Optic Nerve Lipidomics Reveal Impaired Glucosylsphingosine Lipids Pathway in Glaucoma
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Implications in Parkinson's Disease
Journal of Clinical Medicine Review Lysosomal Ceramide Metabolism Disorders: Implications in Parkinson’s Disease Silvia Paciotti 1,2 , Elisabetta Albi 3 , Lucilla Parnetti 1 and Tommaso Beccari 3,* 1 Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy; [email protected] (S.P.); [email protected] (L.P.) 2 Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy 3 Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti, 06123 Perugia, Italy; [email protected] * Correspondence: [email protected] Received: 29 January 2020; Accepted: 20 February 2020; Published: 21 February 2020 Abstract: Ceramides are a family of bioactive lipids belonging to the class of sphingolipids. Sphingolipidoses are a group of inherited genetic diseases characterized by the unmetabolized sphingolipids and the consequent reduction of ceramide pool in lysosomes. Sphingolipidoses include several disorders as Sandhoff disease, Fabry disease, Gaucher disease, metachromatic leukodystrophy, Krabbe disease, Niemann Pick disease, Farber disease, and GM2 gangliosidosis. In sphingolipidosis, lysosomal lipid storage occurs in both the central nervous system and visceral tissues, and central nervous system pathology is a common hallmark for all of them. Parkinson’s disease, the most common neurodegenerative movement disorder, is characterized by the accumulation and aggregation of misfolded α-synuclein that seem associated to some lysosomal disorders, in particular Gaucher disease. This review provides evidence into the role of ceramide metabolism in the pathophysiology of lysosomes, highlighting the more recent findings on its involvement in Parkinson’s disease. Keywords: ceramide metabolism; Parkinson’s disease; α-synuclein; GBA; GLA; HEX A-B; GALC; ASAH1; SMPD1; ARSA * Correspondence [email protected] 1. -
743914V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/743914; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Cross-talks of glycosylphosphatidylinositol biosynthesis with glycosphingolipid biosynthesis 2 and ER-associated degradation 3 4 Yicheng Wang1,2, Yusuke Maeda1, Yishi Liu3, Yoko Takada2, Akinori Ninomiya1, Tetsuya 5 Hirata1,2,4, Morihisa Fujita3, Yoshiko Murakami1,2, Taroh Kinoshita1,2,* 6 7 1Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan 8 2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, 9 Japan 10 3Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, 11 School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China 12 4Current address: Center for Highly Advanced Integration of Nano and Life Sciences (G- 13 CHAIN), Gifu University, 1-1 Yanagido, Gifu-City, Gifu 501-1193, Japan 14 15 *Correspondence and requests for materials should be addressed to T.K. (email: 16 [email protected]) 17 18 19 Glycosylphosphatidylinositol (GPI)-anchored proteins and glycosphingolipids interact with 20 each other in the mammalian plasma membranes, forming dynamic microdomains. How their 21 interaction starts in the cells has been unclear. Here, based on a genome-wide CRISPR-Cas9 22 genetic screen for genes required for GPI side-chain modification by galactose in the Golgi 23 apparatus, we report that b1,3-galactosyltransferase 4 (B3GALT4), also called GM1 24 ganglioside synthase, additionally functions in transferring galactose to the N- 25 acetylgalactosamine side-chain of GPI. -
Investigation of Candidate Genes and Mechanisms Underlying Obesity
Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between -
Expression Profiling of KLF4
