1
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Kurma K, Eslami-S Z, Alix-Panabières C, Cayrefourcq L. Liquid biopsy: paving a new avenue for cancer research. Cell Adh Migr 2024; 18:1-26. [PMID: 39219215 PMCID: PMC11370957 DOI: 10.1080/19336918.2024.2395807] [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: 04/04/2024] [Revised: 05/21/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The current constraints associated with cancer diagnosis and molecular profiling, which rely on invasive tissue biopsies or clinical imaging, have spurred the emergence of the liquid biopsy field. Liquid biopsy involves the extraction of circulating tumor cells (CTCs), circulating free or circulating tumor DNA (cfDNA or ctDNA), circulating cell-free RNA (cfRNA), extracellular vesicles (EVs), and tumor-educated platelets (TEPs) from bodily fluid samples. Subsequently, these components undergo molecular characterization to identify biomarkers that are critical for early cancer detection, prognosis, therapeutic assessment, and post-treatment monitoring. These innovative biosources exhibit characteristics analogous to those of the primary tumor from which they originate or interact. This review comprehensively explores the diverse technologies and methodologies employed for processing these biosources, along with their principal clinical applications.
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Affiliation(s)
- Keerthi Kurma
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
- CREEC/CANECEV, MIVEGEC (CREES),
University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Zahra Eslami-S
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
- CREEC/CANECEV, MIVEGEC (CREES),
University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
- CREEC/CANECEV, MIVEGEC (CREES),
University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Laure Cayrefourcq
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
- CREEC/CANECEV, MIVEGEC (CREES),
University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
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2
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Bravaccini S, Boldrin E, Gurioli G, Tedaldi G, Piano MA, Canale M, Curtarello M, Ulivi P, Pilati P. The use of platelets as a clinical tool in oncology: opportunities and challenges. Cancer Lett 2024:217044. [PMID: 38876385 DOI: 10.1016/j.canlet.2024.217044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
Platelets are small circulating anucleated cells mainly involved in thrombosis and hemostasis processes. Moreover, platelets play an active role in tumorigenesis and cancer progression, stimulating angiogenesis and vascular remodelling, and protecting circulating cancer cells from shear forces and immune surveillance. Several reports indicate that platelet number in the blood circulation of cancer patients is associated with prognosis and response to treatment. However, the mechanisms of platelets "education" by cancer cells and the crosstalk between platelets and tumor are still unclear, and the role of "tumor educated platelets" (TEPs) is achieving growing interest in cancer research. TEPs are a biological source of cancer-derived biomarkers, especially RNAs that are protected by platelets membrane from circulating RNases, and could serve as a non-invasive tool for tumor detection, molecular profiling and evolution during therapy in clinical practice. Moreover, short platelet lifespan offers the possibility to get a snapshot assessment of cancer molecular profile, providing a real-time tool. We review and discuss the potential and the clinical utility, in terms of cancer diagnosis and monitoring, of platelet count together with other morphological parameters and of the more recent and innovative TEP profiling.
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Affiliation(s)
- Sara Bravaccini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Elisa Boldrin
- Immunology and Molecular Oncology Diagnostics Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padova, Italy.
| | - Giorgia Gurioli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Gianluca Tedaldi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Maria Assunta Piano
- Immunology and Molecular Oncology Diagnostics Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padova, Italy.
| | - Matteo Canale
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Matteo Curtarello
- Immunology and Molecular Oncology Diagnostics Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padova, Italy.
| | - Paola Ulivi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", via P. Maroncelli 40, 47014 Meldola, Italy.
| | - Pierluigi Pilati
- Surgical Oncology of Digestive Tract Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padova, Italy.
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3
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Wurtzel JGT, Lazar S, Askari S, Zhao X, Severa J, Ayombil F, Michael JV, Camire RM, McKenzie SE, Stalker TJ, Ma P, Goldfinger LE. Plasma growth factors maintain constitutive translation in platelets to regulate reactivity and thrombotic potential. Blood Adv 2024; 8:1550-1566. [PMID: 38163324 PMCID: PMC10982986 DOI: 10.1182/bloodadvances.2023011734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
ABSTRACT Mechanisms of proteostasis in anucleate circulating platelets are unknown and may regulate platelet function. We investigated the hypothesis that plasma-borne growth factors/hormones (GFHs) maintain constitutive translation in circulating platelets to facilitate reactivity. Bio-orthogonal noncanonical amino acid tagging (BONCAT) coupled with liquid chromatography-tandem mass spectrometry analysis revealed constitutive translation of a broad-spectrum translatome in human platelets dependent upon plasma or GFH exposure, and in murine circulation. Freshly isolated platelets from plasma showed homeostatic activation of translation-initiation signaling pathways: phosphorylation of p38/ERK upstream kinases, essential intermediate MNK1/2, and effectors eIF4E/4E-BP1. Plasma starvation led to loss of pathway phosphorylation, but it was fully restored with 5-minute stimulation by plasma or GFHs. Cycloheximide or puromycin infusion suppressed ex vivo platelet GpIIb/IIIa activation and P-selectin exposure with low thrombin concentrations and low-to-saturating concentrations of adenosine 5'-diphosphate (ADP) or thromboxane analog but not convulxin. ADP-induced thromboxane generation was blunted by translation inhibition, and secondary-wave aggregation was inhibited in a thromboxane-dependent manner. Intravenously administered puromycin reduced injury-induced clot size in cremaster muscle arterioles, and delayed primary hemostasis after tail tip amputation but did not delay neither final hemostasis after subsequent rebleeds, nor final hemostasis after jugular vein puncture. In contrast, these mice were protected from injury-induced arterial thrombosis and thrombin-induced pulmonary thromboembolism (PE), and adoptive transfer of translation-inhibited platelets into untreated mice inhibited arterial thrombosis and PE. Thus, constitutive plasma GFH-driven translation regulates platelet G protein-coupled receptor reactivity to balance hemostasis and thrombotic potential.
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Affiliation(s)
- Jeremy G. T. Wurtzel
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Sophia Lazar
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Shayan Askari
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Xuefei Zhao
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Jenna Severa
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Francis Ayombil
- Division of Hematology and the Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA
| | - James V. Michael
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Rodney M. Camire
- Division of Hematology and the Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Steven E. McKenzie
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Timothy J. Stalker
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Peisong Ma
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Lawrence E. Goldfinger
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
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4
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Najafi S, Asemani Y, Majidpoor J, Mahmoudi R, Aghaei-Zarch SM, Mortezaee K. Tumor-educated platelets. Clin Chim Acta 2024; 552:117690. [PMID: 38056548 DOI: 10.1016/j.cca.2023.117690] [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: 10/15/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/08/2023]
Abstract
Beyond traditional roles in homeostasis and coagulation, growing evidence suggests that platelets also reflect malignant transformation in cancer. Platelets are present in the tumor microenvironment where they interact with cancer cells. This interaction results in direct and indirect "education" as evident by platelet alterations in adhesion molecules, glycoproteins, nucleic acids, proteins and various receptors. Subsequently, these tumor-educated platelets (TEPs) circulate throughout the body and play pivotal roles in promotion of tumor growth and dissemination. Accordingly, platelet status can be considered a unique blood-based biomarker that can potentially predict prognosis and therapeutic success. Recently, liquid biopsies including TEPs have received much attention as safe, minimally invasive and sensitive alternatives for patient management. Herein, we provide an overview of TEPs and explore their benefits and limitations in cancer.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yahya Asemani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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5
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Bruzek S, Betensky M, Di Paola J, Diacovo T, Goldenberg N, Ignjatovic V. What can the plasma proteome tell us about platelets and (vice versa)? Platelets 2023; 34:2186707. [PMID: 36894508 DOI: 10.1080/09537104.2023.2186707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Multi-omics approaches are being used increasingly to study physiological and pathophysiologic processes. Proteomics specifically focuses on the study of proteins as functional elements and key contributors to, and markers of the phenotype, as well as targets for diagnostic and therapeutic approaches. Depending on the condition, the plasma proteome can mirror the platelet proteome, and hence play an important role in elucidating both physiologic and pathologic processes. In fact, both plasma and platelet protein signatures have been shown to be important in the setting of thrombosis-prone disease states such as atherosclerosis and cancer. Plasma and platelet proteomes are increasingly being studied as a part of a single entity, as is the case with patient-centric sample collection approaches such as capillary blood. Future studies should cut across the plasma and platelet proteome silos, taking advantage of the vast knowledge available when they are considered as part of the same studies, rather than studied as distinct entities.
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Affiliation(s)
- Steven Bruzek
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Marisol Betensky
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA.,Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Johns Hopkins All Children's Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Jorge Di Paola
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas Diacovo
- Departments of Pediatrics and Pharmacology, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Neil Goldenberg
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA.,Department of Pediatrics and Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Vera Ignjatovic
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, USA
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6
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Thibord F, Johnson AD. Sources of variability in the human platelet transcriptome. Thromb Res 2023; 231:255-263. [PMID: 37357099 DOI: 10.1016/j.thromres.2023.06.009] [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: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
Platelets are anucleated cells produced by megakaryocytes, from which they inherit all the components necessary to carry their functions. They circulate in blood vessels where they play essential roles in coagulation, wound repair or inflammation, and have been implicated in various pathological conditions such as thrombosis, viral infection or cancer progression. The importance of these cells has been established over a century ago, and effective anti-platelet medications with different mechanisms of action have since been developed. However, these therapies are not always effective and can incur adverse events, thus a better understanding of platelets molecular processes is needed to address these issues and improve our understanding of platelet functions. In recent years, an increasing number of studies have leveraged OMICs technologies to analyze their content and identify molecular signatures and mechanisms associated with platelet functions and platelet related disorders. In particular, the increased accessibility of microarrays and RNA sequencing opened the way for studies of the platelet transcriptome under a wide array of conditions. These studies revealed distinct expression profiles in diverse pathologies, which could lead to the discovery of novel biomarkers and therapeutic targets, and suggests a dynamic transcriptome that could influence platelet mechanisms. In this review, we highlight the different sources of transcript level variability in platelets while summarizing recent advances and discoveries from this emerging field.
