MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem Cells
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GSK3 Is a Negative Regulator of the Thermogenic Program in Brown Adipocytes
GSK3 is a negative regulator of the thermogenic program in brown adipocytes Markussen, Lasse K.; Winther, Sally; Wicksteed, Barton; Hansen, Jacob B. Published in: Scientific Reports DOI: 10.1038/s41598-018-21795-y Publication date: 2018 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Markussen, L. K., Winther, S., Wicksteed, B., & Hansen, J. B. (2018). GSK3 is a negative regulator of the thermogenic program in brown adipocytes. Scientific Reports, 8, 1-12. [3469]. https://doi.org/10.1038/s41598- 018-21795-y Download date: 01. okt.. 2021 www.nature.com/scientificreports OPEN GSK3 is a negative regulator of the thermogenic program in brown adipocytes Received: 16 January 2017 Lasse K. Markussen1, Sally Winther1, Barton Wicksteed2 & Jacob B. Hansen 1 Accepted: 9 February 2018 Brown adipose tissue is a promising therapeutic target in metabolic disorders due to its ability to Published: xx xx xxxx dissipate energy and improve systemic insulin sensitivity and glucose homeostasis. β-Adrenergic stimulation of brown adipocytes leads to an increase in oxygen consumption and induction of a thermogenic gene program that includes uncoupling protein 1 (Ucp1) and fbroblast growth factor 21 (Fgf21). In kinase inhibitor screens, we have identifed glycogen synthase kinase 3 (GSK3) as a negative regulator of basal and β-adrenergically stimulated Fgf21 expression in cultured brown adipocytes. In addition, inhibition of GSK3 also caused increased Ucp1 expression and oxygen consumption. β-Adrenergic stimulation triggered an inhibitory phosphorylation of GSK3 in a protein kinase A (PKA)- dependent manner. Mechanistically, inhibition of GSK3 activated the mitogen activated protein kinase (MAPK) kinase 3/6-p38 MAPK-activating transcription factor 2 signaling module. -
Quantitative Proteomics Methods for the Analysis of Histone Post-Translational Modifications
Université de Montréal Quantitative Proteomics Methods for the Analysis of Histone Post-translational Modifications par Nebiyu Ali Abshiru Département de Chimie Faculté des arts et des sciences Thèse présentée à la Faculté des études supérieures et postdoctorales en vue de l’obtention du grade de philosophiae doctor (Ph.D.) en chimie Septembre 2015 ©Nebiyu Ali Abshiru, 2015 i Résumé Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. -
Targeting the CDK4/6-Rb Pathway Enhances Response to PI3K
Published OnlineFirst August 9, 2018; DOI: 10.1158/1078-0432.CCR-18-0717 Translational Cancer Mechanisms and Therapy Clinical Cancer Research Targeting the CDK4/6-Rb Pathway Enhances Response to PI3K Inhibition in PIK3CA-Mutant Lung Squamous Cell Carcinoma Ruoshi Shi1,2, Ming Li1, Vibha Raghavan1, Shirley Tam1, Michael Cabanero1, Nhu-An Pham1, Frances A. Shepherd1,3, Nadeem Moghal1,2, and Ming-Sound Tsao1,2,4 Abstract Purpose: Lung squamous cell carcinoma (LUSC) is a major of LUSC PDX models identified PI3K pathway alterations in subtype of non–small cell lung cancer characterized by mul- over 50% of the models. In vivo screening using PI3K tiple genetic alterations, particularly PI3K pathway alterations inhibitors in 12 of these models identified PIK3CA mutation which have been identified in over 50% of LUSC cases. Despite as a predictive biomarker of response (<20% tumor growth being an attractive target, single-agent PI3K inhibitors have compared with baseline/vehicle). Combined inhibition of demonstrated modest response in LUSC. Thus, novel combi- PI3K and CDK4/6 in models with PIK3CA mutation resulted nation therapies targeting LUSC are needed. in greater antitumor effects compared with either mono- Experimental Design: PI3K inhibitors alone and in com- therapy alone. In addition, the combination of the two bination with CDK4/6 inhibitors were evaluated in previously drugs achieved targeted inhibition of the PI3K and cell-cycle established LUSC patient-derived xenografts (PDX) using an pathways. in vivo screening method. Screening results were validated with Conclusions: PIK3CA mutations predict response to PI3K in vivo expansion to 5 to 8 mice per arm. -
Macrophage Activation JUNB Is a Key Transcriptional Modulator Of
JUNB Is a Key Transcriptional Modulator of Macrophage Activation Mary F. Fontana, Alyssa Baccarella, Nidhi Pancholi, Miles A. Pufall, De'Broski R. Herbert and Charles C. Kim This information is current as of October 2, 2021. J Immunol 2015; 194:177-186; Prepublished online 3 December 2014; doi: 10.4049/jimmunol.1401595 http://www.jimmunol.org/content/194/1/177 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2014/12/03/jimmunol.140159 Material 5.DCSupplemental References This article cites 40 articles, 7 of which you can access for free at: http://www.jimmunol.org/content/194/1/177.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 2, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology JUNB Is a Key Transcriptional Modulator of Macrophage Activation Mary F. Fontana,* Alyssa Baccarella,* Nidhi Pancholi,* Miles A. -
