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Peters CH, Singh RK, Langley AA, Nichols WG, Ferris HR, Jeffrey DA, Proenza C, Bankston JR. LRMP inhibits cAMP potentiation of HCN4 channels by disrupting intramolecular signal transduction. eLife 2024; 12:RP92411. [PMID: 38652113 PMCID: PMC11037915 DOI: 10.7554/elife.92411] [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] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Lymphoid restricted membrane protein (LRMP) is a specific regulator of the hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channel. LRMP prevents cAMP-dependent potentiation of HCN4, but the interaction domains, mechanisms of action, and basis for isoform-specificity remain unknown. Here, we identify the domains of LRMP essential for this regulation, show that LRMP acts by disrupting the intramolecular signal transduction between cyclic nucleotide binding and gating, and demonstrate that multiple unique regions in HCN4 are required for LRMP isoform-specificity. Using patch clamp electrophysiology and Förster resonance energy transfer (FRET), we identified the initial 227 residues of LRMP and the N-terminus of HCN4 as necessary for LRMP to associate with HCN4. We found that the HCN4 N-terminus and HCN4-specific residues in the C-linker are necessary for regulation of HCN4 by LRMP. Finally, we demonstrated that LRMP-regulation can be conferred to HCN2 by addition of the HCN4 N-terminus along with mutation of five residues in the S5 region and C-linker to the cognate HCN4 residues. Taken together, these results suggest that LRMP inhibits HCN4 through an isoform-specific interaction involving the N-terminals of both proteins that prevents the transduction of cAMP binding into a change in channel gating, most likely via an HCN4-specific orientation of the N-terminus, C-linker, and S4-S5 linker.
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Affiliation(s)
- Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Rohit K Singh
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
- Skaggs School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Avery A Langley
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - William G Nichols
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Hannah R Ferris
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Danielle A Jeffrey
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Catherine Proenza
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - John R Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
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Peters CH, Singh RK, Langley AA, Nichols WG, Ferris HR, Jeffrey DA, Proenza C, Bankston JR. LRMP inhibits cAMP potentiation of HCN4 channels by disrupting intramolecular signal transduction. bioRxiv 2024:2023.08.29.555242. [PMID: 37693562 PMCID: PMC10491135 DOI: 10.1101/2023.08.29.555242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Lymphoid restricted membrane protein (LRMP) is a specific regulator of the hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channel. LRMP prevents cAMP-dependent potentiation of HCN4 but the interaction domains, mechanisms of action, and basis for isoform-specificity remain unknown. Here we identify the domains of LRMP essential for regulation. We show that LRMP acts by disrupting the intramolecular signal transduction between cyclic nucleotide binding and gating. And we demonstrate that multiple unique regions in HCN4 are required for LRMP isoform-specificity. Using patch clamp electrophysiology and Förster resonance energy transfer (FRET), we showed that the initial 227 residues of LRMP and the N-terminus of HCN4 are necessary for LRMP to interact with HCN4. We found that the HCN4 N-terminus and HCN4-specific residues in the C-linker are necessary for regulation of HCN4 by LRMP. And we demonstrate that LRMP-regulation can be conferred to HCN2 by addition of the HCN4 N-terminus along with mutation of 5 residues in the S5 region and C-linker to the cognate HCN4 residues. Taken together, these results suggest that LRMP inhibits HCN4 through an isoform-specific interaction involving the N-terminals of both proteins that prevents the transduction of cAMP binding into a change in channel gating via an HCN4-specific orientation of the N-terminus, C-linker, and S4-S5 linker.
