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1. Consensus guidelines for the validation of qRT-PCR assays in clinical research by the CardioRNA consortium

Author

EU-CardioRNA COST Action CA17129, de Gonzalo-Calvo, David, Marchese, Monica, Hellemans, Jan, Lakkisto, Päivi, Devaux, Yvan, HUSLAB, Department of Clinical Chemistry and Hematology, and University of Helsinki

Subjects
RNA, 3111 Biomedicine
Abstract

Despite promising findings, quantitative PCR (qPCR)-based tests for RNA quantification have experienced serious limitations in their clinical application. The noticeable lack of technical standardization remains a huge obstacle in the translation of qPCR-based tests. The incorporation of qPCR-based tests into the clinic will benefit from guidelines for clinical research assay validation. This will ultimately impact the clinical management of the patient, including diagnosis, prognosis, prediction, monitoring of the therapeutic response, and evaluation of toxicity. However, clear assay validation protocols for biomarker investigation in clinical trials using molecular assays are currently lacking. Here, we will focus on the necessary steps, including sample acquisition, processing and storage, RNA purification, target selection, assay design, and experimental design, that need to be taken toward the appropriate validation of qRT-PCR assays in clinical research. These recommendations can fill the gap between research use only (RUO) and in vitro diagnostics (IVD). Our contribution provides a tool for basic and clinical research for the development of validated assays in the intermediate steps of biomarker research. These guidelines are based on the current understanding and consensus within the EU-CardioRNA COST Action consortium (www. cardiorna.eu). Their applicability encompasses all clinical areas.

