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Banerjee M, Rowley JW, Stubben CJ, Tolley ND, Freson K, Nelson B, Nagy B, Fejes Z, Blair AM, Turro E, Gresele P, Taranta GC, Bury L, Falcinelli E, Lordkipanidzé M, Alessi MC, Johnson AD, Bakchoul T, Ramstrom S, Frontini M, Camera M, Brambilla M, Campbell RA, Rondina MT. Prospective, international, multisite comparison of platelet isolation techniques for genome-wide transcriptomics: communication from the SSC of the ISTH. J Thromb Haemost 2024:S1538-7836(24)00376-3. [PMID: 38969303 DOI: 10.1016/j.jtha.2024.06.017] [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: 05/09/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024]
Abstract
Genome-wide platelet transcriptomics is increasingly used to uncover new aspects of platelet biology and as a diagnostic and prognostic tool. Nevertheless, platelet isolation methods for transcriptomic studies are not standardized, introducing challenges for cross-study comparisons, data integration, and replication. In this prospective multicenter study, called "Standardizing Platelet Transcriptomics for Discovery, Diagnostics, and Therapeutics in the Thrombosis and Hemostasis Community (STRIDE)" by the International Society on Thrombosis and Haemostasis Scientific and Standardization Committees, we assessed how 3 of the most commonly used platelet isolation protocols influence metrics from next-generation bulk RNA sequencing and functional assays. Compared with washing alone, more stringent removal of leukocytes by anti-CD45 beads or PALL filters resulted in a sufficient quantity of RNA for next-generation sequencing and similar quality of RNA sequencing metrics. Importantly, stringent removal of leukocytes resulted in the lower relative expression of known leukocyte-specific genes and the higher relative expression of known platelet-specific genes. The results were consistent across enrolling sites, suggesting that the techniques are transferrable and reproducible. Moreover, all 3 isolation techniques did not influence basal platelet reactivity, but agonist-induced integrin αIIbβ3 activation is reduced by anti-CD45 bead isolation compared with washing alone. In conclusion, the isolation technique chosen influences genome-wide transcriptional and functional assays in platelets. These results should help the research community make informed choices about platelet isolation techniques in their own platelet studies.
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Affiliation(s)
- Meenakshi Banerjee
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA
| | - Jesse W Rowley
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA; Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Chris J Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Neal D Tolley
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Katholeike Universiteit (KU) Leuven, Leuven, Belgium
| | - Benjamin Nelson
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Antoinette M Blair
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paolo Gresele
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Loredana Bury
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Marie Lordkipanidzé
- Research Center, Montreal Heart Institute, Montreal, Quebec, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, Quebec, Canada
| | - Marie-Christine Alessi
- Cardiovascular and Nutrition Centre (C2VN), Aix Marseille University, Institut National de la Sante et de la Recherche Medicale (INSERM), National Research Institute for Agriculture, Food and Environment (INRAE), Marseille, France
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts, USA; The Framingham Heart Study, Framingham, Massachusetts, USA
| | - Tamam Bakchoul
- Department of Transfusion Medicine, Medical Faculty of Tubingen, University of Tubingen, Tubingen, Germany
| | - Sofia Ramstrom
- Cardiovascular Research Centre, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mattia Frontini
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, Exeter, United Kingdom
| | - Marina Camera
- Unit of Cell and Molecular Biology in Cardiovascular Diseases, Centro Cardiologico Monzino, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Department of Pharmaceutical Sciences, Università Degli Studi Di Milano, Milan, Italy
| | - Marta Brambilla
- Unit of Cell and Molecular Biology in Cardiovascular Diseases, Centro Cardiologico Monzino, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Robert A Campbell
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA; Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Matthew T Rondina
- University of Utah Molecular Medicine Program, Eccles Institute of Human Genetics, Salt Lake City, Utah, USA; Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA; George E. Wahlen Veterans Affairs Medical Center & Geriatric Research Education and Clinical Center (GRECC), Salt Lake City, Utah, USA.