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Affiliation(s)
- Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
| | - Rohit K Singh
- Skaggs School of Pharmacy, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Boulevard, Aurora, CO 80045
| | - Avery A Langley
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
| | - William G Nichols
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
| | - Hannah R Ferris
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
| | - Danielle A Jeffrey
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
| | - Catherine Proenza
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, 12631 E. 17 Avenue, Aurora, CO 80045
| | - John R Bankston
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, 12800 E. 19 Avenue, Aurora, CO 80045
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Jeffrey DA, Russell A, Guerrero MB, Fontaine JT, Romero P, Rosehart AC, Dabertrand F. Estrogen regulates myogenic tone in hippocampal arterioles by enhanced basal release of nitric oxide and endothelial SK Ca channel activity. bioRxiv 2023:2023.08.15.553442. [PMID: 37645715 PMCID: PMC10462022 DOI: 10.1101/2023.08.15.553442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Arteries and arterioles exhibit myogenic tone, a partially constricted state that allows further constriction or dilation in response to moment-to-moment fluctuations in blood pressure. The vascular endothelium that lines the internal surface of all blood vessels controls a wide variety of essential functions, including the contractility of the adjacent smooth muscle cells by providing a tonic vasodilatory influence. Studies conducted on large (pial) arteries on the surface of the brain have shown that estrogen lowers myogenic tone in female mice by enhancing nitric oxide (NO) release from the endothelium, however, whether this difference extends to the intracerebral microcirculation remains ambiguous. The existing incomplete picture of sex differences in cerebrovascular physiology combined with a deficiency in treatments that fully restore cognitive function after cerebrovascular accidents places heavy emphasis on the necessity to investigate myogenic tone regulation in the microcirculation from both male and female mice. We hypothesized that sex-linked hormone regulation of myogenic tone extends its influence on the microcirculation level, and sought to characterize it in isolated arterioles from the hippocampus, a major cognitive brain area. Using diameter measurements both in vivo (acute cranial window vascular diameter) and ex vivo (pressure myography experiments), we measured lower myogenic tone responses in hippocampal arterioles from female than male mice. By using a combined surgical and pharmacological approach, we found myogenic tone in ovariectomized (OVX) female mice matches that of males, as well as in endothelium-denuded arterioles. Interestingly, eNOS inhibition induced a larger constriction in female arterioles but only partially abolished the difference in tone. We identified that the remnant difference was mediated by a higher activity and expression of the small-conductance Ca 2+ -sensitive K + (SK) channels. Collectively, these data indicate that eNOS and SK channels exert greater vasodilatory influence over myogenic tone in female mice at physiological pressures.
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Jeffrey DA, Fontaine JT, Dabertrand F. Ex vivo capillary-parenchymal arteriole approach to study brain pericyte physiology. Neurophotonics 2022; 9:031919. [PMID: 36278784 PMCID: PMC9225307 DOI: 10.1117/1.nph.9.3.031919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/01/2022] [Indexed: 06/16/2023]
Abstract
Significance Vascular mural cells, defined as smooth muscle cells (SMCs) and pericytes, influence brain microcirculation, but how they contribute is not fully understood. Most approaches used to investigate pericyte and capillary interactions include ex vivo retinal/slice preparations or in vivo two-photon microscopy. However, neither method adequately captures mural cell behavior without interfering neuronal tissue. Thus, there is a need to isolate vessels with their respective mural cells to study functional and pathological changes. Aim The aim of our work was to implement an ex vivo method that recapitulates vessel dynamics in the brain. Approach Expanding upon our established ex vivo capillary-parenchymal arteriole (CaPA) preparation, we isolated and pressurized arteriole-capillary branches. Using Alexa Fluor™ 633 Hydrazide, we distinguished arterioles (containing elastin) versus capillaries (lacking elastin). In addition, our transgenic SMMHC-GCaMP6f mice allowed for us to visualize mural cell morphology andCa 2 + signals. Lastly, isolated microvasculature was cultured in DMEM media (up to 72 h), mounted, and pressurized using our CaPA preparation. Results U46619 induced a decrease in capillary lumen diameter using both a bath perfusion and local application. In addition, U46619 increasedCa 2 + signaling both globally and locally in contractile pericytes. In our SMMHC-GCaMP6f mice, we saw that thin strand pericytes had sparse processes while contractile pericytes had long, thick processes that wrapped around the lumen of the capillary. Fresh and cultured pericytes constricted in response to U46619 to the same level, and upstream arteriolar dilation induced by capillary stimulation with 10 mMK + remained unchanged by culture conditions adding another application of longer treatment to our approach. Conclusion Our ex vivo CaPA methodology facilitates observation of arteriolar SMC and pericyte dynamic changes in real-time without environmental factors. This method will help to better understand how mural cells differ based on microvasculature location.
