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Moss A, Kuttippurathu L, Srivastava A, Schwaber JS, Vadigepalli R. Dynamic dysregulation of transcriptomic networks in brainstem autonomic nuclei during hypertension development in the female spontaneously hypertensive rat. Physiol Genomics 2024; 56:283-300. [PMID: 38145287 DOI: 10.1152/physiolgenomics.00073.2023] [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] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023] Open
Abstract
Neurogenic hypertension stems from an imbalance in autonomic function that shifts the central cardiovascular control circuits toward a state of dysfunction. Using the female spontaneously hypertensive rat and the normotensive Wistar-Kyoto rat model, we compared the transcriptomic changes in three autonomic nuclei in the brainstem, nucleus of the solitary tract (NTS), caudal ventrolateral medulla, and rostral ventrolateral medulla (RVLM) in a time series at 8, 10, 12, 16, and 24 wk of age, spanning the prehypertensive stage through extended chronic hypertension. RNA-sequencing data were analyzed using an unbiased, dynamic pattern-based approach that uncovered dominant and several subtle differential gene regulatory signatures. Our results showed a persistent dysregulation across all three autonomic nuclei regardless of the stage of hypertension development as well as a cascade of transient dysregulation beginning in the RVLM at the prehypertensive stage that shifts toward the NTS at the hypertension onset. Genes that were persistently dysregulated were heavily enriched for immunological processes such as antigen processing and presentation, the adaptive immune response, and the complement system. Genes with transient dysregulation were also largely region-specific and were annotated for processes that influence neuronal excitability such as synaptic vesicle release, neurotransmitter transport, and an array of neuropeptides and ion channels. Our results demonstrate that neurogenic hypertension is characterized by brainstem region-specific transcriptomic changes that are highly dynamic with significant gene regulatory changes occurring at the hypertension onset as a key time window for dysregulation of homeostatic processes across the autonomic control circuits.NEW & NOTEWORTHY Hypertension is a major disease and is the primary risk factor for cardiovascular complications and stroke. The gene expression changes in the central nervous system circuits driving hypertension are understudied. Here, we show that coordinated and region-specific gene expression changes occur in the brainstem autonomic circuits over time during the development of a high blood pressure phenotype in a rat model of human essential hypertension.
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Affiliation(s)
- Alison Moss
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
| | - Lakshmi Kuttippurathu
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
| | - Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
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2
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Bekeova C, Han JI, Xu H, Kerr E, Blackburne B, Lynch SC, Mesaros C, Murgia M, Vadigepalli R, Beld J, Leonardi R, Snyder NW, Seifert EL. Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner. bioRxiv 2023:2023.06.27.546724. [PMID: 37425757 PMCID: PMC10327053 DOI: 10.1101/2023.06.27.546724] [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: 07/11/2023]
Abstract
Acyl-Coenzyme A (acyl-CoA) thioesters are compartmentalized intermediates that participate in in multiple metabolic reactions within the mitochondrial matrix. The limited availability of free CoA (CoASH) in the matrix raises the question of how the local acyl-CoA concentration is regulated to prevent trapping of CoASH from overload of any specific substrate. Acyl-CoA thioesterase-2 (ACOT2) hydrolyzes long-chain acyl-CoAs to their constituent fatty acids and CoASH, and is the only mitochondrial matrix ACOT refractory to inhibition by CoASH. Thus, we reasoned that ACOT2 may constitutively regulate matrix acyl-CoA levels. Acot2 deletion in murine skeletal muscle (SM) resulted in acyl-CoA build-up when lipid supply and energy demands were modest. When energy demand and pyruvate availability were elevated, lack of ACOT2 activity promoted glucose oxidation. This preference for glucose over fatty acid oxidation was recapitulated in C2C12 myotubes with acute depletion of Acot2 , and overt inhibition of β-oxidation was demonstrated in isolated mitochondria from Acot2 -depleted glycolytic SM. In mice fed a high fat diet, ACOT2 enabled the accretion of acyl-CoAs and ceramide derivatives in glycolytic SM, and this was associated with worse glucose homeostasis compared to when ACOT2 was absent. These observations suggest that ACOT2 supports CoASH availability to facilitate β-oxidation in glycolytic SM when lipid supply is modest. However, when lipid supply is high, ACOT2 enables acyl-CoA and lipid accumulation, CoASH sequestration, and poor glucose homeostasis. Thus, ACOT2 regulates matrix acyl-CoA concentration in glycolytic muscle, and its impact depends on lipid supply.
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3
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Gee MM, Hornung E, Gupta S, Newton AJH, Cheng ZJ, Lytton WW, Lenhoff AM, Schwaber JS, Vadigepalli R. Unpacking the multimodal, multi-scale data of the fast and slow lanes of the cardiac vagus through computational modelling. Exp Physiol 2023:10.1113/EP090865. [PMID: 37120805 PMCID: PMC10613580 DOI: 10.1113/ep090865] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
NEW FINDINGS What is the topic of this review? The vagus nerve is a crucial regulator of cardiovascular homeostasis, and its activity is linked to heart health. Vagal activity originates from two brainstem nuclei: the nucleus ambiguus (fast lane) and the dorsal motor nucleus of the vagus (slow lane), nicknamed for the time scales that they require to transmit signals. What advances does it highlight? Computational models are powerful tools for organizing multi-scale, multimodal data on the fast and slow lanes in a physiologically meaningful way. A strategy is laid out for how these models can guide experiments aimed at harnessing the cardiovascular health benefits of differential activation of the fast and slow lanes. ABSTRACT The vagus nerve is a key mediator of brain-heart signaling, and its activity is necessary for cardiovascular health. Vagal outflow stems from the nucleus ambiguus, responsible primarily for fast, beat-to-beat regulation of heart rate and rhythm, and the dorsal motor nucleus of the vagus, responsible primarily for slow regulation of ventricular contractility. Due to the high-dimensional and multimodal nature of the anatomical, molecular and physiological data on neural regulation of cardiac function, data-derived mechanistic insights have proven elusive. Elucidating insights has been complicated further by the broad distribution of the data across heart, brain and peripheral nervous system circuits. Here we lay out an integrative framework based on computational modelling for combining these disparate and multi-scale data on the two vagal control lanes of the cardiovascular system. Newly available molecular-scale data, particularly single-cell transcriptomic analyses, have augmented our understanding of the heterogeneous neuronal states underlying vagally mediated fast and slow regulation of cardiac physiology. Cellular-scale computational models built from these data sets represent building blocks that can be combined using anatomical and neural circuit connectivity, neuronal electrophysiology, and organ/organismal-scale physiology data to create multi-system, multi-scale models that enable in silico exploration of the fast versus slow lane vagal stimulation. The insights from the computational modelling and analyses will guide new experimental questions on the mechanisms regulating the fast and slow lanes of the cardiac vagus toward exploiting targeted vagal neuromodulatory activity to promote cardiovascular health.
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Affiliation(s)
- Michelle M Gee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
- Department of Pathology and Genomic Medicine, Daniel Baugh Institute of Functional Genomics/Computational Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Eden Hornung
- Department of Pathology and Genomic Medicine, Daniel Baugh Institute of Functional Genomics/Computational Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Suranjana Gupta
- Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Adam J H Newton
- Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Zixi Jack Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - William W Lytton
- Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - James S Schwaber
- Department of Pathology and Genomic Medicine, Daniel Baugh Institute of Functional Genomics/Computational Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- Department of Pathology and Genomic Medicine, Daniel Baugh Institute of Functional Genomics/Computational Biology, Thomas Jefferson University, Philadelphia, PA, USA
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4
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Gee MM, Lenhoff AM, Schwaber JS, Ogunnaike BA, Vadigepalli R. Closed-loop modeling of central and intrinsic cardiac nervous system circuits underlying cardiovascular control. AIChE J 2023; 69:e18033. [PMID: 37250861 PMCID: PMC10211393 DOI: 10.1002/aic.18033] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/02/2023] [Indexed: 01/16/2023]
Abstract
The baroreflex is a multi-input, multi-output control physiological system that regulates blood pressure by modulating nerve activity between the brainstem and the heart. Existing computational models of the baroreflex do not explictly incorporate the intrinsic cardiac nervous system (ICN), which mediates central control of the heart function. We developed a computational model of closed-loop cardiovascular control by integrating a network representation of the ICN within central control reflex circuits. We examined central and local contributions to the control of heart rate, ventricular functions, and respiratory sinus arrhythmia (RSA). Our simulations match the experimentally observed relationship between RSA and lung tidal volume. Our simulations predicted the relative contributions of the sensory and the motor neuron pathways to the experimentally observed changes in the heart rate. Our closed-loop cardiovascular control model is primed for evaluating bioelectronic interventions to treat heart failure and renormalize cardiovascular physiology.