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2
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Affiliation(s)
- Julie B Larsen
- Thrombosis and Haemostasis Research Unit, Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Lekva T, Sundaram AYF, Roland MCP, Åsheim J, Michelsen AE, Norwitz ER, Aukrust P, Gilfillan GD, Ueland T. Platelet and mitochondrial RNA is decreased in plasma-derived extracellular vesicles in women with preeclampsia-an exploratory study. BMC Med 2023; 21:458. [PMID: 37996819 PMCID: PMC10666366 DOI: 10.1186/s12916-023-03178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Circulating extracellular vesicles (EVs) are increased in preeclampsia (PE) and are associated with severity and progression. We examined in this exploratory cohort study if the mRNAs and long noncoding RNAs (lncRNAs) in plasma-derived EVs were dysregulated in PE compared to normal pregnancy and display different temporal patterns during gestation. METHODS We isolated EVs from plasma at weeks 22-24 and 36-38 in women with and without PE (n=7 in each group) and performed RNA-seq, focusing on mRNAs and lncRNAs. We validated highly expressed mitochondrial and platelet-derived RNAs discovered from central pathways in 60 women with/without PE. We examined further one of the regulated RNAs, noncoding mitochondrially encoded tRNA alanine (MT-TA), in leukocytes and plasma to investigate its biomarker potential and association with clinical markers of PE. RESULTS We found abundant levels of platelet-derived and mitochondrial RNAs in EVs. Expression of these RNAs were decreased and lncRNAs increased in EVs from PE compared to without PE. These findings were further validated by qPCR for mitochondrial RNAs MT-TA, MT-ND2, MT-CYB and platelet-derived RNAs PPBP, PF4, CLU in EVs. Decreased expression of mitochondrial tRNA MT-TA in leukocytes at 22-24 weeks was strongly associated with the subsequent development of PE. CONCLUSIONS Platelet-derived and mitochondrial RNA were highly expressed in plasma EVs and were decreased in EVs isolated from women with PE compared to without PE. LncRNAs were mostly increased in PE. The MT-TA in leukocytes may be a useful biomarker for prediction and/or early detection of PE.
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Affiliation(s)
- Tove Lekva
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.
| | - Arvind Y Fm Sundaram
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | - June Åsheim
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Annika E Michelsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Gregor D Gilfillan
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
- K. G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
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4
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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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Allan HE, Vadgama A, Armstrong PC, Warner TD. Platelet ageing: A review. Thromb Res 2023; 231:214-222. [PMID: 36587993 DOI: 10.1016/j.thromres.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Platelet ageing is an area of research which has gained much interest in recent years. Newly formed platelets, often referred to as reticulated platelets, young platelets or immature platelets, are defined as RNA-enriched and have long been thought to be hyper-reactive. This latter view is largely rooted in associations and observations in patient groups with shortened platelet half-lives who often present with increased proportions of newly formed platelets. Evidence from such groups suggests that an increased proportion of newly formed platelets is associated with an increased risk of thrombotic events and a reduced effectiveness of standard anti-platelet therapies. Whilst research has highlighted the existence of platelet subpopulations based on function, size and age within patient groups, the common intrinsic changes which occur as platelets age within the circulation are only just being explored. By understanding the changes that occur during the natural ageing processes of platelets, we may be able to identify the triggers for alterations in platelet life span and platelet reactivity. Here we review research on platelet ageing in the context of health and disease, paying particular attention to the experimental approaches taken and the robustness of conclusions that can be drawn.
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Affiliation(s)
- Harriet E Allan
- Centre for Immunobiology, Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom.
