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The mechanical regulation of microRNA epitranscriptomics in heart failure

Lead Research Organisation: Imperial College London
Department Name: National Heart and Lung Institute

Abstract

Despite advances in therapies and prevention, heart failure (HF) remains a leading cause of morbidity and mortality worldwide. The heart is exposed to mechanical forces and constantly adapts to its environment in a process known as cardiac remodelling. Excessive mechanical load is a major driver of pathological cardiac remodelling, progressively leading to HF. A set of microRNAs (miRs) are responsive to mechanical forces (mechanomiRs) and contribute to heart pathophysiology and HF. Epitranscriptomics (i.e., the biochemical modification of the RNA) is emerging as a new layer of gene expression regulation affecting both coding and non-coding RNAs. N6-adenosine RNA methylation (m6A) regulate the processing of miR transcripts (pri-miRs) to functional miRs, promoting angiogenesis and cardiac repair after myocardial infarction. However, dysregulation of m6A reportedly contributes to HF. The role played by epitranscriptomics in heart mechanical responses and mechanomiR regulation have not yet been investigated, although crucial to inform transformative therapeutics. Epi-mecHEART aims to unveil the mechanically induced epitranscriptomic mechanisms leading to HF, focussing on mechanomiRs. Combining "living myocardial slice" and computational technologies (available at the host lab) with molecular techniques and biomechanical tools, I will i) identify the mechanosensitive N6-methylation responses in cardiomyocytes subjected to mechanical overload; ii) unveil how mechanical overload modulates the N6-methylation profile of both pri-miRs and miR-mRNA targets; iii) investigate how the mechanically induced N6-methylation on mRNAs impacts miR-targeting function iv) validate the clinical relevance of mechanically-induced N6-methylation changes in HF, by use of clinical samples. Targeting N6-methylation represents a transformative strategy to support the adaptation of the heart to increased workload, thus preventing HF.

Publications

10 25 50
 
Description What has been discovered:
The role of microRNAs in the diseased heart has led to an increasing interest in their regulation as a therapeutic and diagnostic approach . The possibility to target specific microRNAs and their complex regulatory network will offer new therapeutic options. Here we discovered a pool of mechano-sensitive microRNAs, whose expression is altered upon mechanical overload. 
Targeting N6-methyladenosine (m6A) RNA methylation represents a transformative strategy to modulate gene expression in the failing heart via interference with miR networks. Here, we found that mechanical overload affects global m6A levels and the expression of m6A demethylases in the heart.
Exploitation Route Ongoing analysis of the m6A profile on identified microRNA primary transcripts and mRNA targets holds promise for unveiling novel mechanically regulated m6A events, providing insights for transformative therapeutic strategies.  The molecular mechanisms discovered within this project will offer the basis to develop further lines of investigations not only related to cardiovascular diseases but also to other pathological conditions in which mechanical cues play a fundamental role.
Sectors Healthcare

Pharmaceuticals and Medical Biotechnology

 
Title AAV to express METTL-3 
Description Develpment of vector to express METTL3 in vivo 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact On going work and new collaboration with the Japanese National Cerebral and Cardiovascular Center 
 
Title Adenoviruses to express METTL-3 
Description Bulding of viral vectors to express METTL-3 in vivo (mouse work) 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Publication 
 
Title CUT&RUN-m6A-seq in living myocardial slices 
Description To detect m6A profile on microRNA primary transcripts and mRNAs, Dr Martino implemented CUT&RUN-m6A-sequencing technology in living myocardial slices. This technique enables to enrich RNA fragments containing m6A from low input RNA and to prepare library for next generation sequencing. 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact This technique allows to perform the m6A pull down from low input material (only 1 slice, about 5 µg of RNA), opposite to the more commonly used me-RIP technique that requires a high amount of starting RNA (about 500ug). After pulling down m6A modified RNAs and preparing the libraries, the samples were sent to be sequenced (we are now waiting for the results). 
 