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Affiliation(s)
- Michelle M Gee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA 19107
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - James S Schwaber
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA 19107
| | - Babatunde A Ogunnaike
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Rajanikanth Vadigepalli
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA 19107
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5
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Chen CG, Kapoor A, Xie C, Moss A, Vadigepalli R, Ricard-Blum S, Iozzo RV. Conditional expression of endorepellin in the tumor vasculature attenuates breast cancer growth, angiogenesis and hyaluronan deposition. Matrix Biol 2023; 118:92-109. [PMID: 36907428 PMCID: PMC10259220 DOI: 10.1016/j.matbio.2023.03.005] [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] [Received: 08/11/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
The tumor stroma of most solid malignancies is characterized by a pathological accumulation of pro-angiogenic and pro-tumorigenic hyaluronan driving tumorigenesis and metastatic potential. Of all three hyaluronan synthase isoforms, HAS2 is the primary enzyme that promotes the build-up of tumorigenic HA in breast cancer. Previously, we discovered that endorepellin, the angiostatic C-terminal fragment of perlecan, evokes a catabolic mechanism targeting endothelial HAS2 and hyaluronan via autophagic induction. To explore the translational implications of endorepellin in breast cancer, we created a double transgenic, inducible Tie2CreERT2;endorepellin(ER)Ki mouse line that expresses recombinant endorepellin specifically from the endothelium. We investigated the therapeutic effects of recombinant endorepellin overexpression in an orthotopic, syngeneic breast cancer allograft mouse model. First, adenoviral delivery of Cre evoking intratumor expression of endorepellin in ERKi mice suppressed breast cancer growth, peritumor hyaluronan and angiogenesis. Moreover, tamoxifen-induced expression of recombinant endorepellin specifically from the endothelium in Tie2CreERT2;ERKi mice markedly suppressed breast cancer allograft growth, hyaluronan deposition in the tumor proper and perivascular tissues, and tumor angiogenesis. These results provide insight into the tumor suppressing activity of endorepellin at the molecular level and implicate endorepellin as a promising cancer protein therapy that targets hyaluronan in the tumor microenvironment.
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Affiliation(s)
- Carolyn G Chen
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Aastha Kapoor
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Christopher Xie
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Alison Moss
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Rajanikanth Vadigepalli
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sylvie Ricard-Blum
- Institute of Molecular and Supramolecular Chemistry and Biochemistry, University Claude Bernard Lyon 1, Villeurbanne, France
| | - Renato V Iozzo
- Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Barnhart BK, Kan T, Srivastava A, Wessner CE, Waters J, Ambelil M, Eisenbrey JR, Hoek JB, Vadigepalli R. Longitudinal ultrasound imaging and network modeling in rats reveal sex-dependent suppression of liver regeneration after resection in alcoholic liver disease. Front Physiol 2023; 14:1102393. [PMID: 36969577 PMCID: PMC10033530 DOI: 10.3389/fphys.2023.1102393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Liver resection is an important surgical technique in the treatment of cancers and transplantation. We used ultrasound imaging to study the dynamics of liver regeneration following two-thirds partial hepatectomy (PHx) in male and female rats fed via Lieber-deCarli liquid diet protocol of ethanol or isocaloric control or chow for 5–7 weeks. Ethanol-fed male rats did not recover liver volume to the pre-surgery levels over the course of 2 weeks after surgery. By contrast, ethanol-fed female rats as well as controls of both sexes showed normal volume recovery. Contrary to expectations, transient increases in both portal and hepatic artery blood flow rates were seen in most animals, with ethanol-fed males showing higher peak portal flow than any other experimental group. A computational model of liver regeneration was used to evaluate the contribution of physiological stimuli and estimate the animal-specific parameter intervals. The results implicate lower metabolic load, over a wide range of cell death sensitivity, in matching the model simulations to experimental data of ethanol-fed male rats. However, in the ethanol-fed female rats and controls of both sexes, metabolic load was higher and in combination with cell death sensitivity matched the observed volume recovery dynamics. We conclude that adaptation to chronic ethanol intake has a sex-dependent impact on liver volume recovery following liver resection, likely mediated by differences in the physiological stimuli or cell death responses that govern the regeneration process. Immunohistochemical analysis of pre- and post-resection liver tissue validated the results of computational modeling by associating lack of sensitivity to cell death with lower rates of cell death in ethanol-fed male rats. Our results illustrate the potential for non-invasive ultrasound imaging to assess liver volume recovery towards supporting development of clinically relevant computational models of liver regeneration.
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Affiliation(s)
- Benjamin K. Barnhart
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Toshiki Kan
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Corinne E. Wessner
- Department of Radiology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - John Waters
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Manju Ambelil
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - John R. Eisenbrey
- Department of Radiology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jan B. Hoek
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
- *Correspondence: Rajanikanth Vadigepalli,
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Cook D, Manchel A, Ogunnaike BA, Vadigepalli R. Elucidating the Mechanisms of Dynamic and Robust Control of the Liver Homeostatic Renewal Process: Cell Network Modeling and Analysis. Ind Eng Chem Res 2023; 62:2275-2287. [PMID: 36787103 PMCID: PMC9912253 DOI: 10.1021/acs.iecr.2c03579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/06/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/29/2023]
Abstract
Recent experimental investigations of liver homeostatic renewal have identified high replication capacity hepatocyte populations as the primary maintainers of liver mass. However, the molecular and cellular processes controlling liver homeostatic renewal remain unknown. To address this problem, we developed and analyzed a mathematical model describing cellular network interactions underlying liver homeostatic renewal. Model simulation results demonstrate that without feedback control, basic homeostatic renewal is not robust to disruptions, leading to tissue loss under persistent/repetitive insults. Consequently, we extended our basic model to incorporate putative regulatory interactions and investigated how such interactions may confer robustness on the homeostatic renewal process. We utilized a Design of Experiments approach to identify the combination of feedback interactions that yields a cell network model of homeostatic renewal capable of maintaining liver mass robustly during persistent/repetitive injury. Simulations of this robust model indicate that repeated injury destabilizes liver homeostasis within several months, which differs from epidemiological observations of a much slower decay of liver function occurring over several years. To address this discrepancy, we extended the model to include feedback control by liver nonparenchymal cells. Simulations and analysis of the final multicellular feedback control network suggest that achieving robust liver homeostatic renewal requires intrinsic stability in a hepatocellular network combined with feedback control by nonparenchymal cells.
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Affiliation(s)
- Daniel Cook
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States,Daniel
Baugh Institute for Functional Genomics and Computational Biology,
Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania19107, United States,SimBioSys,
Inc., Chicago, Illinois60601, United
States
| | - Alexandra Manchel
- Daniel
Baugh Institute for Functional Genomics and Computational Biology,
Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania19107, United States
| | - Babatunde A. Ogunnaike
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Rajanikanth Vadigepalli
- Daniel
Baugh Institute for Functional Genomics and Computational Biology,
Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania19107, United States,Rajanikanth
Vadigepalli E-mail:
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8
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Manchel A, Mahadevan R, Bataller R, Hoek JB, Vadigepalli R. Genome-Scale Metabolic Modeling Reveals Sequential Dysregulation of Glutathione Metabolism in Livers from Patients with Alcoholic Hepatitis. Metabolites 2022; 12:metabo12121157. [PMID: 36557195 PMCID: PMC9788589 DOI: 10.3390/metabo12121157] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Alcoholic hepatitis (AH) is the most severe form of alcoholic liver disease for which there is no efficacious treatment aiding most patients. AH manifests differently in individuals, with some patients showing debilitating symptoms more so than others. Previous studies showed significant metabolic dysregulation associated with AH. Therefore, we sought to analyze how the activity of metabolic pathways differed in the liver of patients with varying degrees of AH severity. We utilized a genome-scale metabolic modeling approach that allowed for integration of a generic human cellular metabolic model with specific RNA-seq data corresponding to healthy and multiple liver disease states to predict the metabolic fluxes within each disease state. Additionally, we performed a systems-level analysis of the transcriptomic data and predicted metabolic flux data to identify the regulatory and functional differences in liver metabolism with increasing severity of AH. Our results provide unique insights into the sequential dysregulation of the solute transport mechanisms underlying the glutathione metabolic pathway with increasing AH disease severity. We propose targeting of the solute transporters in the glutathione pathway to mimic the flux activity of the healthy liver state as a potential therapeutic intervention for AH.
