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Journal of Molecular and Cellular Cardiology

Elsevier BV

All preprints, ranked by how well they match Journal of Molecular and Cellular Cardiology's content profile, based on 40 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Systems analysis reveals neuregulin-1 control of cardiomyocyte size and shape mediated by distinct PI3K and p38 pathways

Luanpaisanon, P.; Tan, P. M.; Ryall, K. A.; O'Hearn, J. J.; Woo, L. A.; Harris, B. N.; Wissmann, B.; Paap, A.; Rhoads, M.; Saucerman, J. J.

2025-10-03 systems biology 10.1101/2025.10.01.679873 medRxiv
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Pathological and physiological stresses induce diverse forms of cardiac hypertrophy, with distinct manifestations in cardiomyocyte size and shape regulated by still poorly understood signaling networks. Here, we combined high-content morphological profiling, phospho-protein arrays, and systems modeling to characterize the diverse forms of hypertrophy induced by angiotensin II, endothelin-1, insulin growth factor-1, and neuregulin-1. Reverse-phase protein array profiling and partial least squares regression modeling revealed that Akt, GSK3, and MAPK signaling are differentially regulated by hypertrophic agonists and are predictive of distinct phenotypic outcomes. Neuregulin-1 uniquely induced cardiomyocyte elongation in both neonatal rat and human iPSC-derived cardiomyocytes, in addition to increasing cell area. Pharmacological perturbations demonstrated that neuregulin1-induced elongation and area expansion both require PI3K activity, whereas p38 selectively mediates cell area. A logic-based network model incorporating dual-specificity phosphatases were sufficient to capture the amplifying PI3K and transient p38 signaling dynamics driving phenotypic changes. Together, these results identify distinct signaling cascades by which neuregulin-1 coordinates cardiomyocyte size and shape, providing mechanistic insight into how hypertrophic remodeling can be differentially regulated. This systems approach provides new insight into the pathways that drive distinct forms of cardiomyocyte hypertrophy, highlighting opportunities to selectively target maladaptive remodeling in heart failure. Highlights- Reverse-phase protein arrays capture distinct signatures of cellular signaling in response to diverse hypertrophic ligands. - Partial least squares regression model maps proteomic signatures to diverse patterns of cell morphology and gene expression. - Combinatorial ligand-inhibitor screen validates predicted causal regulators of mRNAs and cell morphology - PI3K mediates both neuregulin-1-induced elongation and cell area, validating the PLSR model. In contrast, p38 regulates cell area but not elongation. - Logic-based model demonstrates that the characterized mechanisms are sufficient to predict how distinct PI3K and p38 dynamics drive size and shape.

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Lipid metabolism drives allele-specific early-stage hypertrophic cardiomyopathy

Vaniya, A.; Karlstaedt, A.; Ates Gulkok, D.; Thottakara, T.; Liu, Y.; Fan, S.; Eades, H.; Fukunaga, R.; Vernon, H. J.; Fiehn, O.; Abraham, M. R.

2023-11-15 systems biology 10.1101/2023.11.10.564562 medRxiv
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Hypertrophic cardiomyopathy (HCM) results from pathogenic variants in sarcomeric protein genes, that increase myocyte energy demand and lead to cardiac hypertrophy. But it is unknown whether a common metabolic trait underlies the cardiac phenotype at early disease stage. This study characterized two HCM mouse models (R92W-TnT, R403Q-MyHC) that demonstrate differences in mitochondrial function at early disease stage. Using a combination of cardiac phenotyping, transcriptomics, mass spectrometry-based metabolomics and computational modeling, we discovered allele-specific differences in cardiac structure/function and metabolic changes. TnT-mutant hearts had impaired energy substrate metabolism and increased phospholipid remodeling compared to MyHC-mutants. TnT-mutants showed increased incorporation of saturated fatty acid residues into ceramides, cardiolipin, and increased lipid peroxidation, that could underlie allele-specific differences in mitochondrial function and cardiomyopathy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/564562v1_ufig1.gif" ALT="Figure 1"> O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/564562v1_ufig2.gif" ALT="Figure 1"> O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/564562v1_ufig3.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@195b1d7org.highwire.dtl.DTLVardef@cead88org.highwire.dtl.DTLVardef@e2bf35org.highwire.dtl.DTLVardef@776765_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Proteomics dissection of cardiac protein profiles of humans and model organisms

Linscheid, N.; Santos, A.; Poulsen, P. C.; Mills, R. W.; Stolte, C.; Leurs, U.; Ye, J. Z.; Calloe, K.; Thomsen, M. B.; Bentzen, B. H.; Lundegaard, P. R.; Olesen, M. S.; Jensen, L. J.; Olsen, J. V.; Lundby, A.

2020-01-09 systems biology 10.1101/2020.01.08.897595 medRxiv
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The study of human cardiac pathologies often relies on research conducted in model organisms to gain molecular insight into disease and to develop novel treatment strategies; however, translating findings from model organisms back to human can present a significant challenge, in part due to a lack of knowledge about the differences across species in cardiac protein abundances and their interactions. Here we set out to bridge this knowledge gap by presenting a global analysis of cardiac protein expression profiles in humans and commonly used model organisms. Using quantitative mass spectrometry-based proteomics, we measured the abundance of ~7,000 proteins in samples from the separate chambers of human, pig, horse, rat, mouse and zebrafish hearts. This knowledgebase of cardiac protein signatures is accessible through an online database at: atlas.cardiacproteomics.com. Quantitative comparison of the protein profiles support the pig as model organism of choice for arrhythmogenic right ventricular cardiomyopathy whereas comparison of profiles from the two-chambered zebrafish heart suggests a better resemblance to the right side of mammalian hearts. This proteomics resource facilitates translational prospect of cardiac studies from model organisms to humans by enabling direct comparison of disease-linked protein networks across species.