Title RNA and proteins isolated from rat and human living myocardial slices 
Description Dr Martino learned to prepare and culture living myocardial slices from human and rat left ventricles. Human LMS, obtained from the left ventricle of human donor non-failing hearts (NHS Blood and Transplant INOAR program, IRAS project ID: 189069) and rat LMS have been subjected to two degrees of mechanical preload: physiological and overload. LMS are maintained for 48h under electrical stimulation in circulating oxygenated media at 37C. RNA and proteins were isolated from 8 rats and 6 human donor hearts. 
Type Of Material Biological samples 
Year Produced 2023 
Provided To Others? No  
Impact Living myocardial slices (LMS) are ultra-thin organotypic sections of living adult ventricular myocardium retaining the native multicellularity, architecture, and physiology of the heart. LMS are cultured in biomimetic conditions, thus allowing to study the effect of mechanical overload (volume overload) over time. Using LMS technology, we modulate mechanical load in a multicellular environment while maintaining physiological behavior. 
 
Title RNA isolation 
Description A method to isolate RNA and purified extracellular vesicles from patient urine samples has been developed and refined and is available for researchers to use 
Type Of Material Biological samples 
Year Produced 2022 
Provided To Others? Yes  
Impact Process refinement for RNA samples 
 
Title Small RNA sequencing in living myocardial slices 
Description To detect the microRNAs sensitive to mechanical overload, we performed small RNA sequencing in physiological and overloaded living myocardial slices from both human and rat hearts 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact Identifying microRNAs whose expression is affected by mechanical overload (mechano-miRs) is a step forward towards unveiling the molecular mechanisms underlying pathological cardiac remodeling. 
 
Title sc-RNA sequencing of mouse healthy and diabetic heart 
Description During the last six months, we optimized the protocol to perform sc-RNA sequencing of mouse healthy and diabetic heart. Cardiomyocytes were separated from non-cardiomyocytes cellulome (by Langendorff). Non-cardiomyocytes cellulome was FACS-sorted to select only living cells (PI-negative cells). Next, single cells were prepared for sequencing using 10x chromium technology. This technique will be essential to progress on our project. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? No  
Impact Process improvement for Emanueli lab 
 
Description Michela Noseda Improving protocol for cardiac scRNA-sequencing- 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution We provide additional data
Collaborator Contribution Supervision of 2 postdocs of my team to improve the protocol for scRNA-seq of the mouse heart
Impact not yet
Start Year 2023
 
Description Nanopore for m6A mapping collaboration with Prof. Dr. rer. nat. Christoph Dieterich Section of Bioinformatics and Systems Cardiology MII Site Coordinator HiGHmed UKHD University Hospital Heidelberg German Center for Cardiovascular Research (DZHK) - 
Organisation Heidelberg University
Country Germany 
Sector Academic/University 
PI Contribution We provided heart samples for m6A analyses by Nanopore, together with bulk-RNA-sequencing for small and long RNA.
Collaborator Contribution The Heidelbergh team has done Nanopore and bioinformatically integrating the omic data
Impact This is an interdisciplinary collaboration between laboratory and data science We will write and submit a research paper with the result of the collaboration as we have analysed the data
Start Year 2024
 
Description Abstract Presentation - Investigating N6-methyladenosin RNA modification as a mediator of microRNA mechanical regulation in the heart 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ESC Congress Sep 2024 in London
Year(s) Of Engagement Activity 2024
 
Description Poster Presentation - Investigating M6A RNA Modification As A Mediator Of Heart Response To Mechanical Overload", 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keystone Symposium, RNA modification in Health and Disease, December 12-15, 2023 | Fairmont Banff Springs, Banff, AB, Canada
Year(s) Of Engagement Activity 2023
 
Description Presentation of Epi-mecHEART project at the Multifaculty Centre of Cellular Mechanosensing and Functional Microscopy Inaugural Conference at Imperial College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact This conference, organized by Professor Julia Gorelik, brought together many scientists from other Academic Disciplines working on mechanobiology to discuss their work and promote future collaboration
Year(s) Of Engagement Activity 2023