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Affiliation(s)
- Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
- The Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Jan B. Hoek
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Correspondence:
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9
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O'Sullivan SJ, Srivastava A, Vadigepalli R, Schwaber JS. Investigating Drivers of Antireward in Addiction Behavior with Anatomically Specific Single-Cell Gene Expression Methods. J Vis Exp 2022. [DOI: 10.3791/64014] [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: 10/31/2022] Open
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10
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Verma A, Manchel A, Melunis J, Hengstler JG, Vadigepalli R. From Seeing to Simulating: A Survey of Imaging Techniques and Spatially-Resolved Data for Developing Multiscale Computational Models of Liver Regeneration. Front Syst Biol 2022; 2:917191. [PMID: 37575468 PMCID: PMC10421626 DOI: 10.3389/fsysb.2022.917191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Liver regeneration, which leads to the re-establishment of organ mass, follows a specifically organized set of biological processes acting on various time and length scales. Computational models of liver regeneration largely focused on incorporating molecular and signaling detail have been developed by multiple research groups in the recent years. These modeling efforts have supported a synthesis of disparate experimental results at the molecular scale. Incorporation of tissue and organ scale data using noninvasive imaging methods can extend these computational models towards a comprehensive accounting of multiscale dynamics of liver regeneration. For instance, microscopy-based imaging methods provide detailed histological information at the tissue and cellular scales. Noninvasive imaging methods such as ultrasound, computed tomography and magnetic resonance imaging provide morphological and physiological features including volumetric measures over time. In this review, we discuss multiple imaging modalities capable of informing computational models of liver regeneration at the organ-, tissue- and cellular level. Additionally, we discuss available software and algorithms, which aid in the analysis and integration of imaging data into computational models. Such models can be generated or tuned for an individual patient with liver disease. Progress towards integrated multiscale models of liver regeneration can aid in prognostic tool development for treating liver disease.
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Affiliation(s)
- Aalap Verma
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Justin Melunis
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Jan G. Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
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11
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Srivastava A, Barnhart BK, Hoek JB, Vadigepalli R. MicroRNA Drivers for Regenerative Capacity in Liver Transplantation. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Benjamin K. Barnhart
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Jan B. Hoek
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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Achanta S, Hornung E, Moss A, Schwaber J, Vadigepalli R. Systems‐level Multi‐organ Modeling of Transcriptomic Data to Reveal Sex‐specific Shifts in Regulatory Control During the Development of Hypertension. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sirisha Achanta
- Department of PathologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Eden Hornung
- Department of PathologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Alison Moss
- Department of PathologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - James Schwaber
- Department of PathologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Department of PathologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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Hornung E, Robbins S, Achanta S, Srivastava A, Moss A, Schwaber J, Vadigepalli R. A 3D Anatomical and Molecular Map of Cardiac Vagal Motoneurons. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Eden Hornung
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - Shaina Robbins
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - Sirisha Achanta
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - Ankita Srivastava
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - Alison Moss
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - James Schwaber
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyDaniel Baugh Institute of Functional Genomics and Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson University, Philadelphia, PAPhiladelphiaPA
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14
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Srivastava A, Robbins S, Achanta S, Schwaber JS, Vadigepalli R. Anatomical and Molecular Phenotypes of Fast and Slow Vagal Targets in the Intrinsic Cardiac Nervous System. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Shaina Robbins
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - James S. Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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15
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Manchel A, Barnhart B, Achanta S, Hoek JB, Vadigepalli R. Integrating Single Cell RNAseq and Computational Modeling to Infer Hepatocyte Metabolic Functionalities during Liver Regeneration. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Gupta S, Feldman JM, Newton AJH, Kuttippurathu L, Moss A, Schwaber JS, Vadigepalli R, Lytton WW. Biophysical Models of Minipig Right Atrial Ganglionic Plexus Principal Neurons Identified from Transcriptomics Data. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Suranjana Gupta
- Department of Physiology and PharmacologySUNY Downstate Health Sciences UniversityBrooklynNY
| | - Jessica M. Feldman
- Department of Physiology and PharmacologySUNY Downstate Health Sciences UniversityBrooklynNY
| | - Adam J. H. Newton
- Department of Physiology and PharmacologySUNY Downstate Health Sciences UniversityBrooklynNY
| | - Lakshmi Kuttippurathu
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Alison Moss
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - James S. Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - William W. Lytton
- Department of Physiology and PharmacologySUNY Downstate Health Sciences UniversityBrooklynNY
- NeurologySUNY Downstate Health Sciences UniversityBrooklynNY
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17
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Gee M, Hornung E, Moss A, Kuttippurathu L, Schwaber JS, Ogunnaike B, Vadigepalli R. Modeling and Analysis of Closed‐Loop Control of the Cardiovascular System. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michelle Gee
- Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDE
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Eden Hornung
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Alison Moss
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Lakshmi Kuttippurathu
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - James S. Schwaber
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | | | - Rajanikanth Vadigepalli
- Daniel Baugh Institute of Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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18
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Srivastava A, Parrish A, Hoek JB, Vadigepalli R. Modulation of miR‐21 can reprogram the TGF‐β signaling pathway to alter HSC phenotype in vitro. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Austin Parrish
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Jan B. Hoek
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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19
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Manchel A, Srivastava A, Bataller R, Hoek JB, Vadigepalli R. Deconvolution of Bulk RNAseq Data from Human Liver Samples Reveals a Metabolic Switch in Periportal Hepatocytes in Alcoholic Hepatitis. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Ramon Bataller
- Pittsburgh Liver Research CenterUniversity of Pittsburgh Medical CenterPittsburghPA
| | - Jan B. Hoek
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational BiologyDepartment of Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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20
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Verma A, Manchel A, Narayanan R, Hoek JB, Ogunnaike BA, Vadigepalli R. A Spatial Model of Hepatic Calcium Signaling and Glucose Metabolism Under Autonomic Control Reveals Functional Consequences of Varying Liver Innervation Patterns Across Species. Front Physiol 2021; 12:748962. [PMID: 34899380 PMCID: PMC8662697 DOI: 10.3389/fphys.2021.748962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/28/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Rapid breakdown of hepatic glycogen stores into glucose plays an important role during intense physical exercise to maintain systemic euglycemia. Hepatic glycogenolysis is governed by several different liver-intrinsic and systemic factors such as hepatic zonation, circulating catecholamines, hepatocellular calcium signaling, hepatic neuroanatomy, and the central nervous system (CNS). Of the factors regulating hepatic glycogenolysis, the extent of lobular innervation varies significantly between humans and rodents. While rodents display very few autonomic nerve terminals in the liver, nearly every hepatic layer in the human liver receives neural input. In the present study, we developed a multi-scale, multi-organ model of hepatic metabolism incorporating liver zonation, lobular scale calcium signaling, hepatic innervation, and direct and peripheral organ-mediated communication between the liver and the CNS. We evaluated the effect of each of these governing factors on the total hepatic glucose output and zonal glycogenolytic patterns within liver lobules during simulated physical exercise. Our simulations revealed that direct neuronal stimulation of the liver and an increase in circulating catecholamines increases hepatic glucose output mediated by mobilization of intracellular calcium stores and lobular scale calcium waves. Comparing simulated glycogenolysis between human-like and rodent-like hepatic innervation patterns (extensive vs. minimal) suggested that propagation of calcium transients across liver lobules acts as a compensatory mechanism to improve hepatic glucose output in sparsely innervated livers. Interestingly, our simulations suggested that catecholamine-driven glycogenolysis is reduced under portal hypertension. However, increased innervation coupled with strong intercellular communication can improve the total hepatic glucose output under portal hypertension. In summary, our modeling and simulation study reveals a complex interplay of intercellular and multi-organ interactions that can lead to differing calcium dynamics and spatial distributions of glycogenolysis at the lobular scale in the liver.