Published
2022

2. Catalyzing transcriptomics research in cardiovascular disease: The CardioRNA COST action CA17129

Author

Da Costa Gomes, Clarissa Pedrosa, Ágg, Bence, Andova, Andrejaana, Arslan, Serdal, Baker, Andrew, Barteková, Monika, Beis, Dimitris, Betsou, Fay, Bezzina Wettinger, Stephanie, Bugarski, Branko, Condorelli, Gianluigi, Da Silva, Gustavo José Justo, Danilin, Sabrina, De Gonzalo-Calvo, David, Buil, Alfonso, Carmo-Fonseca, Maria, Enguita, Francisco J., Felekkis, Kyriacos, Ferdinandy, Peter, Gyöngyösi, Mariann, Hackl, Matthias, Karaduzovic-Hadziabdic, Kanita, Hellemans, Jan, Heymans, Stephane, Hlavackova, Markéta, Hoydal, Morten Andre, Jankovic, Aleksandra, Jusic, Amela, Kardassis, Dimitris, Kerkelä, Risto, Kuster, Gabriela M., Lakkisto, Päivi, Leszek, Przemyslaw, Lustrek, Mitja, Maegdefessel, Lars, Martelli, Fabio, Novella, Susana, O’Brien, Timothy, Papaneophytou, Christos, Pedrazzini, Thierry, Pinet, Florence, Popescu, Octavian, Potoˇcnjak, Ines, Robinson, Emma L., Sasson, Shlomo, Scholz, Markus, Simionescu, Maya, Stoll, Monika, Varga, Zoltan V., Vinciguerra, Manlio, Xuereb, Angela, Yilmaz, Mehmet Birhan, Emanueli, Costanza, Devaux, Yvan, Formosa, Melissa Marie, EU-CardioRNA COST Action (CA17129), Repositório da Universidade de Lisboa, Luxembourg Institute of Health (LIH), Semmelweis University [Budapest], Jozef Stefan Institute [Ljubljana] (IJS), Cumhuriyet University [Sivas, Turkey], Queen's Medical Researche Institute, University of Edinburgh, Slovak Academy of Sciences (SAS), Biomedical Research Foundation of the Academy of Athens (BRFAA), Integrated BioBank of Luxembourg (IBBL), University of Malta [Malta], Faculty of Technology and Metallurgy [University of Belgrade], University of Belgrade [Belgrade], Humanitas Clinical and Research Center [Rozzano, Milan, Italy], Oslo University Hospital [Oslo], University of Oslo (UiO), Firalis SAS, Spanish National Research Council (CSIC), Universidade de Lisboa (ULISBOA), University of Cyprus [Nicosia], Medizinische Universität Wien = Medical University of Vienna, International University of Sarajevo, Maastricht University [Maastricht], Czech Academy of Sciences [Prague] (CAS), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Institute for Biological Research Sinisa Stankovic [Belgrade] (IBISS), University of Tuzla, University of Crete [Heraklion] (UOC), Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Foundation for Research and Technology - Hellas (FORTH), University of Oulu, University Hospital Basel [Basel], University of Basel (Unibas), Minerva Foundation Institute for Medical Research, Karolinska Institutet [Stockholm], Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Universitat de València (UV), National University of Ireland [Galway] (NUI Galway), Université de Lausanne (UNIL), Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Babes-Bolyai University [Cluj-Napoca] (UBB), The Hebrew University of Jerusalem (HUJ), Leipzig University, Institute of Cellular Biology and Pathology Nicolae Simionescu, Westfälische Wilhelms-Universität Münster (WWU), Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), National Heart and Lung Institute [London] (NHLI), Royal Brompton and Harefield NHS Foundation Trust-Imperial College London, EU-CardioRNA COST Action (CA17129), European Cooperation in Science and Technology, [Gomes, Clarissa Pedrosa da Costa -- Devaux, Yvan] Luxembourg Inst Hlth, Cardiovasc Res Unit, L-1445 Strassen, Luxembourg -- [Agg, Bence -- Ferdinandy, Peter -- Varga, Zoltan V.] Semmelweis Univ, Dept Pharmacol & Pharmacotherapy, H-1085 Budapest, Hungary -- [Andova, Andrejaana -- Lustrek, Mitja] Jozef Stefan Inst, Dept Intelligent Syst, Ljubljana 1000E, Slovenia -- [Arslan, Serdal] Cumhuriyet Univ, Fac Med, Dept Med Biol, TR-58140 Sivas, Turkey -- [Baker, Andrew] Univ Edinburgh, Ctr Cardiovasc Sci, Queens Med Res Inst, Edinburgh EH16 4TJ, Midlothian, Scotland -- [Bartekova, Monika] Slovak Acad Sci, Ctr Expt Med, Inst Heart Res, Bratislava 84104, Slovakia -- [Beis, Dimitris] Acad Athens, Biomed Res Fdn, Athens 11527, Greece -- [Betsou, Fay] Integrated BioBank Luxembourg, L-3550 Dudelange, Luxembourg -- [Wettinger, Stephanie Bezzina -- Xuereb, Angela] Univ Malta, Fac Hlth Sci, MSD-2080 Msida, Malta -- [Bugarski, Branko] Univ Belgrade, Fac Technol & Met, Belgrade 11000, Serbia -- [Condorelli, Gianluigi] Humanitas Res Hosp, Dept Cardiovasc, I-20089 Rozzano, Italy -- [da Silva, Gustavo Jose Justo] Oslo Univ Hosp, Inst Expt Med Res, PB 4956 Nydalen, NO-0424 Oslo, Norway -- [da Silva, Gustavo Jose Justo] Univ Oslo, PB 4956 Nydalen, NO-0424 Oslo, Norway -- [Danilin, Sabrina] Firalis, F-68330 Huningue, France -- [de Gonzalo-Calvo, David] CSIC, Inst Biomed Res Barcelona IIBB, Barcelona 08036, Spain -- [Buil, Alfonso] Mental Hlth Ctr Sct Hans, DK-4000 Roskilde, Denmark -- [Carmo-Fonseca, Maria -- Enguita, Francisco J.] Univ Lisbon, Fac Med, Inst Med Mol, P-1649028 Lisbon, Portugal -- [Felekkis, Kyriacos -- Papaneophytou, Christos] Univ Nicosia, Sch Sci & Engn, Dept Life & Hlth Sci, CY-2417 Nicosia, Cyprus -- [Gyoengyoesi, Mariann] Med Univ Vienna, Dept Cardiol, A-1090 Vienna, Austria -- [Hackl, Matthias] TAmiRNA, A-1190 Vienna, Austria -- [Karaduzovic-Hadziabdic, Kanita] Int Univ Sarajevo, Fac Engn & Nat Sci, Sarajevo 71210, Bosnia & Herceg -- [Hellemans, Jan] Biogazelle, B-9052 Zwijnaarde, Belgium -- [Heymans, Stephane] Maastricht Univ, Fac Hlth Med & Life Sci, Sch Cardiovasc Dis, NL-6229 ER Maastricht, Netherlands -- [Hlavackova, Marketa] Czech Acad Sci, Inst Physiol, Dept Dev Cardiol, Prague 14220, Czech Republic -- [Hoydal, Morten Andre] NTNU Norwegian Univ Technol & Sci, Fac Med & Hlth Sci, Dept Circulat & Med Imaging, NO-7489 Trondheim, Norway -- [Jankovic, Aleksandra] Univ Belgrade, Inst Biol Res Sinisa Stankovic, Dept Physiol, Belgrade 11000, Serbia -- [Jusic, Amela] Univ Tuzla, Fac Nat Sci & Math, Dept Biol, Tuzla 75000, Bosnia & Herceg -- [Kardassis, Dimitris] Univ Crete, Med Sch, Dept Basic Sci, Iraklion 71003, Crete, Greece -- [Kardassis, Dimitris] Fdn Res & Technol Hellas, Inst Mol Biol & Biotechnol, Iraklion 71003, Crete, Greece -- [Kerkela, Risto] Univ Oulu, Res Unit Biomed, Oulu 90014, Finland -- [Kuster, Gabriela M.] Univ Hosp, Dept Biomed & Clin Cardiol, CH-4031 Basel, Switzerland -- [Kuster, Gabriela M.] Univ Basel, CH-4031 Basel, Switzerland -- [Lakkisto, Paivi] Minerva Fdn, Helsinki 00290, Finland -- [Leszek, Przemyslaw] Cardinal Stefan Wyszynski Inst Cardiol, PL-04628 Warsaw, Poland -- [Maegdefessel, Lars] Karolinska Inst, Ctr Mol Med, S-17176 Stockholm, Sweden -- [Martelli, Fabio] IRCCS Policlin San Donato, Mol Cardiol Lab, I-20097 Milan, Italy -- [Novella, Susana] Univ Valencia, Dept Physiol, Valencia 46010, Spain -- [Novella, Susana] INCLIVA Biomed Res Inst INCLIVA, Valencia 46010, Spain -- [O'Brien, Timothy] Natl Univ Ireland Galway, Regenerat Med Inst REMEDI, Galway H91 TK33, Ireland -- [Pedrazzini, Thierry] Univ Lausanne, Med Sch, Dept Cardiovasc Med, Expt Cardiol Unit,Div Cardiol, CH-1011 Lausanne, Switzerland -- [Pinet, Florence] Inst Pasteur, INSERM, F-59019 Lille, France -- [Popescu, Octavian] Babes Bolyai Univ, Cluj Napoca 400084, Romania -- [Potocnjak, Ines] Univ Hosp Ctr Sisters Char, Inst Clin Med Res & Educ, Zagreb 10000, Croatia -- [Robinson, Emma] Maastricht Univ, Fac Hlth Med & Life Sci, Ctr Heart Failure Res, Dept Cardiol, NL-6229 ER Maastricht, Netherlands -- [Sasson, Shlomo] Hebrew Univ Jerusalem, Fac Med, Inst Drug Res, IL-91120 Jerusalem, Israel -- [Scholz, Markus] Univ Leipzig, Med Fac, Inst Med Informat Stat & Epidemiol, D-04107 Leipzig, Germany -- [Simionescu, Maya] Inst Cellular Biol & Pathol Nicolae Simionescu, Bucharest 050568, Romania -- [Stoll, Monika] Westfalische Wilhelms Univ Munster, Inst Human Genet, Dept Genet Epidemiol, D-48149 Munster, Germany -- [Vinciguerra, Manlio] Int Clin Res Ctr, Brno 65691, Czech Republic -- [Yilmaz, Mehmet Birhan] Dokuz Eylul Univ, Fac Med, Dept Cardiol, TR-35340 Izmir, Turkey -- [Emanueli, Costanza] Imperial Coll London, Fac Med, Natl Heart & Lung Inst, London W12 0HH, England, Hlavackova, Marketa -- 0000-0003-3842-6907, Devaux, Yvan -- 0000-0002-5321-8543, Gyongyosi, Mariann -- 0000-0002-7083-2107, Sasson, Shlomo -- 0000-0002-9343-526X, Buil, Alfonso -- 0000-0002-3097-1014, Hoydal, Morten -- 0000-0003-1804-2578, Justo da Silva, Gustavo -- 0000-0002-1651-7966, Baker, Andrew -- 0000-0003-1441-5576, Lakkisto, Paivi -- 0000-0001-9935-6573, Pinet, Florence -- 0000-0002-5471-1487, Martelli, Fabio -- 0000-0002-8624-7738, Robinson, Emma -- 0000-0002-4866-731X, Novella, Susana -- 0000-0001-8303-7252, Jusic, Amela -- 0000-0003-2835-4284, Beis, Dimitris -- 0000-0003-2579-7848, O'Brien, Timothy -- 0000-0001-9028-5481, Popescu, Octavian -- 0000-0002-2597-7155, Felekkis, Kyriacos -- 0000-0002-0919-0037, de Gonzalo Calvo, David -- 0000-0003-2240-3532, Universidade de Lisboa = University of Lisbon (ULISBOA), University of Cyprus [Nicosia] (UCY), Université de Lausanne = University of Lausanne (UNIL), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, Cardiologie, MUMC+: MA Med Staf Spec Cardiologie (9), RS: CARIM - R2.02 - Cardiomyopathy, RS: CARIM - R2 - Cardiac function and failure, and RS: Carim - H02 Cardiomyopathy

