tbuckley/cabot-search huggingface dataset:
Abstract We003: Identification of CircRNA-miRNA-mRNA Regulatory Network and Crucial Signaling Pathways Related to Cardiomyocyte Proliferation in Neonatal Mice
Authors: Ling Tang, Verah Nyarige, Pengsheng Li, Wuqiang Zhu
Journal: Circulation Research (2024)

Introduction: Neonatal pig hearts exhibit remarkable regenerative capacity within two days post-birth. In this study, we propose that a comprehensive multiomics analysis encompassing circRNA, miRNA, and mRNA data from neonatal mouse hearts can unveil intricate circRNA-miRNA-mRNA relationships associated with cardiac regeneration. Our aim is to identify new novel circRNAs and miRNAs implicated in cardiomyocyte proliferation through leveraging multiomics analysis. Methods: Utilizing neonatal mouse hearts, we conducted circRNA, miRNA, and mRNA sequencing across four different postnatal days (P1, P3, P7, and P28; n=6, encompassing both males and females). We employed integrative bioinformatics analyses across distinct experimental designs (P1 vs P3, P1 vs P7, and P1 vs P28). Back splice junctions generated by CIRCexplorer2’s parse command was utilized to annotate sequenced circRNAs as known or novel. Validation of circRNA, miRNA, and mRNA expression levels was achieved through qRT-PCR, while protein expression levels were assessed via western blotting. Fluorescence in situ hybridization (FISH) technology was employed to determine circRNA localization. The functional significance of key genes involved in cardiomyocyte proliferation was assessed via siRNA-mediated knockdown of circRNAs and miRNAs, accompanied by cell cycle assessment using bioluminescence assay and immunostaining. Results: Intersection of differentially expressed target genes from circRNA, miRNA, and mRNA analyses at each experimental design facilitated the construction of circRNA-miRNA-mRNA regulatory networks, aiding in the development of cardiac regeneration-related regulatory networks and inference of novel relationships between circRNA, miRNA, and mRNA. Integrative bioinformatics analysis revealed significant alterations in circRNA-miRNA-mRNA expression profiles during postnatal cardiomyocyte maturation in mice. Pathway enrichment analysis identified several differentially expressed circRNAs enriched in cell division and proliferation-related pathways. qPCR and cell cycle studies identified 17 potential circRNAs associated with cardiomyocyte proliferation in mice, with knockdown of these circRNAs significantly impacting cardiomyocyte cell cycle. Conclusion: Our findings suggest a crucial role for circRNAs in the regulation of neonatal myocardial regeneration.
Abstract We125: HIV-1 Nef protein induces aging and cardiac dysfunction through autophagy dysregulation
Authors: Olena Kondrachuk, Manish Gupta
Journal: Circulation Research (2024)

Background: Despite highly active antiretroviral therapy (ART), HIV-associated cardiovascular disease and accelerated aging cause increased mortality in people living with HIV/AIDS (PLWHA). Nef protein has been detected in HIV patients even with ART therapy. We hypothesized that the Nef protein may compromise heart function and accelerate aging by dysregulation of autophagy. Methods: We generated a Nef transgenic (Nef-TG) mouse model by cloning the HIV-Nef gene in the CAG-Lox-CAT vector. We used Western blotting to determine protein expression in cardiac tissue. Heart function was evaluated by echocardiography. Nef protein function was also determined by plasmid DNA transfection in the HEK293 cells. Results: Nef-TG mouse shows cardiac dysfunction, increased cardiac fibrosis, and early mortality. Expression of autophagy marker LC3II was significantly decreased in the heart of Nef-TG mice. The data suggest Nef inhibits autophagy in the cell. Mechanistically, we found that senescence-associated markers p21, Bcl2, and Beclin1 levels significantly increased in Nef-TG mice's hearts, which may negatively regulate heart function and promote aging. Conclusion: Our new Nef-TG mouse model revealed the cause of HIV-associated aging in PLWHA. Our mouse model can also be used to elucidate the role of Nef protein on other organ systems and test novel therapeutics for HIV.
Abstract We120: NHE1 Regulates Apoptosis Susceptibility in Sugen-Hypoxia Pulmonary Arterial Smooth Muscle Cells via Modulation of CHOP
Authors: Manuella Ribas Andrade, Xin Yun, Larissa Shimoda
Journal: Circulation Research (2024)