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Affiliation(s)
- Aalap Verma
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States.,Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rahul Narayanan
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Jan B Hoek
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Babatunde A Ogunnaike
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
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21
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O'Sullivan SJ, McIntosh-Clarke D, Park J, Vadigepalli R, Schwaber JS. Single Cell Scale Neuronal and Glial Gene Expression and Putative Cell Phenotypes and Networks in the Nucleus Tractus Solitarius in an Alcohol Withdrawal Time Series. Front Syst Neurosci 2021; 15:739790. [PMID: 34867221 PMCID: PMC8641127 DOI: 10.3389/fnsys.2021.739790] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
Alcohol withdrawal syndrome (AWS) is characterized by neuronal hyperexcitability, autonomic dysregulation, and severe negative emotion. The nucleus tractus solitarius (NTS) likely plays a prominent role in the neurological processes underlying these symptoms as it is the main viscerosensory nucleus in the brain. The NTS receives visceral interoceptive inputs, influences autonomic outputs, and has strong connections to the limbic system and hypothalamic-pituitary-adrenal axis to maintain homeostasis. Our prior analysis of single neuronal gene expression data from the NTS shows that neurons exist in heterogeneous transcriptional states that form distinct functional subphenotypes. Our working model conjectures that the allostasis secondary to alcohol dependence causes peripheral and central biological network decompensation in acute abstinence resulting in neurovisceral feedback to the NTS that substantially contributes to the observed AWS. We collected single noradrenergic and glucagon-like peptide-1 (GLP-1) neurons and microglia from rat NTS and measured a subset of their transcriptome as pooled samples in an alcohol withdrawal time series. Inflammatory subphenotypes predominate at certain time points, and GLP-1 subphenotypes demonstrated hyperexcitability post-withdrawal. We hypothesize such inflammatory and anxiogenic signaling contributes to alcohol dependence via negative reinforcement. Targets to mitigate such dysregulation and treat dependence can be identified from this dataset.
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Affiliation(s)
- Sean J O'Sullivan
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Brain Stimulation Lab, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, United States
| | - Damani McIntosh-Clarke
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James Park
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical Engineering, University of Delaware, Newark, DE, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical Engineering, University of Delaware, Newark, DE, United States
| | - James S Schwaber
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
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22
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Parrish A, Srivastava A, Juskeviciute E, Hoek JB, Vadigepalli R. Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration. Physiol Genomics 2021; 53:546-555. [PMID: 34796728 PMCID: PMC8820682 DOI: 10.1152/physiolgenomics.00113.2021] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Impaired liver regeneration has been considered as a hallmark of progression of alcohol-associated liver disease. Our previous studies demonstrated that in vivo inhibition of the microRNA (miRNA) miR21 can restore regenerative capacity of the liver in chronic ethanol-fed animals. The present study focuses on the role of microRNA regulatory networks that are likely to mediate the miR-21 action. Rats were chronically fed an ethanol-enriched diet along with pair-fed control animals and treated with AM21 (anti-miR-21), a locked nucleic acid antisense to miR-21. Partial hepatectomy (PHx) was performed and miRNA expression profiling over the course of liver regeneration was assessed. Our results showed dynamic expression changes in several miRNAs after PHx, notably with altered miRNA expression profiles between ethanol and control groups. We found that in vivo inhibition of miR-21 led to correlated differential expression of miR-340-5p and anticorrelated expression of miR-365, let-7a, miR-1224, and miR-146a across all sample groups after PHx. Gene set enrichment analysis identified a miRNA signature significantly associated with hepatic stellate cell activation within whole liver tissue data. We hypothesized that at least part of the PHx-induced miRNA network changes responsive to miR-21 inhibition is localized to hepatic stellate cells. We validated this hypothesis using AM21 and TGF-β treatments in LX-2 human hepatic stellate cells in culture and measured expression levels of select miRNAs by quantitative RT-PCR. Based on the in vivo and in vitro results, we propose a hepatic stellate cell miRNA regulatory network as contributing to the restoration of liver regenerative capacity by miR-21 inhibition.
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Affiliation(s)
- Austin Parrish
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Egle Juskeviciute
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jan B Hoek
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
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23
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Parihar M, Bendelac-Kapon L, Gur M, Abbou T, Belorkar A, Achanta S, Kinberg K, Vadigepalli R, Fainsod A. Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis. Front Cell Dev Biol 2021; 9:747969. [PMID: 34746144 PMCID: PMC8564372 DOI: 10.3389/fcell.2021.747969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/27/2021] [Accepted: 09/23/2021] [Indexed: 01/15/2023] Open
Abstract
Robustness is a feature of regulatory pathways to ensure signal consistency in light of environmental changes or genetic polymorphisms. The retinoic acid (RA) pathway, is a central developmental and tissue homeostasis regulatory signal, strongly dependent on nutritional sources of retinoids and affected by environmental chemicals. This pathway is characterized by multiple proteins or enzymes capable of performing each step and their integration into a self-regulating network. We studied RA network robustness by transient physiological RA signaling disturbances followed by kinetic transcriptomic analysis of the recovery during embryogenesis. The RA metabolic network was identified as the main regulated module to achieve signaling robustness using an unbiased pattern analysis. We describe the network-wide responses to RA signal manipulation and found the feedback autoregulation to be sensitive to the direction of the RA perturbation: RA knockdown exhibited an upper response limit, whereas RA addition had a minimal feedback-activation threshold. Surprisingly, our robustness response analysis suggests that the RA metabolic network regulation exhibits a multi-objective optimization, known as Pareto optimization, characterized by trade-offs between competing functionalities. We observe that efficient robustness to increasing RA is accompanied by worsening robustness to reduced RA levels and vice versa. This direction-dependent trade-off in the network-wide feedback response, results in an uneven robustness capacity of the RA network during early embryogenesis, likely a significant contributor to the manifestation of developmental defects.
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Affiliation(s)
- Madhur Parihar
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Liat Bendelac-Kapon
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Michal Gur
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Tali Abbou
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Abha Belorkar
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Keren Kinberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
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24
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McGinnis RW, Sztandera L, Ruane J, Vadigepalli R. Analyzing the relationships between city opioid deaths and socioeconomic factors. J Opioid Manag 2021; 17:363-382. [PMID: 34714537 DOI: 10.5055/jom.2021.0670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The opioid crisis has been increasing in severity over the past several decades. Every year, thousands of people die due to opioid-related issues. The factors that play into the causes of this are complex. Our study aimed to see how commute times, city budget for roads, and city budget for arts and culture contribute to the city's overall opioid death rates. We know that overdose rates are more common in cities rather than rural areas, therefore making one major city per state as part of our design. METHODS We collected data from one city per state (n = 50) and ran two ANOVA tests and 11 logistical regression tests. Both types of tests were run on IBM SPSS Statistical software version 25 at its default settings with a confidence interval set to 95 percent. Opioid deaths were the dependent variable, whereas commute time, budget for roads, and budget for arts and culture were the independent variables. RESULTS Commute time yielded a significant result in almost all the tests it was included in: Table 1, 0.033; Table 3, 0.000; Figure 4, 0.000; Figure 5, 0.000. Budget for roads also showed significant results in most of its tests as well: Table 1, 0.003; Table 2, 0.047; Figure 3, 0.001. Budget for arts and culture showed significant results but not in a pattern that we could interpret: Table 1, 0.002; Table 2, 0.021; Table 4, 0.013. CONCLUSIONS Commute time and the budget for roads are likely to play a role in their city's opioid crisis. Understanding where a city fits in relation to these results may better help them prepare and reduce opioid death rates.
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Affiliation(s)
| | - Les Sztandera
- Thomas Jefferson University, Center City Campus, Philadelphia, Pennsylvania
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25
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Moss A, Robbins S, Achanta S, Kuttippurathu L, Turick S, Nieves S, Hanna P, Smith EH, Hoover DB, Chen J, Cheng Z(J, Ardell JL, Shivkumar K, Schwaber JS, Vadigepalli R. A single cell transcriptomics map of paracrine networks in the intrinsic cardiac nervous system. iScience 2021; 24:102713. [PMID: 34337356 PMCID: PMC8324809 DOI: 10.1016/j.isci.2021.102713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
We developed a spatially-tracked single neuron transcriptomics map of an intrinsic cardiac ganglion, the right atrial ganglionic plexus (RAGP) that is a critical mediator of sinoatrial node (SAN) activity. This 3D representation of RAGP used neuronal tracing to extensively map the spatial distribution of the subset of neurons that project to the SAN. RNA-seq of laser capture microdissected neurons revealed a distinct composition of RAGP neurons compared to the central nervous system and a surprising finding that cholinergic and catecholaminergic markers are coexpressed, suggesting multipotential phenotypes that can drive neuroplasticity within RAGP. High-throughput qPCR of hundreds of laser capture microdissected single neurons confirmed these findings and revealed a high dimensionality of neuromodulatory factors that contribute to dynamic control of the heart. Neuropeptide-receptor coexpression analysis revealed a combinatorial paracrine neuromodulatory network within RAGP informing follow-on studies on the vagal control of RAGP to regulate cardiac function in health and disease.
