1
|
Cao S, Buchholz KS, Tan P, Stowe JC, Wang A, Fowler A, Knaus KR, Khalilimeybodi A, Zambon AC, Omens JH, Saucerman JJ, McCulloch AD. Differential sensitivity to longitudinal and transverse stretch mediates transcriptional responses in mouse neonatal ventricular myocytes. Am J Physiol Heart Circ Physiol 2024; 326:H370-H384. [PMID: 38063811 DOI: 10.1152/ajpheart.00562.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
To identify how cardiomyocyte mechanosensitive signaling pathways are regulated by anisotropic stretch, micropatterned mouse neonatal cardiomyocytes were stretched primarily longitudinally or transversely to the myofiber axis. Four hours of static, longitudinal stretch induced differential expression of 557 genes, compared with 30 induced by transverse stretch, measured using RNA-seq. A logic-based ordinary differential equation model of the cardiac myocyte mechanosignaling network, extended to include the transcriptional regulation and expression of 784 genes, correctly predicted measured expression changes due to anisotropic stretch with 69% accuracy. The model also predicted published transcriptional responses to mechanical load in vitro or in vivo with 63-91% accuracy. The observed differences between transverse and longitudinal stretch responses were not explained by differential activation of specific pathways but rather by an approximately twofold greater sensitivity to longitudinal stretch than transverse stretch. In vitro experiments confirmed model predictions that stretch-induced gene expression is more sensitive to angiotensin II and endothelin-1, via RhoA and MAP kinases, than to the three membrane ion channels upstream of calcium signaling in the network. Quantitative cardiomyocyte gene expression differs substantially with the axis of maximum principal stretch relative to the myofilament axis, but this difference is due primarily to differences in stretch sensitivity rather than to selective activation of mechanosignaling pathways.NEW & NOTEWORTHY Anisotropic stretch applied to micropatterned neonatal mouse ventricular myocytes induced markedly greater acute transcriptional responses when the major axis of stretch was parallel to the myofilament axis than when it was transverse. Analysis with a novel quantitative network model of mechanoregulated cardiomyocyte gene expression suggests that this difference is explained by higher cell sensitivity to longitudinal loading than transverse loading than by the activation of differential signaling pathways.
Collapse
Affiliation(s)
- Shulin Cao
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Kyle S Buchholz
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Philip Tan
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Jennifer C Stowe
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Ariel Wang
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Annabelle Fowler
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Katherine R Knaus
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
| | - Ali Khalilimeybodi
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States
| | - Alexander C Zambon
- Department of Biopharmaceutical Sciences, Keck Graduate Institute, Claremont, California, United States
| | - Jeffrey H Omens
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
- Department of Medicine, University of California San Diego, La Jolla, California, United States
| | - Jeffrey J Saucerman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States
- Department of Medicine, University of California San Diego, La Jolla, California, United States
| |
Collapse
|
2
|
Cao S, Buchholz K, Tan PM, Aboelkassem Y, Stowe JC, Saucerman JJ, Omens J, McCulloch AD. Analysis of Differential Gene Expression in Response to Anisotropic Stretch using a Systems Model of Cardiac Myocyte Mechanotransduction. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
3
|
Gan Z, Powell FL, Zambon AC, Buchholz KS, Fu Z, Ocorr K, Bodmer R, Moya EA, Stowe JC, Haddad GG, McCulloch AD. Transcriptomic analysis identifies a role of PI3K-Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo. J Physiol 2017; 595:5797-5813. [PMID: 28688178 DOI: 10.1113/jp274556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 01/13/2023] Open
Abstract
KEY POINTS Changes in gene expression that occur within hours of exposure to hypoxia in in vivo skeletal muscles remain unexplored. Two hours of hypoxia caused significant down-regulation of extracellular matrix genes followed by a shift at 6 h to altered expression of genes associated with the nuclear lumen while respiratory and blood gases were stabilized. Enrichment analysis of mRNAs classified by stability rates suggests an attenuation of post-transcriptional regulation within hours of hypoxic exposure, where PI3K-Akt signalling was suggested to have a nodal role by pathway analysis. Experimental measurements and bioinformatic analyses suggested that the dephosphorylation of Akt after 2 h of hypoxic exposure might deactivate RNA-binding protein BRF1, hence resulting in the selective degradation of mRNAs. ABSTRACT The effects of acute hypoxia have been widely studied, but there are few studies of transcriptional responses to hours of hypoxia in vivo, especially in hypoxia-tolerant tissues like skeletal muscles. We used RNA-seq to analyse gene expression in plantaris muscles while monitoring respiration, arterial blood gases, and blood glucose in mice exposed to 8% O2 for 2 or 6 h. Rapid decreases in blood gases and a slower reduction in blood glucose suggest stress, which was accompanied by widespread changes in gene expression. Early down-regulation of genes associated with the extracellular matrix was followed by a shift to genes associated with the nuclear lumen. Most of the early down-regulated genes had mRNA half-lives longer than 2 h, suggesting a role for post-transcriptional regulation. These transcriptional changes were enriched in signalling pathways in which the PI3K-Akt signalling pathway was identified as a hub. Our analyses indicated that gene targets of PI3K-Akt but not HIF were enriched in early transcriptional responses to hypoxia. Among the PI3K-Akt targets, 75% could be explained by a deactivation of adenylate-uridylate-rich element (ARE)-binding protein BRF1, a target of PI3K-Akt. Consistent decreases in the phosphorylation of Akt and BRF1 were experimentally confirmed following 2 h of hypoxia. These results suggest that the PI3K-Akt signalling pathway might play a role in responses induced by acute hypoxia in skeletal muscles, partially through the dephosphorylation of ARE-binding protein BRF1.