| | - Ami Vadgama
- Centre for Immunobiology, Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Paul C Armstrong
- Centre for Immunobiology, Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Timothy D Warner
- Centre for Immunobiology, Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
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Collinson RJ, Boey D, Wilson L, Ng ZY, Mirzai B, Chuah H, Leahy MF, Howman R, Linden M, Fuller K, Erber WN, Guo BB. PlateletSeq: A novel method for discovery of blood-based biomarkers. Methods 2023; 219:139-149. [PMID: 37813292 DOI: 10.1016/j.ymeth.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023] Open
Abstract
Platelets are small circulating fragments of cells that play important roles in thrombosis, haemostasis, immune response, inflammation and cancer growth. Although anucleate, they contain a rich RNA repertoire which offers an opportunity to characterise changes in platelet gene expression in health and disease. Whilst this can be achieved with conventional RNA sequencing, a large input of high-quality RNA, and hence blood volume, is required (unless a pre-amplification step is added), along with specialist bioinformatic skills for data analysis and interpretation. We have developed a transcriptomics next-generation sequencing-based approach that overcomes these limitations. Termed PlateletSeq, this method requires very low levels of RNA input and does not require specialist bioinformatic analytical skills. Here we describe the methodology, from sample collection to processing and data analysis. Specifically, blood samples can be stored for up to 8 days at 4 °C prior to analysis. Platelets are isolated using multi-step centrifugation and a purity of ≤ 1 leucocyte per 0.26x106 platelets is optimal for gene expression analysis. We have applied PlateletSeq to normal adult blood samples and show there are no age-associated variations and only minor gender-associated differences. In contrast, platelets from patients with myeloproliferative neoplasms show differences in platelet transcript profiles from normal and between disease subtypes. This illustrates the potential applicability of PlateletSeq for biomarker discovery and studying platelet biology in patient samples. It also opens avenues for assessing platelet quality in other fields such as transfusion research.
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Affiliation(s)
- Ryan J Collinson
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia
| | - Darren Boey
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia
| | - Lynne Wilson
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia
| | - Zi Yun Ng
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia; Royal Perth Hospital, Department of Health Western Australia, Perth, W.A., Australia
| | - Bob Mirzai
- PathWest Laboratory Medicine, Nedlands, W.A., Australia
| | - Hun Chuah
- Royal Perth Hospital, Department of Health Western Australia, Perth, W.A., Australia; PathWest Laboratory Medicine, Nedlands, W.A., Australia; Rockingham General Hospital, Department of Health Western Australia, Rockingham, W.A., Australia
| | - Michael F Leahy
- Royal Perth Hospital, Department of Health Western Australia, Perth, W.A., Australia; PathWest Laboratory Medicine, Nedlands, W.A., Australia; Medical School, The University of Western Australia, Crawley, W.A., Australia
| | - Rebecca Howman
- Sir Charles Gairdner Hospital, Department of Health Western Australia, Nedlands, W.A., Australia
| | - Matthew Linden
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia
| | - Kathy Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia; PathWest Laboratory Medicine, Nedlands, W.A., Australia
| | - Belinda B Guo
- School of Biomedical Sciences, The University of Western Australia, Crawley, W.A., Australia.
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Huber LT, Kraus JM, Ezić J, Wanli A, Groth M, Laban S, Hoffmann TK, Wollenberg B, Kestler HA, Brunner C. Liquid biopsy: an examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for predictive molecular tumor markers. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:422-446. [PMID: 37455825 PMCID: PMC10344902 DOI: 10.37349/etat.2023.00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 07/18/2023] Open
Abstract
Aim Recently, a tumor cell-platelet interaction was identified in different tumor entities, resulting in a transfer of tumor-derived RNA into platelets, named further "tumor-educated platelets (TEP)". The present pilot study aims to investigate whether such a tumor-platelet transfer of RNA occurs also in patients suffering from head and neck squamous cell carcinoma (HNSCC). Methods Sequencing analysis of RNA derived from platelets of tumor patients (TPs) and healthy donors (HDs) were performed. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used for verification of differentially expressed genes in platelets from TPs and HDs in a second cohort of patients and HDs. Data were analyzed by applying bioinformatic tools. Results Sequencing of RNA derived from the tumor as well as from platelets of TPs and HDs revealed 426 significantly differentially existing RNA, at which 406 RNA were more and 20 RNA less abundant in platelets from TPs in comparison to that of HDs. In TPs' platelets, abundantly existing RNA coding for 49 genes were detected, characteristically expressed in epithelial cells and RNA, the products of which are involved in tumor progression. Applying bioinformatic tools and verification on a second TP/HD cohort, collagen type I alpha 1 chain (COL1A1) and zinc finger protein 750 (ZNF750) were identified as the strongest potentially platelet-RNA-sequencing (RNA-seq)-based biomarkers for HNSCC. Conclusions These results indicate a transfer of tumor-derived messenger RNA (mRNA) into platelets of HNSCC patients. Therefore, analyses of a patient's platelet RNA could be an efficient option for liquid biopsy in order to diagnose HNSCC or to monitor tumorigenesis as well as therapeutic responses at any time and in real time.