Pulmonary hypertension (PH) is caused by lung vascular remodeling involving increased pulmonary arterial smooth muscle cell (PASMC) proliferation and apoptosis resistance. Na +/ H + exchanger (NHE) isoform 1 (NHE1) is a membrane protein regulating intracellular pH (pH i ) via movement of H + . Our lab found increased NHE activity is associated with hyperproliferation in PASMCs from the Sugen Hypoxia (SuHx) animal model of PH. In this study, we tested the hypothesis that increased NHE1 activity also causes apoptosis resistance in SuHx PASMCs via dysregulation of pH i . PASMCs isolated from distal pulmonary arteries of control and SuHx rats were treated with NHE inhibitor, [5-(N-ethyl-N-isopropyl)-amiloride; EIPA;1 uM], NHE1 inhibitor [cariporide;10 uM] or vehicle for 24 h before analyzing cell apoptosis via Hoechst staining under baseline and stimulated (250 uM H 2 O 2 ) conditions. Control PASMCs were infected with adenovirus containing green fluorescent protein (GFP), wild-type NHE1 (WT) or NHE1 lacking ion translocation activity (E262I). Protein expression and localization were assessed via immunoblotting. NHE activity was assessed from Na + -dependent recovery following an ammonium pulse. At baseline, apoptosis in SuHx PASMCs was similar to control cells but following H 2 O 2 stimulation , SuHx PASMCs were resistant to apoptosis (p&lt;0.001). EIPA increased basal and stimulated apoptosis in SuHx cells. Surprisingly, treatment with cariporide did not alter SuHx apoptosis, suggesting that EIPA but not cariporide was able to sensitize SuHx cells to apoptosis, despite both drugs significantly inhibiting NHE activity, suggesting EIPA affects PASMC apoptosis through a mechanism other than pH i regulation. To test this possibility, control PASMCs were infected with GFP, WT or E262I. NHE activity was increased in cells with WT, but not E262I, when compared to GFP (p&lt;0.001). Overexpression of either WT or E262I inhibited apoptosis following treatment with H2O2 (p&lt;0.001). We next explored CAAT/enhancer binding protein homologous transcription factor (CHOP), known to be involved in induction of apoptosis. CHOP expression was increased by H2O2 in control cells but was decreased in SuHx PASMCs. EIPA increased CHOP levels in SuHx cells, whereas, expression of both WT and E262I constructs inhibited the H 2 O 2 -induced CHOP increase in control PASMCs. Our results indicate that NHE1 regulates apoptosis susceptibility in PASMCs during PH via modulation of CHOP rather than through pH i regulation.
Abstract We114: Feeding Behavior Underlies the Circadian Rhythm in the Autonomic Input to the Heart and Heart Rate
Authors: Abhilash Prabhat, Isabel Stumpf, Rebecca Stalcup, Allison Ehlman, Tanya Seward, Julie Pendergast, Elizabeth Schroder, Brian Delisle
Journal: Circulation Research (2024)

Objective: The circadian pacemaker located in the suprachiasmatic nucleus (SCN) of the hypothalamus drives circadian rhythms in feeding and activity. Several studies suggest the SCN regulates autonomic input to the heart to generate day-night rhythms in heart rate. Hypothesis: The circadian rhythm in feeding generates day-night rhythms in autonomic input to the heart and heart rate. Methodology: Mice (n=6/sex) were implanted with telemetry probes to continuously record heart rate, core body temperature, and activity in thermoneutral housing conditions. Mice were housed in a 12 h light: 12 h dark cycle (LD) with ad libitum access to food (ALF). In these conditions, mice primarily eat during the dark cycle. Mice were subjected to light phase time-restricted feeding (TRF) for 5 days. This forces the mice to eat during the light cycle. We quantified changes in autonomic input to the heart by injecting mice with the autonomic receptor inhibitors propranolol and methylatropine. To determine if circadian rhythms generate day-night rhythms in autonomic input to the heart, TRF mice were switched from LD to constant darkness (DD) and then returned to ALF in DD. Results: ALF mice housed in LD had 24-hour rhythms in autonomic input to the heart, heart rate, and activity that all peaked in alignment during the dark cycle. One day after starting TRF, the phase of the 24-hour rhythms in heart rate but not activity shifted by 8-10 hours to align with feeding during the light phase. Switching TRF mice in LD to DD did not alter the phase or amplitude of the day-night rhythms in autonomic input to the heart, heart rate, or activity. Returning the TRF mice in DD to ALF showed the autonomic input to the heart and heart rate re-aligned with the free running rhythm in activity. Conclusions: Day-night rhythms in heart rate and autonomic input to the heart align with activity in LD and DD in ad libitum fed but not time-restricted fed conditions. These data demonstrate that feeding behavior, not SCN-signaling or activity rhythms, drives day-night rhythms in autonomic input to the heart and heart rate.
Abstract We111: 3D spheroids composed by induced Skeletal Muscle Progenitor Cells and Mesenchymal Stem Cells derived from human Pluripotent Stem Cells can recapitulate embryonic niches in hindlimb ischemia model
Authors: Jinju Kim, Jae-Hyun Park, Yeon-Jik Choi, Hun Park
Journal: Circulation Research (2024)