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Affiliation(s)
- Danielle A. Jeffrey
- University of Colorado Anschutz Medical Campus, Department of Anesthesiology, Aurora, Colorado, United States
| | - Jackson T. Fontaine
- University of Colorado Anschutz Medical Campus, Department of Anesthesiology, Aurora, Colorado, United States
| | - Fabrice Dabertrand
- University of Colorado Anschutz Medical Campus, Department of Anesthesiology, Aurora, Colorado, United States
- University of Colorado Anschutz Medical Campus, Department of Pharmacology, Aurora, Colorado, United States
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Woulfe KC, Jeffrey DA, Pires Da Silva J, Wilson CE, Mahaffey JH, Lau E, Slavov D, Hailu F, Karimpour-Fard A, Dockstader K, Bristow MR, Stauffer BL, Miyamoto SD, Sucharov CC. Serum response factor deletion 5 regulates phospholamban phosphorylation and calcium uptake. J Mol Cell Cardiol 2021; 159:28-37. [PMID: 34139234 PMCID: PMC8546760 DOI: 10.1016/j.yjmcc.2021.06.007] [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: 04/05/2021] [Revised: 05/25/2021] [Accepted: 06/13/2021] [Indexed: 11/25/2022]
Abstract
AIMS Pediatric dilated cardiomyopathy (pDCM) is characterized by unique age-dependent molecular mechanisms that include myocellular responses to therapy. We previously showed that pDCM, but not adult DCM patients respond to phosphodiesterase 3 inhibitors (PDE3i) by increasing levels of the second messenger cAMP and consequent phosphorylation of phospholamban (PLN). However, the molecular mechanisms involved in the differential pediatric and adult response to PDE3i are not clear. METHODS AND RESULTS Quantification of serum response factor (SRF) isoforms from the left ventricle of explanted hearts showed that PDE3i treatment affects expression of SRF isoforms in pDCM hearts. An SRF isoform lacking exon 5 (SRFdel5) was highly expressed in the hearts of pediatric, but not adult DCM patients treated with PDE3i. To determine the functional consequence of expression of SRFdel5, we overexpressed full length SRF or SRFdel5 in cultured cardiomyocytes with and without adrenergic stimulation. Compared to a control adenovirus, expression of SRFdel5 increased phosphorylation of PLN, negatively affected expression of the phosphatase that promotes dephosphorylation of PLN (PP2Cε), and promoted faster calcium reuptake, whereas expression of full length SRF attenuated calcium reuptake through blunted phosphorylation of PLN. CONCLUSIONS Taken together, these data indicate that expression of SRFdel5 in pDCM hearts in response to PDE3i contributes to improved function through regulating PLN phosphorylation and thereby calcium reuptake.
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Affiliation(s)
- Kathleen C Woulfe
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Danielle A Jeffrey
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Julie Pires Da Silva
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Cortney E Wilson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jennifer H Mahaffey
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Edward Lau
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Dobromir Slavov
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Frehiwet Hailu
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Anis Karimpour-Fard
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Karen Dockstader
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael R Bristow
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brian L Stauffer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; Denver Health Medical Center, Denver, CO, United States
| | - Shelley D Miyamoto
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital of Colorado, Aurora, CO, United States
| | - Carmen C Sucharov
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
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Jeffrey DA, Pires Da Silva J, Garcia AM, Jiang X, Karimpour-Fard A, Toni LS, Lanzicher T, Peña B, Miyano CA, Nunley K, Korst A, Sbaizero O, Taylor MR, Miyamoto SD, Stauffer BL, Sucharov CC. Serum circulating proteins from pediatric dilated cardiomyopathy patients cause pathologic remodeling and cardiomyocyte stiffness. JCI Insight 2021; 6:e148637. [PMID: 34383712 PMCID: PMC8525651 DOI: 10.1172/jci.insight.148637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 08/11/2021] [Indexed: 12/01/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy and main indication for heart transplantation in children. Therapies specific to pediatric DCM remain limited due to lack of a disease model. Our previous study showed that treatment of neonatal rat ventricular myocytes (NRVMs) with serum from nonfailing or DCM pediatric patients activates the fetal gene program (FGP). Here we show that serum treatment with proteinase K prevents activation of the FGP, whereas RNase treatment exacerbates it, suggesting that circulating proteins, but not circulating miRNAs, promote these pathological changes. Evaluation of the protein secretome showed that midkine (MDK) is upregulated in DCM serum, and NRVM treatment with MDK activates the FGP. Changes in gene expression in serum-treated NRVMs, evaluated by next-generation RNA-Seq, indicated extracellular matrix remodeling and focal adhesion pathways were upregulated in pediatric DCM serum and in DCM serum–treated NRVMs, suggesting alterations in cellular stiffness. Cellular stiffness was evaluated by Atomic Force Microscopy, which showed an increase in stiffness in DCM serum–treated NRVMs. Of the proteins increased in DCM sera, secreted frizzled-related protein 1 (sFRP1) was a potential candidate for the increase in cellular stiffness, and sFRP1 treatment of NRVMs recapitulated the increase in cellular stiffness observed in response to DCM serum treatment. Our results show that serum circulating proteins promoted pathological changes in gene expression and cellular stiffness, and circulating miRNAs were protective against pathological changes.