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Missense variants in the myosin binding domains of MYBPC3 and MYBPHL impair sarcomere incorporation

Araujo, K.; Cizauskas, H.; Yildiz, Y.; Fritzmann, G.; Bui, T.; Wittenkeller, L.; Pena, A.; Pak, T.; Barefield, D. Y.

2025-10-01 biochemistry 10.1101/2025.09.29.679322 medRxiv
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Approximately 40% of genetic hypertrophic cardiomyopathy cases involve mutations in MYBPC3, which encodes cardiac myosin binding protein-C (cMyBP-C), a key regulator of sarcomere contractility. The atrial-specific paralog, myosin binding protein-H like (MyBP-HL), has been associated with dilated cardiomyopathy in humans and mice. Both proteins bind to the same binding sites in the thick filament C-zone. In the atria, cMyBP-C and MyBP-HL are found at [~]1:1 ratios, while ventricles only express cMyBP-C, which is found at twice the atrial level, indicating a stoichiometric relationship. In the atria, we hypothesize that missense variants in either gene may cause alterations in thick filament binding affinity and changes in the normal [~]1:1 ratio. Notably, MyBP-HL deletion in atrial myofibrils accelerates relaxation kinetics, suggesting that altered stoichiometry impacts biophysical parameters. We hypothesized that deletion, overexpression, or missense variants in either gene would alter the abundance of the other protein in atrial sarcomeres, affecting sarcomere localization and function. To test this, we engineered two constructs: a mini-C construct comprising thick filament-binding domains of cMyBP-C and a MyBP-HL construct. Selected MYBPC3 and MYBPHL missense variants were introduced and expressed in neonatal rat ventricular cardiomyocytes (NRVMs). Sarcomere localization was assessed by co-localization with endogenous cMyBP-C. MYBPC3 variants were selected across a range of pathogenicity, while MYBPHL variants were based on evolutionary conservation of residues. MYBPHL variants Gly275Ser, Arg285His, and Ala342Thr induced significant sarcomere mislocalization, and MYBPC3 variants Pro1181Ala and Asn1257Lys showed variable effects on sarcomere mislocalization. To assess stoichiometric effects, we developed a T2A/P2A polycistronic construct to co-express mini-C, Td-Tomato, and MyBP-HL. Immunoblotting and mass spectrometry confirmed consistent and reproducible expression. We identified several MYBPC3 and MYBPHL variants that reduced the affinity of their protein for myofilament incorporation. These results suggest that this 2A construct is a useful tool for measuring the effect of myosin binding protein missense variants on sarcomere affinity, with implications for assessing pathogenicity of these variants.

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Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C+/- During Development

Shafaattalab, S.; LI, A. Y.; Maaref, Y.; Jayousi, F.; Hamledari, H.; Baygi, D. H.; Barszczewski, T.; Gunawan, M.; Rupai, B.; Jannati, S.; Nagalingam, R.; Cool, A. M.; Langa, P.; Solaro, R. J.; Sanatani, S.; Toepfer, C.; Lindert, S.; Lange, P. F.; Tibbits, G. F.

2023-06-07 cell biology 10.1101/2023.06.06.542948 medRxiv
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Hypertrophic cardiomyopathy (HCM) is one of the most common heritable cardiovascular diseases and variants of TNNT2 (cardiac troponin T) are linked to increased risk of sudden cardiac arrest despite causing limited hypertrophy. In this study, a TNNT2 variant, R278C+/-, was generated in both human cardiac recombinant/reconstituted thin filaments (hcRTF) and human-induced pluripotent stem cells (hiPSCs) to investigate the mechanisms by which the R278C+/- variant affects cardiomyocytes at the proteomic and functional levels. The results of proteomics analysis showed a significant upregulation of markers of cardiac hypertrophy and remodeling in R278C+/- vs. the isogenic control. Functional measurements showed that R278C+/- variant enhances the myofilament sensitivity to Ca2+, increases the kinetics of contraction, and causes arrhythmia at frequencies >75 bpm. This study uniquely shows the profound impact of the TNNT2 R278C+/- variant on the cardiomyocyte proteomic profile, cardiac electrical and contractile function in the early stages of cardiac development. Translational PerspectiveHypertrophic cardiomyopathy (HCM) is the leading known cause of sudden cardiac arrest in the young. Thin-variant associated HCM variants make up to 15% of familial HCM yet their molecular mechanisms remain less clear relative to thick filament variants. Here, we employ computational modeling, human cardiac recombinant/reconstituted thin filaments (hcRTF), and hiPSC-CMs to study the thin filament TNNT2 R278C+/- variant, revealing its extensive pathogenicity and potential mechanisms by which it can lead to HCM and sudden death. Mavacamten, the recently FDA-approved treatment, was effective in alleviating contractile dysfunction in TNNT2 R278C+/- hiPSC-CMs, positing it as a potential therapy for thin filament HCM. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=117 HEIGHT=200 SRC="FIGDIR/small/542948v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@102a8b0org.highwire.dtl.DTLVardef@190e356org.highwire.dtl.DTLVardef@13d3f9aorg.highwire.dtl.DTLVardef@1a9c33_HPS_FORMAT_FIGEXP M_FIG C_FIG

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MYBPC3 D389V Variant Induces Hypercontractility in Cardiac Organoids

Desai, D.; Song, T.; Singh, R.; Baby, A.; McNamara, J.; Green, L.; Nabavizadeh, P.; Ericksen, M.; Bazrafshan, S.; Natesan, S.; Sadayappan, S.