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Affiliation(s)
- Lisa T. Huber
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Jasmin Ezić
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Amin Wanli
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Marco Groth
- Leibniz Institute of Aging – Fritz Lipmann Institute, CF DNA sequencing, 07745 Jena, Germany
| | - Simon Laban
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Thomas K. Hoffmann
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Barbara Wollenberg
- Clinic for Otorhinolaryngology, Head and Neck Surgery, Technical University of Munich, 80333 Munich, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
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de Sousa DMB, Poupardin R, Villeda SA, Schroer AB, Fröhlich T, Frey V, Staffen W, Mrowetz H, Altendorfer B, Unger MS, Iglseder B, Paulweber B, Trinka E, Cadamuro J, Drerup M, Schallmoser K, Aigner L, Kniewallner KM. The platelet transcriptome and proteome in Alzheimer's disease and aging: an exploratory cross-sectional study. Front Mol Biosci 2023; 10:1196083. [PMID: 37457829 PMCID: PMC10348715 DOI: 10.3389/fmolb.2023.1196083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction: Alzheimer's disease (AD) and aging are associated with platelet hyperactivity. However, the mechanisms underlying abnormal platelet function in AD and aging are yet poorly understood. Methods: To explore the molecular profile of AD and aged platelets, we investigated platelet activation (i.e., CD62P expression), proteome and transcriptome in AD patients, non-demented elderly, and young individuals as controls. Results: AD, aged and young individuals showed similar levels of platelet activation based on CD62P expression. However, AD and aged individuals had a proteomic signature suggestive of increased platelet activation compared with young controls. Transcriptomic profiling suggested the dysregulation of proteolytic machinery involved in regulating platelet function, particularly the ubiquitin-proteasome system in AD and autophagy in aging. The functional implication of these transcriptomic alterations remains unclear and requires further investigation. Discussion: Our data strengthen the evidence of enhanced platelet activation in aging and provide a first glimpse of the platelet transcriptomic changes occurring in AD.
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Affiliation(s)
- Diana M. Bessa de Sousa
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Rodolphe Poupardin
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Experimental and Clinical Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Saul A. Villeda
- Department of Anatomy, University of California San Francisco, San Francisco, CA, United States
| | - Adam B. Schroer
- Department of Anatomy, University of California San Francisco, San Francisco, CA, United States
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Vanessa Frey
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Wolfgang Staffen
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Heike Mrowetz
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Barbara Altendorfer
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Michael S. Unger
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Iglseder
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Paulweber
- Department of Internal Medicine, St. Johanns University Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Eugen Trinka
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
- Department of Public Health, Health Services Research and Health Technology Assessment, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
- Neuroscience Institute, Christian Doppler University Hospital, Paracelsus Medical University and Centre for Cognitive Neuroscience Salzburg, Salzburg, Austria
| | - Janne Cadamuro
- Department of Laboratory Medicine, University Hospital SALK, Salzburg, Austria
| | - Martin Drerup
- Department of Urology, Paracelsus Medical University, Salzburg, Austria
| | - Katharina Schallmoser
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Department of Transfusion Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Kathrin M. Kniewallner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
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Cimmino G, Conte S, Palumbo D, Sperlongano S, Torella M, Della Corte A, Golino P. The Novel Role of Noncoding RNAs in Modulating Platelet Function: Implications in Activation and Aggregation. Int J Mol Sci 2023; 24:ijms24087650. [PMID: 37108819 PMCID: PMC10144470 DOI: 10.3390/ijms24087650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
It is currently believed that plaque complication, with the consequent superimposed thrombosis, is a key factor in the clinical occurrence of acute coronary syndromes (ACSs). Platelets are major players in this process. Despite the considerable progress made by the new antithrombotic strategies (P2Y12 receptor inhibitors, new oral anticoagulants, thrombin direct inhibitors, etc.) in terms of a reduction in major cardiovascular events, a significant number of patients with previous ACSs treated with these drugs continue to experience events, indicating that the mechanisms of platelet remain largely unknown. In the last decade, our knowledge of platelet pathophysiology has improved. It has been reported that, in response to physiological and pathological stimuli, platelet activation is accompanied by de novo protein synthesis, through a rapid and particularly well-regulated translation of resident mRNAs of megakaryocytic derivation. Although the platelets are anucleate, they indeed contain an important fraction of mRNAs that can be quickly used for protein synthesis following their activation. A better understanding of the pathophysiology of platelet activation and the interaction with the main cellular components of the vascular wall will open up new perspectives in the treatment of the majority of thrombotic disorders, such as ACSs, stroke, and peripheral artery diseases before and after the acute event. In the present review, we will discuss the novel role of noncoding RNAs in modulating platelet function, highlighting the possible implications in activation and aggregation.
