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Liu Y, Zhang X, Wang K, Li Q, Yan S, Shi H, Liu L, Liang S, Yang M, Su Z, Ge C, Jia J, Xu Z, Dou T. RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers. Foods 2024; 13:2008. [PMID: 38998514 PMCID: PMC11241438 DOI: 10.3390/foods13132008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine-cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.
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Affiliation(s)
- Yong Liu
- Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China; (Y.L.)
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Guangxi Bufialo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Xia Zhang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
- School of Biological and Food Engineering, Lvliang University, Lvliang 033000, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Qihua Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Shixiong Yan
- Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China; (Y.L.)
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Hongmei Shi
- Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China; (Y.L.)
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Lixian Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
- Institute of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Shuangmin Liang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, College of Computing and Informatics, the University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Junjing Jia
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
| | - Zhiqiang Xu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tengfei Dou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (K.W.); (Q.L.); (C.G.); (J.J.)
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Mazur-Michałek I, Ruciński M, Sowiński M, Pietras P, Leśniczak-Staszak M, Szaflarski W, Isalan M, Mielcarek M. Identification of the Transcriptional Biomarkers Panel Linked to Pathological Remodelling of the Eye Tissues in Various HD Mouse Models. Cells 2022; 11:1675. [PMID: 35626712 PMCID: PMC9139483 DOI: 10.3390/cells11101675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Ocular abnormalities are becoming associated with a spectrum of pathological events in various neurodegenerative diseases. Huntington's disease (HD) is just such an example of a fatal neurological disorder, where mutated genes (CAG trinucleotide expansions in the Huntingtin gene) have widespread expression, leading to the production of mutant Huntingtin (mHTT) protein. It is well known that mutant HTT protein is prone to form toxic aggregates, which are a typical pathological feature, along with global transcriptome alterations. In this study, we employed well-established quantitative methods such as Affymetrix arrays and quantitative PCR (qPCR) to identify a set of transcriptional biomarkers that will track HD progression in three well-established mouse models: R6/2, R6/1, and HdhQ150. Our array analysis revealed significantly deregulated networks that are related to visual processes and muscle contractions. Furthermore, our targeted quantitative analysis identified a panel of biomarkers with some being dysregulated even at the presymptomatic stage of the disease, e.g., Opn1mw, Opn1sw, and Pfkfb2. Some of the deregulated genes identified in this study have been linked to other genetic ocular disorders such as: GNAT2, a source of achromatopsia, and REEP6, linked to Retinitis pigmentosa. It may thus be a useful platform for preclinical evaluations of therapeutic interventions.
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Affiliation(s)
- Iwona Mazur-Michałek
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Marcin Ruciński
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Mateusz Sowiński
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Paulina Pietras
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Marta Leśniczak-Staszak
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (I.M.-M.); (M.R.); (M.S.); (P.P.); (M.L.-S.); (W.S.)
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK;
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK;
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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Lewandowski D, Sander CL, Tworak A, Gao F, Xu Q, Skowronska-Krawczyk D. Dynamic lipid turnover in photoreceptors and retinal pigment epithelium throughout life. Prog Retin Eye Res 2021; 89:101037. [PMID: 34971765 PMCID: PMC10361839 DOI: 10.1016/j.preteyeres.2021.101037] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022]
Abstract
The retinal pigment epithelium-photoreceptor interphase is renewed each day in a stunning display of cellular interdependence. While photoreceptors use photosensitive pigments to convert light into electrical signals, the RPE supports photoreceptors in their function by phagocytizing shed photoreceptor tips, regulating the blood retina barrier, and modulating inflammatory responses, as well as regenerating the 11-cis-retinal chromophore via the classical visual cycle. These processes involve multiple protein complexes, tightly regulated ligand-receptors interactions, and a plethora of lipids and protein-lipids interactions. The role of lipids in maintaining a healthy interplay between the RPE and photoreceptors has not been fully delineated. In recent years, novel technologies have resulted in major advancements in understanding several facets of this interplay, including the involvement of lipids in phagocytosis and phagolysosome function, nutrient recycling, and the metabolic dependence between the two cell types. In this review, we aim to integrate the complex role of lipids in photoreceptor and RPE function, emphasizing the dynamic exchange between the cells as well as discuss how these processes are affected in aging and retinal diseases.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Christopher L Sander
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Fangyuan Gao
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Qianlan Xu
- Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA.
