1
|
Auffret P, Le Luyer J, Sham Koua M, Quillien V, Ky CL. Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing. BMC Genomics 2020; 21:662. [PMID: 32977773 PMCID: PMC7517651 DOI: 10.1186/s12864-020-07015-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation. RESULTS Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially expressed genes in whole juvenile, adult mantle and pearl sac tissue, respectively. These genes were found to be involved in five main molecular pathways, tightly linked to known pigmentation pathways: melanogenesis, calcium signalling pathway, Notch signalling pathway, pigment transport and biomineralization. Additionally, significant phenotype-associated SNPs were selected (N = 159), including two located in the Pif biomineralization gene, which codes for nacre formation. Interestingly, significantly different transcript splicing was detected between juvenile (N = 1366) and adult mantle tissue (N = 313) in, e.g., the tyrosinase Tyr-1 gene, which showed more complex regulation in mantle, and the Notch1 encoding gene, which was upregulated in albino juveniles. CONCLUSION This multiple RNA-seq approach provided new knowledge about genes associated with the P. margaritifera albino phenotype, highlighting: 1) new molecular pathways, such as the Notch signalling pathway in pigmentation, 2) associated SNP markers with biomineraliszation gene of interest like Pif for marker-assisted selection and prevention of inbreeding, and 3) alternative gene splicing for melanin biosynthesis implicating tyrosinase.
Collapse
Affiliation(s)
- Pauline Auffret
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Jérémy Le Luyer
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Manaarii Sham Koua
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Virgile Quillien
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
- Ifremer, UMR LEMAR UBO CNRS Ifremer IRD 6539, ZI Pointe Diable CS 10070, F-29280 Plouzane, France
| | - Chin-Long Ky
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090 Montpellier, France
| |
Collapse
|
2
|
Ganguly K, Saha T, Saha A, Dutta T, Banerjee S, Sengupta D, Bhattacharya S, Ghosh S, Sengupta M. Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools. Arch Dermatol Res 2019; 311:163-171. [PMID: 30756169 DOI: 10.1007/s00403-019-01891-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/26/2018] [Accepted: 02/09/2019] [Indexed: 12/30/2022]
Abstract
Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.
Collapse
Affiliation(s)
- Kausik Ganguly
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Tania Saha
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Arpan Saha
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Tithi Dutta
- Department of Genetics, University of Calcutta, Kolkata, India
| | | | | | | | - Sampurna Ghosh
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, Kolkata, India.
| |
Collapse
|
3
|
Jovancevic N, Khalfaoui S, Weinrich M, Weidinger D, Simon A, Kalbe B, Kernt M, Kampik A, Gisselmann G, Gelis L, Hatt H. Odorant Receptor 51E2 Agonist β-ionone Regulates RPE Cell Migration and Proliferation. Front Physiol 2017; 8:888. [PMID: 29249973 PMCID: PMC5714887 DOI: 10.3389/fphys.2017.00888] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/19/2017] [Indexed: 01/09/2023] Open
Abstract
The odorant receptor 51E2 (OR51E2), which is well-characterized in prostate cancer cells and epidermal pigment cells, was identified for the first time as the most highly expressed OR in human fetal and adult retinal pigment epithelial (RPE) cells. Immunofluorescence staining and Western blot analysis revealed OR51E2 localization throughout the cytosol and in the plasma membrane. Additionally, immunohistochemical staining of diverse layers of the eye showed that the expression of OR51E2 is restricted to the pigment cells of the RPE and choroid. The results of Ca2+-imaging experiments demonstrate that activation of OR51E2 triggers a Ca2+ dependent signal pathway in RPE cells. Downstream signaling of OR51E2 involves the activation of adenylyl cyclase, ERK1/2 and AKT. The activity of these protein kinases likely accounts for the demonstrated increase in the migration and proliferation of RPE cells upon stimulation with the OR51E2 ligand β-ionone. These findings suggest that OR51E2 is involved in the regulation of RPE cell growth. Thus, OR51E2 represents a potential target for the treatment of proliferative disorders.