Introduction: Peripheral artery disease (PAD) is a significant comorbidity in aging population regarding diminished quality of life and increased mortality rates. There are urgent needs for developing advanced therapeutics for functional limb salvage beyond conventional revascularization. We hypothesized that 3D spheroids composed by induced Skeletal Muscle Progenitor Cells (iSKMPs) and Mesenchymal Stem Cells (iMSCs) could recapitulate embryonic niches and provide promising regenerative potentials in hindlimb ischemia (HLI) models. Methods: We manufactured scaffold-free, self-aggregated 3D spheroids using microcavity plates with ultra-low attachment surface. 3D spheroids were designed into 3 groups according to the induced cell types derived from Human Pluripotent Stem Cells (hPSCs); 1) iSKMPs only, 2) iMSCs only, 3) iSKMPs + iMSCs mixed. We transplanted 3D spheroids into the ischemic area and compared their therapeutic potentials using Laser Doppler Perfusion Imaging (LDPI) and immunohistochemical staining analysis. Results: iSKMPs secreted various angiogenic factors including IGF, HGF and FGF and facilitated tube formation and migration of endothelial cells (ECs). iSKMPs also showed the differentiation potential into myofibers in defined 2D culture condition. During the 28-day follow-up period, the transplantation of 3D mixed spheroids not only increased blood perfusion in ischemia limb, but also significantly reduced amputation rate compared with those of control and other 3D single spheroid groups. Notably, in vivo capacity of muscle regeneration was more potent in 3D mixed spheroid group with higher rate of engraftment, myotube formation, and vascularization. These findings suggested that iSKMPs played a significant role in limb salvage via myogenesis and angiogenesis, and their cell-to-cell interaction with iMSCs within 3D spheroids provided a favorable microenvironment to enhance the engraftment and maturation of iSKMPs in ischemic hindlimb. Conclusion: We demonstrated that the transplantation of 3D spheroids composed by iSKMPs and iMSCs could recapitulate developmental embryonic niches and provide potent regenerative potentials in HLI models. These findings provide compelling evidence that this injectable platform of 3D mixed spheroids can be a promising tool to rescue limb amputation in patients with PAD.
Abstract We013: Modeling Sex and Stress using Induced Pluripotent Stem Cell Derived Cardiomyocytes
Authors: Samuel Feinstein, Orlando Chirikian, Beth Pruitt
Journal: Circulation Research (2024)

Despite causing 1 in 3 deaths worldwide, cardiovascular disease and the heart have only recently been studied in women. Contrary to previous belief, the female heart is not just a smaller replica of a male heart. Almost all heart diseases show sexual differences in risk, treatment, and symptoms. Even with these differences there is a lack of female models in animal and cellular studies. Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) are a powerful human model to test baseline and stressed sex differences at the cellular level. We hypothesized that using stressors that mimic disease conditions (drugs, substrate stiffness) in multiple male and female hiPSC-CMs will result in differential sex-based responses. We ran Traction Force Microscopy on 3 male (n = 424 cells, 3 batches) and 3 female (n = 318 cells, 3 batches) cell lines on 10 kPa polyacrylamide hydrogels. Male cells had 42% higher twitch force (p = 8.8E-6) with 25% higher contraction (p = 1.77E-5) and relaxation (p = 0.0006) velocities. However, female cells had a larger spread area (823 +/- 17.32 µm 2 vs. 756 +/- 21.64 µm 2 , p = 0.0018). To validate hiPSC-CMs as a model we compared preliminary RNA-seq to publicly available Heart Cell Atlas sc/snRNA-seq data sets of primary ventricular cardiomyocytes. They had similar differentially expressed genes (DEGs) as our hiPSC-CMs. Furthermore, DEGs had significantly enriched gene sets including a 25-fold enrichment in hypertrophic cardiomyopathy (FDR = 1.6E-7), 23-fold in dilated cardiomyopathy (FDR = 1.6E-7), and 16-fold in cardiac muscle contraction (FDR = 6.3E-4). We analyzed stiffness by differentiating and culturing hiPSC-CMs on 10 kPa and 100 kPa stiffness hydrogels. Our RNA-seq analysis at day 10 and 30 after differentiation found 7000 DEGs at 10 kPa while only 556 DEGs at 100 kPa. We looked hypercontractility caused stres and performed RNA-seq on day 60 wild type and hypercontractile mutant hiPSC-CMs. The wild type was dosed with positive inotrope levosimendan to induce hypercontractility while the hypercontractile mutant was dosed with negative inotrope verapamil to lower contractility. Hypercontractility had significant upregulation of the cellular response to stress including ER stress, stress-activated MAPK cascades, stress fibers, and cardiac muscle hypertrophy in response to stress. These differences can identify possible gene targets for preventing cardiovascular disease and inform personalized medicine.
Abstract Mo084: Stem Cell-Based Functional Genomics Unravel A Novel Vascular Smooth Muscle Cell State Induced By The 9p21 Coronary Artery Disease Risk Locus
Authors: Elsa Salido, Carolina de Medeiros Vieira, Rohan Zade, Valentina Lo Sardo
Journal: Circulation Research (2024)

