Hepatic Transcriptome Profiles of Mice with Diet-Induced Nonalcoholic Steatohepatitis Treated with Astaxanthin and Vitamin E
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A Homozygous FITM2 Mutation Causes a Deafness-Dystonia Syndrome with Motor Regression and Signs of Ichthyosis and Sensory Neuropathy
A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy Zazo Seco, Celia; Castells-Nobau, Anna; Joo, Seol-Hee; Schraders, Margit; Foo, Jia Nee; van der Voet, Monique; Velan, S Sendhil; Nijhof, Bonnie; Oostrik, Jaap; de Vrieze, Erik; Katana, Radoslaw; Mansoor, Atika; Huynen, Martijn; Szklarczyk, Radek; Oti, Martin; Tranebjærg, Lisbeth; van Wijk, Erwin; Scheffer-de Gooyert, Jolanda M; Siddique, Saadat; Baets, Jonathan; de Jonghe, Peter; Kazmi, Syed Ali Raza; Sadananthan, Suresh Anand; van de Warrenburg, Bart P; Khor, Chiea Chuen; Göpfert, Martin C; Qamar, Raheel; Schenck, Annette; Kremer, Hannie; Siddiqi, Saima Published in: Disease models & mechanisms DOI: 10.1242/dmm.026476 Publication date: 2017 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Zazo Seco, C., Castells-Nobau, A., Joo, S-H., Schraders, M., Foo, J. N., van der Voet, M., Velan, S. S., Nijhof, B., Oostrik, J., de Vrieze, E., Katana, R., Mansoor, A., Huynen, M., Szklarczyk, R., Oti, M., Tranebjærg, L., van Wijk, E., Scheffer-de Gooyert, J. M., Siddique, S., ... Siddiqi, S. (2017). A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy. Disease models & mechanisms, 10, 105-118. https://doi.org/10.1242/dmm.026476 Download date: 25. Sep. 2021 © 2017. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2017) 10, 105-118 doi:10.1242/dmm.026476 RESEARCH ARTICLE A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy Celia Zazo Seco1,2,*, Anna Castells-Nobau3,4,*, Seol-hee Joo5, Margit Schraders1,4, Jia Nee Foo6, Monique van der Voet3,4, S. -
13Type 2 Diabetes Genetics: Beyond GWAS
abetes & Di M f e o t a l b a o Sang and Blackett, J Diabetes Metab 2012, 3:5 n l r i s u m o DOI: 10.4172/2155-6156.1000198 J Journal of Diabetes and Metabolism ISSN: 2155-6156 Review Article Open Access Type 2 Diabetes Genetics: Beyond GWAS Dharambir K. Sanghera* and Piers R. Blackett University of Oklahoma Health Sciences Center, Oklahoma City, USA Abstract The global epidemic of type 2 diabetes mellitus (T2D) is one of the most challenging problems of the 21st century and the fifth leading cause of death worldwide. Substantial evidence suggests that T2D is a multifactorial disease with a strong genetic component. Recent genome-wide association studies (GWAS) have successfully identified and replicated nearly 75 susceptibility loci associated with T2D and related metabolic traits, mostly in Europeans, and some in African, and South Asian populations. The GWAS serve as a starting point for future genetic and functional studies since the mechanisms of action by which these associated loci influence disease is still unclear and it is difficult to predict potential implication of these findings in clinical settings. Despite extensive replication, no study has unequivocally demonstrated their clinical role in the disease management beyond progression to T2D from impaired glucose tolerance. However, these studies are revealing new molecular pathways underlying diabetes etiology, gene-environment interactions, epigenetic modifications, and gene function. This review highlights evolving progress made in the rapidly moving field of T2D genetics that is starting to unravel the pathophysiology of a complex phenotype and has potential to show clinical relevance in the near future. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Manuscript for Proximity Interactome Analysis of Lassa