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Affiliation(s)
- Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte, Suite #2, Framingham, MA 01702, USA; The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA 01702, USA.
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte, Suite #2, Framingham, MA 01702, USA; The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA 01702, USA
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7
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Ajanel A, Middleton EA. Alterations in the megakaryocyte transcriptome impacts platelet function in sepsis and COVID-19 infection. Thromb Res 2023; 231:247-254. [PMID: 37258336 PMCID: PMC10198739 DOI: 10.1016/j.thromres.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Platelets and their parent cell, the megakaryocyte (MK), are increasingly recognized for their roles during infection and inflammation. The MK residing in the bone marrow or arising from precursors trafficked to other organs for development go on to form platelets through thrombopoiesis. Infection, by direct and indirect mechanisms, can alter the transcriptional profile of MKs. The altered environment, whether mediated by inflammatory cytokines or other signaling mechanisms results in an altered platelet transcriptome. Platelets released into the circulation, in turn, interact with each other, circulating leukocytes and endothelial cells and contribute to the clearance of pathogens or the potentiation of pathophysiology through such mechanisms as immunothrombosis. In this article we hope to identify key contributions that explore the impact of an altered transcriptomic landscape during severe, systemic response to infection broadly defined as sepsis, and viral infections, including SARS-CoV2. We include current publications that outline the role of MKs from bone-marrow and extra-medullary sites as well as the circulating platelet. The underlying diseases result in thrombotic complications that exacerbate organ dysfunction and mortality. Understanding the impact of platelets on the pathophysiology of disease may drive therapeutic advances to improve the morbidity and mortality of these deadly afflictions.
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Affiliation(s)
- Abigail Ajanel
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth A Middleton
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA; Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA.
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8
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Luan C, Xu Y. Matrix metalloproteinase gene mutations and bioinformatics of telocytes in hepatocellular carcinoma. Cell Biol Int 2023; 47:110-122. [PMID: 36273423 DOI: 10.1002/cbin.11912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 01/01/2023]
Abstract
Telocytes (TCs) have crucial functions to promote the metastasis of hepatocellular carcinoma (HCC) by over-expressing matrix metalloproteinases (MMPs), but the mechanism by which TCs secrete MMPs in the genome is still unknown. We first cultured and isolated primary TCs from distinct liver cancer tissues and hepatic hemangioma surrounding tissues (Control group). Their whole exon genes were tested by Illumina HiSeq family of platforms and by high-throughput sequencing as well as variant mutations. Moreover, immunohistochemistry, Western blot, and quantitative reverse transcription-polymerase chain reaction assays were utilized to assess the expression of MMPs. The perniciousness of signal-nucleotide polymorphism (SNP) mutations of proteins were predicted by the Polyphen-2 database. Divergent expression and overall survival (OS) of MMPs was screened by StarBase-Pan Cancer plate; and MMPs associated signaling pathways were found by Kyoto Encyclopedia Genes and Genomes. The "competing endogenous RNA (ceRNA)" network was constructed by Cytoscape software. We found that 12 specific types of SNP mutations related to 5 types of MMPs occurred in TCs of liver malignant tumors as a potential result of MMP1, MMP9, and MMP17 overexpression. High levels of MMP1, MMP7, and MMP9 represented poor OS in HCC, and an interactive network of MMPs is shown. Allele shifts of C/T (rs20544) and G/C (rs2250889) in MMP9 were risk factors for TCs in HCC by the prediction of the Polyphen-2 Database. (MMP9 (-3 C/T)) mutation might be a genetic mechanism of upregulating MMP9 in TCs.
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Affiliation(s)
- Chaoguang Luan
- General Surgery, Ji 'nan Municipal Three Hospitals, Ji'nan, Shandong, China
| | - Ying Xu
- Postdoctoral Centre, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Ji'nan, Shandong, China
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9
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De Wispelaere K, Freson K. The Analysis of the Human Megakaryocyte and Platelet Coding Transcriptome in Healthy and Diseased Subjects. Int J Mol Sci 2022; 23:ijms23147647. [PMID: 35886993 PMCID: PMC9317744 DOI: 10.3390/ijms23147647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/10/2022] Open
Abstract
Platelets are generated and released into the bloodstream from their precursor cells, megakaryocytes that reside in the bone marrow. Though platelets have no nucleus or DNA, they contain a full transcriptome that, during platelet formation, is transported from the megakaryocyte to the platelet. It has been described that transcripts in platelets can be translated into proteins that influence platelet response. The platelet transcriptome is highly dynamic and has been extensively studied using microarrays and, more recently, RNA sequencing (RNA-seq) in relation to diverse conditions (inflammation, obesity, cancer, pathogens and others). In this review, we focus on bulk and single-cell RNA-seq studies that have aimed to characterize the coding transcriptome of healthy megakaryocytes and platelets in humans. It has been noted that bulk RNA-seq has limitations when studying in vitro-generated megakaryocyte cultures that are highly heterogeneous, while single-cell RNA-seq has not yet been applied to platelets due to their very limited RNA content. Next, we illustrate how these methods can be applied in the field of inherited platelet disorders for gene discovery and for unraveling novel disease mechanisms using RNA from platelets and megakaryocytes and rare disease bioinformatics. Next, future perspectives are discussed on how this field of coding transcriptomics can be integrated with other next-generation technologies to decipher unexplained inherited platelet disorders in a multiomics approach.
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10
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Platelets Purification Is a Crucial Step for Transcriptomic Analysis. Int J Mol Sci 2022; 23:ijms23063100. [PMID: 35328521 PMCID: PMC8953733 DOI: 10.3390/ijms23063100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 01/24/2023] Open
Abstract
Platelets are small anucleate cells derived from the fragmentation of megakaryocytes and are involved in different biological processes especially hemostasis, thrombosis, and immune response. Despite their lack of nucleus, platelets contain a reservoir of megakaryocyte-derived RNAs and all the machinery useful for mRNA translation. Interestingly, platelet transcriptome was analyzed in health and diseases and led to the identification of disease-specific molecular signatures. Platelet contamination by leukocytes and erythrocytes during platelet purification is a major problem in transcriptomic analysis and the presence of few contaminants in platelet preparation could strongly alter transcriptome results. Since contaminant impacts on platelet transcriptome remains theoretical, we aimed to determine whether low leukocyte and erythrocyte contamination could cause great or only minor changes in platelet transcriptome. Using microarray technique, we compared the transcriptome of platelets from the same donor, purified by common centrifugation method or using magnetic microbeads to eliminate contaminating cells. We found that platelet transcriptome was greatly altered by contaminants, as the relative amount of 8274 transcripts was different between compared samples. We observed an increase of transcripts related to leukocytes and erythrocytes in platelet purified without microbeads, while platelet specific transcripts were falsely reduced. In conclusion, serious precautions should be taken during platelet purification process for transcriptomic analysis, in order to avoid platelets contamination and result alteration.
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11
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Finding the “switch” in platelet activation prediction of key mediators involved in reversal of platelet activation using a novel network biology approach. J Proteomics 2022; 261:104577. [DOI: 10.1016/j.jprot.2022.104577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 11/15/2022]
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12
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Correa F, Luise D, Bosi P, Trevisi P. Weaning differentially affects the maturation of piglet peripheral blood and jejunal Peyer's patches. Sci Rep 2022; 12:1604. [PMID: 35102264 PMCID: PMC8803882 DOI: 10.1038/s41598-022-05707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The study aimed to assess how the post-weaning condition changes piglet peripheral blood (PB) and jejunal Peyer's patches (JPPs) as compared to the suckling period, and how these changes are associated with intestinal microbiota evolution. Sixteen pigs were slaughtered and sampled for PB, JPPs and jejunal content (JC) at weaning (26 days) or at 12 days fed on a pre-starter diet. The PB and JPP transcriptomes were analysed using mRNA-seq. The Gene Set Enrichment Analysis was used to demonstrate enriched gene clusters, depending on sampling time. Jejunal microbiota was profiled using 16S rRNA gene sequencing. Post-weaning JPPs were enriched for processes related to the activation of IFN-γ and major histocompatibility complex (MHC) class I antigen processing which clustered with the reduced abundance of the Weisella genus and Faecalibacterium prausnitzii in JC. The post-weaning microbiome differed from that seen in just-weaned pigs. For just-weaned PB, the enrichment of genes related to hemoglobin and the iron metabolism indicated the greater presence of reticulocytes and immature erythrocytes. The JPP genes involved in the I MHC and IFN-γ activations were markers of the post-weaning phase. Several genes attributable to reticulocyte and erythrocyte maturation could be interesting for testing the iron nutrition of piglets.