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Lipids in Pathophysiology and Development of the Membrane Lipid Therapy: New Bioactive Lipids. MEMBRANES 2021; 11:membranes11120919. [PMID: 34940418 PMCID: PMC8708953 DOI: 10.3390/membranes11120919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022]
Abstract
Membranes are mainly composed of a lipid bilayer and proteins, constituting a checkpoint for the entry and passage of signals and other molecules. Their composition can be modulated by diet, pathophysiological processes, and nutritional/pharmaceutical interventions. In addition to their use as an energy source, lipids have important structural and functional roles, e.g., fatty acyl moieties in phospholipids have distinct impacts on human health depending on their saturation, carbon length, and isometry. These and other membrane lipids have quite specific effects on the lipid bilayer structure, which regulates the interaction with signaling proteins. Alterations to lipids have been associated with important diseases, and, consequently, normalization of these alterations or regulatory interventions that control membrane lipid composition have therapeutic potential. This approach, termed membrane lipid therapy or membrane lipid replacement, has emerged as a novel technology platform for nutraceutical interventions and drug discovery. Several clinical trials and therapeutic products have validated this technology based on the understanding of membrane structure and function. The present review analyzes the molecular basis of this innovative approach, describing how membrane lipid composition and structure affects protein-lipid interactions, cell signaling, disease, and therapy (e.g., fatigue and cardiovascular, neurodegenerative, tumor, infectious diseases).
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Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures. Cell Rep 2021; 30:1644-1659.e4. [PMID: 32023475 PMCID: PMC7901645 DOI: 10.1016/j.celrep.2020.01.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 12/31/2019] [Indexed: 12/18/2022] Open
Abstract
To study the development of the human retina, we use single-cell RNA sequencing (RNA-seq) at key fetal stages and follow the development of the major cell types as well as populations of transitional cells. We also analyze stem cell (hPSC)-derived retinal organoids; although organoids have a very similar cellular composition at equivalent ages as the fetal retina, there are some differences in gene expression of particular cell types. Moreover, the inner retinal lamination is disrupted at more advanced stages of organoids compared with fetal retina. To determine whether the disorganization in the inner retina is due to the culture conditions, we analyze retinal development in fetal retina maintained under similar conditions. These retinospheres develop for at least 6 months, displaying better inner retinal lamination than retinal organoids. Our single-cell RNA sequencing (scRNA-seq) comparisons of fetal retina, retinal organoids, and retinospheres provide a resource for developing better in vitro models for retinal disease.
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Fan YY, Liu CH, Wu AL, Chen HC, Hsueh YJ, Chen KJ, Lai CC, Huang CY, Wu WC. MicroRNA-126 inhibits pathological retinal neovascularization via suppressing vascular endothelial growth factor expression in a rat model of retinopathy of prematurity. Eur J Pharmacol 2021; 900:174035. [PMID: 33727052 DOI: 10.1016/j.ejphar.2021.174035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 01/11/2023]
Abstract
Vascular endothelial growth factor (VEGF) is the principal growth factor responsible for the retinal neovascularization in the pathogenesis of retinopathy of prematurity (ROP). Current therapies for ROP include laser ablation and intravitreal anti-VEGF injection. However, these treatments either destroy the peripheral retina or associate with problems of persistent peripheral avascular retina or later recurrence of ROP. In the present study we investigated a new therapeutic approach by exploring the potential role of a specific microRNA, miR-126, in regulating VEGFA expression and retinal neovascularization in a rat oxygen-induced retinopathy (OIR) model. We demonstrated that miR-126 mimic and plasmid effectively suppresses VEGFA mRNA expression in both human and rat retinal pigment epithelium cell lines, quantified with qRT-PCR. Animal experiments on rat OIR model revealed that intravitreal injection of miR-126 plasmid efficiently downregulated VEGFA expression in the intraocular fluid and retinal tissues measured by ELISA, and significantly suppressed retinal neovascularization, which was confirmed by calculating sizes of neovascularization areas on fluorescence microscopic images of flat mounted retina stained with Alexa Fluor 594-conjugated isolectin B4 to visualize blood vessels. Together, these results showed that intravitreal injection of miR-126 plasmid could inhibit retinal neovascularization by down-regulating VEGFA expression, suggesting a potential therapeutic effect for ROP.
