Transcriptomic research in atherosclerosis: Unravelling plaque phenotype and overcoming methodological challenges

Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that...

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Published inJournal of Molecular and Cellular Cardiology Plus (Online) Vol. 6; p. 100048
Main Authors Sopić, Miron, Karaduzovic-Hadziabdic, Kanita, Kardassis, Dimitris, Maegdefessel, Lars, Martelli, Fabio, Meerson, Ari, Munjas, Jelena, Niculescu, Loredan S., Stoll, Monika, Magni, Paolo, Devaux, Yvan
Format Journal Article
LanguageEnglish
Published England Elsevier Ltd 01.12.2023
Elsevier
Subjects
Atherosclerotic plaque
Data integration, machine learning
Transcriptomics
Data integration, machine learning
Atherosclerotic plaque
Transcriptomics
Online AccessGet full text
ISSN2772-9761
2772-9761
DOI10.1016/j.jmccpl.2023.100048

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Abstract Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that drive atherosclerosis. However, low reproducibility of research findings and lack of standardization of procedures pose significant challenges in this field. In this review, we discuss how transcriptomic research can help in understanding the different phenotypes of the atherosclerotic plaque that contribute to the development and progression of atherosclerosis. We highlight the methodological challenges that need to be addressed to improve research outputs, and emphasize the importance of research protocols harmonization. We also discuss recent advances in transcriptomic research, including bulk or single-cell sequencing, and their added value in plaque phenotyping. Finally, we explore how integrated multiomics data and machine learning improve understanding of atherosclerosis and provide directions for future research. [Display omitted] •A deep characterization of the molecular mechanisms responsible for atherosclerotic plaque development is needed.•RNAs and particularly non-coding RNAs regulate gene expression and play a major role in atherosclerotic plaque development.•Methodological challenges in transcriptomic studies hinder the translation of basic research findings to clinics.•Tips and tricks are provided to improve translational capacity of basic transcriptomic research for patient’s benefit.
AbstractList Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that drive atherosclerosis. However, low reproducibility of research findings and lack of standardization of procedures pose significant challenges in this field. In this review, we discuss how transcriptomic research can help in understanding the different phenotypes of the atherosclerotic plaque that contribute to the development and progression of atherosclerosis. We highlight the methodological challenges that need to be addressed to improve research outputs, and emphasize the importance of research protocols harmonization. We also discuss recent advances in transcriptomic research, including bulk or single-cell sequencing, and their added value in plaque phenotyping. Finally, we explore how integrated multiomics data and machine learning improve understanding of atherosclerosis and provide directions for future research.
Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that drive atherosclerosis. However, low reproducibility of research findings and lack of standardization of procedures pose significant challenges in this field. In this review, we discuss how transcriptomic research can help in understanding the different phenotypes of the atherosclerotic plaque that contribute to the development and progression of atherosclerosis. We highlight the methodological challenges that need to be addressed to improve research outputs, and emphasize the importance of research protocols harmonization. We also discuss recent advances in transcriptomic research, including bulk or single-cell sequencing, and their added value in plaque phenotyping. Finally, we explore how integrated multiomics data and machine learning improve understanding of atherosclerosis and provide directions for future research. [Display omitted] •A deep characterization of the molecular mechanisms responsible for atherosclerotic plaque development is needed.•RNAs and particularly non-coding RNAs regulate gene expression and play a major role in atherosclerotic plaque development.•Methodological challenges in transcriptomic studies hinder the translation of basic research findings to clinics.•Tips and tricks are provided to improve translational capacity of basic transcriptomic research for patient’s benefit.
Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that drive atherosclerosis. However, low reproducibility of research findings and lack of standardization of procedures pose significant challenges in this field. In this review, we discuss how transcriptomic research can help in understanding the different phenotypes of the atherosclerotic plaque that contribute to the development and progression of atherosclerosis. We highlight the methodological challenges that need to be addressed to improve research outputs, and emphasize the importance of research protocols harmonization. We also discuss recent advances in transcriptomic research, including bulk or single-cell sequencing, and their added value in plaque phenotyping. Finally, we explore how integrated multiomics data and machine learning improve understanding of atherosclerosis and provide directions for future research.Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized and patient-centered healthcare. Transcriptomic research has proven to be a powerful tool for unravelling the complex molecular pathways that drive atherosclerosis. However, low reproducibility of research findings and lack of standardization of procedures pose significant challenges in this field. In this review, we discuss how transcriptomic research can help in understanding the different phenotypes of the atherosclerotic plaque that contribute to the development and progression of atherosclerosis. We highlight the methodological challenges that need to be addressed to improve research outputs, and emphasize the importance of research protocols harmonization. We also discuss recent advances in transcriptomic research, including bulk or single-cell sequencing, and their added value in plaque phenotyping. Finally, we explore how integrated multiomics data and machine learning improve understanding of atherosclerosis and provide directions for future research.
ArticleNumber 100048
Author Meerson, Ari
Kardassis, Dimitris
Munjas, Jelena
Magni, Paolo
Devaux, Yvan
Karaduzovic-Hadziabdic, Kanita
Niculescu, Loredan S.
Sopić, Miron
Martelli, Fabio
Stoll, Monika
Maegdefessel, Lars
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  givenname: Dimitris
  surname: Kardassis
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  givenname: Jelena
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  fullname: Munjas, Jelena
  organization: Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Serbia
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  surname: Niculescu
  fullname: Niculescu, Loredan S.
  organization: Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B.P. Hasdeu Street, Bucharest 050568, Romania
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  surname: Magni
  fullname: Magni, Paolo
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  givenname: Yvan
  surname: Devaux
  fullname: Devaux, Yvan
  email: yvan.devaux@lih.lu
  organization: Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
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Keywords Data integration, machine learning
Atherosclerotic plaque
Transcriptomics
Language English
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2023 The Authors. Published by Elsevier Ltd.
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Snippet Atherosclerotic disease is a major cause of acute cardiovascular events. A deeper understanding of its underlying mechanisms will allow advancing personalized...
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SubjectTerms Atherosclerotic plaque
Data integration, machine learning
Transcriptomics
Title Transcriptomic research in atherosclerosis: Unravelling plaque phenotype and overcoming methodological challenges
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https://dx.doi.org/10.1016/j.jmccpl.2023.100048
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