2024-05-30 cell biology 10.1101/2024.05.29.596463 medRxiv
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BACKGROUNDMYBPC3, encoding cardiac myosin binding protein-C (cMyBP-C), is the most mutated gene known to cause hypertrophic cardiomyopathy (HCM). However, since little is known about the underlying etiology, additional in vitro studies are crucial to defining the underlying molecular mechanisms. Accordingly, this study aimed to investigate the molecular mechanisms underlying the pathogenesis of HCM associated with a polymorphic variant (D389V) in MYBPC3 by using human-induced pluripotent stem cell (hiPSC)-derived cardiac organoids (hCOs). METHODSThe hiPSC-derived cardiomyocytes (hiPSC-CMs) and hCOs were generated from human subjects to define the molecular, cellular, and functional changes caused by the MYBPC3D389V variant. This variant is associated with increased fractional shortening and is highly prevalent in South Asian descendants. Recombinant C0-C2, N-region of cMyBP-C (wildtype and D389V), and myosin S2 proteins were also utilized to perform binding and motility assays in vitro. RESULTSConfocal and electron microscopic analyses of hCOs generated from noncarriers (NC) and carriers of the MYBPC3D389V variant revealed the presence of highly organized sarcomeres. Furthermore, functional experiments showed hypercontractility with increased contraction velocity, faster calcium cycling, and faster contractile kinetics in hCOs expressing MYBPC3D389V than NC hCOs. Interestingly, significantly increased cMyBP-C phosphorylation in MYBPC3D389V hCOs was observed, but without changes in total protein levels, in addition to higher oxidative stress and lower mitochondrial membrane potential ({Delta}{Psi}m). Next, spatial mapping revealed the presence of endothelial cells, fibroblasts, macrophages, immune cells, and cardiomyocytes in the hCOs. The hypercontractile function was significantly improved after treatment with the myosin inhibitor mavacamten (CAMZYOS(R)) in MYBPC3D389V hCOs. Lastly, various in vitro binding assays revealed a significant loss of affinity in the presence of MYBPC3D389V with myosin S2 region as a likely mechanism for hypercontraction. CONCLUSIONSConceptually, we showed the feasibility of assessing the functional and molecular mechanisms of HCM using highly translatable hCOs through pragmatic experiments that led to determining the MYBPC3D389V hypercontractile phenotype, which was rescued by administration of a myosin inhibitor. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIMYBPC3 mutations have been implicated in hypertrophic cardiomyopathy. C_LIO_LID389V is a polymorphic variant of MYBPC3 predicted to be present in 53000 US South Asians owing to the founder effect. D389V carriers have shown evidence of hyperdynamic heart, and human-induced pluripotent stem cells (hiPSC)-derived cardiomyocytes with D389V show cellular hypertrophy and irregular calcium transients. C_LIO_LIThe molecular mechanism by which the D389V variant develops pathological cardiac dysfunction remains to be conclusively determined. C_LI What New Information Does This Article Contribute?O_LIThe authors leveraged a highly translational cardiac organoid model to explore the role of altered cardiac calcium handling and cardiac contractility as a common pathway leading to pathophysiological phenotypes in patients with early HCM. C_LIO_LIThe MYBPC3D389V-mediated pathological pathway is first studied here by comparing functional properties using three-dimensional cardiac organoids differentiated from hiPSC and determining the presence of hypercontraction. C_LIO_LIOur data demonstrate that faster sarcomere kinetics resulting from lower binding affinity between D389V-mutated cMyBP-C protein and myosin S2, as evidenced by in vitro studies, could cause hypercontractility which was rescued by administration of mavacamten (CAMZYOS(R)), a myosin inhibitor. C_LIO_LIIn addition, hypercontractility causes secondary mitochondrial defects such as higher oxidative stress and lower mitochondrial membrane potential ({Delta}{Psi}m), highlighting a possible early adaptive response to primary sarcomeric changes. C_LIO_LIEarly treatment of MYBPC3D389V carriers with mavacamten may prevent or reduce early HCM-related pathology. C_LI GRAPHICAL ABSTRACTA graphical abstract is available for this article. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/596463v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1489301org.highwire.dtl.DTLVardef@1ab60c1org.highwire.dtl.DTLVardef@5d49d1org.highwire.dtl.DTLVardef@9944d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Cardiac Adaptations in the Cave Nectar Bat Eonycteris spelaea: Insights into Metabolic Resilience and Stress Response

Yu, F.; Gamage, A. M.; Kp, M. M. J.; Foo, R.; Lin, Y.-H.; Wang, L.; Pua, C. J.; Chan, W.; Crespo-Avilan, G. E.; Pena, E. M.; Hong, L. Z.; Iyer, A.; Ghosh, S.; Liehn, E. A.; Kovalik, J.-P.; Wang, L.-F.; Ramachandra, C. J.; Hausenloy, D. J.

2025-05-18 systems biology 10.1101/2025.05.15.653669 medRxiv
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AimsBats are unique mammals with remarkable adaptations, including powered flight, which demands significant energy expenditure. While previous studies have documented basic structural characteristics of bat hearts, a comprehensive understanding of their response to physiological stress remains unexplored. This study investigates the cardiac adaptations of the cave nectar bat Eonycteris spelaea to elucidate the mechanisms underlying their unique physiological capabilities. Methods and ResultsWe performed RNA sequencing to analyse the cardiac gene expression profile of E. spelaea and 6 other bat species in comparison to mouse and human hearts, revealing enriched transcriptomic signatures related to oxidative phosphorylation and fatty acid metabolism across multiple bat species. Metabolomic profiling compared acylcarnitine metabolites and tricarboxylic acid (TCA) cycle intermediates between bat and mouse hearts, indicating a distinct acylcarnitine profile and increased levels of TCA cycle intermediates in bats, suggesting enhanced metabolic capacity. Structural adaptations were assessed through anatomical and histological analyses on cardiac tissues, showing thicker left ventricular walls and increased vascular density in bats without pathological hypertrophy. Functional characteristics were evaluated using dobutamine stress echocardiography, demonstrating superior cardiac reserve in bats with significant increases in ejection fraction, stroke volume, and cardiac output under stress conditions. Additionally, isolated cardiomyocytes were treated with Angiotensin II (Ang II) to assess stress responses. Bat cardiomyocytes displayed resistance to Ang II-induced hypertrophy and mitochondrial dysfunction compared to mice, further highlighting their resilience to stress-induced damage. ConclusionThe unique adaptations observed in bat hearts, including enhanced metabolic pathways, structural remodelling, and cellular resilience contribute to their ability to meet the high energy demands of powered flight while maintain cardiac function under stress. These insights into bat cardiac physiology provide valuable information on cardioprotective mechanisms that could be applicable to other species. Translational PerspectiveBats exhibit remarkable cardiac adaptations that sustain the high energy demands of powered flight while resisting stress-induced damage. These insights into evolutionarily conserved cardioprotective mechanisms highlight potential therapeutic pathways for preventing heart failure, including resistance to hypertrophy and mitochondrial dysfunction under stress. Studying non-model organisms like bats may offer innovative approaches to enhance metabolic and stress resilience in human hearts, paving the way for translational research in cardiovascular disease management and treatment.