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Affiliation(s)
- Danielle A Jeffrey
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Julie Pires Da Silva
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Anastacia M Garcia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Xuan Jiang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Anis Karimpour-Fard
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Lee S Toni
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Thomas Lanzicher
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Brisa Peña
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Carissa A Miyano
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Karin Nunley
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Armin Korst
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Matthew Rg Taylor
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Shelley D Miyamoto
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Brian L Stauffer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
| | - Carmen C Sucharov
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, United States of America
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Garcia AM, McPhaul JC, Sparagna GC, Jeffrey DA, Jonscher R, Patel SS, Sucharov CC, Stauffer BL, Miyamoto SD, Chatfield KC. Alteration of cardiolipin biosynthesis and remodeling in single right ventricle congenital heart disease. Am J Physiol Heart Circ Physiol 2020; 318:H787-H800. [PMID: 32056460 DOI: 10.1152/ajpheart.00494.2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 11/22/2022]
Abstract
Despite advances in both medical and surgical therapies, individuals with single ventricle heart disease (SV) remain at high risk for the development of heart failure (HF). However, the molecular mechanisms underlying remodeling and eventual HF in patients with SV are poorly characterized. Cardiolipin (CL), an inner mitochondrial membrane phospholipid, is critical for proper mitochondrial function, and abnormalities in CL content and composition are known in various cardiovascular disease etiologies. The purpose of this study was to investigate myocardial CL content and composition in failing and nonfailing single right ventricle (RV) samples compared with normal control RV samples, to assess mRNA expression of CL biosynthetic and remodeling enzymes, and to quantitate relative mitochondrial copy number. A cross-sectional analysis of RV myocardial tissue from 22 failing SV (SVHF), 9 nonfailing SV (SVNF), and 10 biventricular control samples (BVNF) was performed. Expression of enzymes involved in CL biosynthesis and remodeling were analyzed using RT-qPCR and relative mitochondrial DNA copy number determined by qPCR. Normal phase high-pressure liquid chromatography coupled to electrospray ionization mass spectrometry was used to quantitate total and specific CL species. While mitochondrial copy number was not significantly different between groups, total CL content was significantly lower in SVHF myocardium compared with BVNF controls. Despite having lower total CL content however, the relative percentage of the major tetralinoleoyl CL species is preserved in SVHF samples relative to BVNF controls. Correspondingly, expression of enzymes involved in CL biosynthesis and remodeling were upregulated in SVHF samples when compared with both SVNF samples and BVNF controls.NEW & NOTEWORTHY The mechanisms underlying heart failure in the single ventricle (SV) congenital heart disease population are largely unknown. In this study we identify alterations in cardiac cardiolipin metabolism, composition, and content in children with SV heart disease. These findings suggest that cardiolipin could be a novel therapeutic target in this unique population of patients.