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.16.452739; this version posted July 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Main Manuscript for 2 Proximity interactome analysis of Lassa polymerase reveals 3 eRF3a/GSPT1 as a druggable target for host directed antivirals. 4 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen5, Kelvin Frank Cho6, Alice 5 Y. Ting7,8, Alexander Bukreyev3,4,9, Erica Ollmann Saphire2* and Juan Carlos de la Torre1* 6 1 Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 2La Jolla Institute for Immunology, La Jolla CA 92037 8 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 9 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 10 5Proteomics Core, Scripps Research, Jupiter, FL 33458 11 6Cancer Biology Program, Stanford University, Stanford, CA 94305 12 7Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 8Chan Zuckerberg Biohub, San Francisco, CA 94158 15 9Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 *Erica Ollmann Saphire; Juan Carlos de la Torre. 18 Email: [email protected] and [email protected] 19 Author Contributions: J.F., E.O.S., and J.C.T designed research; J.F. performed all non-BSL4 20 experiments and analyzed data; C.P. -
Regulation of Steatohepatitis and PPARΓ Signaling
Cell Metabolism Article Regulation of Steatohepatitis and PPARg Signaling by Distinct AP-1 Dimers Sebastian C. Hasenfuss,1,2 Latifa Bakiri,1 Martin K. Thomsen,1 Evan G. Williams,3 Johan Auwerx,3 and Erwin F. Wagner1,* 1Genes, Development, and Disease Group, F-BBVA Cancer Cell Biology Programme, National Cancer Research Centre (CNIO), 28029 Madrid, Spain 2Faculty Biology, University of Freiburg, 79104 Freiburg, Germany 3Laboratory of Integrative and Systems Physiology, School of Life Sciences, E´ cole Polytechnique Fe´ de´ rale, 1015 Lausanne, Switzerland *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cmet.2013.11.018 SUMMARY development (Smedile and Bugianesi, 2005). Understanding the cellular and molecular mechanisms leading to NAFLD, as Nonalcoholic fatty liver disease (NAFLD) affects up well as the identification of novel targets for NAFLD therapy, to 30% of the adult population in Western societies, has therefore become a priority (Cohen et al., 2011; Lazo and yet the underlying molecular pathways remain Clark, 2008). poorly understood. Here, we identify the dimeric The Activator Protein 1 (AP-1) (Fos/Jun) protein complex is a Activator Protein 1 as a regulator of NAFLD. Fos- dimeric leucine zipper (bZIP) transcription factor. Three different related antigen 1 (Fra-1) and Fos-related antigen 2 Jun proteins (c-Jun, JunB, and JunD) and four different Fos proteins (c-Fos, FosB, Fra-1, and Fra-2) form AP-1 dimer. Jun (Fra-2) prevent dietary NAFLD by inhibiting prostea- proteins can either form homodimers, such as c-Jun/c-Jun or totic PPARg signaling. Moreover, established c-Jun/JunB, or heterodimers, such as c-Jun/c-Fos. -
Functional Interactomes of the Ebola Virus Polymerase Identified by Proximity Proteomics 2 in the Context of Viral Replication
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.20.453153; this version posted July 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Functional interactomes of the Ebola virus polymerase identified by proximity proteomics 2 in the context of viral replication 3 Jingru Fang1,2, Colette Pietzsch3,4, George Tsaprailis5, Gogce Crynen6, Kelvin Frank Cho7, Alice 4 Y. Ting8,9, Alexander Bukreyev3,4,10*, Juan Carlos de la Torre2*, Erica Ollmann Saphire1* 5 1La Jolla Institute for Immunology, La Jolla CA 92037 6 2Department of Immunology and Microbiology, Scripps Research, La Jolla CA 92037 7 3Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550 8 4Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550 9 5Proteomics Core, Scripps Research, Jupiter, FL 33458 10 6Bioinformatics and Statistics Core, Scripps Research, Jupiter, FL 33458 11 7Cancer Biology Program, Stanford University, Stanford, CA 94305 12 8Department of Genetics, Department of Biology and Department of Chemistry, Stanford 13 University, Stanford, CA 94305 14 9Chan Zuckerberg Biohub, San Francisco, CA 94158 15 10 Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 16 TX 77550 17 Correspondence: [email protected], [email protected], [email protected] 18 Lead contact: [email protected] 19 SUMMARY 20 Ebola virus (EBOV) critically depends on the viral polymerase to replicate and transcribe the viral 21 RNA genome. -
Influence of Erf3a/GSPT1 Gene Expression on Susceptibility to Carcinogenesis