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PGM1 deficiency disrupts sarcomere and mitochondrial function in a stem-cell cardiomyocyte model

Radenkovic, S.; Preston, G.; Budhraja, R.; Muffels, I.; Ligezka, A. N.; Hrstka, R.; Staff, N. P.; Balakrishan, B.; Shah, R.; Verberkmoes, S.; Shammas, I.; Bosnyak, I.; Stiers, K. M.; Lai, K.; Beamer, L. J.; Pandey, A.; Morava, E.; Kozicz, T.

2025-07-04 biochemistry 10.1101/2025.07.01.662580 medRxiv
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BackgroundPhosphoglucomutase-1 (PGM1) plays a pivotal role in glycolysis, glycogen metabolism, and glycosylation. Pathogenic variants in PGM1 cause PGM1-congenital disorder of glycosylation (PGM1-CDG), a multisystem disorder with cardiac involvement. While glycosylation abnormalities in PGM1-CDG are treatable with galactose, cardiomyopathy does not improve suggesting a glycosylation-independent pathomechanism. Recently, mitochondrial abnormalities have been shown in a heart of a PGM1-deficicient patient and PGM1-mouse model. In addition, PGM1 has been associated with LDB3 (ZASP/Cypher), a sarcomeric Z-disk protein also associated with cardiomyopathy. However, the cardiac-specific role of PGM1 remains poorly understood, and targeted therapies for PGM1-related cardiomyopathy are currently lacking. MethodsInduced pluripotent stem cell-derived cardiomyocytes (iCMs) were generated from PGM1-deficient patient fibroblasts. Multielectrode array (MEA) recordings, untargeted (glyco)proteomics, and pathway analysis were performed to assess functional and molecular changes. Key findings were validated using tracer metabolomics and mitochondrial respiration assays. ResultsPGM1-deficient iCMs exhibited reduced beating frequency, impaired contractility, and prolonged contraction kinetics. Proteomic analyses revealed depletion of Z-disk components, including LDB3. AlphaFold3 structural modeling predicted a direct interaction between PGM1 and LDB3, implicating PGM1 in Z-disk integrity, which was confirmed in vitro. In addition, mitochondrial proteins were severely depleted, prompting us to investigate mitochondrial function. Functional validation confirmed extensive metabolic rewiring, energy depletion, and severely impaired mitochondrial respiration. Finally, the in silico drug repurposing identified possible therapeutic options that could target PGM1-deficient cardiomyopathy. ConclusionPGM1 is a key regulator of cardiomyocyte function, linking sarcomeric Z-disk integrity with mitochondrial metabolism. These mechanistic insights offer a foundation for developing targeted therapies for PGM1-CDG and potentially other cardiomyopathies involving Z-disk dysfunction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/662580v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17da449org.highwire.dtl.DTLVardef@1acb669org.highwire.dtl.DTLVardef@1fbbeecorg.highwire.dtl.DTLVardef@b38b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Multiomics reveals the genomic, proteomic and metabolic influences of histidyl dipeptides on heart

Baba, S.; Yan, K.; Mei, Z.; Zhao, J.; Prodhan, M. A.; Obal, D.; Katragadda, K.; Doelling, B.; Hoetker, D.; Posa, D. K.; He, L.; Yin, X.; Shah, J.; Pan, J.; Rai, S.; Lorkiewicz, P. K.; Zhang, X.; Li, S.; Bhatnagar, A.

2021-08-10 systems biology 10.1101/2021.08.10.455864 medRxiv
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Histidyl dipeptides, are synthesized in the heart via enzyme carnosine synthase (Carns), which facilitates glycolysis and glucose oxidation by proton buffering and attenuate ischemia and reperfusion injury. However, a composite understanding of the histidyl dipeptide mediated responses in the heart are lacking. We performed multilayer omics in the cardio specific Carns overexpressing mice, showing higher myocardial levels of histidyl dipeptides lead to extensive changes in microRNAs that could target the expression of contractile proteins and enzymes involved in {beta}-fatty acid oxidation and citric acid cycle (TCA). Similarly, global proteomics showed contractile function, fatty acid degradation and TCA cycle, pathways were enriched in the CarnsTg heart. Parallel with these changes, free fatty acids, and TCA intermediate-succinic acid were lower under aerobic and significantly attenuated under anaerobic conditions in the CarnsTg heart. Integration of multiomics data shows {beta}-fatty acid oxidation and TCA cycle exhibit correlative changes at all three levels in CarnsTg heart, suggesting histidyl dipeptides are critical regulators of myocardial structure, function and energetics.

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Metabolic Adaptations in Adult Spiny Mouse (Acomys) Cardiomyocytes Facilitate Enhanced Cardiac Recovery Following Myocardial Infarction

Kuppa, A.; Alzamrooni, A.; Suhan, T.; Chaudhary, R.; Lopez, R.; Collins, N.; Van Den Bergh, F.; Abouleisa, R.; Wang, H.; Mohamed, T.; Satin, J.; Seifert, A. W.; Lyssiotis, C. A.; Beard, D.; Abdel-Latif, A.