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Affiliation(s)
- Alison Moss
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Shaina Robbins
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sirisha Achanta
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lakshmi Kuttippurathu
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Scott Turick
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sean Nieves
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peter Hanna
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Elizabeth H. Smith
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Donald B. Hoover
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Jin Chen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Zixi (Jack) Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jeffrey L. Ardell
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Kalyanam Shivkumar
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - James S. Schwaber
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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26
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Leung C, Robbins S, Moss A, Heal M, Osanlouy M, Christie R, Farahani N, Monteith C, Chen J, Hunter P, Tappan S, Vadigepalli R, Cheng Z(J, Schwaber JS. 3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system. iScience 2021; 24:102795. [PMID: 34355144 PMCID: PMC8324857 DOI: 10.1016/j.isci.2021.102795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/05/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
We developed and analyzed a single cell scale anatomical map of the rat intrinsic cardiac nervous system (ICNS) across four male and three female hearts. We find the ICNS has a reliable structural organizational plan across individuals that provide the foundation for further analyses of the ICNS in cardiac function and disease. The distribution of the ICNS was evaluated by 3D visualization and data-driven clustering. The pattern, distribution, and clustering of ICNS neurons across all male and female rat hearts is highly conserved, demonstrating a coherent organizational plan where distinct clusters of neurons are consistently localized. Female hearts had fewer neurons, lower packing density, and slightly reduced distribution, but with identical localization. We registered the anatomical data from each heart to a geometric scaffold, normalizing their 3D coordinates for standardization of common anatomical planes and providing a path where multiple experimental results and data types can be integrated and compared.
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Affiliation(s)
- Clara Leung
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Shaina Robbins
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alison Moss
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Mahyar Osanlouy
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Richard Christie
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | | | - Jin Chen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | - Rajanikanth Vadigepalli
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zixi (Jack) Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - James S. Schwaber
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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27
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Vadigepalli R, Schwaber JS. Mapping the little brain at the heart by an interdisciplinary systems biology team. iScience 2021; 24:102433. [PMID: 34113808 PMCID: PMC8169792 DOI: 10.1016/j.isci.2021.102433] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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28
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Hanna P, Dacey MJ, Brennan J, Moss A, Robbins S, Achanta S, Biscola NP, Swid MA, Rajendran PS, Mori S, Hadaya JE, Smith EH, Peirce SG, Chen J, Havton LA, Cheng Z(J, Vadigepalli R, Schwaber J, Lux RL, Efimov I, Tompkins JD, Hoover DB, Ardell JL, Shivkumar K. Innervation and Neuronal Control of the Mammalian Sinoatrial Node a Comprehensive Atlas. Circ Res 2021; 128:1279-1296. [PMID: 33629877 PMCID: PMC8284939 DOI: 10.1161/circresaha.120.318458] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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] [Indexed: 01/01/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Peter Hanna
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
- UCLA Molecular, Cellular & Integrative Physiology Program, UCLA
| | - Michael J. Dacey
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
- UCLA Molecular, Cellular & Integrative Physiology Program, UCLA
| | - Jaclyn Brennan
- Bioengineering, George Washington University, Washington, DC
| | - Alison Moss
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | - Shaina Robbins
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | - Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | | | - Mohammed A. Swid
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | - Pradeep S. Rajendran
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | - Shumpei Mori
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | - Joseph E. Hadaya
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | | | | | - Jin Chen
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine, Orlando, FL
| | - Leif A. Havton
- Neurology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
- VA RR&D National Center of Excellence for the Medical Consequences of Spinal and; Cord Injury and Neurology Service, James J. Peters Veterans Administration Medical Center, Bronx, NY
| | - Zixi (Jack) Cheng
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine, Orlando, FL
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | - James Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA
| | - Robert L. Lux
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | - Igor Efimov
- Bioengineering, George Washington University, Washington, DC
| | - John D. Tompkins
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
| | - Donald B. Hoover
- Biomedical Sciences
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University
| | - Jeffrey L. Ardell
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
- UCLA Molecular, Cellular & Integrative Physiology Program, UCLA
| | - Kalyanam Shivkumar
- University of California Los Angeles (UCLA) Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, Department of Medicine
- UCLA Molecular, Cellular & Integrative Physiology Program, UCLA
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29
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Massey V, Parrish A, Argemi J, Moreno M, Mello A, García-Rocha M, Altamirano J, Odena G, Dubuquoy L, Louvet A, Martinez C, Adrover A, Affò S, Morales-Ibanez O, Sancho-Bru P, Millán C, Alvarado-Tapias E, Morales-Arraez D, Caballería J, Mann J, Cao S, Sun Z, Shah V, Cameron A, Mathurin P, Snider N, Villanueva C, Morgan TR, Guinovart J, Vadigepalli R, Bataller R. Integrated Multiomics Reveals Glucose Use Reprogramming and Identifies a Novel Hexokinase in Alcoholic Hepatitis. Gastroenterology 2021; 160:1725-1740.e2. [PMID: 33309778 PMCID: PMC8613537 DOI: 10.1053/j.gastro.2020.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 02/23/2020] [Revised: 11/06/2020] [Accepted: 12/01/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND & AIMS We recently showed that alcoholic hepatitis (AH) is characterized by dedifferentiation of hepatocytes and loss of mature functions. Glucose metabolism is tightly regulated in healthy hepatocytes. We hypothesize that AH may lead to metabolic reprogramming of the liver, including dysregulation of glucose metabolism. METHODS We performed integrated metabolomic and transcriptomic analyses of liver tissue from patients with AH or alcoholic cirrhosis or normal liver tissue from hepatic resection. Focused analyses of chromatin immunoprecipitation coupled to DNA sequencing was performed. Functional in vitro studies were performed in primary rat and human hepatocytes and HepG2 cells. RESULTS Patients with AH exhibited specific changes in the levels of intermediates of glycolysis/gluconeogenesis, the tricarboxylic acid cycle, and monosaccharide and disaccharide metabolism. Integrated analysis of the transcriptome and metabolome showed the used of alternate energetic pathways, metabolite sinks and bottlenecks, and dysregulated glucose storage in patients with AH. Among genes involved in glucose metabolism, hexokinase domain containing 1 (HKDC1) was identified as the most up-regulated kinase in patients with AH. Histone active promoter and enhancer markers were increased in the HKDC1 genomic region. High HKDC1 levels were associated with the development of acute kidney injury and decreased survival. Increased HKDC1 activity contributed to the accumulation of glucose-6-P and glycogen in primary rat hepatocytes. CONCLUSIONS Altered metabolite levels and messenger RNA expression of metabolic enzymes suggest the existence of extensive reprogramming of glucose metabolism in AH. Increased HKDC1 expression may contribute to dysregulated glucose metabolism and represents a novel biomarker and therapeutic target for AH.