Background: Genome-wide association studies have identified common genetic variants (Single Nucleotide Polymorphisms – SNPs) at ~300 human genomic loci linked to coronary artery disease (CAD) susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert and encompasses ~80 SNPs in high linkage disequilibrium. We have previously generated isogenic induced Pluripotent Stem Cells (iPSCs) lines from risk and non-risk donors at 9p21.3 and performed a complete deletion of the locus. By using iPSC-derived vascular smooth muscle cells (iPSC-VSMCs) we demonstrated that the risk haplotype at 9p21.3 causes altered expression of numerous genes essential for muscle function, including contraction and adhesion. Notably, deletion of the risk haplotype restores the non-risk phenotype, suggesting a gain of function effect. Here, we aimed to identify the transcriptomic signature and state trajectories of VSMCs induced by the 9p21.3 risk haplotype and validate them through functional assays and ex-vivo analysis of human coronary arteries. Methods: We have used iPSCs from individuals carrying the risk and non-risk haplotype at 9p21.3 and isogenic knockout lines. After VSMCs differentiation induction, mature VSMCs were used for single cell RNA sequencing using 10X Chromium platform and functional assays. Results: Our analysis revealed that the 9p21.3 risk haplotype prompts VSMCs to acquire a novel cellular state showing reduced plasticity and divergent from other VSMC states previously linked to CAD. We found markers of alternative lineages, including osteogenic and neuronal, coupled with altered expression of genes within other CAD loci, and functional defects. We identified a set of new molecular markers crucial to define risk-associated VSMCs and uncovered their upstream regulators. Conclusions: Our study provides insights into CAD pathogenesis driven by the 9p21.3 risk locus and identified new gene regulatory networks essential for maintaining the normal functionality of the muscle layer of the arteries. Leveraging the power of iPSCs we present novel concepts about the biology of VSMCs and shed light on the impact of the strongest CAD genetic risk factor in preserving a healthy cellular state within the vasculature.
Abstract We010: In Vivo Partial Reprogramming of Cardiomyocytes to a Molecularly Rejuvenated State Ameliorates Cardiac Failure
Authors: Irene De Lazaro, Bohan Zhang, Nadezhda Makarova, Marco Mariotti, Vadim Gladyshev, David Mooney
Journal: Circulation Research (2024)

Introduction: i n vivo partial cell reprogramming through transient overexpression of Oct3/4 , Klf4 , Sox2 and cMyc (OKSM) transcription factors generates de-differentiated or molecularly rejuvenated cells that may contribute to tissue regeneration. However, not all cell types are equally amenable to reprogramming, and tools to induce cell type-specific reprogramming in vivo are scarce. Here, we generated cardiomyocyte-specific, “reprogrammable” mice (CM-OKSM) that enabled inducible OKSM expression specifically in this cell type, characterized by its remarkably poor regenerative capacity after birth. Using this model, we investigated if partial, in situ , cardiomyocyte reprogramming was feasible and able to enhance cardiac regeneration. Methods: To generate lineage-traceable CM-OKSM mice, we combined Cre recombination driven by a cardiomyocyte-specific promoter ( Myh6 ), conditional GFP labelling and conditional, doxycycline (dox)-inducible, control of OKSM expression. We administered 1 mg/ml dox in the drinking water of CM-OKSM mice, and investigated reprogramming at the molecular level (immunostaining, RT-qPCR, RNAseq, DNA methylation), histological level (H&amp;E, electron microscopy) and functional level (teratoma assay, echocardiography). We compared dox administration for six cycles of a two-day ON/five-day OFF regime, and for eighteen continuous days, to investigate partial and full reprogramming to pluripotency, respectively. We conducted studies in young adult mice (8 to 12 weeks old) and on older mice (9 months old) with heart failure, to assess the effects of cardiomyocyte reprogramming in cardiac performance. Results and Discussion: In young CM-OKSM mice, adult cardiomyocytes can be fully reprogrammed to pluripotency in vivo by eighteen-day overexpression of OKSM. This was evidenced by significant upregulation of endogenous pluripotency markers, loss of sarcomere organization, cell de-differentiation, and the appearance of GFP+ teratomas with trilineage contribution. We then found that cyclic OKSM induction prevented reacquisition of pluripotency and tumorigenesis, both in young and old mice. In the latter, partial reprogramming of cardiomyocytes induced significant rejuvenation of their epigenetic age and halted the progression of congestive heart failure. Our results confirm that the OKSM cocktail can reprogram adult mouse cardiomyocytes in vivo and that partial reprogramming can contribute to functional improvements in cardiac disease.
Abstract We019: YAP Overcomes Mechanical Barriers to Induce Adult Cardiomyocyte Division
Authors: Yuka Morikawa, Jong Kim, Rich Gang Li, James Martin
Journal: Circulation Research (2024)