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Affiliation(s)
- Giovanni Cimmino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Stefano Conte
- Department of Translational Medical Sciences, Section of Lung Diseases, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Domenico Palumbo
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Simona Sperlongano
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
- Cardiology Unit, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Piazza Miraglia, 80138 Naples, Italy
| | - Michele Torella
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Alessandro Della Corte
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
| | - Paolo Golino
- Department of Translational Medical Sciences, Section of Cardiology, University of Campania Luigi Vanvitelli, L. Bianchi Street, 80131 Naples, Italy
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Cygert S, Pastuszak K, Górski F, Sieczczyński M, Juszczyk P, Rutkowski A, Lewalski S, Różański R, Jopek MA, Jassem J, Czyżewski A, Wurdinger T, Best MG, Żaczek AJ, Supernat A. Platelet-Based Liquid Biopsies through the Lens of Machine Learning. Cancers (Basel) 2023; 15:cancers15082336. [PMID: 37190262 DOI: 10.3390/cancers15082336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid biopsies offer minimally invasive diagnosis and monitoring of cancer disease. This biosource is often analyzed using sequencing, which generates highly complex data that can be used using machine learning tools. Nevertheless, validating the clinical applications of such methods is challenging. It requires: (a) using data from many patients; (b) verifying potential bias concerning sample collection; and (c) adding interpretability to the model. In this work, we have used RNA sequencing data of tumor-educated platelets (TEPs) and performed a binary classification (cancer vs. no-cancer). First, we compiled a large-scale dataset with more than a thousand donors. Further, we used different convolutional neural networks (CNNs) and boosting methods to evaluate the classifier performance. We have obtained an impressive result of 0.96 area under the curve. We then identified different clusters of splice variants using expert knowledge from the Kyoto Encyclopedia of Genes and Genomes (KEGG). Employing boosting algorithms, we identified the features with the highest predictive power. Finally, we tested the robustness of the models using test data from novel hospitals. Notably, we did not observe any decrease in model performance. Our work proves the great potential of using TEP data for cancer patient classification and opens the avenue for profound cancer diagnostics.
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Affiliation(s)
- Sebastian Cygert
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
- Ideas NCBR, 00-801 Warsaw, Poland
| | - Krzysztof Pastuszak
- Department of Algorithms and System Modeling, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Franciszek Górski
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | - Michał Sieczczyński
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | - Piotr Juszczyk
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | - Antoni Rutkowski
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | - Sebastian Lewalski
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | | | - Maksym Albin Jopek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Jacek Jassem
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Andrzej Czyżewski
- Department of Multimedia Systems, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, 80-233 Gdańsk, Poland
| | - Thomas Wurdinger
- Department of Neurosurgery, Amsterdam University Medical Center, 1081 Amsterdam, The Netherlands
| | - Myron G Best
- Department of Neurosurgery, Amsterdam University Medical Center, 1081 Amsterdam, The Netherlands
| | - Anna J Żaczek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Anna Supernat
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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11
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Liefaard MC, Moore KS, Mulder L, van den Broek D, Wesseling J, Sonke GS, Wessels LFA, Rookus M, Lips EH. Tumour-educated platelets for breast cancer detection: biological and technical insights. Br J Cancer 2023; 128:1572-1581. [PMID: 36765174 PMCID: PMC10070267 DOI: 10.1038/s41416-023-02174-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. METHODS Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses. RESULTS Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals. CONCLUSIONS We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.