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Affiliation(s)
- Federico Correa
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Paolo Bosi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
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13
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Mikaelsdottir E, Thorleifsson G, Stefansdottir L, Halldorsson G, Sigurdsson JK, Lund SH, Tragante V, Melsted P, Rognvaldsson S, Norland K, Helgadottir A, Magnusson MK, Ragnarsson GB, Kristinsson SY, Reykdal S, Vidarsson B, Gudmundsdottir IJ, Olafsson I, Onundarson PT, Sigurdardottir O, Sigurdsson EL, Grondal G, Geirsson AJ, Geirsson G, Gudmundsson J, Holm H, Saevarsdottir S, Jonsdottir I, Thorgeirsson G, Gudbjartsson DF, Thorsteinsdottir U, Rafnar T, Stefansson K. Genetic variants associated with platelet count are predictive of human disease and physiological markers. Commun Biol 2021; 4:1132. [PMID: 34580418 PMCID: PMC8476563 DOI: 10.1038/s42003-021-02642-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
Platelets play an important role in hemostasis and other aspects of vascular biology. We conducted a meta-analysis of platelet count GWAS using data on 536,974 Europeans and identified 577 independent associations. To search for mechanisms through which these variants affect platelets, we applied cis-expression quantitative trait locus, DEPICT and IPA analyses and assessed genetic sharing between platelet count and various traits using polygenic risk scoring. We found genetic sharing between platelet count and counts of other blood cells (except red blood cells), in addition to several other quantitative traits, including markers of cardiovascular, liver and kidney functions, height, and weight. Platelet count polygenic risk score was predictive of myeloproliferative neoplasms, rheumatoid arthritis, ankylosing spondylitis, hypertension, and benign prostate hyperplasia. Taken together, these results advance understanding of diverse aspects of platelet biology and how they affect biological processes in health and disease. Evgenia Mikaelsdottir et al. report a study of variants associated with platelet count among European individuals where they identify 577 associations. They also report a genetic overlap between platelet count and human diseases, including myeloproliferative neoplasms, rheumatoid arthritis, and hypertension, as well as a genetic overlap between platelet count and various physiological markers.
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Affiliation(s)
| | | | | | | | | | - Sigrun H Lund
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Magnus K Magnusson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Gunnar B Ragnarsson
- Department of Oncology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Sigurdur Y Kristinsson
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.,Department of Hematology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Sigrun Reykdal
- Department of Hematology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Department of Hematology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Pall T Onundarson
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.,Laboratory Hematology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Olof Sigurdardottir
- Department of Clinical Biochemistry, Akureyri Hospital, 600, Akureyri, Iceland
| | | | - Gerdur Grondal
- Department of Rheumatology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Arni J Geirsson
- Department of Rheumatology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Gudmundur Geirsson
- Department of Urology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.,Department of Rheumatology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Department of Cardiology, Landspitali-University Hospital, 101, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, 101, Reykjavik, Iceland. .,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.
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14
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Cacic D, Nordgård O, Meyer P, Hervig T. Platelet Microparticles Decrease Daunorubicin-Induced DNA Damage and Modulate Intrinsic Apoptosis in THP-1 Cells. Int J Mol Sci 2021; 22:ijms22147264. [PMID: 34298882 PMCID: PMC8304976 DOI: 10.3390/ijms22147264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/26/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Platelets can modulate cancer through budding of platelet microparticles (PMPs) that can transfer a plethora of bioactive molecules to cancer cells upon internalization. In acute myelogenous leukemia (AML) this can induce chemoresistance, partially through a decrease in cell activity. Here we investigated if the internalization of PMPs protected the monocytic AML cell line, THP-1, from apoptosis by decreasing the initial cellular damage inflicted by treatment with daunorubicin, or via direct modulation of the apoptotic response. We examined whether PMPs could protect against apoptosis after treatment with a selection of inducers, primarily associated with either the intrinsic or the extrinsic apoptotic pathway, and protection was restricted to the agents targeting intrinsic apoptosis. Furthermore, levels of daunorubicin-induced DNA damage, assessed by measuring gH2AX, were reduced in both 2N and 4N cells after PMP co-incubation. Measuring different BCL2-family proteins before and after treatment with daunorubicin revealed that PMPs downregulated the pro-apoptotic PUMA protein. Thus, our findings indicated that PMPs may protect AML cells against apoptosis by reducing DNA damage both dependent and independent of cell cycle phase, and via direct modulation of the intrinsic apoptotic pathway by downregulating PUMA. These findings further support the clinical relevance of platelets and PMPs in AML.
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Affiliation(s)
- Daniel Cacic
- Department of Hematology and Oncology, Stavanger University Hospital, 4068 Stavanger, Norway; (O.N.); (P.M.)
- Correspondence:
| | - Oddmund Nordgård
- Department of Hematology and Oncology, Stavanger University Hospital, 4068 Stavanger, Norway; (O.N.); (P.M.)
| | - Peter Meyer
- Department of Hematology and Oncology, Stavanger University Hospital, 4068 Stavanger, Norway; (O.N.); (P.M.)
| | - Tor Hervig
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
- Laboratory of Immunology and Transfusion Medicine, Haugesund Hospital, 5528 Haugesund, Norway
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15
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Huang J, Swieringa F, Solari FA, Provenzale I, Grassi L, De Simone I, Baaten CCFMJ, Cavill R, Sickmann A, Frontini M, Heemskerk JWM. Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions. Sci Rep 2021; 11:12358. [PMID: 34117303 PMCID: PMC8196183 DOI: 10.1038/s41598-021-91661-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome-wide transcriptomes (57.8 k mRNAs). For 14.8 k protein-coding transcripts, we assigned the proteins to 21 UniProt-based classes, based on their preferential intracellular localization and presumed function. This classified transcriptome-proteome profile of platelets revealed: (i) Absence of 37.2 k genome-wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein-coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43-0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identified proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma-derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identified proteome of nuclear-related, membrane and signaling proteins, as well proteins with low-level transcripts. We then constructed a prediction model, based on protein function, transcript level and (peri)nuclear localization, and calculated the achievable proteome at ~ 10 k proteins. Model validation identified 1.0 k additional proteins in the predicted classes. Network and database analysis revealed the presence of 2.4 k proteins with a possible role in thrombosis and hemostasis, and 138 proteins linked to platelet-related disorders. This genome-wide platelet transcriptome and (non)identified proteome database thus provides a scaffold for discovering the roles of unknown platelet proteins in health and disease.
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Affiliation(s)
- Jingnan Huang
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-E.V, Dortmund, Germany.
| | - Frauke Swieringa
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-E.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-E.V, Dortmund, Germany
| | - Isabella Provenzale
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge, UK
| | - Ilaria De Simone
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Constance C F M J Baaten
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH, Aachen, Germany
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, FSE, Maastricht University, Maastricht, The Netherlands
| | - Albert Sickmann
- Leibniz-Institut Für Analytische Wissenschaften-ISAS-E.V, Dortmund, Germany
- Medizinische Fakultät, Medizinische Proteom-Center, Ruhr-Universität Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, Exeter, UK
| | - Johan W M Heemskerk
- Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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16
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Rolfes V, Ribeiro LS, Hawwari I, Böttcher L, Rosero N, Maasewerd S, Santos MLS, Próchnicki T, Silva CMDS, Wanderley CWDS, Rothe M, Schmidt SV, Stunden HJ, Bertheloot D, Rivas MN, Fontes CJ, Carvalho LH, Cunha FQ, Latz E, Arditi M, Franklin BS. Platelets Fuel the Inflammasome Activation of Innate Immune Cells. Cell Rep 2021; 31:107615. [PMID: 32402278 PMCID: PMC7225754 DOI: 10.1016/j.celrep.2020.107615] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
The inflammasomes control the bioactivity of pro-inflammatory cytokines of the interleukin (IL)-1 family. The inflammasome assembled by NLRP3 has been predominantly studied in homogeneous cell populations in vitro, neglecting the influence of cellular interactions that occur in vivo. Here, we show that platelets boost the inflammasome capacity of human macrophages and neutrophils and are critical for IL-1 production by monocytes. Platelets license NLRP3 transcription, thereby enhancing ASC oligomerization, caspase-1 activity, and IL-1β secretion. Platelets influence IL-1β production in vivo, and blood platelet counts correlate with plasmatic IL-1β levels in malaria. Furthermore, we reveal an enriched platelet gene signature among the highest-expressed transcripts in IL-1β-driven autoinflammatory diseases. The platelet effect is independent of cell-to-cell contact, platelet-derived lipid mediators, purines, nucleic acids, and a host of platelet cytokines, and it involves the triggering of calcium-sensing receptors on macrophages. Hence, platelets provide an additional layer of regulation of inflammasomes and IL-1-driven inflammation. Platelets license NLRP3 for inflammasome activattion in innate immune cells Platelets are required for optimal monocyte inflammasome activation Platelets shape IL-1β in vivo, and platelet counts correlate with IL-1β in plasma A constitutive, heat-sensitive soluble platelet-factor boost IL-1β in macrophages
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Affiliation(s)
- Verena Rolfes
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Lucas Secchim Ribeiro
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany.
| | - Ibrahim Hawwari
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Lisa Böttcher
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Nathalia Rosero
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Salie Maasewerd
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Marina Lima Silva Santos
- Laboratório de Malária, Instituto René Rachou, Fundação Oswaldo Cruz, 30190-002 Belo Horizonte, MG, Brazil
| | - Tomasz Próchnicki
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Camila Meirelles de Souza Silva
- Center for Research in Inflammatory Diseases, School of Medicine of Ribeirão Preto, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Carlos Wagner de Souza Wanderley
- Center for Research in Inflammatory Diseases, School of Medicine of Ribeirão Preto, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Maximilian Rothe
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - H James Stunden
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Damien Bertheloot
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany
| | - Magali Noval Rivas
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Cor Jesus Fontes
- Departamento de Clínica Médica, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil
| | - Luzia Helena Carvalho
- Laboratório de Malária, Instituto René Rachou, Fundação Oswaldo Cruz, 30190-002 Belo Horizonte, MG, Brazil
| | - Fernando Queiroz Cunha
- Center for Research in Inflammatory Diseases, School of Medicine of Ribeirão Preto, University of Sao Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, NRW, Germany; Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01655, USA; German Center for Neurodegenerative Diseases, 53127 Bonn, NRW, Germany
| | - Moshe Arditi
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA.
