Periodic Reporting for period 4 - CodingHeart (Novel Coding Factors in Heart Disease)
Okres sprawozdawczy: 2023-07-01 do 2024-12-31
Heart failure affects over 23 million people globally and remains a leading cause of mortality and hospitalization. Particularly underexplored are cases related to diastolic dysfunction and primary cardiomyopathies, including dilated and hypertrophic forms. Addressing a major knowledge gap, our project aimed to comprehensively characterize the role of novel micropeptides—small proteins encoded by previously annotated non-coding RNAs—in cardiac health and disease.
Using advanced ribosome profiling, we mapped a previously uncharted landscape of translated small open reading frames (sORFs) in human and animal hearts. This led to the discovery of hundreds of stable, functional micropeptides, many of which were non-conserved and primate- or human-specific, suggesting evolutionary innovations. We complemented this with in vivo and in vitro validation, including mass spectrometry, single-cell transcriptomics, and CRISPR-based functional screens.
Our work sheds light on novel molecular mechanisms in heart function, identifying potential therapeutic targets and biomarkers for heart failure. Beyond the cardiovascular field, the findings are relevant for other organ systems, offering new insight into gene regulation, translation, and evolutionary biology.
Using advanced ribosome profiling, we mapped a previously uncharted landscape of translated small open reading frames (sORFs) in human and animal hearts. This led to the discovery of hundreds of stable, functional micropeptides, many of which were non-conserved and primate- or human-specific, suggesting evolutionary innovations. We complemented this with in vivo and in vitro validation, including mass spectrometry, single-cell transcriptomics, and CRISPR-based functional screens.
Our work sheds light on novel molecular mechanisms in heart function, identifying potential therapeutic targets and biomarkers for heart failure. Beyond the cardiovascular field, the findings are relevant for other organ systems, offering new insight into gene regulation, translation, and evolutionary biology.
Over the course of the project, we:
• Generated the first comprehensive genome-wide catalog of cardiac micropeptides in humans and rats.
• Identified 339 micropeptides encoded by lncRNAs in human hearts and over 1,000 micropeptides from 5’UTRs of canonical mRNAs.
• Published our human dataset in Cell (2019), rat dataset in Genome Biology (2021), and co-led the inclusion of micropeptide annotations into GENCODE, published in Nature Biotechnology (2022).
• Performed high-resolution single-nucleus and single-cell RNA sequencing of 14 human hearts (Nature, 2020), revealing cell-type-specific expression patterns.
• Identified micropeptides with mitochondrial localization, potential secretory roles, and others with transmembrane domains, suggesting diverse functionality.
• Found over 500 primate-specific micropeptides using an innovative evolutionary pipeline and comparative translatome analysis (Nature Cardiovascular Research, 2024).
• Validated micropeptide-protein interactions via high-throughput PRISMA screens (Molecular Cell, 2023), showing relevance in translation, endocytosis, and splicing.
• Conducted a pooled CRISPR screen across 169 translated lncRNAs, with downstream phenotyping in iPSC-derived cardiomyocytes, uncovering regulatory lncRNAs like LINC01405.
Exploitation of Results
• Our micropeptide catalogs and methodologies have been made openly available, serving as a valuable resource for basic researchers, bioinformaticians, and clinicians working in cardiac and translational genomics.
• The standardized annotations in GENCODE-Ensembl and UniProt provide the foundation for clinical genome interpretation, especially in the context of rare genetic diseases and cardiomyopathies.
• Micropeptides identified with functional effects on mitochondrial activity and protein synthesis are now being considered as pre-clinical targets for therapeutic development.
• Our computational pipeline for evolutionary annotation has been integrated into collaborative platforms and can now be used by other labs for species-specific gene discovery.
• Intellectual property generated (e.g. around candidate therapeutic micropeptides) is currently under review for patent protection and potential industry partnerships.
Dissemination of Results
• We published peer-reviewed articles in high-impact journals (Cell, Nature, Nature Biotechnology, Molecular Cell, etc.).
• Our team presented results at major conferences in cardiology, functional genomics, and translational biology.
• All major datasets and tools were deposited in open-access repositories (e.g. GEO, ProteomeXchange, ENA) and linked to web-based tools enabling community use.
• Through our international consortium efforts, we engaged over 65 collaborators worldwide, laying the groundwork for sustained dissemination and future funding proposals.
• Workshops and training sessions were held to support early-career scientists and data users in using ribosome profiling and our evolutionary tools.
