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Li W, Qiu L, Guan J, Sun Y, Zhao J, Du M. Comparative transcriptome analysis of longissimus dorsi tissues with different intramuscular fat contents from Guangling donkeys. BMC Genomics 2022; 23:644. [PMID: 36085018 PMCID: PMC9463830 DOI: 10.1186/s12864-022-08857-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Donkey meat has low fat and high protein contents and is rich in various unsaturated fatty acids and trace elements that are beneficial to human digestion and absorption. IMF (intramuscular fat), also known as marbling, is an important indicator of the lean meat to fat ratio, which directly affects the tenderness and juiciness of the meat. At present, the underlying molecular variations affecting IMF content among donkey breeds are unclear. The Guangling donkey is an indigenous species in China. This study explored candidate regulatory genes that affect IMF content in Guangling donkeys. The IMF content of the longissimus dorsi muscle in 30 Guangling donkeys was measured. Six donkeys of similar age were selected according to age factors and divided into two groups, the high (H) and low (L) fat groups, according to their IMF content.
Results
RNA-seq technology was used to compare the muscle transcriptome between the two groups. More than 75.0% of alternative splicing (AS) events were of the skipped exon (SE) type. A total of 887 novel genes were identified; only 386 novel genes were aligned to the annotation information of various databases. Transcriptomics analysis revealed 167 differentially expressed genes (DEGs), of which 64 were upregulated and 103 were downregulated between the H and L groups. Gene ontology analysis showed that the DEGs were enriched in multiple biological processes and pathways that are related to adipocyte differentiation, lipid synthesis, and neutral lipid metabolism. KEGG pathway analysis suggested that arachidonic acid metabolism, the HIF-1 signalling pathway, fructose and mannose metabolism, glycerophospholipid metabolism, and the AMPK signalling pathway were involved in lipid deposition. In addition, a gene–gene interaction network was constructed that revealed that the DEGs, including SCD, LEPR, CIDEA, DLK1, DGAT2, ITGAL, HMOX1, WNT10B, and DGKA, had significant roles in adipocyte differentiation and adipogenesis. The selected DEGs were further validated by qRT–PCR.
Conclusion
This study improves the in-depth understanding of gene regulation and protein expression regarding IMF deposition and lays a basis for subsequent molecular breeding studies in Guangling donkeys.
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Sharma P, Yadav SK, Shah SD, Javed E, Lim JM, Pan S, Nayak AP, Panettieri RA, Penn RB, Kambayashi T, Deshpande DA. Diacylglycerol Kinase Inhibition Reduces Airway Contraction by Negative Feedback Regulation of Gq-signaling. Am J Respir Cell Mol Biol 2021; 65:658-671. [PMID: 34293268 DOI: 10.1165/rcmb.2021-0106oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Exaggerated airway smooth muscle (ASM) contraction regulated by the Gq family of G protein-coupled receptors (GPCRs) causes airway hyperresponsiveness (AHR) in asthma. Activation of Gq-coupled GPCRs leads to phospholipase C (PLC)-mediated generation of inositol triphosphate (IP3) and diacylglycerol (DAG). DAG signaling is terminated by the action of DAG kinase (DGK) that converts DAG into phosphatidic acid (PA). Our previous study demonstrated that DGKα and ζ isoform knockout mice are protected from the development of allergen-induced AHR. Here we aimed at determining the mechanism by which DGK regulates ASM contraction. Activity of DGK isoforms was inhibited in human ASM cells by siRNA-mediated knockdown of DGKα and ζwhile pharmacological inhibition was achieved by pan DGK inhibitor I (R59022). Effects of DGK inhibition on contractile agonist-induced activation of PLC and myosin light chain (MLC) kinase, elevation of IP3, and calcium levels were assessed. Further, we employed human precision-cut lung slices and assessed the role of DGK in agonist-induced bronchoconstriction. DGK inhibitor I attenuated histamine- and methacholine-induced bronchoconstriction. DGKα and ζ knockdown or pre-treatment with DGK inhibitor I resulted in attenuated agonist-induced phosphorylation of MLC and myosin light chain phosphatase in ASM cells. Further, DGK inhibition decreased Gq agonist-induced calcium elevation, generation of IP3, and increased histamine-induced production of PA. Finally, DGK inhibition or treatment with DAG analog resulted in attenuation of activation of PLC in human ASM cells. Our findings suggest that DGK inhibition perturbed the DAG:PA ratio resulting in inhibition of Gq-PLC activation in a negative feedback manner, resulting in protection against ASM contraction.