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Affiliation(s)
- Anastacia M Garcia
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Jessica C McPhaul
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Genevieve C Sparagna
- Division of Cardiology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Danielle A Jeffrey
- Division of Cardiology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Raleigh Jonscher
- Division of Cardiology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Sonali S Patel
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Carmen C Sucharov
- Division of Cardiology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Brian L Stauffer
- Division of Cardiology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,Division of Cardiology, Denver Health Medical Center, Denver, Colorado
| | - Shelley D Miyamoto
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Kathryn C Chatfield
- Division of Cardiology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
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Toni LS, Garcia AM, Jeffrey DA, Jiang X, Stauffer BL, Miyamoto SD, Sucharov CC. Optimization of phenol-chloroform RNA extraction. MethodsX 2018; 5:599-608. [PMID: 29984193 PMCID: PMC6031757 DOI: 10.1016/j.mex.2018.05.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/21/2018] [Indexed: 11/24/2022] Open
Abstract
Accurate and reliable analysis of gene expression depends on the extraction of pure and high-quality RNA. However, while the conventional phenol-chloroform RNA extraction is preferable over silica-based columns, particularly when cost is a concern or higher RNA yield is desired, it can result in significant RNA contamination. Contaminants including excess phenol, chloroform, or salts, can have significant impacts on downstream applications, including RNA quantification and reverse transcription, that can skew data collection and interpretation. To overcome the issue of RNA contamination in the conventional phenol-chloroform based RNA extraction method, we have optimized the protocol by adding one chloroform extraction step, and several RNA washing steps. Importantly, RNA quality and purity and accuracy in the quantification of RNA concentration were significantly improved with the modified protocol, resulting in reliable data collection and interpretation in downstream gene expression analysis. Our protocol is customized by the addition of a second chloroform extraction step. Chloroform is carefully pipetted so as to not disturb the interphase layer. Any contaminants accidentally removed from interphase will be present in subsequent steps and can result in RNA contaminated with protein or phenol. The additional chloroform step increases RNA purity. Additionally, the addition of 2 additional ethanol washes, initially intended to remove any residual salts from the isopropanol RNA precipitation step, also removed residual phenol contamination, enhancing RNA purity. In summary, these modifications serve to enhance not only the purity of the RNA but, also increase the accuracy and reliability of RNA quantification.
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Affiliation(s)
- Lee S Toni
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Anastacia M Garcia
- Department of Pediatrics, Division of Cardiology, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, United States
| | - Danielle A Jeffrey
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Xuan Jiang
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Brian L Stauffer
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Medicine, Division of Cardiology, Denver Health and Hospital Authority, Denver, CO, United States
| | - Shelley D Miyamoto
- Department of Pediatrics, Division of Cardiology, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, United States
| | - Carmen C Sucharov
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Jeffrey DA, Sucharov CC. CELF1 regulates gap junction integrity contributing to dilated cardiomyopathy. Noncoding RNA Investig 2018; 2:10. [PMID: 30198017 PMCID: PMC6128295 DOI: 10.21037/ncri.2018.02.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Danielle A Jeffrey
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carmen C Sucharov
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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10
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Woulfe KC, Tatman PD, Karimpour-Fard A, Jeffrey DA, Nunley K, Taylor MR, Miyamoto SD, Stauffer BL, Sucharov CC. Pediatric dilated cardiomyopathy hearts display a gene expression profile consistent with pluripotency and dedifferentiation. J Mol Cell Cardiol 2017. [DOI: 10.1016/j.yjmcc.2017.07.033] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tatman PD, Woulfe KC, Karimpour-Fard A, Jeffrey DA, Jaggers J, Cleveland JC, Nunley K, Taylor MR, Miyamoto SD, Stauffer BL, Sucharov CC. Pediatric dilated cardiomyopathy hearts display a unique gene expression profile. JCI Insight 2017; 2:94249. [PMID: 28724804 DOI: 10.1172/jci.insight.94249] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 03/27/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022] Open
Abstract
Our previous work showed myocellular differences in pediatric and adult dilated cardiomyopathy (DCM). However, a thorough characterization of the molecular pathways involved in pediatric DCM does not exist, limiting the development of age-specific therapies. To characterize this patient population, we investigated the transcriptome profile of pediatric patients. RNA-Seq from 7 DCM and 7 nonfailing (NF) explanted age-matched pediatric left ventricles (LV) was performed. Changes in gene expression were confirmed by real-time PCR (RT-PCR) in 36 DCM and 21 NF pediatric hearts and in 20 DCM and 10 NF adult hearts. The degree of myocyte hypertrophy was investigated in 4 DCM and 7 NF pediatric hearts and in 4 DCM and 9 NF adult hearts. Changes in gene expression in response to pluripotency-inducing factors were investigated in neonatal rat ventricular myocytes (NRVMs). Transcriptome analysis identified a gene expression profile in children compared with adults with DCM. Additionally, myocyte hypertrophy was not observed in pediatric hearts but was present in adult hearts. Furthermore, treatment of NRVMs with pluripotency-inducing factors recapitulated changes in gene expression observed in the pediatric DCM heart. Pediatric DCM is characterized by unique changes in gene expression that suggest maintenance of an undifferentiated state.