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17
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Gutmann C, Joshi A, Zampetaki A, Mayr M. The Landscape of Coding and Noncoding RNAs in Platelets. Antioxid Redox Signal 2021; 34:1200-1216. [PMID: 32460515 DOI: 10.1089/ars.2020.8139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Levels of platelet noncoding RNAs (ncRNAs) are altered by disease, and ncRNAs may exert functions inside and outside of platelets. Their role in physiologic hemostasis and pathologic thrombosis remains to be explored. Recent Advances: The number of RNA classes identified in platelets has been growing since the past decade. Apart from coding messenger RNAs, the RNA landscape in platelets comprises ncRNAs such as microRNAs, circular RNAs, long ncRNAs, YRNAs, and potentially environmentally derived exogenous ncRNAs. Recent research has focused on the function of platelet RNAs beyond platelets, mediated through protective RNA shuttles or even cellular uptake of entire platelets. Multiple studies have also explored the potential of platelet RNAs as novel biomarkers. Critical Issues: Platelet preparations can contain contaminating leukocytes. Even few leukocytes may contribute a substantial amount of RNA. As biomarkers, platelet RNAs have shown associations with platelet activation, but it remains to be seen whether their measurements could improve diagnostics. It also needs to be clarified whether platelet RNAs influence processes beyond platelets. Future Directions: Technological advances such as single-cell RNA-sequencing might help to identify hyperreactive platelet subpopulations on a single-platelet level, avoid the common problem of leukocyte contamination in platelet preparations, and allow simultaneous profiling of native megakaryocytes and their platelet progeny to clarify to what extent the platelet RNA content reflects their megakaryocyte precursors or changes in the circulation. Antioxid. Redox Signal. 34, 1200-1216.
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Affiliation(s)
- Clemens Gutmann
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Abhishek Joshi
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
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18
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Abstract
Until recently, the nucleic acid content of platelets was considered to be fully determined by their progenitor megakaryocyte. However, it is now well understood that additional mediators (eg, cancer cells) can intervene, thereby influencing the RNA repertoire of platelets. Platelets are highly dynamic cells that are able to communicate and influence their environment. For instance, platelets have been involved in various steps of cancer development and progression by supporting tumor growth, survival, and dissemination. Cancer cells can directly and/or indirectly influence platelet RNA content, resulting in tumor-mediated "education" of platelets. Alterations in the tumor-educated platelet RNA profile have been described as a novel source of potential biomarkers. Individual platelet RNA biomarkers as well as complex RNA signatures may be used for early detection of cancer and treatment monitoring. Here, we review the RNA transfer occurring between cancer cells and platelets. We explore the potential use of platelet RNA biomarkers as a liquid biopsy biosource and discuss methods to evaluate the transcriptomic content of platelets.
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19
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Savage AK, Gutschow MV, Chiang T, Henderson K, Green R, Chaudhari M, Swanson E, Heubeck AT, Kondza N, Burley KC, Genge PC, Lord C, Smith T, Thomson Z, Beaubien A, Johnson E, Goldy J, Bolouri H, Buckner JH, Meijer P, Coffey EM, Skene PJ, Torgerson TR, Li XJ, Bumol TF. Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing. iScience 2021; 24:102404. [PMID: 34113805 PMCID: PMC8169801 DOI: 10.1016/j.isci.2021.102404] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/28/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMC up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from native in vivo biology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states. Studies of human blood cells and plasma are highly sensitive to process variability Time variability distorts biology in cutting-edge single-cell and multiplex assays Longitudinal, multi-modal, and aligned data enable data qualification and exploration Dataset holds potential novel, multi-modal biological correlations and hypotheses
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Affiliation(s)
- Adam K Savage
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Tony Chiang
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Richard Green
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | | | | | - Nina Kondza
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Palak C Genge
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Cara Lord
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Tanja Smith
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | | | - Ed Johnson
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hamid Bolouri
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Jane H Buckner
- Center for Translational Research, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Paul Meijer
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Peter J Skene
- Allen Institute for Immunology, Seattle, WA 98109, USA
| | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA 98109, USA
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20
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Kammers K, Taub MA, Rodriguez B, Yanek LR, Ruczinski I, Martin J, Kanchan K, Battle A, Cheng L, Wang ZZ, Johnson AD, Leek JT, Faraday N, Becker LC, Mathias RA. Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole-genome and RNA sequencing. Blood 2021; 137:959-968. [PMID: 33094331 PMCID: PMC7918180 DOI: 10.1182/blood.2020006115] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/29/2020] [Indexed: 01/04/2023] Open
Abstract
Genome-wide association studies have identified common variants associated with platelet-related phenotypes, but because these variants are largely intronic or intergenic, their link to platelet biology is unclear. In 290 normal subjects from the GeneSTAR Research Study (110 African Americans [AAs] and 180 European Americans [EAs]), we generated whole-genome sequence data from whole blood and RNA sequence data from extracted nonribosomal RNA from 185 induced pluripotent stem cell-derived megakaryocyte (MK) cell lines (platelet precursor cells) and 290 blood platelet samples from these subjects. Using eigenMT software to select the peak single-nucleotide polymorphism (SNP) for each expressed gene, and meta-analyzing the results of AAs and EAs, we identify (q-value < 0.05) 946 cis-expression quantitative trait loci (eQTLs) in derived MKs and 1830 cis-eQTLs in blood platelets. Among the 57 eQTLs shared between the 2 tissues, the estimated directions of effect are very consistent (98.2% concordance). A high proportion of detected cis-eQTLs (74.9% in MKs and 84.3% in platelets) are unique to MKs and platelets compared with peak-associated SNP-expressed gene pairs of 48 other tissue types that are reported in version V7 of the Genotype-Tissue Expression Project. The locations of our identified eQTLs are significantly enriched for overlap with several annotation tracks highlighting genomic regions with specific functionality in MKs, including MK-specific DNAse hotspots, H3K27-acetylation marks, H3K4-methylation marks, enhancers, and superenhancers. These results offer insights into the regulatory signature of MKs and platelets, with significant overlap in genes expressed, eQTLs detected, and enrichment within known superenhancers relevant to platelet biology.
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Affiliation(s)
- Kai Kammers
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Benjamin Rodriguez
- National Heart, Lung, and Blood Institute, Population Sciences Branch, The Framingham Heart Study, Framingham, MA; and
| | | | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | | | | | - Linzhao Cheng
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Zack Z Wang
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute, Population Sciences Branch, The Framingham Heart Study, Framingham, MA; and
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | | | - Rasika A Mathias
- The GeneSTAR Research Program
- Division of Allergy and Clinical Immunology
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21
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Neu CT, Gutschner T, Haemmerle M. Post-Transcriptional Expression Control in Platelet Biogenesis and Function. Int J Mol Sci 2020; 21:ijms21207614. [PMID: 33076269 PMCID: PMC7589263 DOI: 10.3390/ijms21207614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Platelets are highly abundant cell fragments of the peripheral blood that originate from megakaryocytes. Beside their well-known role in wound healing and hemostasis, they are emerging mediators of the immune response and implicated in a variety of pathophysiological conditions including cancer. Despite their anucleate nature, they harbor a diverse set of RNAs, which are subject to an active sorting mechanism from megakaryocytes into proplatelets and affect platelet biogenesis and function. However, sorting mechanisms are poorly understood, but RNA-binding proteins (RBPs) have been suggested to play a crucial role. Moreover, RBPs may regulate RNA translation and decay following platelet activation. In concert with other regulators, including microRNAs, long non-coding and circular RNAs, RBPs control multiple steps of the platelet life cycle. In this review, we will highlight the different RNA species within platelets and their impact on megakaryopoiesis, platelet biogenesis and platelet function. Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs.
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Affiliation(s)
- Carolin T. Neu
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
- Correspondence: ; Tel.: +49-345-557-3964
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Yan S, Liu X, Ke X, Xian Z, Peng C, Wang X, Chen M. Screening on platelet LncRNA expression profile discloses novel residual platelet reactivity biomarker. Int J Lab Hematol 2020; 42:661-668. [PMID: 32567809 DOI: 10.1111/ijlh.13261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/15/2020] [Accepted: 05/13/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Double antiplatelet therapy (DAPT) has wide inter-individual variabilities in coronary heart disease (CHD) patients' responses, which undermines the prognosis effect in clinical practice. Long noncoding RNAs (lncRNAs) have been reported to be widely existed in platelets, albeit their potential roles in platelet responses to DAPT largely remains in the realm of the unknown. This study aims to screen differentially expressed lncRNAs responsible for high residual platelet reactivities under DAPT. METHODS We enrolled 144 CHD patients that received DAPT and assigned them to high platelet reactivity (HPR) group and baseline group according to their residual platelet reactivities. Statistical analysis and a series of experiments including microarray analysis, platelet reactivity screening, RNA isolation and lncRNA microarray analysis were explored to the research. RESULTS We detected a total of 22,424 kinds of co-expressed lncRNAs in three pairs of patients between the HPR and baseline groups. We identified twenty differentially expressed lncRNAs and successfully validated three of them in the 144 patients. Ultimately, the expression of ensemble transcript ENST00000433442 was demonstrated as significantly correlated with high platelet reactivity (OR = 0.487, P = .035) by logistic regression analysis. CONCLUSION There is a considerable amount of lncRNAs in platelets, and the downregulated expression of ENST00000433442 is an independent risk factor for high residual platelet reactivity in CHD patients under DAPT.