Collapse
Affiliation(s)
- Zhuohui Gan
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.,Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Frank L Powell
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexander C Zambon
- Department of Biopharmaceutical Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kyle S Buchholz
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhenxing Fu
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Esteban A Moya
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer C Stowe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA.,Rady Children's Hospital San Diego, 3020 Children's Way, San Diego, CA, 92123, USA
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
4
|
Pfeiffer ER, Wright AT, Edwards AG, Stowe JC, McNall K, Tan J, Niesman I, Patel HH, Roth DM, Omens JH, McCulloch AD. Caveolae in ventricular myocytes are required for stretch-dependent conduction slowing. J Mol Cell Cardiol 2014; 76:265-74. [PMID: 25257915 DOI: 10.1016/j.yjmcc.2014.09.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/25/2014] [Accepted: 09/13/2014] [Indexed: 12/23/2022]
Abstract
Mechanical stretch of cardiac muscle modulates action potential propagation velocity, causing potentially arrhythmogenic conduction slowing. The mechanisms by which stretch alters cardiac conduction remain unknown, but previous studies suggest that stretch can affect the conformation of caveolae in myocytes and other cell types. We tested the hypothesis that slowing of action potential conduction due to cardiac myocyte stretch is dependent on caveolae. Cardiac action potential propagation velocities, measured by optical mapping in isolated mouse hearts and in micropatterned mouse cardiomyocyte cultures, decreased reversibly with volume loading or stretch, respectively (by 19±5% and 26±4%). Stretch-dependent conduction slowing was not altered by stretch-activated channel blockade with gadolinium or by GsMTx-4 peptide, but was inhibited when caveolae were disrupted via genetic deletion of caveolin-3 (Cav3 KO) or membrane cholesterol depletion by methyl-β-cyclodextrin. In wild-type mouse hearts, stretch coincided with recruitment of caveolae to the sarcolemma, as observed by electron microscopy. In myocytes from wild-type but not Cav3 KO mice, stretch significantly increased cell membrane capacitance (by 98±64%), electrical time constant (by 285±149%), and lipid recruitment to the bilayer (by 84±39%). Recruitment of caveolae to the sarcolemma during physiologic cardiomyocyte stretch slows ventricular action potential propagation by increasing cell membrane capacitance.
Collapse
Affiliation(s)
- E R Pfeiffer
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - A T Wright
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - A G Edwards
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - J C Stowe
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - K McNall
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - J Tan
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - I Niesman
- Department of Anesthesiology, VA San Diego Healthcare System, and University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-9125, USA
| | - H H Patel
- Department of Anesthesiology, VA San Diego Healthcare System, and University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-9125, USA
| | - D M Roth
- Department of Anesthesiology, VA San Diego Healthcare System, and University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-9125, USA
| | - J H Omens
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613, USA
| | - A D McCulloch
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613, USA.
| |
Collapse
|
5
|
Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC. MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. BMC Bioinformatics 2014; 15:69. [PMID: 24621103 PMCID: PMC3975178 DOI: 10.1186/1471-2105-15-69] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/27/2014] [Indexed: 12/16/2022] Open
Abstract
Background Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons. Results We developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila. MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour. Conclusions MAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Alexander C Zambon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
6
|
Abstract
Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.
Collapse
Affiliation(s)
- Zhuohui Gan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer C. Stowe
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ilkay Altintas
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Alexander C. Zambon
- Departments of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|