Subjects
Project Report, 0301 basic medicine, medicine.medical_specialty, Biochemistry & Molecular Biology, Knowledge management, lcsh:QH426-470, BIOMARKERS, best practices and guidelines, cardiovascular disease, personalized medicine, transcriptomics, translational research, Context (language use), Translational research, Disease, 030204 cardiovascular system & hematology, Biology, Biochemistry, LONG NONCODING RNAS, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, CIRCULATING MICRORNAS, TARGETS, Genetics, medicine, Cost action, Set (psychology), Molecular Biology, ComputingMilieux_MISCELLANEOUS, Genetics & Heredity, Science & Technology, business.industry, Cardiovascular system -- Diseases, Public health, Medicine -- Research -- International cooperation, 3. Good health, lcsh:Genetics, 030104 developmental biology, Action (philosophy), PERSPECTIVES, Personalized medicine, Translational research, biomedical, business, Transcriptome, Life Sciences & Biomedicine
Abstract

WOS: 000474931400001, PubMed ID: 30934986, Cardiovascular disease (CVD) remains the leading cause of death worldwide and, despite continuous advances, better diagnostic and prognostic tools, as well as therapy, are needed. The human transcriptome, which is the set of all RNA produced in a cell, is much more complex than previously thought and the lack of dialogue between researchers and industrials and consensus on guidelines to generate data make it harder to compare and reproduce results. This European Cooperation in Science and Technology (COST) Action aims to accelerate the understanding of transcriptomics in CVD and further the translation of experimental data into usable applications to improve personalized medicine in this field by creating an interdisciplinary network. It aims to provide opportunities for collaboration between stakeholders from complementary backgrounds, allowing the functions of different RNAs and their interactions to be more rapidly deciphered in the cardiovascular context for translation into the clinic, thus fostering personalized medicine and meeting a current public health challenge. Thus, this Action will advance studies on cardiovascular transcriptomics, generate innovative projects, and consolidate the leadership of European research groups in the field. COST (European Cooperation in Science and Technology) is a funding organization for research and innovation networks (www.cost.eu)., COST (European Cooperation in Science and Technology) Action EU-CardioRNA [CA17129], This work is supported by COST (European Cooperation in Science and Technology) Action EU-CardioRNA CA17129. YD is the chair and CE is the vice-chair of the European COST Action CA17129, CardioRNA.

Published
2019

3. Regulatory RNAs in Heart Failure.

Author

Gomes, Clarissa Pedrosa da Costa, Schroen, Blanche, Kuster, Gabriela M., Robinson, Emma L., Ford, Kerrie, Squire, Iain B., Heymans, Stephane, Martelli, Fabio, Emanueli, Costanza, Devaux, Yvan, Gomes, Clarissa Pedrosa Costa, and EU-CardioRNA COST Action (CA17129)

Published
2020
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4. Noncoding RNAs in Hypertension.