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Affiliation(s)
- Shaodi Yan
- Shenzhen University School of Medicine, Shenzhen, China.,Department of Cardiology, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China.,Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaojing Liu
- Laboratory of Cardiovascular Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Ke
- Shenzhen University School of Medicine, Shenzhen, China.,Department of Cardiology, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
| | - Zhanchao Xian
- Department of Cardiology, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
| | - Changnong Peng
- Department of Cardiology, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
| | - Xiaoqing Wang
- Department of Cardiology, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
| | - Mao Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
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Tini G, Marchetti L, Priami C, Scott-Boyer MP. Multi-omics integration-a comparison of unsupervised clustering methodologies. Brief Bioinform 2020; 20:1269-1279. [PMID: 29272335 DOI: 10.1093/bib/bbx167] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
With the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these factors is explored when solving the problem of sample classification, by comparing the performances of five unsupervised algorithms: Multiple Canonical Correlation Analysis, Multiple Co-Inertia Analysis, Multiple Factor Analysis, Joint and Individual Variation Explained and Similarity Network Fusion. These methods were applied to three real data sets taken from literature and several ad hoc simulated scenarios to discuss classification performance in different conditions of noise and signal strength across the data types. The impact of experimental design, feature selection and parameter training has been also evaluated to unravel important conditions that can affect the accuracy of the result.
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Riley DRJ, Khalil JS, Naseem KM, Rivero F. Biochemical and immunocytochemical characterization of coronins in platelets. Platelets 2019; 31:913-924. [PMID: 31801396 PMCID: PMC7497283 DOI: 10.1080/09537104.2019.1696457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Rapid reorganization of the actin cytoskeleton in response to receptor-mediated signaling cascades allows platelets to transition from a discoid shape to a flat spread shape upon adhesion to damaged vessel walls. Coronins are conserved regulators of the actin cytoskeleton turnover but they also participate in signaling events. To gain a better picture of their functions in platelets we have undertaken a biochemical and immunocytochemical investigation with a focus on Coro1. We found that class I coronins Coro1, 2 and 3 are abundant in human and mouse platelets whereas little Coro7 can be detected. Coro1 is mainly cytosolic, but a significant amount associates with membranes in an actin-independent manner and does not translocate from or to the membrane fraction upon exposure to thrombin, collagen or prostacyclin. Coro1 rapidly translocates to the Triton insoluble cytoskeleton upon platelet stimulation with thrombin or collagen. Coro1, 2 and 3 show a diffuse cytoplasmic localization with discontinuous accumulation at the cell cortex and actin nodules of human platelets, where all three coronins colocalize. Our data are consistent with a role of coronins as integrators of extracellular signals with actin remodeling and suggests a high extent of functional overlap among class I coronins in platelets.
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Affiliation(s)
- David R J Riley
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Faculty of Health Sciences, University of Hull , Hull, UK
| | - Jawad S Khalil
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Faculty of Health Sciences, University of Hull , Hull, UK.,School of Physiology, Pharmacology and Neuroscience, Faculty of Life Sciences, University of Bristol , Bristol, UK
| | - Khalid M Naseem
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds , Leeds, UK
| | - Francisco Rivero
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Faculty of Health Sciences, University of Hull , Hull, UK
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Heffron SP, Marier C, Parikh M, Fisher EA, Berger JS. Severe obesity and bariatric surgery alter the platelet mRNA profile. Platelets 2019; 30:967-974. [PMID: 30388921 PMCID: PMC6642854 DOI: 10.1080/09537104.2018.1536261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mechanisms explaining the relationship between obesity and cardiovascular disease (CVD) are needed. Despite growing recognition of the importance of the anucleate platelet transcriptome, low levels of RNA in platelets make assessment difficult. We sought to perform unbiased platelet RNA profiling in obesity by performing a prospective study of severe obesity and weight loss via bariatric surgery on platelet characteristics and mRNA profile in 26 pre-menopausal, non-diabetic women (31.6 ± 8.4 years; BMI 43.0 ± 6.5 kg/m2) who underwent sleeve gastrectomy. Totally, 10 women of similar age with normal BMI served as controls. Platelet activation via flow cytometry was assessed before and after surgery. RNA-sequencing (RNAseq) was performed on platelet isolates from a subset of 13 subjects (eight obese women and five normal-BMI subjects). Platelet count, size, and age did not differ between control and obese women. However, platelet surface P-selectin and CD40 were higher in obesity. RNAseq demonstrated 629 differentially abundant transcripts in obesity. Notably, S100A9 and AGER, established markers of cardiovascular risk, were two of the most highly upregulated transcripts (each > 2.5 fold). At 6 months post-operatively, subjects lost 26.1 ± 5.8% body weight and inducible platelet P-selectin expression was reduced. Expression of 170 transcripts was affected by surgery, but only a small fraction (46/629) were genes found altered in obesity. We demonstrate that obesity is associated with an altered platelet transcriptome and increased platelet activation, which is partly attenuated by bariatric surgery. These observations suggest that platelets may contribute to increased cardiovascular risk in obesity through a variety of mechanisms.
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Affiliation(s)
- Sean P Heffron
- Department of Medicine, Leon H. Charney Division of Cardiology and the Center for the Prevention of Cardiovascular Disease;,Address for Correspondence: Sean P. Heffron MD, MS, MSc, Instructor in Medicine, Leon H. Charney Division of Cardiology, New York University School of Medicine, 227 East 30th St., #834, New York, NY 10016, Tel: -1- 646-501-2735,
| | - Christian Marier
- Genome Technology Core Laboratory, New York University School of Medicine, New York, NY
| | - Manish Parikh
- Department of Surgery, New York University Langone Medical Center
| | - Edward A Fisher
- Department of Medicine, Leon H. Charney Division of Cardiology and the Center for the Prevention of Cardiovascular Disease
| | - Jeffrey S Berger
- Department of Medicine, Leon H. Charney Division of Cardiology and the Center for the Prevention of Cardiovascular Disease;,Department of Surgery, Division of Vascular Surgery, New York University Langone Medical Center
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27
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Impacts of Cancer on Platelet Production, Activation and Education and Mechanisms of Cancer-Associated Thrombosis. Cancers (Basel) 2018; 10:cancers10110441. [PMID: 30441823 PMCID: PMC6266827 DOI: 10.3390/cancers10110441] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/31/2018] [Accepted: 11/10/2018] [Indexed: 12/12/2022] Open
Abstract
Platelets are small anucleate cells that are traditionally described as the major effectors of hemostasis and thrombosis. However, increasing evidence indicates that platelets play several roles in the progression of malignancies and in cancer-associated thrombosis. A notable cross-communication exists between platelets and cancer cells. On one hand, cancer can “educate” platelets, influencing their RNA profiles, the numbers of circulating platelets and their activation states. On the other hand, tumor-educated platelets contain a plethora of active biomolecules, including platelet-specific and circulating ingested biomolecules, that are released upon platelet activation and participate in the progression of malignancy. The numerous mechanisms by which the primary tumor induces the production, activation and aggregation of platelets (also known as tumor cell induced platelet aggregation, or TCIPA) are directly related to the pro-thrombotic state of cancer patients. Moreover, the activation of platelets is critical for tumor growth and successful metastatic outbreak. The development or use of existing drugs targeting the activation of platelets, adhesive proteins responsible for cancer cell-platelet interactions and platelet agonists should be used to reduce cancer-associated thrombosis and tumor progression.
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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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Zhang Q, Hu H, Liu H, Jin J, Zhu P, Wang S, Shen K, Hu Y, Li Z, Zhan P, Zhu S, Fan H, Zhang J, Lv T, Song Y. RNA sequencing enables systematic identification of platelet transcriptomic alterations in NSCLC patients. Biomed Pharmacother 2018; 105:204-214. [PMID: 29857300 DOI: 10.1016/j.biopha.2018.05.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/24/2018] [Accepted: 05/15/2018] [Indexed: 02/02/2023] Open
Abstract
Platelets are implicated as key players in the metastatic dissemination of tumor cells. Previous evidence demonstrated platelets retained cytoplasmic RNAs with physiologically activity, splicing pre-mRNA to mRNA and translating into functional proteins in response to external stimulation. Recently, platelets gene profile of healthy or diseased individuals were characterized with the help of RNA sequencing (RNA-Seq) in some studies, leading to new insights into the mechanisms underlying disease pathogenesis. In this study, we performed RNA-seq in platelets from 7 healthy individuals and 15 non-small cell lung cancer (NSCLC) patients. Our data revealed a subset of near universal differently expressed gene (DEG) profiles in platelets of metastatic NSCLC compared to healthy individuals, including 626 up-regulated RNAs (mRNAs and ncRNAs) and 1497 down-regulated genes. The significant over-expressed genes showed enrichment in focal adhesion, platelets activation, gap junction and adherens junction pathways. The DEGs also included previously reported tumor-related genes such as PDGFR, VEGF, EGF, etc., verifying the consistence and significance of platelet RNA-Seq in oncology study. We also validated several up-regulated DEGs involved in tumor cell-induced platelet aggregation (TCIPA) and tumorigenesis. Additionally, transcriptomic comparison analyses of NSCLC subgroups were conducted. Between non-metastatic and metastatic NSCLC patients, 526 platelet DEGs were identified with the most altered expression. The outcomes from subgroup analysis between lung adenocarcinoma and lung squamous cell carcinoma demonstrated the diagnostic potential of platelet RNA-Seq on distinguishing tumor histological types.