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Affiliation(s)
- Marte C Liefaard
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kat S Moore
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Clinical Chemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Matti Rookus
- Department of Psychosocial and Epidemiology Research, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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12
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LL-37 Triggers Antimicrobial Activity in Human Platelets. Int J Mol Sci 2023; 24:ijms24032816. [PMID: 36769137 PMCID: PMC9917488 DOI: 10.3390/ijms24032816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Platelets play a crucial role in hemostasis and the immune response, mainly by recognizing signals associated with vascular damage. However, it has recently been discovered that the antimicrobial peptide LL-37 activates platelets in functions related to thrombus formation and inflammation. Therefore, this work aims to evaluate the effect of LL-37 on the activation of antimicrobial functions of human platelets. Our results show that platelets treated with LL-37 increase the surface expression of receptors (Toll-like receptors (TLRs) 2 and -4, CD32, CD206, Dectin-1, CD35, LOX-1, CD41, CD62P, and αIIbβ3 integrins) for the recognition of microorganisms, and molecules related to antigen presentation to T lymphocytes (CD80, CD86, and HLA-ABC) secrete the antimicrobial molecules: bactericidal/permeability-increasing protein (BPI), azurocidin, human neutrophil peptide (HNP) -1, and myeloperoxidase. They also translate azurocidin, and have enhanced binding to Escherichia coli, Staphylococcus aureus, and Candida albicans. Furthermore, the supernatant of LL-37-treated platelets can inhibit E. coli growth, or platelets can employ their LL-37 to inhibit microbial growth. In conclusion, these findings demonstrate that LL-37 participates in the antimicrobial function of human platelets.
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13
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An Insight into Platelets at Older Age: Cellular and Clinical Perspectives. Subcell Biochem 2023; 102:343-363. [PMID: 36600139 DOI: 10.1007/978-3-031-21410-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Higher access to medical care, advanced diagnostic tools, and overall public health improvements have favored increased humans lifespan. With a growing proportion of older adults, the associated costs to care for ageing-associated conditions will continue to grow. This chapter highlights recent cellular and clinical evidence of platelets at an older age, from the hyperreactive phenotype associated with thrombosis to the well-known hallmarks of ageing identifiable in platelets and their potential functional implications on platelets at an older age. Therefore, it is imperative to understand platelets' molecular and cellular mechanisms during ageing in health and disease. New knowledge will favor the development of new ways to prevent some of the age-associated complications where platelets are key players.
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14
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Xiang Y, Xiang P, Zhang L, Li Y, Zhang J. A narrative review for platelets and their RNAs in cancers: New concepts and clinical perspectives. Medicine (Baltimore) 2022; 101:e32539. [PMID: 36596034 PMCID: PMC9803462 DOI: 10.1097/md.0000000000032539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recent years have witnessed a growing body of evidence suggesting that platelets are involved in several stages of the metastatic process via direct or indirect interactions with cancer cells, contributing to the progression of neoplastic malignancies. Cancer cells can dynamically exchange components with platelets in and out of blood vessels, and directly phagocytose platelets to hijack their proteome, transcriptome, and secretome, or be remotely regulated by metabolites or microparticles released by platelets, resulting in phenotypic, genetic, and functional modifications. Moreover, platelet interactions with stromal and immune cells in the tumor microenvironment lead to alterations in their components, including the ribonucleic acid (RNA) profile, and complicate the impact of platelets on cancers. A deeper understanding of the roles of platelets and their RNAs in cancer will contribute to the development of anticancer strategies and the optimization of clinical management. Encouragingly, advances in high-throughput sequencing, bioinformatics data analysis, and machine learning have allowed scientists to explore the potential of platelet RNAs for cancer diagnosis, prognosis, and guiding treatment. However, the clinical application of this technique remains controversial and requires larger, multicenter studies with standardized protocols. Here, we integrate the latest evidence to provide a broader insight into the role of platelets in cancer progression and management, and propose standardized recommendations for the clinical utility of platelet RNAs to facilitate translation and benefit patients.