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL INFLUENCE OF ERF3 A/GSPT1 GENE EXPRESSI ON ON SUSCEPTIBILITY TO CARCINOGENESIS JOANA FERREIRA TOMÉ MALTA VACAS Tese orientada por: Professor Doutor Rui Miguel Brito Professora Doutora Maria Manuela Coelho DOUTORAMENTO EM BIOLOGIA (Biologia Molecular) 2009 This study was supported by the Fundação Para a Ciência e a Tecnologia: PhD fellowship SFRH/BD/21468/2005, projects POCTI/MGI/40071/2001 and PTDC/SAU-GMG/67031/2006. This dissertation should be cited as: Malta-Vacas J. (2009) Influence of eRF3a/GSPT1 gene expression on susceptibility to carcinogenesis. PhD Thesis, University of Lisbon, Portugal. “O erro é a noite dos espíritos e a armadilha da inocência” Luc de Clapiers, Marquês de Vauvenargues NOTAS PRÉVIAS Nos termos do n.º 1 do Artigo 40, Capítulo V, do Regulamento de Estudos Pós-Graduados da Universidade de Lisboa, publicado no Diário da República – II Série N.º 153, de 5 de Julho de 2003, esclarece-se que na elaboração da presente dissertação foram usados integralmente artigos científicos já publicados (4) ou submetidos para publicação (1) em revistas indexadas de circulação internacional, os quais integram os Capítulos II e III da presente tese. Tendo os referidos trabalhos sido realizados em colaboração, a candidata esclarece que participou integralmente no planeamento e na elaboração de todos os trabalhos, assim como na análise e discussão dos resultados. Esclarece-se ainda que a formatação dos vários artigos que integram a presente dissertação obedece às regras das revistas em que foram publicados ou submetidos para publicação. Por este motivo, não foi possível adoptar um critério uniforme ao longo dos vários capítulos. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Meta-Analysis of Genome-Wide Association Studies Identifies Eight New Loci for Type 2 Diabetes in East Asians
LETTERS Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians Yoon Shin Cho1,46, Chien-Hsiun Chen2,3,46, Cheng Hu4,46, Jirong Long5,46, Rick Twee Hee Ong6,46, Xueling Sim7,46, Fumihiko Takeuchi8,46, Ying Wu9,46, Min Jin Go1,46, Toshimasa Yamauchi10,46, Yi-Cheng Chang11,46, Soo Heon Kwak12,46, Ronald C W Ma13,46, Ken Yamamoto14,46, Linda S Adair15, Tin Aung16,17, Qiuyin Cai5, Li-Ching Chang2, Yuan-Tsong Chen2, Yutang Gao18, Frank B Hu19, Hyung-Lae Kim1,20, Sangsoo Kim21, Young Jin Kim1, Jeannette Jen-Mai Lee22, Nanette R Lee23, Yun Li9,24, Jian Jun Liu25, Wei Lu26, Jiro Nakamura27, Eitaro Nakashima27,28, Daniel Peng-Keat Ng22, Wan Ting Tay16, Fuu-Jen Tsai3, Tien Yin Wong16,17,29, Mitsuhiro Yokota30, Wei Zheng5, Rong Zhang4, Congrong Wang4, Wing Yee So13, Keizo Ohnaka31, Hiroshi Ikegami32, Kazuo Hara10, Young Min Cho12, Nam H Cho33, Tien-Jyun Chang11, Yuqian Bao4, Åsa K Hedman34, Andrew P Morris34, Mark I McCarthy34,35, DIAGRAM Consortium36, MuTHER Consortium36, Ryoichi Takayanagi37,47, Kyong Soo Park12,38,47, Weiping Jia4,47, Lee-Ming Chuang11,39,47, Juliana C N Chan13,47, Shiro Maeda39,47, Takashi Kadowaki10,47, Jong-Young Lee1,47, Jer-Yuarn Wu2,3,47, Yik Ying Teo6,7,22,25,41,47, E Shyong Tai22,42,43,47, Xiao Ou Shu5,47, Karen L Mohlke9,47, Norihiro Kato8,47, Bok-Ghee Han1,47 & Mark Seielstad25,44,45,47 We conducted a three-stage genetic study to identify have been identified for T2D10,11. -
Uncovering RNA Binding Proteins Associated with Age and Gender During Liver Maturation
OPEN Uncovering RNA binding proteins SUBJECT AREAS: associated with age and gender during GENOME-WIDE ASSOCIATION STUDIES liver maturation REGULATORY NETWORKS Praneet Chaturvedi1, Yaseswini Neelamraju1, Waqar Arif2, Auinash Kalsotra2 & Sarath Chandra Janga1,3,4 AGEING GENE REGULATORY NETWORKS 1Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202, 2Departments of Biochemistry and Medical Biochemistry, University Received of Illinois, Urbana-Champaign, Illinois 61801, USA, 3Center for Computational Biology and Bioinformatics, Indiana University 11 December 2014 School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana, 46202, 4Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Accepted Building, 975 West Walnut Street, Indianapolis, Indiana, 46202. 