Adult mammalian cardiomyocytes (CMs) are among the least able to renew of all cell types. CMs exit the cell cycle soon after birth and remain cell cycle arrested by unknown mechanisms. We previously found that in adult CMs, the active form of the Hippo signaling pathway effector YAP, YAP5SA, induces cell division in vivo . Here, we analyze the mechanism by which YAP5SA regulates the cell cycle in adult CMs. YAP5SA-expressing adult CMs reenter the cell cycle at the G1/S transition and have a prolonged S-phase lasting approximately 48 hours. Molecular and functional analysis revealed that progression from S to G2 phase, and the induction of mitotic rounding, requires sarcomere disassembly. Transition from G2 to M phase requires overcoming DNA damage checkpoint facilitated by the activation of the P21 degradation pathway. Clonal analysis showed that approximately 20% of CMs progress through cytokinesis. Our results show that multiple barriers are involved in suppressing the adult CM cell cycle. These include the structural block caused by the highly structured CM cytoskeleton and the P21 regulated DNA damage checkpoint.
Abstract We007: High Throughput 3D-Printed Human Engineered Heart Tissues for Cardiac Disease Modeling
Authors: Miranda Juarros, Abhishek Dhand, Thomas Martin, Henry Valle-Ayala, Dakota Hunt, Jason Burdick, Leslie Leinwand
Journal: Circulation Research (2024)

While cell models have been used to study cardiac diseases, there is currently no standardization or fully mature in vitro system. Obtaining a mature cardiomyocyte (CM) phenotype is necessary to create a physiologically relevant environment and accurately model and study cardiac diseases. Increased success in maturation of human induced pluripotent stem cell derived CMs (hiPS-CMs) has been achieved in 3D in vitro models in the form of engineered heart tissues (EHTs). Digital light processing (DLP) offers a high throughput and efficient method to fabricate hydrogels that recapitulate properties of native tissues. In this study, we use DLP-printed EHTs to seed and mature differentiated hiPS-CMs and test their potential for modeling pathological cardiac hypertrophy. To further encourage maturity of CMs, we utilized a low glucose maturation medium supplemented with fatty acids. DLP-printed EHTs displayed high reproducibility and increased CM maturity. To determine degree of maturity of our system, we performed RT-qPCR, western blot analysis, and immunofluorescence (IF) microscopy. We found increased expression of fatty-acid transport and beta oxidation genes and improved sarcomere alignment compared to 2D hiPS-CMs. To model pathological cardiac hypertrophy, we used two different approaches: 1. acute adrenergic agonism with isoproterenol and phenylephrine; 2. chronic culturing of EHTs in pathologically stiff conditions. To assess pathology, we conducted RT-qPCR, western blot, ELISA, IF microscopy, and functional analyses. We found that agonist-treated EHTs displayed increased pathology-associated gene expression compared to standard 2D hiPS-CMs. Both agonist-treated and stiff EHTs had increased secreted B-Type Natriuretic Peptide (BNP) and phosphorylation of proteins involved in pathological remodeling, including ERK and P38. Additionally, we observed increased nuclear area, increased calcium handling, and increased contractile force in the treatment groups. In conclusion, we have established a high throughput, reproducible, mature EHT platform that can be used to model pathological cardiac hypertrophy. This platform can be easily adopted by other laboratories to study a wide array of cardiac diseases.