Expression Profiling of KLF4 AJCR0000006 Supplemental Data Figure S1. Snapshot of enriched gene sets identified by GSEA in Klf4-null MEFs. Figure S2. Snapshot of enriched gene sets identified by GSEA in wild type MEFs. 98 Am J Cancer Res 2011;1(1):85-97 Table S1: Functional Annotation Clustering of Genes Up-Regulated in Klf4 -Null MEFs ILLUMINA_ID Gene Symbol Gene Name (Description) P -value Fold-Change Cell Cycle 8.00E-03 ILMN_1217331 Mcm6 MINICHROMOSOME MAINTENANCE DEFICIENT 6 40.36 ILMN_2723931 E2f6 E2F TRANSCRIPTION FACTOR 6 26.8 ILMN_2724570 Mapk12 MITOGEN-ACTIVATED PROTEIN KINASE 12 22.19 ILMN_1218470 Cdk2 CYCLIN-DEPENDENT KINASE 2 9.32 ILMN_1234909 Tipin TIMELESS INTERACTING PROTEIN 5.3 ILMN_1212692 Mapk13 SAPK/ERK/KINASE 4 4.96 ILMN_2666690 Cul7 CULLIN 7 2.23 ILMN_2681776 Mapk6 MITOGEN ACTIVATED PROTEIN KINASE 4 2.11 ILMN_2652909 Ddit3 DNA-DAMAGE INDUCIBLE TRANSCRIPT 3 2.07 ILMN_2742152 Gadd45a GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE 45 ALPHA 1.92 ILMN_1212787 Pttg1 PITUITARY TUMOR-TRANSFORMING 1 1.8 ILMN_1216721 Cdk5 CYCLIN-DEPENDENT KINASE 5 1.78 ILMN_1227009 Gas2l1 GROWTH ARREST-SPECIFIC 2 LIKE 1 1.74 ILMN_2663009 Rassf5 RAS ASSOCIATION (RALGDS/AF-6) DOMAIN FAMILY 5 1.64 ILMN_1220454 Anapc13 ANAPHASE PROMOTING COMPLEX SUBUNIT 13 1.61 ILMN_1216213 Incenp INNER CENTROMERE PROTEIN 1.56 ILMN_1256301 Rcc2 REGULATOR OF CHROMOSOME CONDENSATION 2 1.53 Extracellular Matrix 5.80E-06 ILMN_2735184 Col18a1 PROCOLLAGEN, TYPE XVIII, ALPHA 1 51.5 ILMN_1223997 Crtap CARTILAGE ASSOCIATED PROTEIN 32.74 ILMN_2753809 Mmp3 MATRIX METALLOPEPTIDASE -
Transcriptome Alteration in the Diabetic Heart by Rosiglitazone: Implications for Cardiovascular Mortality
Transcriptome Alteration in the Diabetic Heart by Rosiglitazone: Implications for Cardiovascular Mortality Kitchener D. Wilson1,3., Zongjin Li1., Roger Wagner2, Patrick Yue2, Phillip Tsao2, Gergana Nestorova4, Mei Huang1, David L. Hirschberg4, Paul G. Yock2,3, Thomas Quertermous2, Joseph C. Wu1,2* 1 Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America, 2 Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, United States of America, 3 Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America, 4 Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, California, United States of America Abstract Background: Recently, the type 2 diabetes medication, rosiglitazone, has come under scrutiny for possibly increasing the risk of cardiac disease and death. To investigate the effects of rosiglitazone on the diabetic heart, we performed cardiac transcriptional profiling and imaging studies of a murine model of type 2 diabetes, the C57BL/KLS-leprdb/leprdb (db/db) mouse. Methods and Findings: We compared cardiac gene expression profiles from three groups: untreated db/db mice, db/db mice after rosiglitazone treatment, and non-diabetic db/+ mice. Prior to sacrifice, we also performed cardiac magnetic resonance (CMR) and echocardiography. As expected, overall the db/db gene expression signature was markedly different from control, but to our surprise was -
Cholesterol-Dependent Increases in Glucosylceramide
Neuropharmacology 110 (2016) 458e469 Contents lists available at ScienceDirect Neuropharmacology journal homepage: www.elsevier.com/locate/neuropharm Cholesterol-dependent increases in glucosylceramide synthase activity in Niemann-Pick disease type C model cells: Abnormal trafficking of endogenously formed ceramide metabolites by inhibition of the enzyme Naohiro Hashimoto 1, Ikiru Matsumoto 1, Hiromasa Takahashi, Hitomi Ashikawa, * Hiroyuki Nakamura , Toshihiko Murayama Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan article info abstract Article history: Sphingolipids such as sphingomyelin and glycosphingolipids (GSLs) derived from glucosylceramide Received 1 February 2016 (GlcCer), in addition to cholesterol, accumulate in cells/neurons in Niemann-Pick disease type C (NPC). Received in revised form The activities of acid sphingomyelinase and lysosomal glucocerebrosidase (GCase), which degrade 10 August 2016 sphingomyelin and GlcCer, respectively, are down-regulated in NPC cells, however, changes in GlcCer Accepted 12 August 2016 synthase activity have not yet been elucidated. We herein demonstrated for the first time that GlcCer Available online 15 August 2016 synthase activity for the fluorescent ceramide, 4-nitrobenzo-2-oxa-1,3-diazole-labeled C6-ceramide À À (NBD-ceramide) increased in intact NPC1( / ) cells and cell lysates without affecting the protein levels. Keywords: (À/À) fl Niemann-Pick disease type C In NBD-ceramide-labeled NPC1 cells, NBD- uorescence preferentially accumulated in the Golgi Cholesterol complex and vesicular specks in the cytoplasm 40 and 150 min, respectively, after labeling, while a Glucosylceramide synthase treatment for 48 h with the GlcCer synthase inhibitors, N-butyldeoxynojirimycin (NB-DNJ) and 1-phenyl- Sphingomyelin 2-palmitoylamino-3-morpholino-1-propanol, accelerated the appearance of vesicular specks emitting À À Vesicular trafficking NBD-fluorescence within 40 min. -