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Affiliation(s)
- Veronica Massey
- Division of Gastroenterology and Hepatology, Departments of Medicine and Nutrition, and Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, North Carolina
| | - Austin Parrish
- Daniel Baugh Institute, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Josepmaria Argemi
- Department of Gastroenterology and Hepatology, Division of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Liver Unit, Clinica Universidad de Navarra. Hepatology Program, Center for Applied Medical Research, IdisNA, Pamplona, Spain
| | - Montserrat Moreno
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Aline Mello
- Department of Gastroenterology and Hepatology, Division of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mar García-Rocha
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Altamirano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Liver Unit, Internal Medicine Department, Hospital Universitari Vall d'Hebrón, Vall d'Hebrón Institut de Recerca, Barcelona, Spain
| | - Gemma Odena
- Division of Gastroenterology and Hepatology, Departments of Medicine and Nutrition, and Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, North Carolina
| | - Laurent Dubuquoy
- Service des Maladies de l'appareil digestif, CHU Lille, Inserm LIRIC-UMR995, University of Lille, Lille, France
| | - Alexandre Louvet
- Service des Maladies de l'appareil digestif, CHU Lille, Inserm LIRIC-UMR995, University of Lille, Lille, France
| | - Carlos Martinez
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Adrover
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Affò
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | | | - Pau Sancho-Bru
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Cristina Millán
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Edilmar Alvarado-Tapias
- Department of Gastroenterology, Hospital Santa Creu i Sant Pau, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain
| | - Dalia Morales-Arraez
- Department of Gastroenterology and Hepatology, Division of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Juan Caballería
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Liver Unit, Hospital Clínic, CIBER de Enfermedades Hepáticas y Digestivas, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Jelena Mann
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Sheng Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Zhaoli Sun
- Johns Hopkins School of Medicine, Department of Surgery and Transplant Biology Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Vijay Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Andrew Cameron
- Johns Hopkins School of Medicine, Department of Surgery and Transplant Biology Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Phillipe Mathurin
- Service des Maladies de l'appareil digestif, CHU Lille, Inserm LIRIC-UMR995, University of Lille, Lille, France
| | - Natasha Snider
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina
| | - Càndid Villanueva
- Department of Gastroenterology, Hospital Santa Creu i Sant Pau, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain; Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Timothy R Morgan
- Gastroenterology Services, VA Long Beach Healthcare, VA Long Beach Healthcare System, Long Beach, California
| | - Joan Guinovart
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ramon Bataller
- Division of Gastroenterology and Hepatology, Departments of Medicine and Nutrition, and Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, North Carolina; Department of Gastroenterology and Hepatology, Division of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
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30
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Erdemir A, Mulugeta L, Ku JP, Drach A, Horner M, Morrison TM, Peng GCY, Vadigepalli R, Lytton WW, Myers JG. Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective. J Transl Med 2020; 18:369. [PMID: 32993675 PMCID: PMC7526418 DOI: 10.1186/s12967-020-02540-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 05/27/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022] Open
Abstract
The complexities of modern biomedicine are rapidly increasing. Thus, modeling and simulation have become increasingly important as a strategy to understand and predict the trajectory of pathophysiology, disease genesis, and disease spread in support of clinical and policy decisions. In such cases, inappropriate or ill-placed trust in the model and simulation outcomes may result in negative outcomes, and hence illustrate the need to formalize the execution and communication of modeling and simulation practices. Although verification and validation have been generally accepted as significant components of a model’s credibility, they cannot be assumed to equate to a holistic credible practice, which includes activities that can impact comprehension and in-depth examination inherent in the development and reuse of the models. For the past several years, the Committee on Credible Practice of Modeling and Simulation in Healthcare, an interdisciplinary group seeded from a U.S. interagency initiative, has worked to codify best practices. Here, we provide Ten Rules for credible practice of modeling and simulation in healthcare developed from a comparative analysis by the Committee’s multidisciplinary membership, followed by a large stakeholder community survey. These rules establish a unified conceptual framework for modeling and simulation design, implementation, evaluation, dissemination and usage across the modeling and simulation life-cycle. While biomedical science and clinical care domains have somewhat different requirements and expectations for credible practice, our study converged on rules that would be useful across a broad swath of model types. In brief, the rules are: (1) Define context clearly. (2) Use contextually appropriate data. (3) Evaluate within context. (4) List limitations explicitly. (5) Use version control. (6) Document appropriately. (7) Disseminate broadly. (8) Get independent reviews. (9) Test competing implementations. (10) Conform to standards. Although some of these are common sense guidelines, we have found that many are often missed or misconstrued, even by seasoned practitioners. Computational models are already widely used in basic science to generate new biomedical knowledge. As they penetrate clinical care and healthcare policy, contributing to personalized and precision medicine, clinical safety will require established guidelines for the credible practice of modeling and simulation in healthcare.
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Affiliation(s)
- Ahmet Erdemir
- Department of Biomedical Engineering and Computational Biomodeling (CoBi) Core, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue (ND20), Cleveland, OH, 44195, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Lealem Mulugeta
- InSilico Labs LLC, 2617 Bissonnet St. Suite 435, Houston, TX, 77005, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Joy P Ku
- Department of Bioengineering, Clark Center, Stanford University, 318 Campus Drive, Stanford, CA, 94305-5448, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Andrew Drach
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, 201 E. 24th st, Austin, TX, 78712, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Marc Horner
- ANSYS, Inc, 1007 Church Street, Suite 250, Evanston, IL, 60201, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Tina M Morrison
- Division of Applied Mechanics, United States Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Grace C Y Peng
- National Institute of Biomedical Imaging & Bioengineering, Suite 200, MSC 6707 Democracy Blvd5469, Bethesda, MD, 20892, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - William W Lytton
- State University of New York, Kings County Hospital, 450 Clarkson Ave., MSC 31, Brooklyn, NY, 11203, USA.,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA
| | - Jerry G Myers
- Human Research Program, Cross-Cutting Computational Modeling Project, National Aeronautics and Space Administration - John H. Glenn Research Center, 21000 Brookpark Road, Cleveland, OH, 44135, USA. .,Committee on Credible Practice of Modeling, & Simulation in Healthcare, Interagency Modeling and Analysis Group and Multiscale Modeling Consortium, Bethesda, MD, USA.
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31
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Achanta S, Gorky J, Leung C, Moss A, Robbins S, Eisenman L, Chen J, Tappan S, Heal M, Farahani N, Huffman T, England S, Cheng ZJ, Vadigepalli R, Schwaber JS. A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System. iScience 2020; 23:101140. [PMID: 32460006 PMCID: PMC7327996 DOI: 10.1016/j.isci.2020.101140] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 01/17/2020] [Revised: 03/11/2020] [Accepted: 05/01/2020] [Indexed: 12/21/2022] Open
Abstract
We have developed and integrated several technologies including whole-organ imaging and software development to support an initial precise 3D neuroanatomical mapping and molecular phenotyping of the intracardiac nervous system (ICN). While qualitative and gross anatomical descriptions of the anatomy of the ICN have each been pursued, we here bring forth a comprehensive atlas of the entire rat ICN at single-cell resolution. Our work precisely integrates anatomical and molecular data in the 3D digitally reconstructed whole heart with resolution at the micron scale. We now display the full extent and the position of neuronal clusters on the base and posterior left atrium of the rat heart, and the distribution of molecular phenotypes that are defined along the base-to-apex axis, which had not been previously described. The development of these approaches needed for this work has produced method pipelines that provide the means for mapping other organs. Comprehensive single-neuron-scale mapping of the intrinsic cardiac nervous system Whole-organ high-throughput imaging and reconstruction at a cellular resolution 3D anatomical framework for spatially tracked single-neuron molecular phenotypes Integrated histology, neuron mapping, and molecular profiles for 3D organ reconstruction
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Affiliation(s)
- Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan Gorky
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Clara Leung
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Alison Moss
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Shaina Robbins
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leonard Eisenman
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jin Chen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | | | | | | | | | | | - Zixi Jack Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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32
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Park JH, Gorky J, Ogunnaike B, Vadigepalli R, Schwaber JS. Investigating the Effects of Brainstem Neuronal Adaptation on Cardiovascular Homeostasis. Front Neurosci 2020; 14:470. [PMID: 32508573 PMCID: PMC7251082 DOI: 10.3389/fnins.2020.00470] [Citation(s) in RCA: 5] [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: 02/02/2019] [Accepted: 04/16/2020] [Indexed: 01/01/2023] Open
Abstract
Central coordination of cardiovascular function is accomplished, in part, by the baroreceptor reflex, a multi-input multi-output physiological control system that regulates the activity of the parasympathetic and sympathetic nervous systems via interactions among multiple brainstem nuclei. Recent single-cell analyses within the brain revealed that individual neurons within and across brain nuclei exhibit distinct transcriptional states contributing to neuronal function. Such transcriptional heterogeneity complicates the task of understanding how neurons within and across brain nuclei organize and function to process multiple inputs and coordinate cardiovascular functions within the larger context of the baroreceptor reflex. However, prior analysis of brainstem neurons revealed that single-neuron transcriptional heterogeneity reflects an adaptive response to synaptic inputs and that neurons organize into distinct subtypes with respect to synaptic inputs received. Based on these results, we hypothesize that adaptation of neuronal subtypes support robust biological function through graded cellular responses. We test this hypothesis by examining the functional impact of neuronal adaptation on parasympathetic activity within the context of short-term baroreceptor reflex regulation. In this work, we extend existing quantitative closed-loop models of the baroreceptor reflex by incorporating into the model distinct input-driven neuronal subtypes and neuroanatomical groups that modulate parasympathetic activity. We then use this extended model to investigate, via simulation, the functional role of neuronal adaptation under conditions of health and systolic heart failure. Simulation results suggest that parasympathetic activity can be modulated appropriately by the coordination of distinct neuronal subtypes to maintain normal cardiovascular functions under systolic heart failure conditions. Moreover, differing degrees of adaptation of these neuronal subtypes contribute to cardiovascular behaviors corresponding to distinct clinical phenotypes of heart failure, such as exercise intolerance. Further, our results suggest that an imbalance between sympathetic and parasympathetic activity regulating ventricular contractility contributes to exercise intolerance in systolic heart failure patients, and restoring this balance can improve the short-term cardiovascular performance of these patients.