Collapse
Affiliation(s)
| | | | | | | | - Annika Simon
- Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Benjamin Kalbe
- Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Marcus Kernt
- Ophthalmology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Anselm Kampik
- Ophthalmology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Lian Gelis
- Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Hanns Hatt
- Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| |
Collapse
|
4
|
Kim JM, Lee H, Shin JP, Ahn J, Yoo JM, Song SJ, Kim SJ, Kang SW. Epiretinal Membrane: Prevalence and Risk Factors from the Korea National Health and Nutrition Examination Survey, 2008 through 2012. KOREAN JOURNAL OF OPHTHALMOLOGY 2017; 31:514-523. [PMID: 29022294 PMCID: PMC5726986 DOI: 10.3341/kjo.2016.0098] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/13/2017] [Indexed: 11/23/2022] Open
Abstract
PURPOSE To investigate the prevalence and risk factors for an epiretinal membrane (ERM) in Korean population. METHODS Using the database of the Korea National Health and Nutrition Examination Survey from 2008 through 2012, 14,772 participants 40 years of age or older with gradable fundus photographs were included. The presence of ERM was determined by using fundus photographs. The prevalence of ERM was estimated and possible risk factors including systemic factors, nutritional status, and blood tests were analyzed via multiple logistic regression analyses. RESULTS The prevalence of ERM was 2.9% (95% confidence interval [CI], 2.6% to 3.3%). On multiple logistic regression analysis, the prevalence of ERM was affected by age. The odds ratios (ORs) against the forties were 2.70, 5.48, and 5.69 in the fifties, sixties, and seventies, respectively. ERM was also significantly affected by cataract surgery (OR, 2.82; 95% CI, 2.08 to 3.81) and by the increase in intake of 100-mg calcium (OR, 1.05; 95% CI, 1.00 to 1.11). ERM had negative associations with red blood cell count (OR, 0.66; 95% CI, 0.45 to 0.95). CONCLUSIONS The estimated nation-wide prevalence of ERM in Korea is 2.9%. The presence of ERM in the general population is associated with age, cataract surgery, increased dietary calcium, and a low red blood cell count.
Collapse
Affiliation(s)
- Jong Min Kim
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hoyoung Lee
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Pil Shin
- Department of Ophthalmology, Kyungpook National University Hospital, Daegu, Korea
| | - Jeeyun Ahn
- Department of Ophthalmology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Je Moon Yoo
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Su Jeong Song
- Department of Ophthalmology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Jin Kim
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Woong Kang
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | | |
Collapse
|
5
|
Glenn JV, Mahaffy H, Dasari S, Oliver M, Chen M, Boulton ME, Xu H, Curry WJ, Stitt AW. Proteomic profiling of human retinal pigment epithelium exposed to an advanced glycation-modified substrate. Graefes Arch Clin Exp Ophthalmol 2011; 250:349-59. [PMID: 22081232 DOI: 10.1007/s00417-011-1856-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/20/2011] [Accepted: 10/26/2011] [Indexed: 01/07/2023] Open
Abstract
PURPOSE The retinal pigment epithelium (RPE) and underlying Bruch's membrane undergo significant modulation during ageing. Progressive, age-related modifications of lipids and proteins by advanced glycation end products (AGEs) at this cell-substrate interface have been implicated in RPE dysfunction and the progression to age-related macular degeneration (AMD). The pathogenic nature of these adducts in Bruch's membrane and their influence on the overlying RPE remains unclear. This study aimed to identify alterations in RPE protein expression in cells exposed to AGE-modified basement membrane (AGE-BM), to determine how this "aged" substrate impacts RPE function and to map the localisation of identified proteins in ageing retina. METHODS Confluent ARPE-19 monolayers were cultured on AGE-BM and native, non-modified BM (BM). Following 28-day incubation, the proteome was profiled using 2-dimensional gel electrophoresis (2D), densitometry and image analysis was employed to map proteins of interest that were identified by electrospray ionisation mass spectrometry (ESI MS/MS). Immunocytochemistry was employed to localise identified proteins in ARPE-19 monolayers cultured on unmodified and AGE-BM and to analyze aged human retina. RESULTS Image analysis detected altered protein spot densities between treatment groups, and proteins of interest were identified by LC ESI MS/MS which included heat-shock proteins, cytoskeletal and metabolic regulators. Immunocytochemistry revealed deubiquitinating enzyme ubiquitin carboxyterminal hydrolase-1 (UCH-L1), which was upregulated in AGE-exposed RPE and was also localised to RPE in human retinal sections. CONCLUSIONS This study has demonstrated that AGE-modification of basement membrane alters the RPE proteome. Many proteins are changed in this ageing model, including UCHL-1, which could impact upon RPE degradative capacity. Accumulation of AGEs at Bruch"s membrane could play a significant role in age-related dysfunction of the RPE.