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Affiliation(s)
- Qun Zhang
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Huan Hu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jiajia Jin
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, 210002, China
| | - Peiyuan Zhu
- Department of Blood Transfusion, Jinling Hospital, Nanjing, 210002, China
| | - Shujun Wang
- Department of Blood Transfusion, Jinling Hospital, Nanjing, 210002, China
| | - Kaikai Shen
- Department of Respiratory Medicine, Jinling Hospital, Wannan Medical College, Wuhu, Anhui, China
| | - Yangbo Hu
- Department of Respiratory Medicine, Jinling Hospital, Southeast University School of Medicine, Nanjing, 210002, China
| | - Zhou Li
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Ping Zhan
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Suhua Zhu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Hang Fan
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Jianya Zhang
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Tangfeng Lv
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China.
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China.
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30
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de la Salle H, Angénieux C, Lanza F, Gachet C. Retinoic acid receptor-α regulates synthetic events in human platelets: comment. J Thromb Haemost 2018; 16:1013-1014. [PMID: 29504265 DOI: 10.1111/jth.13992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 11/28/2022]
Affiliation(s)
- H de la Salle
- INSERM UMR_S949, Université de Strasbourg, Etablissement Français du Sang Grand-Est (EFS Grand-Est), Strasbourg, France
| | - C Angénieux
- INSERM UMR_S949, Université de Strasbourg, Etablissement Français du Sang Grand-Est (EFS Grand-Est), Strasbourg, France
| | - F Lanza
- INSERM UMR_S949, Université de Strasbourg, Etablissement Français du Sang Grand-Est (EFS Grand-Est), Strasbourg, France
| | - C Gachet
- INSERM UMR_S949, Université de Strasbourg, Etablissement Français du Sang Grand-Est (EFS Grand-Est), Strasbourg, France
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Massolt ET, Meima ME, Swagemakers SMA, Leeuwenburgh S, van den Hout-van Vroonhoven MCGM, Brigante G, Kam BLR, van der Spek PJ, van IJcken WFJ, Visser TJ, Peeters RP, Visser WE. Thyroid State Regulates Gene Expression in Human Whole Blood. J Clin Endocrinol Metab 2018; 103:169-178. [PMID: 29069456 DOI: 10.1210/jc.2017-01144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023]
Abstract
CONTEXT Despite the well-recognized clinical features resulting from insufficient or excessive thyroid hormone (TH) levels in humans, it is largely unknown which genes are regulated by TH in human tissues. OBJECTIVE To study the effect of TH on human gene expression profiles in whole blood, mainly consisting of T3 receptor (TR) α-expressing cells. METHODS We performed next-generation RNA sequencing on whole blood samples from eight athyroid patients (four females) on and after 4 weeks off levothyroxine replacement. Gene expression changes were analyzed through paired differential expression analysis and confirmed in a validation cohort. Weighted gene coexpression network analysis (WGCNA) was applied to identify thyroid state-related networks. RESULTS We detected 486 differentially expressed genes (fold-change >1.5; multiple testing corrected P value < 0.05), of which 76% were positively and 24% were negatively regulated. Gene ontology (GO) enrichment analysis revealed that three biological processes were significantly overrepresented, of which the process translational elongation showed the highest fold enrichment (7.3-fold, P = 1.8 × 10-6). WGCNA analysis independently identified various gene clusters that correlated with thyroid state. Further GO analysis suggested that thyroid state affects platelet function. CONCLUSIONS Changes in thyroid state regulate numerous genes in human whole blood, predominantly TRα-expressing leukocytes. In addition, TH may regulate gene transcripts in platelets.
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Affiliation(s)
- Elske T Massolt
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Marcel E Meima
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Selmar Leeuwenburgh
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Giulia Brigante
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Boen L R Kam
- Department of Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | | | | | - Theo J Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - W Edward Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
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Telonis AG, Rigoutsos I. Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. Cancer Res 2017; 78:1140-1154. [PMID: 29229607 DOI: 10.1158/0008-5472.can-17-1947] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/19/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancer (TNBC) is a breast cancer subtype characterized by marked differences between White and Black/African-American women. We performed a systems-level analysis on datasets from The Cancer Genome Atlas to elucidate how the expression patterns of mRNAs are shaped by regulatory noncoding RNAs (ncRNA). Specifically, we studied isomiRs, that is, isoforms of miRNAs, and tRNA-derived fragments (tRF). In normal breast tissue, we observed a marked cohesiveness in both the ncRNA and mRNA layers and the associations between them. This cohesiveness was widely disrupted in TNBC. Many mRNAs become either differentially expressed or differentially wired between normal breast and TNBC in tandem with isomiR or tRF dysregulation. The affected pathways included energy metabolism, cell signaling, and immune responses. Within TNBC, the wiring of the affected pathways with isomiRs and tRFs differed in each race. Multiple isomiRs and tRFs arising from specific miRNA loci (e.g., miR-200c, miR-21, the miR-17/92 cluster, the miR-183/96/182 cluster) and from specific tRNA loci (e.g., the nuclear tRNAGly and tRNALeu, the mitochondrial tRNAVal and tRNAPro) were strongly associated with the observed race disparities in TNBC. We highlight the race-specific aspects of transcriptome wiring by discussing in detail the metastasis-related MAPK and the Wnt/β-catenin signaling pathways, two of the many key pathways that were found differentially wired. In conclusion, by employing a data- and knowledge-driven approach, we comprehensively analyzed the normal and cancer transcriptomes to uncover novel key contributors to the race-based disparities of TNBC.Significance: This big data-driven study comparing normal and cancer transcriptomes uncovers RNA expression differences between Caucasian and African-American patients with triple-negative breast cancer that might help explain disparities in incidence and aggressive character. Cancer Res; 78(5); 1140-54. ©2017 AACR.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania.
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania.
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Beaulieu L, Tanriverdi K, Freedman J, Clancy L. The role of RNA uptake in platelet heterogeneity. Thromb Haemost 2017; 117:948-961. [DOI: 10.1160/th16-11-0873] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/10/2017] [Indexed: 12/29/2022]
Abstract
SummaryThe role of platelets in regulating vascular homeostasis has expanded beyond mediation of haemostasis and thrombosis. The discovery of platelet RNA and the presence of subpopulations of platelets containing varying amounts of RNA suggest a role for platelet transcripts in vascular function. As the RNA in anucleated platelets is biologically functional and may transfer to other vascular cells, we hypothesised that platelet RNA diminishes over the lifespan of the platelet with diminishing platelet size due to horizontal cellular transfer. The purpose of this study is to determine if platelet RNA variance is the result of horizontal cellular transfer between platelets and other vascular cells. Utilising platelet sorting and RNA sequencing, we found that smaller platelets contained a more diverse set of transcripts than larger platelets. Further investigation using fluorescence imaging, gene expression analyses and in vitro and in vivo modelling revealed that platelets take up RNA from other vascular cells in a complex manner, revealing a dynamic role for platelets in modulating vascular homeostasis through bidirectional RNA transfer. The resultant RNA profile heterogeneity suggests unique functional roles for platelets dependent on size and complexity. This study expands our basic understanding of platelet function and heterogeneity and is the first to evaluate endogenous vascular RNA uptake and its relation to platelet processes. Our findings describe a novel endogenous phenomenon that can help elucidate the platelet’s role in these non-thrombotic and haemostatic fields, as well as present potential for diagnostic and therapeutic development.Supplementary Material to this article is available online at www.thrombosis-online.com.
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The potential role of platelets in the consensus molecular subtypes of colorectal cancer. Cancer Metastasis Rev 2017; 36:273-288. [DOI: 10.1007/s10555-017-9678-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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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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Deng G, Yu S, He Y, Sun T, Liang W, Yu L, Xu D, Li Q, Zhang R. MicroRNA profiling of platelets from immune thrombocytopenia and target gene prediction. Mol Med Rep 2017; 16:2835-2843. [PMID: 28677771 DOI: 10.3892/mmr.2017.6901] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 04/24/2017] [Indexed: 01/28/2023] Open
Abstract
Immune thrombocytopenia (ITP) is an autoimmune disease characterized by a low platelet count and insufficient platelet production. Previous studies identified that microRNAs (miRNAs/miRs) are important for platelet function. However, the regulatory role of miRNAs in the pathogenesis of thrombocytopenia in ITP remains unclear. The aim of the present study is to isolate differentially expressed miRNAs, and identify their roles in platelets from ITP. A total of 5 ml blood from 22 patients with ITP and 8 healthy controls was isolated for platelet collection. A microarray assay was performed to analyze the differentially expressed miRNAs in the patients with ITP and healthy patients. Furthermore, the expression of differentially expressed miRNAs was verified by reverse transcription‑quantitative polymerase chain reaction. In addition, the target mRNAs of the differentially expressed miRNAs were predicted via miRWalk databases, and the target genes and miRNAs were classified by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analyses. In the present study, 115 miRNAs were identified to be differentially expressed in platelets from patients with ITP compared with the healthy controls (>3‑fold alteration; P<0.05). Among them, 57 miRNAs were upregulated in ITP, while 58 miRNAs were downregulated. Bioinformatic prediction demonstrated that hsa‑miR‑548a‑5p, hsa‑miR‑1185‑2‑3p, hsa‑miR‑30a‑3p, hsa‑miR‑6867‑5p, hsa‑miR‑765 and hsa‑miR‑3125 were associated with platelet apoptosis and adhesion in ITP. The present study performed miRNA profiling of platelets from patients with ITP and the results may aid in the understanding of the regulatory mechanism of ITP.