Supplementary Methods
Supplementary methods Human lung tissues and tissue microarray (TMA) All human tissues were obtained from the Lung Cancer Specialized Program of Research Excellence (SPORE) Tissue Bank at the M.D. Anderson Cancer Center (Houston, TX). A collection of 26 lung adenocarcinomas and 24 non-tumoral paired tissues were snap-frozen and preserved in liquid nitrogen for total RNA extraction. For each tissue sample, the percentage of malignant tissue was calculated and the cellular composition of specimens was determined by histological examination (I.I.W.) following Hematoxylin-Eosin (H&E) staining. All malignant samples retained contained more than 50% tumor cells. Specimens resected from NSCLC stages I-IV patients who had no prior chemotherapy or radiotherapy were used for TMA analysis by immunohistochemistry. Patients who had smoked at least 100 cigarettes in their lifetime were defined as smokers. Samples were fixed in formalin, embedded in paraffin, stained with H&E, and reviewed by an experienced pathologist (I.I.W.). The 413 tissue specimens collected from 283 patients included 62 normal bronchial epithelia, 61 bronchial hyperplasias (Hyp), 15 squamous metaplasias (SqM), 9 squamous dysplasias (Dys), 26 carcinomas in situ (CIS), as well as 98 squamous cell carcinomas (SCC) and 141 adenocarcinomas. Normal bronchial epithelia, hyperplasia, squamous metaplasia, dysplasia, CIS, and SCC were considered to represent different steps in the development of SCCs. All tumors and lesions were classified according to the World Health Organization (WHO) 2004 criteria. The TMAs were prepared with a manual tissue arrayer (Advanced Tissue Arrayer ATA100, Chemicon International, Temecula, CA) using 1-mm-diameter cores in triplicate for tumors and 1.5 to 2-mm cores for normal epithelial and premalignant lesions. -
Integration of Lipidomics and Transcriptomics Data Towards A
Gupta et al. BMC Systems Biology 2011, 5:26 http://www.biomedcentral.com/1752-0509/5/26 RESEARCHARTICLE Open Access Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism Shakti Gupta1, Mano R Maurya1, Alfred H Merrill Jr2, Christopher K Glass3, Shankar Subramaniam1,3,4* Abstract Background: Sphingolipids play important roles in cell structure and function as well as in the pathophysiology of many diseases. Many of the intermediates of sphingolipid biosynthesis are highly bioactive and sometimes have antagonistic activities, for example, ceramide promotes apoptosis whereas sphingosine-1-phosphate can inhibit apoptosis and induce cell growth; therefore, quantification of the metabolites and modeling of the sphingolipid network is imperative for an understanding of sphingolipid biology. Results: In this direction, the LIPID MAPS Consortium is developing methods to quantitate the sphingolipid metabolites in mammalian cells and is investigating their application to studies of the activation of the RAW264.7 macrophage cell by a chemically defined endotoxin, Kdo2-Lipid A. Herein, we describe a model for the C16-branch of sphingolipid metabolism (i.e., for ceramides with palmitate as the N-acyl-linked fatty acid, which is selected because it is a major subspecies for all categories of complex sphingolipids in RAW264.7 cells) integrating lipidomics and transcriptomics data and using a two-step matrix-based approach to estimate the rate constants from experimental data. The rate constants obtained from the first step are further refined using generalized constrained nonlinear optimization. The resulting model fits the experimental data for all species. The robustness of the model is validated through parametric sensitivity analysis. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Shaping the Sperm Head: an ER Enzyme Leaves Its Mark