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Affiliation(s)
- Yunhui Xiang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Pinpin Xiang
- Department of Laboratory Medicine, Xiping Community Health Service Center of Longquanyi District Chengdu City, Chengdu, China
| | - Liuyun Zhang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanying Li
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Juan Zhang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- * Correspondence: Juan Zhang, Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, 32# West Second Section, First Ring Road, Qingyang District, Chengdu City, Sichuan Province 610072, China (e-mail: )
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15
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Pablo‐Torres C, Delgado‐Dolset MI, Sanchez‐Solares J, Mera‐Berriatua L, Núñez Martín Buitrago L, Reaño Martos M, Bueno JL, Escribese MM, Barber D, Gomez‐Casado C. A method based on plateletpheresis to obtain functional platelet, CD3 + and CD14 + matched populations for research immunological studies. Clin Exp Allergy 2022; 52:1157-1168. [PMID: 35757844 PMCID: PMC9796013 DOI: 10.1111/cea.14192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND In previous studies with peripheral blood cells, platelet factors were found to be associated with severe allergic phenotypes. A reliable method yielding highly concentrated and pure platelet samples is usually not available for immunological studies. Plateletpheresis is widely used in the clinics for donation purposes. In this study, we designed a protocol based on plateletpheresis to obtain Platelet-Rich Plasma (PRP), Platelet-Poor Plasma (PPP) as well as CD3+ and CD14+ cells matched samples from a waste plateletpheresis product for immunological studies. METHODS Twenty-seven subjects were voluntarily subjected to plateletpheresis. PRP, PPP and blood cell concentrate contained in a leukocyte reduction system chamber (LRSC) were obtained in this process. CD3+ and CD14+ cells were isolated from the LRSC by density-gradient centrifugation and positive magnetic bead isolation. RNA was isolated from PRP, CD3+ and CD14+ cell samples and used for transcriptomic studies by Affymetrix. PRP and PPP samples were used for platelet protein quantification by multiplex assays. RESULTS A reliable high yield method to obtain matched samples of PRP, PPP, CD3+ and CD14+ from a single donor for RNA and protein analyses has been designed. The RNA quality indicators (RQI) routinely used for other cell types were not suitable for platelet RNA characterization. Despite this, the platelet RNA was valid for transcriptomic studies by Affymetrix, as platelet transcripts obtained in our previous studies were confirmed in PRP samples. Platelet samples were enriched in platelet factors as determined in protein multiplex analysis. CONCLUSIONS We have developed a method that yields not only high content and pure platelet samples from a single donor but also CD3+ and CD14+ matched samples that can be used for RNA and protein analyses in immunological studies.
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Affiliation(s)
- Carmela Pablo‐Torres
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | - María Isabel Delgado‐Dolset
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain,Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistrySchool of PharmacySan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | - Javier Sanchez‐Solares
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | - Leticia Mera‐Berriatua
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | | | - Mar Reaño Martos
- Department of Allergy and ImmunologyPuerta de Hierro‐Majadahonda University HospitalMadridSpain
| | - José Luis Bueno
- Department of Hematology and HemotherapyPuerta de Hierro‐Majadahonda University HospitalMadridSpain
| | - Maria M. Escribese
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain
| | - Cristina Gomez‐Casado
- Institute of Applied Molecular Medicine (IMMA) Nemesio DíezDepartment of Basic Medical SciencesSchool of MedicineSan Pablo‐CEU UniversityCEU UniversitiesBoadilla del MonteSpain,Department of DermatologyMedical FacultyUniversity Hospital DüsseldorfHeinrich‐Heine‐University DüsseldorfDüsseldorfGermany
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16
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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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17
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Lee SH, Park NR, Kim JE. Bioinformatics of Differentially Expressed Genes in Phorbol 12-Myristate 13-Acetate-Induced Megakaryocytic Differentiation of K562 Cells by Microarray Analysis. Int J Mol Sci 2022; 23:ijms23084221. [PMID: 35457039 PMCID: PMC9031040 DOI: 10.3390/ijms23084221] [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: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/09/2022] [Indexed: 01/27/2023] Open
Abstract
Megakaryocytes are large hematopoietic cells present in the bone marrow cavity, comprising less than 0.1% of all bone marrow cells. Despite their small number, megakaryocytes play important roles in blood coagulation, inflammatory responses, and platelet production. However, little is known about changes in gene expression during megakaryocyte maturation. Here we identified the genes whose expression was changed during K562 leukemia cell differentiation into megakaryocytes using an Affymetrix GeneChip microarray to determine the multifunctionality of megakaryocytes. K562 cells were differentiated into mature megakaryocytes by treatment for 7 days with phorbol 12-myristate 13-acetate, and a microarray was performed using RNA obtained from both types of cells. The expression of 44,629 genes was compared between K562 cells and mature megakaryocytes, and 954 differentially expressed genes (DEGs) were selected based on a p-value < 0.05 and a fold change >2. The DEGs was further functionally classified using five major megakaryocyte function-associated clusters—inflammatory response, angiogenesis, cell migration, extracellular matrix, and secretion. Furthermore, interaction analysis based on the STRING database was used to generate interactions between the proteins translated from the DEGs. This study provides information on the bioinformatics of the DEGs in mature megakaryocytes after K562 cell differentiation.