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Affiliation(s)
- Pawan Sharma
- Thomas Jefferson University - Center City Campus, 6559, Medicine, Philadelphia, Pennsylvania, United States.,University of Tasmania Faculty of Health, 60119, Hobart, Tasmania, Australia
| | - Santosh K Yadav
- Thomas Jefferson University, 6559, Medicine, Philadelphia, Pennsylvania, United States
| | - Sushrut D Shah
- Thomas Jefferson University, 6559, Medicine, Philadelphia, Pennsylvania, United States
| | - Elham Javed
- Thomas Jefferson University, 6559, Medicine, Philadelphia, Pennsylvania, United States
| | - John M Lim
- Thomas Jefferson University Sidney Kimmel Medical College, 12313, Philadelphia, Pennsylvania, United States
| | - Shi Pan
- Thomas Jefferson University, 6559, Philadelphia, Pennsylvania, United States
| | - Ajay P Nayak
- Thomas Jefferson University, 6559, Medicine, Philadelphia, Pennsylvania, United States
| | - Reynold A Panettieri
- Rutgers University, 242612, Rutgers Institute for Translational Medicine and Science, Child Health Institute, New Brunswick, New Jersey, United States
| | - Raymond B Penn
- Thomas Jefferson University, 6559, Medicine, Philadelphia, Pennsylvania, United States
| | - Taku Kambayashi
- University of Pennsylvania, 6572, Pathology, Philadelphia, Pennsylvania, United States
| | - Deepak A Deshpande
- Thomas Jefferson University, 6559, Center for Translational Medicine, Philadelphia, Pennsylvania, United States;
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3
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Kambayashi T, Deshpande DA. The role of diacylglycerol kinases in allergic airway disease. Curr Opin Pharmacol 2020; 51:50-58. [PMID: 32836013 DOI: 10.1016/j.coph.2020.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022]
Abstract
Asthma is an obstructive inflammatory airway disease. Airway obstruction is mediated by hyperresponsive airway smooth muscle cell contraction, which is induced and compounded by inflammation caused by T lymphocytes. One important signal transduction pathway that is involved in the activation of these cell types involves the generation of a lipid second messenger known as diacylglycerol (DAG). DAG levels are controlled in cells by a negative regulator known as DAG kinase (DGK). In this review, we discuss how the DAG signaling pathway attenuates the pathological function of immune cells and airway smooth muscle cells in allergic airway disease and asthma. Furthermore, we discuss how the enhancement of the DAG signaling pathway through the inhibition of DGK may represent a novel therapeutic strategy for these diseases.
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Affiliation(s)
- Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Deepak A Deshpande
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, USA.
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4
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Whole-Genome Uterine Artery Transcriptome Profiling and Alternative Splicing Analysis in Rat Pregnancy. Int J Mol Sci 2020; 21:ijms21062079. [PMID: 32197362 PMCID: PMC7139363 DOI: 10.3390/ijms21062079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 01/27/2023] Open
Abstract
During pregnancy, the uterine artery (UA) undergoes extensive remodeling to permit a 20–40 fold increase in blood flow with associated changes in the expression of a multitude of genes. This study used next-gen RNA sequencing technology to identify pathways and genes potentially involved in arterial adaptations in pregnant rat UA (gestation day 20) compared with non-pregnant rat UA (diestrus). A total of 2245 genes were differentially expressed, with 1257 up-regulated and 970 down-regulated in pregnant UA. Gene clustering analysis revealed a unique cluster of suppressed genes implicated in calcium signaling pathway and vascular smooth muscle contraction in pregnant UA. Transcription factor binding site motif scanning identified C2H2 ZF, AP-2 and CxxC as likely factors functional on the promoters of down-regulated genes involved in calcium signaling and vascular smooth muscle contraction. In addition, 1686 genes exhibited alternative splicing that were mainly implicated in microtubule organization and smooth muscle contraction. Cross-comparison analysis identified novel genes that were both differentially expressed and alternatively spliced; these were involved in leukocyte and B cell biology and lipid metabolism. In conclusion, this first comprehensive study provides a valuable resource for understanding the molecular mechanism underlying gestational uterine arterial adaptations during pregnancy.