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Affiliation(s)
- Gang Deng
- Department of Hematology, The First Affiliated Hospital of Soochow University, Soochow, Jiangsu 215006, P.R. China
| | - Shifang Yu
- Department of Transfusion Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yunlei He
- The Ningbo Central Blood Station, Ningbo, Zhejiang 31501, P.R. China
| | - Tao Sun
- Department of Transfusion Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Wei Liang
- The Ningbo Central Blood Station, Ningbo, Zhejiang 31501, P.R. China
| | - Lu Yu
- The Ningbo Central Blood Station, Ningbo, Zhejiang 31501, P.R. China
| | - Deyi Xu
- The Ningbo Central Blood Station, Ningbo, Zhejiang 31501, P.R. China
| | - Qiang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Ri Zhang
- Department of Hematology, The First Affiliated Hospital of Soochow University, Soochow, Jiangsu 215006, P.R. China
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Mills EW, Green R, Ingolia NT. Slowed decay of mRNAs enhances platelet specific translation. Blood 2017; 129:e38-e48. [PMID: 28213379 PMCID: PMC5409447 DOI: 10.1182/blood-2016-08-736108] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/31/2016] [Indexed: 11/20/2022] Open
Abstract
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of messenger RNAs (mRNAs), ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA sequencing (RNA-Seq) and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro-derived MK cells and that these platelet-enriched transcripts are broadly occupied by ribosomes. We use RNA-Seq of synchronized populations of in vitro-derived platelet-like particles to show that mRNA decay strongly shapes the nascent platelet transcriptome. Our data suggest that the decay of platelet mRNAs is slowed by the natural loss of the mRNA surveillance and ribosome rescue factor Pelota.
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Affiliation(s)
- Eric W Mills
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD; and
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicholas T Ingolia
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD; and
- Department of Molecular Cell Biology, Center for RNA Systems Biology, Glenn Center for Aging Research, University of California Berkeley, Berkeley, CA
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38
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Abstract
A wide variety of clinical conditions, associated with low circulating platelet counts, require platelet transfusion in order to normalize hemostatic function. Although single-donor apheresis platelets bear the lowest risk of transfusion-transmitted infections, pathogen reduction technologies (PRT) are being implemented worldwide to reduce this risk further through inactivation of known, emergent and as yet to be discovered nucleic acid-based pathogens. Human blood platelets are now known to harbor a diverse transcriptome, important to their function and comprised of >5000 protein-coding messenger RNAs and different classes of non-coding RNAs, including microRNAs. Our appreciation of the nucleic acid-dependent functions of platelets is likely to increase. On the other hand, the side effects of PRT on platelet function are underappreciated. Recent evidences suggest that PRT may compromise platelets' responsiveness to agonists, and induce platelet activation. For instance, platelets have the propensity to release proinflammatory microparticles (MPs) upon activation, and the possibility that PRT may enhance the production of platelet MPs in platelet concentrates (PCs) appears likely. With this in mind, it would be timely and appropriate to investigate other means to inactivate pathogens more specifically, or to modify the currently available PRT so to better preserve the platelet function and improve the safety of PCs; platelets' perspective to PRT deserves to be considered.
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Affiliation(s)
- Abdimajid Osman
- a Department of Clinical Chemistry , Region Östergötland , Linköping , Sweden.,b Department of Clinical and Experimental Medicine , University of Linköping , Linköping , Sweden
| | - Walter E Hitzler
- c Transfusion Center, University Medical Center of the Johannes Gutenberg University Mainz , Hochhaus Augustusplatz , Mainz , Germany
| | - Patrick Provost
- d CHUQ Research Center/CHUL , 2705 Blvd Laurier, Quebec , QC , Canada.,e Faculty of Medicine , Université Laval , Quebec , QC , Canada
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39
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Provost P. The clinical significance of platelet microparticle-associated microRNAs. ACTA ACUST UNITED AC 2017; 55:657-666. [DOI: 10.1515/cclm-2016-0895] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/30/2016] [Indexed: 02/06/2023]
Abstract
AbstractCirculating blood platelets play a central role in the maintenance of hemostasis. They adhere to subendothelial extracellular matrix proteins that become exposed upon vessel wall damage, which is followed by platelet activation, further platelet recruitment, platelet aggregation and formation of an occlusive, or non-occlusive, platelet thrombus. Platelets host a surprisingly diverse transcriptome, which is comprised of ~9500 messenger RNAs (mRNAs) and different classes of non-coding RNAs, including microRNAs, as well as a significant repertoire of proteins that contribute to their primary (adhesion, aggregation, granule secretion) and alternative (RNA transfer, mRNA translation, immune regulation) functions. Platelets have the propensity to release microparticles (MPs; 0.1–1 μm in diameter) upon activation, which may mediate inflammatory responses and contribute to exacerbate inflammatory diseases and conditions. Carrying components of the platelets’ cytoplasm, platelet MPs may exert their effects on recipient cells by transferring their content in platelet-derived bioactive lipid mediators, cytokines, mRNAs and microRNAs. Platelet MP-associated microRNAs may thus function also outside of platelets and play an important role in intercellular signaling and gene expression programming across the entire circulatory system. The role and importance of platelet MP-associated microRNAs in various aspects of biology and pathophysiology are increasingly recognized, and now provide the scientific basis and rationale to support further translational research and clinical studies. The clinical significance, pathophysiological role as well as the diagnostic and therapeutic potential of platelet MP-associated microRNAs in cardiovascular diseases, platelet transfusion and cancer will be discussed.
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40
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Pienimaeki‐Roemer A, Konovalova T, Musri MM, Sigruener A, Boettcher A, Meister G, Schmitz G. Transcriptomic profiling of platelet senescence and platelet extracellular vesicles. Transfusion 2016; 57:144-156. [DOI: 10.1111/trf.13896] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 07/09/2016] [Accepted: 07/17/2016] [Indexed: 12/12/2022]
Affiliation(s)
| | - Tatiana Konovalova
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Melina M. Musri
- Institute for Biochemistry I, Faculty of Biology and Preclinical Medicine, University of RegensburgRegensburg Germany
| | - Alexander Sigruener
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Alfred Boettcher
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Gunter Meister
- Institute for Biochemistry I, Faculty of Biology and Preclinical Medicine, University of RegensburgRegensburg Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
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41
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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42
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Mogilyansky E, Clark P, Quann K, Zhou H, Londin E, Jing Y, Rigoutsos I. Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b. Front Genet 2016; 7:143. [PMID: 27630665 PMCID: PMC5005319 DOI: 10.3389/fgene.2016.00143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/21/2016] [Indexed: 12/31/2022] Open
Abstract
Breast cancer type 2, early onset susceptibility gene (BRCA2) is a major component of the homologous recombination DNA repair pathway. It acts as a tumor suppressor whose function is often lost in cancers. Patients with specific mutations in the BRCA2 gene often display discrete clinical, histopathological, and molecular features. However, a subset of sporadic cancers has wild type BRCA2 and display defects in the homology-directed repair pathway, which is the hallmark of ‘BRCAness.’ The mechanisms by which BRCAness arises are not well understood but post-transcriptional regulation of BRCA2 gene expression by microRNAs (miRNAs) may contribute to this phenotype. Here, we examine the post-transcriptional effects that some members of the six-miRNA cluster known as the miR-17/92 cluster have on the abundance of BRCA2’s messenger RNA (mRNA) and protein. We discuss two interactions involving the miR-19a and miR-19b members of the cluster and the 3′UTR of BRCA2’s mRNA. We investigated these miRNA:mRNA interactions in 15 cell lines derived from pancreatic, breast, colon, and kidney tissue. We show that over-expression of these two miRNAs results in a concomitant decrease of BRCA2’s mRNA and protein expression in a subset of the tested cell lines. Additionally, using luciferase reporter assays we identified direct interactions between miR-19a/miR-19b and a miRNA response element (MRE) in BRCA2’s 3′UTR. Our results suggest that BRCA2 is subject to a complex post-transcriptional regulatory program that has specific dependencies on the genetic and phenotypic background of cell types.
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Affiliation(s)
- Elena Mogilyansky
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Peter Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia PA, USA
| | - Kevin Quann
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Honglei Zhou
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA
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43
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Abstract
In this issue of Blood, Alhasan et al report the existence of circular RNAs (circRNAs) in circulating human platelets, thereby revealing yet another facet of their already diverse transcriptome.