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Affiliation(s)
- Yuan-Yao Fan
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Hsien Liu
- Graduate Institute of Biochemical and Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - An-Lun Wu
- Department of Ophthalmology, Mackay Memorial Hospital, Hsinchu, Taiwan
| | - Hung-Chi Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Center for Tissue Engineering, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Jen Hsueh
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Center for Tissue Engineering, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Chun Lai
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Ying Huang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Crofton EJ, Nenov MN, Zhang Y, Tapia CM, Donnelly J, Koshy S, Laezza F, Green TA. Topographic transcriptomics of the nucleus accumbens shell: Identification and validation of fatty acid binding protein 5 as target for cocaine addiction. Neuropharmacology 2021; 183:108398. [PMID: 33181146 PMCID: PMC7755097 DOI: 10.1016/j.neuropharm.2020.108398] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/09/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022]
Abstract
Substance use disorders for cocaine are major public health concerns with few effective treatment options. Therefore, identification of novel pharmacotherapeutic targets is critical for future therapeutic development. Evolution has ensured that genes are expressed largely only where they are needed. Therefore, examining the gene expression landscape of the nucleus accumbens shell (NAcSh), a brain region important for reward related behaviors, may lead to the identification of novel targets for cocaine use disorder. In this study, we conducted a novel two-step topographic transcriptomic analysis using five seed transcripts with enhanced expression in the NAcSh to identify transcripts with similarly enhanced expression utilizing the correlation feature to search the more than 20,000 in situ hybridization experiments of the Allen Mouse Brain Atlas. Transcripts that correlated with at least three seed transcripts were analyzed with Ingenuity Pathway Analysis (IPA). We identified 7-fold more NAcSh-enhanced transcripts than our previous analysis using single voxels in the NAcSh as the seed. Analysis of the resulting transcripts with IPA identified many previously identified signaling pathways such as retinoic acid signaling as well as novel pathways. Manipulation of the retinoic acid pathway specifically in the NAcSh of male rats via viral vector-mediated RNA interference targeting fatty acid binding protein 5 (FABP5) decreased cocaine self-administration and modulates excitability of medium spiny neurons in the NAcSh. These results not only validate the prospective strategy of conducting a topographic transcriptomic analysis, but also further validate retinoic acid signaling as a promising pathway for pharmacotherapeutic development against cocaine use disorder.
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Affiliation(s)
- Elizabeth J Crofton
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA; Neuroscience Graduate Program University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Miroslav N Nenov
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yafang Zhang
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA; Pharmacology and Toxicology Graduate Program University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Cynthia M Tapia
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA; Pharmacology and Toxicology Graduate Program University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Joseph Donnelly
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Shyny Koshy
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Fernanda Laezza
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Thomas A Green
- Dept. of Pharmacology and Toxicology, Center for Addiction Research, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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Epigenetic activation of a RAS/MYC axis in H3.3K27M-driven cancer. Nat Commun 2020; 11:6216. [PMID: 33277484 PMCID: PMC7718276 DOI: 10.1038/s41467-020-19972-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022] Open
Abstract
Histone H3 lysine 27 (H3K27M) mutations represent the canonical oncohistone, occurring frequently in midline gliomas but also identified in haematopoietic malignancies and carcinomas. H3K27M functions, at least in part, through widespread changes in H3K27 trimethylation but its role in tumour initiation remains obscure. To address this, we created a transgenic mouse expressing H3.3K27M in diverse progenitor cell populations. H3.3K27M expression drives tumorigenesis in multiple tissues, which is further enhanced by Trp53 deletion. We find that H3.3K27M epigenetically activates a transcriptome, enriched for PRC2 and SOX10 targets, that overrides developmental and tissue specificity and is conserved between H3.3K27M-mutant mouse and human tumours. A key feature of the H3K27M transcriptome is activation of a RAS/MYC axis, which we find can be targeted therapeutically in isogenic and primary DIPG cell lines with H3.3K27M mutations, providing an explanation for the common co-occurrence of alterations in these pathways in human H3.3K27M-driven cancer. Taken together, these results show how H3.3K27M-driven transcriptome remodelling promotes tumorigenesis and will be critical for targeting cancers with these mutations. Histone H3 at lysine 27 (H3K27M) is often mutated in cancer but its role in tumour initiation is unclear. Here, the authors generated a transgenic model expressing H3.3K27M from the Fabp7 gene promoter, demonstrating that H3.3K27M can initiate diverse tumorigesis on its own, acting through a RAS/MYC transcriptomic programme.