2024-05-24 cell biology 10.1101/2024.05.22.595229 medRxiv
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The adult mammalian heart has limited regenerative capacity following injury, leading to progressive heart failure and mortality. Recent studies have identified the spiny mouse (Acomys) as a unique model for mammalian cardiac regeneration, exhibiting enhanced recovery after myocardial infarction compared to commonly used laboratory mouse strains. However, the cellular and molecular mechanisms underlying this regenerative response remain poorly understood. In this study, we performed a comprehensive characterization of the metabolic adaptations to ischemic injury in cardiomyocytes of Acomys in comparison to the non-regenerative Mus Musculus. To investigate the transcriptomic and metabolomic profiles of cardiomyocytes in response to myocardial infarction, we utilized single-nucleus RNA sequencing (snRNA-seq) in sham-operated animals and 1, 3, and 7 days post-myocardial infarction. Complementary targeted metabolomics, stable isotope-resolved metabolomics, and functional mitochondrial assays were performed on heart tissues from both species to validate the transcriptomic findings and elucidate the metabolic adaptations in cardiomyocytes following ischemic injury. Transcriptomic analysis revealed that Acomys cardiomyocytes upregulate genes associated with glycolysis, the pentose phosphate pathway, and glutathione metabolism while downregulating genes involved in oxidative phosphorylation following injury. These metabolic changes were linked to decreased production of reactive oxygen species and increased antioxidant capacity, evidenced by the upregulation of genes such as Prdx1, Sod1, Sod2, and G6pd. Our targeted metabolomic studies supported these findings, showing a shift from fatty acid oxidation to glycolysis and ancillary biosynthetic pathways in Acomys cardiomyocytes post-injury. Functional mitochondrial studies indicated a higher reliance on glycolysis in Acomys compared to Mus, underscoring the unique metabolic adaptations of Acomys cardiomyocytes. Stable isotope tracing experiments confirmed a shift in glucose utilization from oxidative phosphorylation in Acomys. In conclusion, our study identifies unique metabolic adaptations in Acomys cardiomyocytes that contribute to their enhanced regenerative capacity following myocardial infarction. These findings provide novel insights into the role of metabolism in regulating cardiomyocyte proliferation and cardiac repair in adult mammals. By targeting the specific metabolic pathways and regulators identified in Acomys, such as glycolytic enzymes and PCK2, we may be able to develop innovative therapies to promote cardiac regeneration in patients with ischemic heart disease. Our work highlights the importance of metabolic flexibility in determining cardiomyocyte regenerative responses and establishes Acomys as a valuable model for studying cardiac regeneration in adult mammals. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/595229v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@dba53aorg.highwire.dtl.DTLVardef@3c8a74org.highwire.dtl.DTLVardef@a60251org.highwire.dtl.DTLVardef@e2142c_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Dissociation of disease phenotype and allele silencing in hypertrophic cardiomyopathy

Dainis, A.; Zaleta-Rivera, K.; Ribeiro, A.; Chang, A. C. H.; Shang, C.; Lan, F.; Burridge, P. W.; Wu, J. C.; Chang, A. C. Y.; Pruitt, B. L.; Wheeler, M.; Ashley, E.

2019-06-12 genetics 10.1101/642421 medRxiv
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Allele-specific RNA silencing has been shown to be an effective therapeutic treatment in a number of diseases, including neurodegenerative disorders. Studies of allele-specific silencing in hypertrophic cardiomyopathy to date have focused on mouse models of disease. Here, we investigate two methods of allele-specific silencing, short hairpin RNA (shRNA) and antisense oligonucleotide (ASO) silencing, using a human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model of disease. We used cellular micropatterning devices with traction force microscopy and automated video analysis to examine each strategys effects on contractile defects underlying disease. We find that shRNA silencing ameliorates contractile phenotypes of disease, reducing disease-associated increases in cardiomyocyte velocity, force, and power. We find that ASO silencing, while better able to target and knockdown a specific disease-associated allele, showed more modest improvements in contractile phenotypes. We find a dissociation between allelic-specificity and functional improvements between the two tested therapeutic strategies, suggesting a more complex method of allelic control underlying HCM-associated transcripts.\n\nAuthor summaryAllele-specific silencing, whereby a therapeutic molecule is used to lower the expression of just one of the two copies or alleles of a gene, may be a potential therapeutic strategy in diseases caused by a single mutation. In this paper, we examine two such strategies in hypertrophic cardiomyopathy, a disease characterized by an overgrowth of the left-ventricular heart muscle as well as contractile dysfunction. We used a human cell model of disease, creating induced pluripotent stem cell derived cardiomyocytes from a patient with HCM caused by a single base pair change in just one allele of the gene MYH7. We used two strategies to silence the disease-associated copy of MYH7, both focused on reducing RNA expression from the mutated allele, as well as state-of-the-art biophysical techniques for measuring contractility. We found that one silencing strategy, which reduced expression of both the disease-associated and the healthy alleles of MYH7, showed great improvements in contractility between treated and untreated cells. Our second strategy, which silenced only the disease-associated copy of MYH7, showed more modest improvements in contractility. This suggests that the disease mechanism underlying this type of hypertrophic cardiomyopathy may be more complex than just presence or absence of the mutated RNA.

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Purkinje cardiomyocytes of the ventricular conduction system are highly diploid but not regenerative

Watanabe, H.; Tao, G.; Gan, P.; Westbury, B. C.; Cox, K. D.; Tjen, K.; Song, R.; Fishman, G. I.; Makita, T.; Sucov, H. M.