9 March 2015 Published In the present study, we perform an association analysis focusing on the expression changes of 1344 RNA 31 March 2015 Binding proteins (RBPs) as a function of age and gender in human liver. We identify 88 and 45 RBPs to be significantly associated with age and gender respectively. Experimental verification of several of the predicted associations in mice confirmed our findings. Our results suggest that a small fraction of the gender-associated RBPs (,40%) are expressed higher in males than females. Altogether, these observations Correspondence and show that several of these RBPs are important and conserved regulators in maintaining liver function. requests for materials Further analysis of the protein interaction network of RBPs associated with age and gender based on the should be addressed to centrality measures like degree, betweenness and closeness revealed that several of these RBPs might be S.C.J. -
A Homozygous FITM2 Mutation Causes a Deafness-Dystonia
© 2017. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2017) 10, 105-118 doi:10.1242/dmm.026476 RESEARCH ARTICLE AhomozygousFITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy Celia Zazo Seco1,2,*, Anna Castells-Nobau3,4,*, Seol-hee Joo5, Margit Schraders1,4, Jia Nee Foo6, Monique van der Voet3,4, S. Sendhil Velan7,8, Bonnie Nijhof3,4, Jaap Oostrik1,4, Erik de Vrieze1,4, Radoslaw Katana5, Atika Mansoor9, Martijn Huynen10, Radek Szklarczyk10, Martin Oti2,10,11, Lisbeth Tranebjærg12,13,14, Erwin van Wijk1,4, Jolanda M. Scheffer-de Gooyert3,4, Saadat Siddique15, Jonathan Baets16,17,18, Peter de Jonghe16,17,18, Syed Ali Raza Kazmi9, Suresh Anand Sadananthan7,8, Bart P. van de Warrenburg4,19, Chiea Chuen Khor6,20,21, Martin C. Gö pfert5, Raheel Qamar22,23,‡, Annette Schenck3,4,‡, Hannie Kremer1,3,4,‡ and Saima Siddiqi9,‡ ABSTRACT constitute an evolutionary conserved protein family involved in A consanguineous family from Pakistan was ascertained to have a partitioning of triglycerides into cellular lipid droplets. Despite the role novel deafness-dystonia syndrome with motor regression, ichthyosis- of FITM2 in neutral lipid storage and metabolism, no indications for like features and signs of sensory neuropathy. By applying a combined lipodystrophy were observed in the affected individuals. In order to strategy of linkage analysis and whole-exome sequencing in obtain independent evidence for the involvement of FITM2 in the the presented family, a homozygous nonsense mutation, c.4G>T human pathology, downregulation of the single Fitm ortholog, (p.Glu2*), in FITM2 was identified. -
Rnaseq Analysis of Heart Tissue from Mice Treated with Atenolol and Isoproterenol Reveals a Reciprocal Transcriptional Response Andrea Prunotto1,2, Brian J
Prunotto et al. BMC Genomics (2016) 17:717 DOI 10.1186/s12864-016-3059-6 RESEARCH ARTICLE Open Access RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response Andrea Prunotto1,2, Brian J. Stevenson2, Corinne Berthonneche3, Fanny Schüpfer3, Jacques S. Beckmann1,2,3, Fabienne Maurer3*† and Sven Bergmann1,2,4*† Abstract Background: The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strains treated with the β-blocker atenolol (ATE) and the β-agonist isoproterenol (ISO). Results: Differential expression analyses revealed a large set of genes responding to ISO (n = 1770 at FDR = 0.0001) and a comparatively small one responding to ATE (n =23atFDR = 0.0001). At a less stringent definition of differential expression, the transcriptional responses to these two antagonistic drugs are reciprocal for many genes, with an overall anti-correlation of r = −0.3. This trend is also observed at the level of most individual strains even though the power to detect differential expression is significantly reduced. The inversely expressed gene sets are enriched with genes annotated for heart-related functions. Modular analysis revealed gene sets that exhibit coherent transcription profiles across some strains and/or treatments. Correlations between these modules and a broad spectrum of cardiovascular traits are stronger than expected by chance. This provides evidence for the overall importance of transcriptional regulation for these organismal responses and explicits links between co-expressed genes and the traits they are associated with.