Collapse
Affiliation(s)
- J V Glenn
- School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Guo CM, Wang YS, Hu D, Han QH, Wang JB, Hou X, Hui YN. Modulation of migration and Ca2+ signaling in retinal pigment epithelium cells by recombinant human CTGF. Curr Eye Res 2010; 34:852-62. [PMID: 19895313 DOI: 10.3109/02713680903128935] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The migration of retinal pigment epithelium (RPE) cells is an initial step in the development of proliferative vitreoretinopathy (PVR). We investigated the expression of connective tissue growth factor (CTGF) in an in vitro model of wound healing and effects of recombinant human CTGF (rhCTGF) on modulating migration and Ca(2+) signaling in RPE cells. METHODS Cultured human RPE monolayers were used to establish a wound-healing model. Western blot and in situ hybridization were used to detect the CTGF expression in RPE cells. Migration of RPE cells was measured under the stimulation of rhCTGF alone or in combination with dexamethasone (DEX) or 8-Br-cAMP. To determine the concentration of cytoplasmic-free Ca(2+) ([Ca(2+)]i) responding to CTGF, the fluo-3/AM-loaded RPE cells were observed with a laser scanning confocal microscope. RESULTS The CTGF expression first increased after being wounded in RPE cells, then reached a peak and maintained at a high level. The positive expression was mainly at the edge of scrape and in motile RPE cells. rhCTGF-stimulated RPE cells migrated in a dose-dependent manner, and both DEX and 8-Br-cAMP could significantly inhibit the CTGF-induced migrations. CTGF induced a (Ca(2+))i elevation in RPE cells in a concentration-dependent manner. Moreover, stimulation of RPE cells with CTGF and DEX or 8-Br-cAMP counteracted the elevation of (Ca(2+))i induced by CTGF. CONCLUSIONS The CTGF expression could be induced by an in vitro model of scrape wounding. rhCTGF stimulated the migration and Ca(2+) signal pathway in RPE cells in a dose-dependent manner, and DEX and 8-Br-cAMP suppressed this effect. Our results indicate that CTGF is involved in the wound-healing process and plays an important role in the pathogenesis of intraocular proliferative diseases.
Collapse
Affiliation(s)
- Chang-Mei Guo
- Department of Ophthalmology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | | | | | | | | | | | | |
Collapse
|
7
|
Yamaguchi T, Wallace DP, Magenheimer BS, Hempson SJ, Grantham JJ, Calvet JP. Calcium restriction allows cAMP activation of the B-Raf/ERK pathway, switching cells to a cAMP-dependent growth-stimulated phenotype. J Biol Chem 2004; 279:40419-30. [PMID: 15263001 DOI: 10.1074/jbc.m405079200] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
cAMP can be either mitogenic or anti-mitogenic, depending on the cell type. We demonstrated previously that cAMP inhibited the proliferation of normal renal epithelial cells and stimulated the proliferation of cells derived from the cysts of polycystic kidney disease (PKD) patients. The protein products of the genes causing PKD, polycystin-1 and polycystin-2, are thought to regulate intracellular calcium levels, suggesting that abnormal polycystin function may affect calcium signaling and thus cause a switch to the cAMP growth-stimulated phenotype. To test this hypothesis, we disrupted intracellular calcium mobilization by treating immortalized mouse M-1 collecting duct cells and primary cultures of human kidney epithelial cells with calcium channel blockers and by lowering extracellular calcium with EGTA. Calcium restriction for 3-5 h converted both cell types from a normal cAMP growth-inhibited phenotype to an abnormal cAMP growth-stimulated phenotype, characteristic of PKD. In M-1 cells, we showed that calcium restriction was associated with an elevation in B-Raf protein levels and cAMP-stimulated, Ras-dependent activation of B-Raf and ERK. Moreover, the activity of Akt, a negative regulator of B-Raf, was decreased by calcium restriction. Inhibition of Akt or phosphatidylinositol 3-kinase also allowed cAMP-dependent activation of B-Raf and ERK in normal calcium. These results suggest that calcium restriction causes an inhibition of the phosphatidylinositol 3-kinase/Akt pathway, which relieves the inhibition of B-Raf to allow the cAMP growth-stimulated phenotypic switch. Finally, M-1 cells stably overexpressing an inducible polycystin-1 C-terminal cytosolic tail construct were shown to exhibit a cAMP growth-stimulated phenotype involving B-Raf and ERK activation, which was reversed by the calcium ionophore A23187. We conclude that disruption of calcium mobilization in cells that are normally growth-inhibited by cAMP can derepress the B-Raf/ERK pathway, thus converting these cells to a phenotype that is growth-stimulated by cAMP.