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Affiliation(s)
- Seung-Hoon Lee
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (S.-H.L.); (N.R.P.)
- BK21 Four KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, Kyungpook National University, Daegu 41944, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
| | - Na Rae Park
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (S.-H.L.); (N.R.P.)
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
| | - Jung-Eun Kim
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (S.-H.L.); (N.R.P.)
- BK21 Four KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, Kyungpook National University, Daegu 41944, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
- Correspondence: ; Tel.: +82-53-420-4949
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18
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Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12040870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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19
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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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20
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Guettler J, Forstner D, Gauster M. Maternal platelets at the first trimester maternal-placental interface - Small players with great impact on placenta development. Placenta 2021; 125:61-67. [PMID: 34920861 DOI: 10.1016/j.placenta.2021.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022]
Abstract
In human pregnancy, maternal platelet counts decrease with each trimester, reaching a reduction by approximately ten percent at term in uncomplicated cases and recover to the levels of the non-pregnant state a few weeks postpartum. The time when maternal platelets start to occur in the early human placenta most likely coincides with the appearance of loosely cohesive endovascular trophoblast plugs showing capillary-sized channels by mid first trimester. At that time, platelets accumulate in intercellular gaps of anchoring parts of trophoblast columns and start to adhere to the surface of placental villi and the chorionic plate. This is considered as normal process that contributes to placenta development by acting on both the extravillous- and the villous trophoblast compartment. Release of platelet cargo into intercellular gaps of anchoring cell columns may affect partial epithelial-to-mesenchymal transition and invasiveness of extravillous trophoblasts as well as deposition of fibrinoid in the basal plate. Activation of maternal platelets on the villous surface leads to perivillous fibrin-type fibrinoid deposition, contributing to the shaping of the developing placental villi and the intervillous space. In contrast, excess platelet activation at the villous surface leads to deregulation of the endocrine activity, sterile inflammation and local apoptosis of the syncytiotrophoblast. Platelets and their released cargo are adapted to pregnancy, and may be altered in high-risk pregnancies. Identification of different maternal platelet subpopulations, which show differential procoagulant ability and different response to anti-platelet therapy, are promising new future directions in deciphering the role of maternal platelets in human placenta physiology.
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Affiliation(s)
- Jacqueline Guettler
- Division of Cell Biology, Histology and Embryology; Gottfried Schatz Research Center, Medical University of Graz; Graz, Austria
| | - Désirée Forstner
- Division of Cell Biology, Histology and Embryology; Gottfried Schatz Research Center, Medical University of Graz; Graz, Austria
| | - Martin Gauster
- Division of Cell Biology, Histology and Embryology; Gottfried Schatz Research Center, Medical University of Graz; Graz, Austria.
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21
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Shapiro S, Murphy L, Psaila B. Message in a platelet: decoding platelet transcriptomes in myeloproliferative neoplasms. Cell Rep Med 2021; 2:100433. [PMID: 34755142 PMCID: PMC8561304 DOI: 10.1016/j.xcrm.2021.100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Platelets are anucleate but contain a rich repertoire of mRNAs. In this issue of Cell Reports Medicine, Shen and colleagues1 present platelet transcriptomes from patients with myeloproliferative neoplasms to study disease mechanisms and generate a predictive algorithm for fibrotic progression.
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Affiliation(s)
- Susan Shapiro
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine and National Institutes for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lauren Murphy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine and National Institutes for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Bethan Psaila
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine and National Institutes for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
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