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Affiliation(s)
- Philip D Tatman
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA.,Medical Scientist Training Program and
| | - Kathleen C Woulfe
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Danielle A Jeffrey
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | | | - Karin Nunley
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Matthew Rg Taylor
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Shelley D Miyamoto
- Department of Paediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Brian L Stauffer
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA.,Division of Cardiology, Denver Health and Hospital Authority, Denver, Colorado, USA
| | - Carmen C Sucharov
- Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Jull AJ, Courtney C, Jeffrey DA, Beck JW. Isotopic evidence for a terrestrial source of organic compounds found in martian meteorites Allan Hills 84001 and Elephant Moraine 79001. Science 1998; 279:366-9. [PMID: 9430584 DOI: 10.1126/science.279.5349.366] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Stepped-heating experiments on martian meteorites Allan Hills 84001 (ALH84001) and Elephant Moraine 79001 (EETA79001) revealed low-temperature (200 to 430 degrees Celsius) fractions with a carbon isotopic composition delta13C between -22 and -33 per mil and a carbon-14 content that is 40 to 60 percent of that of modern terrestrial carbon, consistent with a terrestrial origin for most of the organic material. Intermediate-temperature (400 to 600 degrees Celsius) carbonate-rich fractions of ALH84001 have delta13C of +32 to +40 per mil with a low carbon-14 content, consistent with an extraterrestrial origin, whereas some of the carbonate fraction of EETA79001 is terrestrial. In addition, ALH84001 contains a small preterrestrial carbon component of unknown origin that combusts at intermediate temperatures. This component is likely a residual acid-insoluble carbonate or a more refractory organic phase.
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Affiliation(s)
- A J Jull
- National Science Foundation-Arizona Accelerator Mass Spectrometer Facility, University of Arizona, Tucson, AZ 85721, USA
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Peakall DB, Jeffrey DA, Boersma D. Mixed-function oxidase activity in seabirds and its relationship to oil pollution. Comp Biochem Physiol C Comp Pharmacol Toxicol 1987; 88:151-4. [PMID: 2890477 DOI: 10.1016/0742-8413(87)90059-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
1. The hepatic activity of epoxide hydrolase, aldrin epoxidase, aminopyrine N-demethylase, 7-ethoxyresorufin O-deethylase, benzo(a)pyrene 3-hydroxylase and UDP glucuronyl transferase was determined in adult herring gulls (Larus argentatus) at various stages of the breeding season. 2. MFO activity was measured for adult Leach's storm-petrels (Oceanodroma leucorhoa), guillemot (Uria aalge) and Atlantic puffins (Fratercula arctica). For most assays the values were highest for the puffin. 3. MFO activity in both nestling and adult Atlantic puffins was determined. The degree of induction caused by a single internal dose of Prudhoe Bay crude oil in adult puffins and that caused by multiple internal doses in nestling puffins was measured.
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Affiliation(s)
- D B Peakall
- National Wildlife Research Center, Canadian Wildlife Service, Ottawa, Ontario
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Jeffrey DA, Peakall DB, Miller DS, Herzberg GR. Blood chemistry changes in food-deprived herring gulls. Comp Biochem Physiol A Comp Physiol 1985; 81:911-3. [PMID: 2863080 DOI: 10.1016/0300-9629(85)90929-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Blood chemistry changes caused by food-stress was measured in fledgling herring gulls (Larus argentatus). Increases of corticosterone, T3, free fatty acids, glucose, cholesterol and alpha-amino n-butyric acid were observed. Significant decreases were found in the concentrations of 14 of the 26 free amino acids studied.
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Jeffrey DA. A living environment for the physically disabled. Rehabil Lit 1973; 34:99-103. [PMID: 4266401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Jeffrey DA. Administration in rehabilitation. Rehabil Lit 1967; 28:248-50. [PMID: 6075044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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