• Generated the first comprehensive genome-wide catalog of cardiac micropeptides in humans and rats.
• Identified 339 micropeptides encoded by lncRNAs in human hearts and over 1,000 micropeptides from 5’UTRs of canonical mRNAs.
• Published our human dataset in Cell (2019), rat dataset in Genome Biology (2021), and co-led the inclusion of micropeptide annotations into GENCODE, published in Nature Biotechnology (2022).
• Performed high-resolution single-nucleus and single-cell RNA sequencing of 14 human hearts (Nature, 2020), revealing cell-type-specific expression patterns.
• Identified micropeptides with mitochondrial localization, potential secretory roles, and others with transmembrane domains, suggesting diverse functionality.
• Found over 500 primate-specific micropeptides using an innovative evolutionary pipeline and comparative translatome analysis (Nature Cardiovascular Research, 2024).
• Validated micropeptide-protein interactions via high-throughput PRISMA screens (Molecular Cell, 2023), showing relevance in translation, endocytosis, and splicing.
• Conducted a pooled CRISPR screen across 169 translated lncRNAs, with downstream phenotyping in iPSC-derived cardiomyocytes, uncovering regulatory lncRNAs like LINC01405.
Exploitation of Results
• Our micropeptide catalogs and methodologies have been made openly available, serving as a valuable resource for basic researchers, bioinformaticians, and clinicians working in cardiac and translational genomics.
• The standardized annotations in GENCODE-Ensembl and UniProt provide the foundation for clinical genome interpretation, especially in the context of rare genetic diseases and cardiomyopathies.
• Micropeptides identified with functional effects on mitochondrial activity and protein synthesis are now being considered as pre-clinical targets for therapeutic development.
• Our computational pipeline for evolutionary annotation has been integrated into collaborative platforms and can now be used by other labs for species-specific gene discovery.
• Intellectual property generated (e.g. around candidate therapeutic micropeptides) is currently under review for patent protection and potential industry partnerships.
Dissemination of Results
• We published peer-reviewed articles in high-impact journals (Cell, Nature, Nature Biotechnology, Molecular Cell, etc.).
• Our team presented results at major conferences in cardiology, functional genomics, and translational biology.
• All major datasets and tools were deposited in open-access repositories (e.g. GEO, ProteomeXchange, ENA) and linked to web-based tools enabling community use.
• Through our international consortium efforts, we engaged over 65 collaborators worldwide, laying the groundwork for sustained dissemination and future funding proposals.
• Workshops and training sessions were held to support early-career scientists and data users in using ribosome profiling and our evolutionary tools.
This project achieved key breakthroughs in both method development and biological discovery:
• Developed a new ribosome profiling protocol, now widely adopted due to the discontinuation of commercial kits.
• Discovered mitochondrial-associated lncRNAs and micropeptides, opening new research directions in cellular energy metabolism.
• Introduced a computational tool to trace evolutionary origins of micropeptides, now used for cross-species functional predictions.
• Established an international standard for sORF annotation, actively shaping future research across proteomics, genomics, and biomedical disciplines.
Conclusion
Our project revealed a hidden layer of molecular regulation in the heart, introducing hundreds of novel, functional micropeptides with clear biological and clinical significance. Through a combination of high-throughput technologies, deep evolutionary analysis, and broad dissemination, we laid the foundation for a new frontier in cardiac biology—one that bridges basic science and translational medicine. We expect these findings to fuel future therapeutic strategies, including micropeptide-based diagnostics and treatments, with the potential to improve patient outcomes in heart failure and related diseases.
• Developed a new ribosome profiling protocol, now widely adopted due to the discontinuation of commercial kits.
• Discovered mitochondrial-associated lncRNAs and micropeptides, opening new research directions in cellular energy metabolism.
• Introduced a computational tool to trace evolutionary origins of micropeptides, now used for cross-species functional predictions.
• Established an international standard for sORF annotation, actively shaping future research across proteomics, genomics, and biomedical disciplines.
Conclusion
Our project revealed a hidden layer of molecular regulation in the heart, introducing hundreds of novel, functional micropeptides with clear biological and clinical significance. Through a combination of high-throughput technologies, deep evolutionary analysis, and broad dissemination, we laid the foundation for a new frontier in cardiac biology—one that bridges basic science and translational medicine. We expect these findings to fuel future therapeutic strategies, including micropeptide-based diagnostics and treatments, with the potential to improve patient outcomes in heart failure and related diseases.