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Small-Molecule Modulation of PPARs for the Treatment of Prevalent Vascular Retinal Diseases. Int J Mol Sci 2020; 21:ijms21239251. [PMID: 33291567 PMCID: PMC7730325 DOI: 10.3390/ijms21239251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 02/08/2023] Open
Abstract
Vascular-related retinal diseases dramatically impact quality of life and create a substantial burden on the healthcare system. Age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity are leading causes of irreversible blindness. In recent years, the scientific community has made great progress in understanding the pathology of these diseases and recent discoveries have identified promising new treatment strategies. Specifically, compelling biochemical and clinical evidence is arising that small-molecule modulation of peroxisome proliferator-activated receptors (PPARs) represents a promising approach to simultaneously address many of the pathological drivers of these vascular-related retinal diseases. This has excited academic and pharmaceutical researchers towards developing new and potent PPAR ligands. This review highlights recent developments in PPAR ligand discovery and discusses the downstream effects of targeting PPARs as a therapeutic approach to treating retinal vascular diseases.
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Buenaventura DF, Corseri A, Emerson MM. Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. Invest Ophthalmol Vis Sci 2019; 60:2787-2799. [PMID: 31260032 PMCID: PMC6607928 DOI: 10.1167/iovs.19-26951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose The early transcriptional events that occur in newly generated cone photoreceptors are not well described. Knowledge of these events is critical to provide benchmarks for in vitro-derived cone photoreceptors and to understand the process of cone and rod photoreceptor diversification. We sought to identify genes with differential gene expression in embryonic mouse cone photoreceptors. Methods The specificity of expression of the LHX4 transcription factor in developing cone photoreceptors was examined using immunofluorescence visualization in both mouse and chicken retinas. A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early-stage cone photoreceptors for profiling by single-cell RNA sequencing. Comparisons were made to previous datasets targeting photoreceptors. Results The LHX4 transcription factor and a transgenic reporter were determined to be highly specific to early developing cone photoreceptors in the mouse. Single-cell transcriptional profiling identified new genes with enriched expression in cone photoreceptors relative to concurrent cell populations. Comparison to previous profiling datasets allowed for further characterization of these genes across developmental time, species, photoreceptor type, and gene regulatory network. Conclusions The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones. Many of these cone-enriched genes do not show obvious de-repression in profiling of retinas mutant for the rod-specific transcription factor NRL, highlighting differences between endogenous cones and those induced in NRL mutants.
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Affiliation(s)
- Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States
| | - Adrianne Corseri
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States.,Biochemistry PhD Program, Graduate Center, City University of New York, New York, New York, United States
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Cai L, Li J, Yu L, Wei Y, Miao Z, Chen M, Huang R. Characterization of transcriptional responses mediated by benzo[a]pyrene stress in a new marine fish model of goby, Mugilogobius chulae. Genes Genomics 2018; 41:113-123. [PMID: 30242742 DOI: 10.1007/s13258-018-0743-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Benzo[a]pyrene (BaP) is one of the most studied targets among polycyclic aromatic hydrocarbons (PAHs). Because of the complexity of the toxicity mechanism in BaP, little is known about the molecular mechanism at the level of transcription of BaP in marine fishes. The primary objective of this study was to investigate the molecular basis of the effects of BaP on marine fish, using Mugilogobius chulae (Smith 1932) as the model. A closed colony of M. chulae was used for the BaP toxicity test. Two fish liver samples per replicate from each group were excised and blended into one sample by pooling an equal amount of liver tissue. Total RNA of all samples was extracted separately. Equal quantities of total RNA from the three replicates of the two groups were pooled for sequencing. The sequencing cDNA libraries were sequenced using Illumina HiSeq 2000 system. Differentially expressed genes were detected with the DEGSeq R package. In total, 52,364,032 and 53,771,748 clean nucleotide reads were obtained in the control and BaP-exposed libraries, respectively, with N50 lengths of 1277 and 1288 bp, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a significant enrichment of genes related to detoxification, transportation, and lipid metabolism. We also identified, for the first time, an association between endoplasmic reticulum dysfunction and lipid metabolism resulting from BaP exposure. Using quantitative real-time PCR, some effective molecular biomarkers for monitoring of BaP-polluted seawater were identified. The results demonstrate that BaP enhanced the expression of genes involved in detoxification in M. chulae and inhibited that of genes related to lipid metabolism, possibly by suppressing the expression of numerous ER-related genes involved in fat digestion and absorption.