Author

Jusic, Amela, Devaux, Yvan, and EU-CardioRNA COST Action (CA17129)

Abstract

The article highlights blood pressure or hypertension, public health problem that affect 40 percent of the World's adult population; and mentions figuring out the complex multifactorial nature of hypertension.

Published
2019
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5. A role for m6A RNA methylation in heart failure development?

Author

Devaux, Yvan, Nossent, Anne Yaël, and EU-CardioRNA COST Action CA17129

Subjects
RNA methylation, GENETIC translation, SCIENTIFIC knowledge, HEART failure, COMPARATIVE studies, RESEARCH methodology, MEDICAL cooperation, METHYLATION, RESEARCH, RNA, EVALUATION research, DISEASE progression
Published
2020
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6. Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129

Author

Stephanie Bezzina Wettinger, Maarten Vanhaverbeke, Costanza Emanueli, Johannes Grillari, Rosienne Farrugia, Monika Bartekova, Barbora Kalocayova, Soumaya Ben-Aicha, EU-CardioRNA Cost Action Ca, Markus Scholz, R. Attard, Yvan Devaux, Matthias Hackl, Fabio Martelli, David de Gonzalo-Calvo, Timo Brandenburger, and EU-CardioRNA COST Action (CA17129)

Subjects
Cardiovascular system -- Diseases, Physiology, business.industry, RNA, Genomics, Disease, Cardiovascular system -- Diseases -- Diagnosis, Bioinformatics, medicine.disease, Transcriptome, Physiology (medical), Heart failure, Cardiovascular system -- Diseases -- Treatment, Gene expression, medicine, Biomarker (medicine), Position paper, Cardiology and Cardiovascular Medicine, business
Abstract

Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners., peer-reviewed

Published
2021

7. Catalyzing Transcriptomics Research in Cardiovascular Disease: The CardioRNA COST Action CA17129.

Author

Gomes CPC, Ágg B, Andova A, Arslan S, Baker A, Barteková M, Beis D, Betsou F, Wettinger SB, Bugarski B, Condorelli G, Silva GJJD, Danilin S, de Gonzalo-Calvo D, Buil A, Carmo-Fonseca M, Enguita FJ, Felekkis K, Ferdinandy P, Gyöngyösi M, Hackl M, Karaduzovic-Hadziabdic K, Hellemans J, Heymans S, Hlavackova M, Hoydal MA, Jankovic A, Jusic A, Kardassis D, Kerkelä R, Kuster GM, Lakkisto P, Leszek P, Lustrek M, Maegdefessel L, Martelli F, Novella S, O'Brien T, Papaneophytou C, Pedrazzini T, Pinet F, Popescu O, Potočnjak I, Robinson E, Sasson S, Scholz M, Simionescu M, Stoll M, Varga ZV, Vinciguerra M, Xuereb A, Yilmaz MB, Emanueli C, Devaux Y, and on behalf of the EU-CardioRNA COST Action (CA17129)

Abstract

Cardiovascular disease (CVD) remains the leading cause of death worldwide and, despite continuous advances, better diagnostic and prognostic tools, as well as therapy, are needed. The human transcriptome, which is the set of all RNA produced in a cell, is much more complex than previously thought and the lack of dialogue between researchers and industrials and consensus on guidelines to generate data make it harder to compare and reproduce results. This European Cooperation in Science and Technology (COST) Action aims to accelerate the understanding of transcriptomics in CVD and further the translation of experimental data into usable applications to improve personalized medicine in this field by creating an interdisciplinary network. It aims to provide opportunities for collaboration between stakeholders from complementary backgrounds, allowing the functions of different RNAs and their interactions to be more rapidly deciphered in the cardiovascular context for translation into the clinic, thus fostering personalized medicine and meeting a current public health challenge. Thus, this Action will advance studies on cardiovascular transcriptomics, generate innovative projects, and consolidate the leadership of European research groups in the field.COST (European Cooperation in Science and Technology) is a funding organization for research and innovation networks (www.cost.eu).

Published
2019
Full Text
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