2022-10-31 developmental biology 10.1101/2022.10.29.514354 medRxiv
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Inefficiency of regeneration underlies many of the pathologies associated with heart injury and disease. Ventricular diploid cardiomyocytes (CMs) are a candidate population that may have enhanced proliferative and regenerative properties [1-3], but subpopulations of diploid CMs and their regenerative capacities are not yet known. Here, using the expression marker Cntn2-GFP and the lineage marker Etv1CreERT2, we demonstrate that peripheral ventricular conduction CMs (Purkinje CMs) are disproportionately diploid (35%, vs. 4% of bulk ventricular CMs). However, this lineage had no enhanced competence to support regeneration after adult infarction. Furthermore, the CM-specific kinase Tnni3k, which strongly influences bulk ventricular CM ploidy [3] and is also associated with conduction system defects [4], had no influence on the ploidy or organization of the ventricular conduction system. Unlike the bulk diploid CM population, a significant fraction of conduction CMs remain diploid by avoiding neonatal cell cycle activity, likely contributing to these properties.

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Reverse remodelling of the mitochondria and cytoskeleton after respiratory heart rate variability pacing of the failing sheep heart

Crossman, D. J.; Guo, G.; Shanks, J.; Pachen, M.; Bai, J.; Moammer, H.; Middleditch, M. J.; Grey, G.; Paton, J. F.; Ramchandra, R.

2025-05-30 cell biology 10.1101/2025.05.29.656916 medRxiv
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We have previously demonstrated that pacing the failing sheep heart with respiratory heart rate variability (RespHRV), a natural variability in the heart rate that is linked to respiration on a breath-by-breath basis, improves cardiac output dramatically. In this study, we used proteomics and super-resolution microscopy to explore the role of energetics and T-tubule cellular remodelling in response to ResPHRV pacing in an ischaemic ovine model of heart failure (HF). After 2 weeks of RespHRV pacing, cardiac output improved by 1.1 {+/-} 0.2 L/min (**p=0.003). Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) was used to probe differences between three groups: HF without any intervention, HF with RespHRV pacing and a healthy control group. Orthogonal Partial Least Squares (OPLS) discriminant analysis demonstrated a clear separation of all three groups by T score (***p<0.001) with the HF+RespHRV pacing group placed intermediate between the HF and control groups. The top 50 proteins negatively correlated with T score (down in HF, restored after RespHRV) were dominated by mitochondrial proteins, as confirmed by Pathway Enrichment Analysis (***p<0.001). Multiple Reaction Monitoring Mass Spectrometry (MRM-MS) analysis confirmed this finding in selected targets (ACAA2, ACADS, CRAT, NDUFA8, and SUCLG1, *p<0.05). STimulated Emission Depletion (STED) microscopy identified a disruption of mitochondria structure in HF (*p<0.05) that was restored in the HF+R group (p=0.051). The area of mitochondria labelling was increased in the HF+RespHRV group compared to HF (**p=0.005). Many cytoskeletal proteins linked to mitochondria regulation and T-tubule remodelling were upregulated in HF and were reduced by RespHRV. MRM-MS was able to confirm these findings for selected targets (ANAXA2, CAVIN2, SPTBN1, TUBA4A). STED microscopy of collagen VI and the ryanodine receptor revealed cellular hypertrophy and remodelling of the T-tubules and cardiac junctions in HF sheep (*p<0.05), RespHRV showed a trend for reversing these structural changes. These data support the hypothesis that within the first two weeks of RespHRV pacing, there is an increase in mitochondrial repair and function coupled with re-organisation of the cellular cytoskeleton, which is consistent with the improvement in cardiac pump function.

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Differential Bioenergetics In Adult Rat Cardiomyocytes Isolated From The Right Versus Left Ventricle

Nguyen, Q.; Rao, K.; Mullett, S.; Wendell, S.; St. Croix, C.; Goetzman, E.; Shiva, S.

2020-06-09 cell biology 10.1101/2020.06.08.133769 medRxiv
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The right and left ventricle of the heart have distinctly different developmental origins and are affected differently by similar pathological stimuli. Though it is well established that the heart relies almost entirely on mitochondrial function to sustain energy production, it remains unclear whether bioenergetics differ in the two ventricles. Herein, we define a novel methodology to optimize the isolation of intact cardiomyocytes from the right versus the left ventricle. We demonstrate that this segmental Langendorff-free methodology yields viable cardiomyocytes with intact mitochondrial function. Further, we compare bioenergetics in right versus left ventricle cardiomyocytes and show that cardiomyocytes from the right ventricle have a greater maximal capacity for respiration and enhanced glycolytic rate. This increase in respiration was concomitant with increased fatty acid oxidation and levels of fatty acid oxidation proteins, but no change in mitochondrial electron transport complex expression. These data validate a potentially powerful tool to evaluate differences in right and left ventricular function and advance the understanding of cardiac bioenergetic differences. These data will be discussed in the context of differential responses by the right versus ventricle in pathology.

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Expression, subcellular localization, and phosphorylation of MK5 in adult cardiac ventricular fibroblasts

Sahadevan, P.; Nawaito, S. A.; Trepanier, J.; Benamar, S.; Sahmi, F.; Theberge-Julien, G.; Villeneuve, L. R.; Gaestel, M.; Tardif, J.-C.; Allen, B. G.

2020-07-24 biochemistry 10.1101/2020.07.24.219790 medRxiv
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MAP kinase-activated protein kinase-5 (MK5) plays an important role in cardiac fibroblast function. Although p38 MAPK and atypical MAPKs and ERK3 and ERK4 have been identified as activators of MK5, the kinases that activate MK5 remain controversial. Here we examined the expression, subcellular distribution, and regulation of MK5 in cardiac ventricular myofibroblasts and myocytes. The copy numbers for MK5 and ERK4 mRNA were comparable in myocytes and myofibroblasts, whereas that of ERK3 was much higher in myofibroblasts. Interestingly, MK5 and ERK3 immunoreactivity was detected in myofibroblasts but not myocytes whereas ERK4 immunoreactivity was detected in myocytes: treating in myocytes with a proteasome inhibitor or hypertrophic agonists failed to rescue MK5 immunoreactivity. In myofibroblasts, MK5 and ERK3 immunoreactivity was predominantly nuclear and cytosolic, respectively. In serum-starved cardiac myofibroblasts, phosphothreonine-182 MK5 (pT182-MK5) immunoreactivity was predominantly nuclear but increased in intensity and relocated to the cytoplasm in response to serum, sorbitol, angiotensin II, TGF{beta}, or H2O2 and this was prevented by inhibition of p38/{beta}. Phos-tag SDS-PAGE revealed multiple slower migrating bands of MK5 immunoreactivity, indicating phosphorylation of MK5 at multiple sites. Phos-tag PAGE also revealed MK5 phosphorylation was increased with fibroblast activation and in hearts exposed to a chronic increase in afterload. MK5 and ERK3 co-immunoprecipitated and proximity ligation assays revealed ERK3 and MK5 in close proximity in myofibroblast cytoplasmic compartment. Furthermore, p38/{beta} inhibition decreased the abundance of MK5 immunoreactivity in ERK3 immunoprecipitates. Finally, deleting MK5 did not reduce the abundance of ERK3 immunoreactivity. These observations suggest that p38 and/or p38{beta} are the primary mediators of T182-MK5 phosphorylation and hence MK5 activation in cardiac myofibroblasts.