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Singh BK, Lu W, Schmidt Paustian AM, Ge MQ, Koziol-White CJ, Flayer CH, Killingbeck SS, Wang N, Dong X, Riese MJ, Deshpande DA, Panettieri RA, Haczku A, Kambayashi T. Diacylglycerol kinase ζ promotes allergic airway inflammation and airway hyperresponsiveness through distinct mechanisms. Sci Signal 2019; 12:12/597/eaax3332. [PMID: 31481522 DOI: 10.1126/scisignal.aax3332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Asthma is a chronic allergic inflammatory airway disease caused by aberrant immune responses to inhaled allergens, which leads to airway hyperresponsiveness (AHR) to contractile stimuli and airway obstruction. Blocking T helper 2 (TH2) differentiation represents a viable therapeutic strategy for allergic asthma, and strong TCR-mediated ERK activation blocks TH2 differentiation. Here, we report that targeting diacylglycerol (DAG) kinase zeta (DGKζ), a negative regulator of DAG-mediated cell signaling, protected against allergic asthma by simultaneously reducing airway inflammation and AHR though independent mechanisms. Targeted deletion of DGKζ in T cells decreased type 2 inflammation without reducing AHR. In contrast, loss of DGKζ in airway smooth muscle cells decreased AHR but not airway inflammation. T cell-specific enhancement of ERK signaling was only sufficient to limit type 2 airway inflammation, not AHR. Pharmacological inhibition of DGK diminished both airway inflammation and AHR in mice and also reduced bronchoconstriction of human airway samples in vitro. These data suggest that DGK is a previously unrecognized therapeutic target for asthma and reveal that the inflammatory and AHR components of asthma are not as interdependent as generally believed.
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Affiliation(s)
- Brenal K Singh
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wen Lu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amanda M Schmidt Paustian
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moyar Q Ge
- Pulmonary, Critical Care and Sleep Division, University of California, Davis, Davis, CA 95616, USA
| | - Cynthia J Koziol-White
- Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cameron H Flayer
- Pulmonary, Critical Care and Sleep Division, University of California, Davis, Davis, CA 95616, USA
| | - Sara S Killingbeck
- Pulmonary, Critical Care and Sleep Division, University of California, Davis, Davis, CA 95616, USA
| | - Nadan Wang
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Center for Sensory Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Matthew J Riese
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - Deepak A Deshpande
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Angela Haczku
- Pulmonary, Critical Care and Sleep Division, University of California, Davis, Davis, CA 95616, USA
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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Ariff A, Melton PE, Brennecke SP, Moses EK. Analysis of the Epigenome in Multiplex Pre-eclampsia Families Identifies SORD, DGKI, and ICA1 as Novel Candidate Risk Genes. Front Genet 2019; 10:227. [PMID: 30941163 PMCID: PMC6434177 DOI: 10.3389/fgene.2019.00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/28/2019] [Indexed: 01/04/2023] Open
Abstract
Pre-eclampsia is a serious heritable disorder that affects 5-8% of pregnancies worldwide. While classical genetic studies have identified several susceptibility genes they do not fully explain the heritability of pre-eclampsia. An additional contribution to risk can be quantified by examining the epigenome, in particular the methylome, which is a representation of interactions between environmental and genetic influences on the phenotype. Current array-based epigenetic studies only examine 2-5% of the methylome. Here, we used whole-genome bisulfite sequencing (WGBS) to determine the entire methylome of 13 individuals from two multiplex pre-eclampsia families, comprising one woman with eclampsia, six women with pre-eclampsia, four women with uncomplicated normotensive pregnancies and two male relatives. The analysis of WGBS profiles using two bioinformatics platforms, BSmooth and Bismark, revealed 18,909 differentially methylated CpGs and 4157 differentially methylated regions (DMRs) concordant in females. The methylation patterns support the involvement of previously reported candidate genes, including COL4A1, SLC2A4, PER3, FLT1, GPI, LCT, DDAH1, TGFB3, DLX5, and LRP1B. Statistical analysis of DMRs revealed three novel genes significantly correlated with pre-eclampsia: sorbitol dehydrogenase (SORD, p = 9.98 × 10-6), diacylglycerol kinase iota (DGKI, p = 2.52 × 10-5), and islet cell autoantigen 1 (ICA1, 7.54 × 10-3), demonstrating the potential of WGBS in families for elucidating the role of epigenome in pre-eclampsia and other complex diseases.
