Computational modeling identifies embolic stroke of undetermined source patients with potential arrhythmic substrate
Abstract
Cardiac magnetic resonance imaging (MRI) has revealed fibrosis in embolic stroke of undetermined source (ESUS) patients comparable to levels seen in atrial fibrillation (AFib). We used computational modeling to understand the absence of arrhythmia in ESUS despite the presence of putatively pro-arrhythmic fibrosis. MRI-based atrial models were reconstructed for 45 ESUS and 45 AFib patients. The fibrotic substrate's arrhythmogenic capacity in each patient was assessed computationally. Reentrant drivers were induced in 24/45 (53%) ESUS and 22/45 (49%) AFib models. Inducible models had more fibrosis (16.7±5.45%) than non-inducible models (11.07±3.61%; P<0.0001); however, inducible subsets of ESUS and AFib models had similar fibrosis levels (P=0.90), meaning the intrinsic pro-arrhythmic substrate properties of fibrosis in ESUS and AFib are indistinguishable. This suggests some ESUS patients have latent pre-clinical fibrotic substrate that could be a future source of arrhythmogenicity. Thus, our work prompts the hypothesis that ESUS patients with fibrotic atria are spared from AFib due to an absence of arrhythmia triggers.
Data availability
Where possible (Figs. 2, 3, 5, 6), raw numerical data underlying figures are available via figshare: https://doi.org/10.6084/m9.figshare.14348042. Patient-derived data related to this article, including processed versions thereof, are not publicly available out of respect for the privacy of the patients involved. Interested parties wishing to obtain these data for non-commercial reuse should contact the co-corresponding authors via email. Upon all reasonable requests for access to these data, the co-corresponding authors will work to pursue negotiation of a Data Transfer and Use Agreement with the requesting party; administrators at the requesting party's institution, the University of Washington, and Klinikum Coburg; and relevant Institutional Review Boards at all the latter institutions. Source files for a complete example of computational modeling and simulation of the fibrotic atria, using publicly available data sets and software tools only, can be found via the following permanent link: https://doi.org/10.6084/m9.figshare.14347979. Documentation provided with this example includes instructions on the use of the openCARP cardiac electrophysiology simulator and the meshalyzer visualization software (both available via https://opencarp.org/) to precisely reproduce the computational protocol applied to patient-specific left atria models in this study.
Article and author information
Author details
Funding
Achievement Rewards for College Scientists Foundation
- Savannah F Bifulco
National Institutes of Health (T32-EB001650)
- Savannah F Bifulco
Medical Research Council (MR/S015086/1)
- Caroline H Roney
National Institutes of Health (R01-HL152256)
- Steven A Niederer
H2020 European Research Council (PREDICT-HF (864055))
- Steven A Niederer
British Heart Foundation (RG/20/4/34803)
- Steven A Niederer
Engineering and Physical Sciences Research Council (EP/P01268X/1)
- Steven A Niederer
Wellcome Trust (203148/Z/16/Z)
- Steven A Niederer
National Institutes of Health (NIH 5-U01-NS095869)
- David Tirschwell
- W T Longstreth Jr
John Locke Charitable Trust
- Nazem Akoum
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: This study was approved by the Institutional Review Board (IRB) of the University of Washington (UW) and the Ethikkommission der Bayerischen Ländesärztekammer München, Bayern, Deutschland; all participants provided written informed consent. Associated reference numbers: IRB5350 for ESUS patients; IRB8763 for AFib patients.
Copyright
© 2021, Bifulco et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,342
- views
-
- 154
- downloads
-
- 17
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Computational and Systems Biology
- Genetics and Genomics
Untranslated regions (UTRs) contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA-dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA-dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.
-
- Computational and Systems Biology
- Medicine
Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunction‐associated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modeling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.