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44
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Klein‐Bosgoed C, Schubert P, Devine DV. Riboflavin and ultraviolet illumination affects selected platelet mRNA transcript amounts differently. Transfusion 2016; 56:2286-95. [DOI: 10.1111/trf.13715] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/17/2016] [Accepted: 05/31/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Christa Klein‐Bosgoed
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
| | - Peter Schubert
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
- Canadian Blood Services Centre for InnovationVancouver BC Canada
| | - Dana V. Devine
- Department of Pathology and Laboratory Medicine and Centre for Blood ResearchUniversity of British Columbia
- Canadian Blood Services Centre for InnovationVancouver BC Canada
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45
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Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 2016; 6:24797-822. [PMID: 26325506 PMCID: PMC4694795 DOI: 10.18632/oncotarget.4695] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/20/2015] [Indexed: 12/21/2022] Open
Abstract
We analyzed transcriptomic data from 452 healthy men and women representing five different human populations and two races, and, 311 breast cancer samples from The Cancer Genome Atlas. Our studies revealed numerous constitutive, distinct fragments with overlapping sequences and quantized lengths that persist across dozens of individuals and arise from the genomic loci of all nuclear and mitochondrial human transfer RNAs (tRNAs). Surprisingly, we discovered that the tRNA fragments' length, starting and ending points, and relative abundance depend on gender, population, race and also on amino acid identity, anticodon, genomic locus, tissue, disease, and disease subtype. Moreover, the length distribution of mitochondrially-encoded tRNAs differs from that of nuclearly-encoded tRNAs, and the specifics of these distributions depend on tissue. Notably, tRNA fragments from the same anticodon do not have correlated abundances. We also report on a novel category of tRNA fragments that significantly contribute to the differences we observe across tissues, genders, populations, and races: these fragments, referred to as i-tRFs, are abundant in human tissues, wholly internal to the respective mature tRNA, and can straddle the anticodon. HITS-CLIP data analysis revealed that tRNA fragments are loaded on Argonaute in a cell-dependent manner, suggesting cell-dependent functional roles through the RNA interference pathway. We validated experimentally two i-tRF molecules: the first was found in 21 of 22 tested breast tumor and adjacent normal samples and was differentially abundant between health and disease whereas the second was found in all eight tested breast cancer cell lines.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Juan Palazzo
- Department of Pathology Anatomy and Cell Biology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
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46
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Wright JR, Amisten S, Goodall AH, Mahaut-Smith MP. Transcriptomic analysis of the ion channelome of human platelets and megakaryocytic cell lines. Thromb Haemost 2016; 116:272-84. [PMID: 27277069 PMCID: PMC5080539 DOI: 10.1160/th15-11-0891] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/30/2016] [Indexed: 11/05/2022]
Abstract
Ion channels have crucial roles in all cell types and represent important therapeutic targets. Approximately 20 ion channels have been reported in human platelets; however, no systematic study has been undertaken to define the platelet channelome. These membrane proteins need only be expressed at low copy number to influence function and may not be detected using proteomic or transcriptomic microarray approaches. In our recent work, quantitative real-time PCR (qPCR) provided key evidence that Kv1.3 is responsible for the voltage-dependent K+ conductance of platelets and megakaryocytes. The present study has expanded this approach to assess relative expression of 402 ion channels and channel regulatory genes in human platelets and three megakaryoblastic/erythroleukaemic cell lines. mRNA levels in platelets are low compared to other blood cells, therefore an improved method of isolating platelets was developed. This used a cocktail of inhibitors to prevent formation of leukocyte-platelet aggregates, and a combination of positive and negative immunomagnetic cell separation, followed by rapid extraction of mRNA. Expression of 34 channel-related transcripts was quantified in platelets, including 24 with unknown roles in platelet function, but that were detected at levels comparable to ion channels with established roles in haemostasis or thrombosis. Trace expression of a further 50 ion channel genes was also detected. More extensive channelomes were detected in MEG-01, CHRF-288-11 and HEL cells (195, 185 and 197 transcripts, respectively), but lacked several channels observed in the platelet. These "channelome" datasets provide an important resource for further studies of ion channel function in the platelet and megakaryocyte.
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Affiliation(s)
| | | | | | - Martyn P Mahaut-Smith
- Prof. Martyn Mahaut-Smith, PhD, Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LEI 7RH, UK, Tel.: +44 116 229 7135, E-mail:
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47
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Osman A, Hitzler WE, Provost P. Peculiarities of studying the effects of pathogen reduction technologies on platelets. Proteomics Clin Appl 2016; 10:805-15. [PMID: 27095411 DOI: 10.1002/prca.201500124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/27/2016] [Accepted: 04/14/2016] [Indexed: 12/31/2022]
Abstract
The transfusion of platelet concentrates (PCs) is mainly used for treatment of thrombocytopenic, trauma or surgery patients. The integrity and safety of these platelet preparations, however, is compromised by the presence of pathogens, such as viruses, bacteria and parasites. The transfer of allogeneic donor leukocytes contaminating PCs can also potentially cause adverse reactions in recipients. These considerations prompted the development and implementation of pathogen reduction technologies (PRT), which are based on chemically induced cross-linking and inactivation of nucleic acids. While the incumbent PRT may provide some protection against transfusion-transmitted infections, they are ineffective against infectious prions and may not inactivate other emerging pathogens. In addition, the safety of PRT concerning platelet viability and function has been questioned in several reports. Recent studies suggest that PRT, such as Intercept, may adversely affect the messenger RNA (mRNA) and microRNA content of platelets, as well as their functional integrity, which may compromise the clinical benefits of PRT. Here, we will discuss about the peculiarities of studying the effects of PRT on platelets, which will need to be taken into account in future studies aimed to characterize further, and polish, the rugged side of this otherwise useful and potentially important approach in transfusion medicine.
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Affiliation(s)
- Abdimajid Osman
- Department of Clinical Chemistry, Region Östergötland, Linköping, Sweden.,Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden
| | - Walter E Hitzler
- Transfusion Center, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Patrick Provost
- CHUQ Research Center/CHUL, Quebec, QC, Canada.,Faculty of Medicine, Université Laval, Quebec, QC, Canada
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48
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Simon L, Chen E, Edelstein L, Kong X, Bhatlekar S, Rigoutsos I, Bray P, Shaw C. Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. Am J Hum Genet 2016; 98:883-897. [PMID: 27132591 DOI: 10.1016/j.ajhg.2016.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/11/2016] [Indexed: 02/07/2023] Open
Abstract
Platelets play a central role in ischemic cardiovascular events. Cardiovascular disease (CVD) is a major cause of death worldwide. Numerous genome-wide association studies (GWASs) have identified loci associated with CVD risk. However, our understanding of how these variants contribute to disease is limited. Using data from the platelet RNA and expression 1 (PRAX1) study, we analyzed cis expression quantitative trait loci (eQTLs) in platelets from 154 normal human subjects. We confirmed these results in silico by performing allele-specific expression (ASE) analysis, which demonstrated that the allelic directionality of eQTLs and ASE patterns correlate significantly. Comparison of platelet eQTLs with data from the Genotype-Tissue Expression (GTEx) project revealed that a number of platelet eQTLs are platelet specific and that platelet eQTL peaks localize to the gene body at a higher rate than eQTLs from other tissues. Upon integration with data from previously published GWASs, we found that the trait-associated variant rs1474868 coincides with the eQTL peak for mitofusin 2 (MFN2). Additional experimental and computational analyses revealed that this eQTL is linked to an unannotated alternate MFN2 start site preferentially expressed in platelets. Integration of phenotype data from the PRAX1 study showed that MFN2 expression levels were significantly associated with platelet count. This study links the variant rs1474868 to a platelet-specific regulatory role for MFN2 and demonstrates the utility of integrating multi-omic data with eQTL analysis in disease-relevant tissues for interpreting GWAS results.
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49
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New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach. Hum Genet 2016; 135:403-414. [DOI: 10.1007/s00439-016-1642-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/23/2016] [Indexed: 10/22/2022]
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50
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Angénieux C, Maître B, Eckly A, Lanza F, Gachet C, de la Salle H. Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity. PLoS One 2016; 11:e0148064. [PMID: 26808079 PMCID: PMC4726520 DOI: 10.1371/journal.pone.0148064] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/12/2016] [Indexed: 01/23/2023] Open
Abstract
Previous investigations have indicated that RNAs are mostly present in the minor population of the youngest platelets, whereas translation in platelets could be biologically important. To attempt to solve this paradox, we studied changes in the RNA content of reticulated platelets, i.e., young cells brightly stained by thiazole orange (TObright), a fluorescent probe for RNAs. We provoked in mice strong thrombocytopenia followed by dramatic thrombocytosis characterized by a short period with a vast majority of reticulated platelets. During thrombocytosis, the TObright platelet count rapidly reached a maximum, after which TOdim platelets accumulated, suggesting that most of the former were converted into the latter within 12 h. Experiments on platelets, freshly isolated or incubated ex vivo at 37°C, indicated that their “RNA content”, here corresponding to the amounts of extracted RNA, and the percentage of TObright platelets were positively correlated. The “RNA Content” normalized to the number of platelets could be 20 to 40 fold higher when 80–90% of the cells were reticulated (20–40 fg/platelet), than when only 5–10% of control cells were TObright (less than 1fg/platelet). TObright platelets, incubated ex vivo at 37°C or transfused into mice, became TOdim within 24 h. Ex vivo at 37°C, platelets lost about half of their ribosomal and beta actin RNAs within 6 hours, and more than 98% of them after 24 hours. Accordingly, fluorescence in situ hybridization techniques confirmed the presence of beta actin mRNAs in most reticulated-enriched platelets, but detected them in only a minor subset of control platelets. In vitro, constitutive translation decreased considerably within less than 6 hours, questioning how protein synthesis in platelets, especially in non-reticulated ones, could have a biological function in vivo. Nevertheless, constitutive transient translation in young platelets under pathological conditions characterized by a dramatic increase in circulating reticulated platelets could deserve to be investigated.
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Affiliation(s)
- Catherine Angénieux
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Blandine Maître
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Anita Eckly
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - François Lanza
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Christian Gachet
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Henri de la Salle
- UMR_S949, INSERM, Strasbourg, France
- Etablissement Français du Sang-Alsace (EFS-Alsace), Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- * E-mail:
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