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Lactate and Immunomagnetic-purified iPSC-derived Cardiomyocytes Generate Comparable Engineered Cardiac Tissue Constructs

Rossler, K. J.; de Lange, W.; Mann, M. W.; Aballo, T. J.; Melby, J. A.; Zhang, J.; Kim, G.; Bayne, E. F.; Zhu, Y.; Farrell, E. T.; Kamp, T. J.; Ralphe, J. C.; Ge, Y.

2023-05-06 molecular biology 10.1101/2023.05.05.539642 medRxiv
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Three-dimensional engineered cardiac tissue (ECT) using purified human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has emerged as an appealing model system for the study of human cardiac biology and disease. A recent study reported widely-used metabolic (lactate) purification of monolayer hiPSC-CM cultures results in an ischemic cardiomyopathy-like phenotype compared to magnetic antibody-based cell sorting (MACS) purification, complicating the interpretation of studies using lactate-purified hiPSC-CMs. Herein, our objective was to determine if use of lactate relative to MACs-purified hiPSC-CMs impacts the properties of resulting hiPSC-ECTs. Therefore, hiPSC-CMs were differentiated and purified using either lactate-based media or MACS. After purification, hiPSC-CMs were combined with hiPSC-cardiac fibroblasts to create 3D hiPSC-ECT constructs maintained in culture for four weeks. There were no structural differences observed, and there was no significant difference in sarcomere length between lactate and MACS hiPSC-ECTs. Assessment of isometric twitch force, Ca2+ transients, and {beta}-adrenergic response revealed similar functional performance between purification methods. High-resolution mass spectrometry (MS)-based quantitative proteomics showed no significant difference in any protein pathway expression or myofilament proteoforms. Taken together, this study demonstrates lactate- and MACS-purified hiPSC-CMs generate ECTs with comparable molecular and functional properties, and suggests lactate purification does not result in an irreversible change in hiPSC-CM phenotype. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/539642v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@54b370org.highwire.dtl.DTLVardef@d0bbc8org.highwire.dtl.DTLVardef@1d847e3org.highwire.dtl.DTLVardef@578c1b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Desmoplakin Haploinsufficiency Underlies Cell-Cell Adhesion Failure in DSP Cardiomyopathy and is Rescued by Transcriptional Activation

Smith, E. D.; Jin, K.; Ferguson, B.; Tsan, Y.-C.; DePalma, S. J.; Meisner, J. K.; Renberg, A.; Bedi, K.; Friedline, S.; Margulies, K. B.; Baker, B. M.; Helms, A. S.

2025-06-03 genetics 10.1101/2025.06.01.657304 medRxiv
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BackgroundTruncating variants in desmoplakin (DSPtv), are a leading cause of arrhythmogenic cardiomyopathy (ACM), often presenting with early fibrosis and arrhythmias disproportionate to systolic dysfunction. DSP is critical for cardiac mechanical integrity, linking desmosomes to the cytoskeleton to withstand contractile forces. While loss-of-function is implicated, direct evidence, both for DSP haploinsufficiency in human hearts and for the impact of mechanical stress on cardiomyocyte adhesion, has been limited, leaving the pathogenic mechanism unclear. MethodsWe analyzed explanted human heart tissue from patients with DSPtv (N=3), titin truncating variants (TTNtv, N=5), and controls (N=5) using RNA-sequencing and mass spectrometry. We generated human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) harboring patient-derived or CRISPR-Cas9 engineered DSPtv to model a range of DSP expression levels. Using a 2D cardiac muscle bundle (CMB) platform enabling live visualization of cell junctions, we developed an assay to assess cell-cell adhesion upon heightened contractile stress in response to the contractile agonist endothelin-1. CRISPR-interference (CRISPRi) was used to confirm the role of DSP loss, and CRISPR-activation (CRISPRa) was tested for therapeutic rescue. ResultsCompared to both control and TTNtv hearts, DSPtv human hearts exhibited reduced DSP at both the mRNA and protein level, as well as broadly disrupted desmosomal stoichiometry. Transcriptomic and proteomic analyses implicated cell adhesion, extracellular matrix, and inflammatory pathways. iPSC-CM models recapitulated DSP haploinsufficiency and desmosomal disruption. DSPtv CMBs showed normal baseline contractile function. However, they displayed marked cell-cell adhesion failure with contractile stress (75% failure vs. 8% in controls, p<0.001). Adhesion failure was prevented by the myosin inhibitor, mavacamten. CRISPRi-mediated DSP knockdown replicated this susceptibility to adhesion failure. Conversely, CRISPRa robustly increased DSP expression and rescued cell-cell adhesion failure in DSPtv CMBs (9% failure post-CRISPRa, p<0.001 vs. un-treated). Rescue occurred even when only the DSPII isoform was upregulated in a model with biallelic DSP transcript 1 loss of function. ConclusionsDSP haploinsufficiency is the major cause of DSP cardiomyopathy with a primary consequence of conferring vulnerability to cardiomyocyte cell-cell adhesion failure under heightened contractile stress. Transcriptional activation of DSP reverses this defect in preclinical models, establishing proof-of-concept for a potential therapeutic strategy in DSP cardiomyopathy.