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Affiliation(s)
- Amir Ariff
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, Curtin University, The University of Western Australia, Perth, WA, Australia.,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Phillip E Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, Curtin University, The University of Western Australia, Perth, WA, Australia.,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Shaun P Brennecke
- Department of Maternal-Fetal Medicine Pregnancy Research Centre, The Royal Women's Hospital, Melbourne, VIC, Australia.,Department of Obstetrics and Gynaecology, The University of Melbourne, Melbourne, VIC, Australia
| | - Eric K Moses
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, Curtin University, The University of Western Australia, Perth, WA, Australia.,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, WA, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia
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Shimomura T, Nakano T, Goto K, Wakabayashi I. R59949, a diacylglycerol kinase inhibitor, inhibits inducible nitric oxide production through decreasing transplasmalemmal L-arginine uptake in vascular smooth muscle cells. Naunyn Schmiedebergs Arch Pharmacol 2016; 390:207-214. [PMID: 27909743 DOI: 10.1007/s00210-016-1316-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/14/2016] [Indexed: 01/26/2023]
Abstract
Although diacylglycerol kinase (DGK) is known to be expressed in vascular smooth muscle cell, its functional significance remains to be clarified. We hypothesized that DGK is involved in the pathway of cytokine-induced nitric oxide (NO) production in vascular smooth muscle cells. The purpose of this study was to investigate the effects of R59949, a diacylglycerol kinase inhibitor, on inducible nitric oxide production in vascular smooth muscle cell. Cultured rat aortic smooth muscle cells (RASMCs) were used to elucidate the effects of R59949 on basal and interleukin-1β (IL-1β)-induced NO production. The effects of R59949 on protein and mRNA expression of induced nitric oxide synthase (iNOS) and on transplasmalemmal L-arginine uptake were also evaluated using RASMCs. Treatment of RASMCs with R59949 (10 μM) inhibited IL-1β (10 ng/ml)-induced NO production but not basal NO production. Neither protein nor mRNA expression level of iNOS after stimulation with IL-1β was significantly affected by R59949. Estimated enzymatic activities of iNOS in RASMCs were comparable in the absence and presence of R59949. Stimulation of RASMCs with IL-1β caused a marked increase in transplasmalemmal L-arginine uptake into RASMCs. L-Arginine uptake in the presence of IL-1β was markedly inhibited by R59949, while basal L-arginine uptake was not significantly affected by R59949. Both IL-1β-induced NO production and L-arginine uptake were abolished in the presence of cycloheximide (1 μM). The results indicate that R59949 inhibits inducible NO production through decreasing transplasmalemmal L-arginine uptake. DGK is suggested to be involved in cytokine-stimulated L-arginine transport and regulate its intracellular concentration in vascular smooth muscle cell.
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Affiliation(s)
- Tomoko Shimomura
- Department of Environmental and Preventive Medicine, Hyogo College of Medicine, Mukogawa-cho 1-1, Nishinomiya, Hyogo, 663-8501, Japan
| | - Tomoyuki Nakano
- Department of Anatomy and Cell Biology, Yamagata University Faculty of Medicine, Iida-nishi 2-2-2, Yamagata, 990-9585, Japan
| | - Kaoru Goto
- Department of Anatomy and Cell Biology, Yamagata University Faculty of Medicine, Iida-nishi 2-2-2, Yamagata, 990-9585, Japan
| | - Ichiro Wakabayashi
- Department of Environmental and Preventive Medicine, Hyogo College of Medicine, Mukogawa-cho 1-1, Nishinomiya, Hyogo, 663-8501, Japan.
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