Collapse
Affiliation(s)
- Tamio Yamaguchi
- Department of Biochemistry, the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | | | | | | | | | | |
Collapse
|
8
|
Abstract
The physiological and pathological importance of lysophosphatidic acid (LPA) in the nervous system is underscored by its presence, as well as the expression of its receptors in neural tissues. In fact, LPA produces responses in a broad range of cell types related to the function of the nervous system. These cell types include neural cell lines, neural progenitors, primary neurons, oligodendrocytes, Schwann cells, astrocytes, microglia, and brain endothelial cells. LPA-induced cell type-specific effects include changes in cell morphology, promotion of cell proliferation and cell survival, induction of cell death, changes in ion conductance and Ca2+ mobilization, induction of pain transmission, and stimulation of vasoconstriction. These effects are mediated through a number of G protein-coupled LPA receptors that activate various downstream signaling cascades. This review provides a current summary of LPA-induced effects in neural cells in vitro or in vivo in combination with our current understanding of the signaling pathways responsible for these effects.
Collapse
Affiliation(s)
- Xiaoqin Ye
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0636, USA
| | | | | | | |
Collapse
|
9
|
Engelke M, Tykhonova S, Zorn-Kruppa M, Diehl H. Tamoxifen induces changes in the lipid composition of the retinal pigment epithelium cell line D407. PHARMACOLOGY & TOXICOLOGY 2002; 91:13-21. [PMID: 12193256 DOI: 10.1034/j.1600-0773.2002.910103.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Tamoxifen, the antioestrogenic drug prescribed for long-term, low-dose therapy of breast cancer, induces retinopathy. This study evaluates the effects of tamoxifen on the human retinal pigment epithelial cell line D407, attempting to identify the underlying mechanisms on tamoxifen-induced retinopathy and the involvement of cellular membranes in the cytotoxic action mechanism. We demonstrate that the tamoxifen-induced decrease in the cell growth of the D407 cell line results from pyknosis and cell cycle arrest rather than from necrosis. Furthermore, D407 cells influence the lipid composition of both plasma membrane and intracellular membranes in response to tamoxifen. Tamoxifen increases the physical order of the lipid bilayer. We observed a compensatory decrease in the cholesterol content of the plasma membrane which results in an increase of the plasma membrane fluidity. In intracellular membranes the phosphatidylcholine content is reduced to 50% of the controls. This reduction may be related to the formation of a second messenger via phospholipase pathway and sustained activation of protein kinase C. Since increased plasma membrane fluidity as well as sustained activation of protein kinase C influence the rod outer segments binding and/or ingestion by retinal pigment epithelial cells, our results suggest that membrane-mediated pathways contribute to the tamoxifen-induced retinopathy.
Collapse
Affiliation(s)
- Maria Engelke
- Department of Biophysics, Institute of Experimental Physics, University of Bremen, Bremen, Germany.
| | | | | | | |
Collapse
|
10
|
Abstract
The effects of ethanol on muscarinic receptor-mediated calcium responses were investigated in individual primary rat astrocytes and human 132 1N1 astrocytoma cells using indo-1/AM and image cytometry. After a 30-min incubation, carbachol-induced calcium responses were inhibited only at 100 or 250 mM ethanol. The effects of ethanol were more pronounced and occurred at lower concentrations with longer exposures, with significant inhibition seen at 10 mM following a 24-hr incubation. Thapsigargin- and glutamate-induced responses were unaffected by ethanol, indicating some selectivity in this inhibition. Upon removal of ethanol, inhibition of calcium responses persisted for up to 6-12 hr, with carbachol responses returning to control levels by 24 hr after washout. Ethanol exposure did not affect muscarinic-receptor binding in astrocytoma cells, but inhibited carbachol-induced IP(3) formation. Inhibition of (3)H-thymidine incorporation by ethanol also persisted upon removal of the alcohol, with a time-dependency similar to that of the calcium responses. These results indicate that ethanol inhibits muscarinic receptor-induced calcium responses in astroglia in a concentration- and duration-dependent manner. They also show that co-incubation with ethanol is not necessary for this effect, suggesting that long-term exposure to ethanol may modify, in a reversible manner, the coupling of muscarinic receptors with its effector. This effect of ethanol may play a role in ethanol's inhibition of carbachol-induced thymidine incorporation.
Collapse
Affiliation(s)
- M C Catlin
- Department of Environmental Health, University of Washington, Seattle, WA 98105, USA
| | | | | |
Collapse
|