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Affiliation(s)
- James H Park
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical and Biochemical Engineering, University of Delaware, Newark, DE, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - Jonathan Gorky
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Babatunde Ogunnaike
- Department of Chemical and Biochemical Engineering, University of Delaware, Newark, DE, United States
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - James S Schwaber
- Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
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33
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Staehle MM, O’Sullivan S, Vadigepalli R, Kernan KF, Gonye GE, Ogunnaike BA, Schwaber JS. Diurnal Patterns of Gene Expression in the Dorsal Vagal Complex and the Central Nucleus of the Amygdala - Non-rhythm-generating Brain Regions. Front Neurosci 2020; 14:375. [PMID: 32477043 PMCID: PMC7233260 DOI: 10.3389/fnins.2020.00375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Genes that establish the circadian clock have differential expression with respect to solar time in central and peripheral tissues. Here, we find circadian-time-induced differential expression in a large number of genes not associated with circadian rhythms in two brain regions lacking overt circadian function: the dorsal vagal complex (DVC) and the central nucleus of the amygdala (CeA). These regions primarily engage in autonomic, homeostatic, and emotional regulation. However, we find striking diurnal shifts in gene expression in these regions of male Sprague Dawley rats with no obvious patterns that could be attributed to function or region. These findings have implications for the design of gene expression studies as well as for the potential effects of xenobiotics on these regions that regulate autonomic and emotional states.
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Affiliation(s)
- Mary M. Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ, United States
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
- Department of Chemical Engineering, University of Delaware, Newark, DE, United States
| | - Sean O’Sullivan
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Kate F. Kernan
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Gregory E. Gonye
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | | | - James S. Schwaber
- Department of Pathology, Anatomy, and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States
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Gorky J, Vadigepalli R, Schwaber JS. SPARC: The Emergence Of Cardioprotection From The Vagus Nerve Mediated Brain‐Heart Network. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Barnhart B, Kan T, Wessner CE, Eisenbrey JR, Hoek JB, Vadigepalli R. Sex‐dependent Liver Volume Recovery and Hemodynamics Measured by Non‐Invasive Ultrasound Imaging after Partial Hepatectomy in Rats. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Chen J, Tappan S, Vadigepalli R, Schwaber JS, Cheng ZJ. SPARC Distribution of Intrinsic Cardiac Neurons Projecting to the Sinoatrial Node in Male and Female Rats: A Comparison. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Moss A, Achanta S, Robbins S, Turick S, Nieves S, Hanna P, Dacey M, Swid MA, Ardell J, Shivkumar K, Schwaber JS, Vadigepalli R. SPARC: A Comprehensive Single Neuron Molecular Phenotype Map of the Right Atrial Ganglionated Plexus in the Pig Heart. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Moss A, Kuttippurathu L, Achanta S, Schwaber JS, Vadigepalli R. SPARC: Time Series Transcriptomic Analysis of the Nucleus of the Solitary Tract During the Development of Hypertension. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Moss A, Kuttippurathu L, Achanta S, Schwaber JS, Vadigepalli R. SPARC: Different MicroRNA Regulatory Networks Are Active In The Nucleus Of The Solitary Tract During The Development Of Hypertension In Male And Female Spontaneously Hypertensive Rats. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Barnhart B, Chopra C, Achanta S, Hoek JB, Vadigepalli R. Compensatory Enzyme Expression In Response To Chronic Ethanol Intake And Partial Hepatectomy Disrupts Zone‐Specific Organization Of Lobular Metabolism In The Rat Liver. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Leung C, Robbins S, Moss A, Heal M, Chen J, Tappan S, Huffman T, Farahani N, Vadigepalli R, Schwaber J, Cheng ZJ. SPARC: Distribution of Intrinsic Cardiac Neurons in 3D Reconstructed Hearts of F344 Rat. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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O'Sullivan SJ, Reyes BAS, Vadigepalli R, Van Bockstaele EJ, Schwaber JS. Combining Laser Capture Microdissection and Microfluidic qPCR to Analyze Transcriptional Profiles of Single Cells: A Systems Biology Approach to Opioid Dependence. J Vis Exp 2020. [PMID: 32202523 DOI: 10.3791/60612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Profound transcriptional heterogeneity in anatomically adjacent single cells suggests that robust tissue functionality may be achieved by cellular phenotype diversity. Single-cell experiments investigating the network dynamics of biological systems demonstrate cellular and tissue responses to various conditions at biologically meaningful resolution. Herein, we explain our methods for gathering single cells from anatomically specific locations and accurately measuring a subset of their gene expression profiles. We combine laser capture microdissection (LCM) with microfluidic reverse transcription quantitative polymerase chain reactions (RT-qPCR). We also use this microfluidic RT-qPCR platform to measure the microbial abundance of gut contents.
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Affiliation(s)
- Sean J O'Sullivan
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University; Sidney Kimmel Medical College, Thomas Jefferson University;
| | - Beverly A S Reyes
- Department of Pharmacology & Physiology, Drexel University College of Medicine
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University
| | | | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University
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Campos G, Schmidt-Heck W, De Smedt J, Widera A, Ghallab A, Pütter L, González D, Edlund K, Cadenas C, Marchan R, Guthke R, Verfaillie C, Hetz C, Sachinidis A, Braeuning A, Schwarz M, Weiß TS, Banhart BK, Hoek J, Vadigepalli R, Willy J, Stevens JL, Hay DC, Hengstler JG, Godoy P. Inflammation-associated suppression of metabolic gene networks in acute and chronic liver disease. Arch Toxicol 2020; 94:205-217. [PMID: 31919559 DOI: 10.1007/s00204-019-02630-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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] [Received: 08/13/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Inflammation has been recognized as essential for restorative regeneration. Here, we analyzed the sequential processes during onset of liver injury and subsequent regeneration based on time-resolved transcriptional regulatory networks (TRNs) to understand the relationship between inflammation, mature organ function, and regeneration. Genome-wide expression and TRN analysis were performed time dependently in mouse liver after acute injury by CCl4 (2 h, 8 h, 1, 2, 4, 6, 8, 16 days), as well as lipopolysaccharide (LPS, 24 h) and compared to publicly available data after tunicamycin exposure (mouse, 6 h), hepatocellular carcinoma (HCC, mouse), and human chronic liver disease (non-alcoholic fatty liver, HBV infection and HCC). Spatiotemporal investigation differentiated lobular zones for signaling and transcription factor expression. Acute CCl4 intoxication induced expression of gene clusters enriched for inflammation and stress signaling that peaked between 2 and 24 h, accompanied by a decrease of mature liver functions, particularly metabolic genes. Metabolism decreased not only in pericentral hepatocytes that underwent CCl4-induced necrosis, but extended to the surviving periportal hepatocytes. Proliferation and tissue restorative TRNs occurred only later reaching a maximum at 48 h. The same upstream regulators (e.g. inhibited RXR function) were implicated in increased inflammation and suppressed metabolism. The concomitant inflammation/metabolism TRN occurred similarly after acute LPS and tunicamycin challenges, in chronic mouse models and also in human liver diseases. Downregulation of metabolic genes occurs concomitantly to induce inflammation-associated genes as an early response and appears to be initiated by similar upstream regulators in acute and chronic liver diseases in humans and mice. In the acute setting, proliferation and restorative regeneration associated TRNs peak only later when metabolism is already suppressed.
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Affiliation(s)
- Gisela Campos
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll Institute, Jena, Germany
| | | | - Agata Widera
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Ahmed Ghallab
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
- Department of Forensic and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Larissa Pütter
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Daniela González
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Karolina Edlund
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Cristina Cadenas
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Rosemarie Marchan
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll Institute, Jena, Germany
| | | | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- The Buck Institute for Research in Aging, Novato, CA, 94945, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Agapios Sachinidis
- Medical Faculty, Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Albert Braeuning
- Department of Experimental and Clinical Pharmacology and Toxicology, University of Tübingen, Tübingen, Germany
- Department of Food Safety, Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Michael Schwarz
- Department of Experimental and Clinical Pharmacology and Toxicology, University of Tübingen, Tübingen, Germany
| | - Thomas S Weiß
- Department of Pediatrics and Juvenile Medicine, Center for Liver Cell Research, University of Regensburg Hospital, Regensburg, Germany
| | - Benjamin K Banhart
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jan Hoek
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeffrey Willy
- Vertex Pharmaceuticals, 3215 Merryfield Row, San Diego, CA, 92121, USA
| | - James L Stevens
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - David C Hay
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, E16 4UU, UK
| | - Jan G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany.
| | - Patricio Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Ardeystrasse 67, 44139, Dortmund, Germany.