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Affiliation(s)
- Lei Cai
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Jianjun Li
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Lujun Yu
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Yuanzheng Wei
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Zongyu Miao
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Meili Chen
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Ren Huang
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China.
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Chaurasia SS, Lim RR, Parikh BH, Wey YS, Tun BB, Wong TY, Luu CD, Agrawal R, Ghosh A, Mortellaro A, Rackoczy E, Mohan RR, Barathi VA. The NLRP3 Inflammasome May Contribute to Pathologic Neovascularization in the Advanced Stages of Diabetic Retinopathy. Sci Rep 2018; 8:2847. [PMID: 29434227 PMCID: PMC5809448 DOI: 10.1038/s41598-018-21198-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/29/2018] [Indexed: 12/11/2022] Open
Abstract
Diabetic retinopathy (DR) is a retinal microvascular disease characterized by inflammatory and angiogenic pathways. In this study, we evaluated NLRP3 inflammasome in a double transgenic mouse model, Akimba (Ins2 Akita xVEGF+/-), which demonstrates hyperglycemia, vascular hyperpermeability and neovascularization seen in the proliferative DR. Retinal structural integrity, vascular leakage and function were examined by fundus photography, fluorescein angiography, optical coherence tomography, retinal flat mounts, laser speckle flowgraphy (LSFG), and electroretinography in Akimba and its parental strains, Akita (Ins2 Akita ) and Kimba (trVEGF029) mice. Inflammatory mechanisms involving NLRP3 inflammasome were investigated using real time-PCR, immunohistochemistry, ELISA and western blots. We observed an increased vascular leakage, reduced retinal thickness, and function in Akimba retina. Also, Akimba retina depicts decreased relative flow volume measured by LSFG. Most importantly, high levels of IL-1β along with increased NLRP3, ASC, and Caspase-1 at mRNA and protein levels were observed in Akimba retina. However, the in vivo functional role remains undefined. In conclusion, increased activation of macroglia (GFAP), microglia (Iba-1 and OX-42) and perivascular macrophages (F4/80 and CD14) together with pro-inflammatory (IL-1β and IL-6) and pro-angiogenic markers (PECAM-1, ICAM-1, VEGF, Flt-1, and Flk-1), suggested a critical role for NLRP3 inflammasome in the Akimba mouse model depicting advanced stages of DR pathogenesis.
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Affiliation(s)
- Shyam S Chaurasia
- Ocular Immunology and Angiogenesis Lab, Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA.
- Department of Biomedical Sciences, University of Missouri, Columbia, MO, USA.
- Ophthalmology, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA.
| | - Rayne R Lim
- Ocular Immunology and Angiogenesis Lab, Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
- Department of Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Ophthalmology, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Bhav H Parikh
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Yeo Sia Wey
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Bo Bo Tun
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
| | - Tien Yin Wong
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
- The Ophthalmology & Visual Sciences Academic Clinical Program, DUKE-NUS Graduate Medical School, Singapore, Singapore
| | - Chi D Luu
- Centre for Eye Research Australia, Department of Surgery (Ophthalmology), University of Melbourne, Melbourne, Australia
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | | | - Alessandra Mortellaro
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Elizabeth Rackoczy
- Centre for Ophthalmology and Visual Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Rajiv R Mohan
- Ocular Immunology and Angiogenesis Lab, Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
- Department of Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Ophthalmology, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
- Mason Eye Institute, University of Missouri, Columbia, MO, USA
| | - Veluchamy A Barathi
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute, Singapore, Singapore
- The Ophthalmology & Visual Sciences Academic Clinical Program, DUKE-NUS Graduate Medical School, Singapore, Singapore
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