Shaping the sperm head: an ER enzyme leaves its mark Angshumoy Roy, … , Yi-Nan Lin, Martin M. Matzuk J Clin Invest. 2006;116(11):2860-2863. https://doi.org/10.1172/JCI30221. Commentary Lipid storage diseases are debilitating inherited metabolic disorders that stem from the absence of specific lysosomal enzymes that degrade selected lipids. Most characteristically, these disorders affect the nervous and the reticulo- endothelial systems, with massive organomegaly resulting from the presence of engorged, lipid-laden macrophages. In this issue of the JCI, Yildiz et al. describe the role of the ER-resident enzyme β-glucosidase 2 (GBA2) in mice (see the related article beginning on page 2985). Surprisingly, GBA2 deficiency leaves bile acid and cholesterol metabolism intact, instead causing lipid accumulation in the ER of testicular Sertoli cells, round-headed sperm (globozoospermia), and impaired male fertility. Find the latest version: https://jci.me/30221/pdf commentaries 1. Niederkorn, J.Y. 2006. See no evil, hear no evil, do no 7. Asheuer, M., et al. 2004. Human CD34+ cells dif- 13. Nimmerjahn, A., Kirchhoff, F., and Helmchen, F. evil: the lessons of immune privilege. Nat. Immunol. ferentiate into microglia and express recombinant 2005. Resting microglial cells are highly dynamic 7:354–359. therapeutic protein. Proc. Natl. Acad. Sci. U. S. A. surveillants of brain parenchyma in vivo. Science. 2. Pardridge, W.M. 2005. The blood-brain barrier: 101:3557–3562. 308:1314–1318. bottleneck in brain drug development. NeuroRx. 8. Biffi, A., et al. 2006. Gene therapy of metachromat- 14. Matzner, U., and Gieselmann, V. 2005. Gene thera- 2:3–14. -
Generation of Sphingosine-1-Phosphate Is Enhanced in Biliary Tract Cancer Patients and Is Associated with Lymphatic Metastasis
www.nature.com/scientificreports OPEN Generation of sphingosine- 1-phosphate is enhanced in biliary tract cancer patients and Received: 5 April 2018 Accepted: 4 July 2018 is associated with lymphatic Published: xx xx xxxx metastasis Yuki Hirose1, Masayuki Nagahashi1, Eriko Katsuta2, Kizuki Yuza1, Kohei Miura1, Jun Sakata1, Takashi Kobayashi1, Hiroshi Ichikawa1, Yoshifumi Shimada1, Hitoshi Kameyama1, Kerry-Ann McDonald2, Kazuaki Takabe 1,2,3,4,5 & Toshifumi Wakai1 Lymphatic metastasis is known to contribute to worse prognosis of biliary tract cancer (BTC). Recently, sphingosine-1-phosphate (S1P), a bioactive lipid mediator generated by sphingosine kinase 1 (SPHK1), has been shown to play an important role in lymphangiogenesis and lymph node metastasis in several types of cancer. However, the role of the lipid mediator in BTC has never been examined. Here we found that S1P is elevated in BTC with the activation of ceramide-synthetic pathways, suggesting that BTC utilizes SPHK1 to promote lymphatic metastasis. We found that S1P, sphingosine and ceramide precursors such as monohexosyl-ceramide and sphingomyelin, but not ceramide, were signifcantly increased in BTC compared to normal biliary tract tissue using LC-ESI-MS/MS. Utilizing The Cancer Genome Atlas cohort, we demonstrated that S1P in BTC is generated via de novo pathway and exported via ABCC1. Further, we found that SPHK1 expression positively correlated with factors related to lymphatic metastasis in BTC. Finally, immunohistochemical examination revealed that gallbladder cancer with lymph node metastasis had signifcantly higher expression of phospho-SPHK1 than that without. Taken together, our data suggest that S1P generated in BTC contributes to lymphatic metastasis. Biliary tract cancer (BTC), the malignancy of the bile ducts and gallbladder, is a highly lethal disease in which a strong prognostic predictor is lymph node metastasis1–5. -
SIRT1 Regulates Sphingolipid Metabolism and Neural
RESEARCH ARTICLE SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc- SMPDL3B Wei Fan1, Shuang Tang1†, Xiaojuan Fan2, Yi Fang1, Xiaojiang Xu3, Leping Li4, Jian Xu5, Jian-Liang Li3, Zefeng Wang2*, Xiaoling Li1* 1Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States; 2CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; 3Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States; 4Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States; 5Children’s Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer *For correspondence: Center, and Hamon Center for Regenerative Science and Medicine, University of [email protected] (ZW); Texas Southwestern Medical Center, Dallas, United States [email protected] (XL) Present address: †Cancer Institute and Department of Nuclear Medicine, Fudan Abstract Sphingolipids are important structural components of cell membranes and prominent University Shanghai Cancer signaling