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44
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Furuya S, Argemi J, Uehara T, Katou Y, Fouts DE, Schnabl B, Dubuquoy L, Belorkar A, Vadigepalli R, Kono H, Bataller R, Rusyn I. A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis. Alcohol Clin Exp Res 2019; 44:87-101. [PMID: 31710124 DOI: 10.1111/acer.14234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/18/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Alcohol-related liver disease is the main cause of liver-related mortality worldwide. The development of novel targeted therapies for patients with advanced forms (i.e., alcoholic hepatitis, AH) is hampered by the lack of suitable animal models. Here, we developed a novel mouse model of acute-on-chronic alcohol liver injury with cholestasis and fibrosis and performed an extensive molecular comparative analysis with human AH. METHODS For the mouse model of acute-on-chronic liver injury, we used 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC, 0.05% w/w) diet for 8 weeks to establish cholestatic liver fibrosis. After 1-week washout period, male mice were fed intragastrically for 4 weeks with up to 24 g/kg of ethyl alcohol in a high-fat diet. This animal model was phenotyped using histopathology, clinical chemistry, microbiome, and gene expression approaches. Data were compared to the phenotypes of human alcohol-related liver disease, including AH. RESULTS Mice with cholestatic liver fibrosis and subsequent alcohol exposure (DDC + EtOH) exhibited exacerbated liver fibrosis with a pericellular pattern, increased neutrophil infiltration, and ductular proliferation, all characteristics of human AH. DDC administration had no effect on urine alcohol concentration or liver steatosis. Importantly, DDC- and alcohol-treated mice showed a transcriptomic signature that resembled that of patients with AH. Finally, we show that mice in the DDC + EtOH group had an increased gut barrier dysfunction, mimicking an important pathophysiological mechanism of human AH. CONCLUSIONS We developed a novel mouse model of acute-on-chronic cholestatic alcoholic liver injury that has considerable translational potential and can be used to test novel therapeutic modalities for AH.
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Affiliation(s)
- Shinji Furuya
- From the , Department of Veterinary Integrative Biosciences (SF, IR), Texas A&M University, College Station, Texas
| | - Josepmaria Argemi
- Center for Liver Diseases, (JA, RB), Pittsburgh Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Takeki Uehara
- Laboratory of Veterinary Pathology, (TU, YK), Osaka Prefecture University, Osaka, Japan
| | - Yuuki Katou
- Laboratory of Veterinary Pathology, (TU, YK), Osaka Prefecture University, Osaka, Japan
| | | | - Bernd Schnabl
- Department of Medicine, (BS), University of California San Diego, La Jolla, California
| | - Laurent Dubuquoy
- Unité INSERM 995, (LD), Faculté de Médecine, Hôpital Huriez, Lille Service des Maladies de l'Appareil Digestif, Lille, France
| | - Abha Belorkar
- Department of Pathology, Anatomy and Cell Biology, (AB, RV), Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy and Cell Biology, (AB, RV), Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hiroshi Kono
- First Department of Surgery, (HK), University of Yamanashi, Yamanashi Prefecture, Japan
| | - Ramon Bataller
- Center for Liver Diseases, (JA, RB), Pittsburgh Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Ivan Rusyn
- From the , Department of Veterinary Integrative Biosciences (SF, IR), Texas A&M University, College Station, Texas
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45
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O'Sullivan SJ, Malahias E, Park J, Srivastava A, Reyes BAS, Gorky J, Vadigepalli R, Van Bockstaele EJ, Schwaber JS. Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis. Front Neurosci 2019; 13:665. [PMID: 31333398 PMCID: PMC6619439 DOI: 10.3389/fnins.2019.00665] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 03/27/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
Drug-seeking in opioid dependence is due in part to the severe negative emotion associated with the withdrawal syndrome. It is well-established that negative emotional states emerge from activity in the amygdala. More recently, gut microflora have been shown to contribute substantially to such emotions. We measured gene expression in single glia and neurons gathered from the amygdala using laser capture microdissection and simultaneously measured gut microflora in morphine-dependent and withdrawn rats to investigate drivers of negative emotion in opioid withdrawal. We found that neuroinflammatory genes, notably Tnf, were upregulated in the withdrawal condition and that astrocytes, in particular, were highly active. We also observe a decreased Firmicutes to Bacteroides ratio in opioid withdrawal indicating gut dysbiosis. We speculate that these inflammatory and gut microflora changes contribute to the negative emotion experienced in opioid withdrawal that motivates dependence.
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Affiliation(s)
- Sean J O'Sullivan
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Evangelia Malahias
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - James Park
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States.,Department of Chemical Engineering, University of Delaware, Newark, DE, United States.,Institute for Systems Biology, Seattle, WA, United States
| | - Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Beverly A S Reyes
- Department of Pharmacology & Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jon Gorky
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Elisabeth J Van Bockstaele
- Department of Pharmacology & Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
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46
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Achanta S, Verma A, Srivastava A, Nilakantan H, Hoek JB, Vadigepalli R. Single-Cell Gene Expression Analysis Identifies Chronic Alcohol-Mediated Shift in Hepatocyte Molecular States After Partial Hepatectomy. Gene Expr 2019; 19:97-119. [PMID: 30189915 PMCID: PMC6466177 DOI: 10.3727/105221618x15361728786767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/24/2022]
Abstract
The analysis of molecular states of individual cells, as defined by their mRNA expression profiles and protein composition, has gained widespread interest in studying biological phenomena ranging from embryonic development to homeostatic tissue function and genesis and evolution of cancers. Although the molecular content of individual cells in a tissue can vary widely, their molecular states tend to be constrained within a transcriptional landscape partly described by the canonical archetypes of a population of cells. In this study, we sought to characterize the effects of an acute (partial hepatectomy) and chronic (alcohol consumption) perturbation on the molecular states of individual hepatocytes during the onset and progression of liver regeneration. We analyzed the expression of 84 genes across 233 individual hepatocytes acquired using laser capture microdissection. Analysis of the single-cell data revealed that hepatocyte molecular states can be considered as distributed across a set of four states irrespective of perturbation, with the proportions of hepatocytes in these states being dependent on the perturbation. In addition to the quiescent, primed, and replicating hepatocytes, we identified a fourth molecular state lying between the primed and replicating subpopulations. Comparison of the proportions of hepatocytes from each experimental condition in these four molecular states suggested that, in addition to aberrant priming, a slower transition from primed to replication state could contribute toward ethanol-mediated suppression of liver regenerative response to partial hepatectomy.
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Affiliation(s)
- Sirisha Achanta
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aalap Verma
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
- †Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Ankita Srivastava
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Harshavardhan Nilakantan
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jan B. Hoek
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- *Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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47
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Chong W, Balycheva M, Schwaber J, Vadigepalli R. Investigating Single‐cell Transcriptome Dynamics of the Dorsal Motor Nucleus of the Vagus (DMV) in a Rat Model of Remote Ischemic‐Reperfusion Cardioprotection (RIPC). FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.742.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Weelic Chong
- Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Marina Balycheva
- Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - James Schwaber
- Pathology, Anatomy and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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48
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Barnhart BK, Hengstler JG, Hoek JB, Vadigepalli R. High‐Resolution Chronology of Murine Biological Responses to 70% Partial Hepatectomy. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.496.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin Karl Barnhart
- Department of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IFADO)DortmundGermany
| | - Jan B Hoek
- Department of Pathology, Anatomy, and Cell BiologyThomas Jefferson UniversityPhiladelphiaPA
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49
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Srivastava A, Parrish A, Hoek J, Vadigepalli R. Changes in Hepatic Stellate Cell MicroRNA Regulation Leads to Altered Activation States Through Modulation of TGF‐β Signaling Pathway Activity. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.496.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Jan Hoek
- Thomas Jefferson UniversityPhiladelphiaPA
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50
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Chen J, Hanna P, Ardell JL, Hoover DB, Vadigepalli R, Schwaber J, Shivkumar K, Cheng ZJ. Intrinsic Cardiac Ganglionic Neurons Projecting to the SA node in the Rat and Pig Hearts: Retrograde Labeling and Neurolucida 3‐D Reconstruction. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.773.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jin Chen
- Neuroscience DivisionCollege of Medicine, University of Central FloridaOrlandoFL
| | - Peter Hanna
- Cardiac Arrhythmia Center and Neurocardiology Research Program of ExcellenceUniversity of California Los AngelesLos AngelesCA
| | - Jeffrey L Ardell
- Cardiac Arrhythmia Center and Neurocardiology Research Program of ExcellenceUniversity of California Los AngelesLos AngelesCA
| | - Donald B Hoover
- Department of Biomedical SciencesEast Tennessee State UniversityJohnson CityTN
| | | | - James Schwaber
- Department of PathologyThomas Jefferson UniversityPhiladelphiaPA
| | - Kalyanam Shivkumar
- Cardiac Arrhythmia Center and Neurocardiology Research Program of ExcellenceUniversity of California Los AngelesLos AngelesCA
| | - Zixi J Cheng
- Neuroscience DivisionCollege of Medicine, University of Central FloridaOrlandoFL
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