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Glucose metabolism promotes neonatal heart regeneration

Fajardo Martinez, V. M.; Feng, I.; Chen, B. Y.; Perez, C. A.; Shi, B.; Clark, P.; Tian, R.; Lien, C.-L.; Pellegrini, M. M.; Christofk, H.; Nakano, H.; Nakano, A.

2019-12-09 developmental biology 10.1101/865790 medRxiv
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The mammalian heart switches its main metabolic substrate from glucose to fatty acids shortly after birth. This metabolic switch coincides with the loss of regenerative capacity in the heart. However, it is unknown whether glucose metabolism itself regulates heart regeneration. Here, we report that glucose metabolism is a determinant of regenerative capacity in the neonatal mammalian heart. Cardiac-specific overexpression of Glut1, the embryonic form of constitutively active glucose transporter, resulted in an increase in glucose uptake and concomitant glycogen storage in postnatal heart. Upon cryoinjury, Glut1 transgenic hearts showed higher regenerative capacity with less fibrosis than non-transgenic control hearts. Interestingly, flow cytometry analysis revealed two distinct populations of ventricular cardiomyocytes: Tnnt2-high and Tnnt2-low cardiomyocytes, the latter of which showed significantly higher mitotic activity in response to high intracellular glucose in Glut1 transgenic hearts. Metabolic profiling shows that Glut1-transgenic hearts have a significant increase in the glucose metabolites upon injury, and inhibition of the nucleotide biosynthesis abrogated the regenerative advantage of high intra-cardiomyocyte glucose level. Our data suggest that the increased in glucose metabolism promotes cardiac regeneration in neonatal mouse heart.

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Nucleoli as drivers of nuclear remodelling in cardiomyocytes during Heart Failure

Matzer, I.; Wang, H.; Kozyrina, A. N.; Fu, J.; Iskratsch, T.; Vassalli, M.; Ljubojevic-Holzer, S.; Gorelik, J.; Swiatlowska, P.

2026-02-25 cell biology 10.64898/2026.02.24.707499 medRxiv
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Cardiomyocyte mechanotransduction has traditionally focused on the sarcomere and cytoskeleton, yet emerging evidence highlights the nucleus as an active mechanical responder. To adapt to the dynamic mechanical environment, the nucleus forms nuclear invaginations (NIs), double-membrane folds that provide structural support to chromatin and incorporate nuclear pore complexes to facilitate nucleo-cytoplasmic transport, including Ca2+ transport. However, how these structures are formed is not yet understood. We leveraged advances in high-resolution microscopy, mechanical stimulation, rat models and human samples, to study the formation, function and remodelling of cardiac NIs in Heart Failure (HF). Here, we demonstrate that the formation of NI in cardiomyocytes is regulated by both, cytoskeleton such as actin and detyrosinated microtubules as well as intranuclear nucleolar interactions with NI disruption resulting in elevated baseline nuclear Ca2+. In a 16-week post-Myocardial Infarction (MI) end-stage HF rat model, as well as in human Dilated Cardiomyopathy samples, a marked reduction in NIs was observed. Importantly, NI loss was already evident at 8 weeks post-MI, preceding detectable cytoskeletal stiffening. At this stage, we observed increased DNA damage in the peri-nucleolar region, accompanied by nucleolar remodelling and a shift in nucleolar biomechanical properties. In conclusion, preserving nucleolar integrity emerges as a potential target for intervention.

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Impact of Serum Circulating Factors and PDE5 Inhibitor Therapy on Cardiomyocyte Metabolism in Single Ventricle Heart Disease

Garcia, A. M.; Pietra, A. E.; Turner, M. E.; Pires Da Silva, J.; Baybayon-Grandgeorge, A. N.; Sparagna, G. C.; Jeffrey, D. A.; Stauffer, B. L.; Sucharov, C. C.; Miyamoto, S. D.

2025-04-01 cell biology 10.1101/2025.03.31.646497 medRxiv
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BackgroundWhile operative and perioperative care continues to improve for single ventricle congenital heart disease (SV), long-term morbidities and mortality remain high. Importantly, phosphodiesterase-5 inhibitor therapies (PDE5i) are increasingly used, however, little is known regarding the direct myocardial effects of PDE5i therapy in the SV population. ObjectivesOur group has previously demonstrated that the failing SV myocardium is characterized by increased PDE5 activity and impaired mitochondrial bioenergetics. Here we sought to determine whether serum circulating factors contribute to pathological metabolic remodeling in SV, and whether PDE5i therapy abrogates these changes. MethodsUsing an established in vitro model whereby primary cardiomyocytes are treated with patient sera +/- PDE5i, we assessed the impact of circulating factors on cardiomyocyte metabolism. Mass spectrometry-based lipidomics and metabolomics were performed to identify phospholipid and metabolite changes. Mitochondrial bioenergetics were assessed using the Seahorse Bioanalyzer and a stable isotope based mitochondrial enzyme activity assay. Relative mitochondrial copy number was quantified using RT-qPCR. ResultsOur data suggest that serum circulating factors contribute to fundamental changes in cardiomyocyte bioenergetics, including impaired mitochondrial function associated with decreased cardiolipin and other phospholipid species, increased reactive oxygen species (ROS) generation, and altered metabolite milieu. Treatment with PDE5i therapy was sufficient to abrogate a number of these metabolic changes, including a rescue of phosphatidylglycerol levels, a reduction in ROS, improved energy production, and normalization of several key metabolic intermediates. ConclusionsTogether, these data suggest PDE5i therapy has direct cardiomyocyte effects and contributes to beneficial cardiomyocyte metabolic remodeling in SV failure.