LIAO-DISSERTATION-2019.Pdf (4.688Mb)
A Genetic Interaction Analysis Identifies Novel Cancer Driver Modifiers and a Combination Therapy The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Liao, Sida. 2019. A Genetic Interaction Analysis Identifies Novel Cancer Driver Modifiers and a Combination Therapy. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42029794 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA A genetic interaction analysis identifies novel cancer driver modifiers and a combination therapy A dissertation presented by Sida Liao To The Division of Medical Sciences In partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts April 2019 © 2019 Sida Liao All rights reserved. Dissertation Advisor: Dr. Stephen J. Elledge Sida Liao A genetic interaction analysis identifies novel cancer driver modifiers and a combination therapy Abstract A large number of cancer drivers have been identified through tumor sequencing efforts but how they interact and the degree to which they can substitute for each other has not been systematically explored. To comprehensively investigate how cancer drivers genetically interact, I searched for modifiers of EGFR dependency by performing CRISPR, shRNA and expression screens in a non-small cell lung cancer model. I elucidated a broad spectrum of TSGs and OGs that can genetically modify proliferation and survival of cancer cells when EGFR signaling is altered. -
Characterization of the Small Molecule Kinase Inhibitor SU11248 (Sunitinib/ SUTENT in Vitro and in Vivo
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Genetik Characterization of the Small Molecule Kinase Inhibitor SU11248 (Sunitinib/ SUTENT in vitro and in vivo - Towards Response Prediction in Cancer Therapy with Kinase Inhibitors Michaela Bairlein Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ. -Prof. Dr. K. Schneitz Prüfer der Dissertation: 1. Univ.-Prof. Dr. A. Gierl 2. Hon.-Prof. Dr. h.c. A. Ullrich (Eberhard-Karls-Universität Tübingen) 3. Univ.-Prof. A. Schnieke, Ph.D. Die Dissertation wurde am 07.01.2010 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 19.04.2010 angenommen. FOR MY PARENTS 1 Contents 2 Summary ................................................................................................................................................................... 5 3 Zusammenfassung .................................................................................................................................................... 6 4 Introduction .............................................................................................................................................................. 8 4.1 Cancer .............................................................................................................................................................. -
Lysine Benzoylation Is a Histone Mark Regulated by SIRT2
ARTICLE DOI: 10.1038/s41467-018-05567-w OPEN Lysine benzoylation is a histone mark regulated by SIRT2 He Huang1, Di Zhang1, Yi Wang2, Mathew Perez-Neut1, Zhen Han3, Y. George Zheng3, Quan Hao2 & Yingming Zhao1 Metabolic regulation of histone marks is associated with diverse biological processes through dynamically modulating chromatin structure and functions. Here we report the identification 1234567890():,; and characterization of a histone mark, lysine benzoylation (Kbz). Our study identifies 22 Kbz sites on histones from HepG2 and RAW cells. This type of histone mark can be stimulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbz marks are associated with gene expression and have physiological relevance distinct from histone acetylation. In addition, we demonstrate that SIRT2, a NAD+-dependent protein deacetylase, removes histone Kbz both in vitro and in vivo. This study therefore reveals a new type of histone marks with potential physiological relevance and identifies possible non-canonical functions of a widely used chemical food preservative. 1 Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA. 2 School of Biomedical Sciences, University of Hong Kong, Hong Kong, China. 3 Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA. Correspondence and requests for materials should be addressed to Y.Z. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:3374 | DOI: 10.1038/s41467-018-05567-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-05567-w hromatin structure and transcriptional activity of genes and coelution analysis were performed to compare the synthetic are regulated by diverse protein posttranslational mod- peptide with its in vivo counterpart (Fig. -
Molecular Signatures Differentiate Immune States in Type 1 Diabetes Families
Page 1 of 65 Diabetes Molecular signatures differentiate immune states in Type 1 diabetes families Yi-Guang Chen1, Susanne M. Cabrera1, Shuang Jia1, Mary L. Kaldunski1, Joanna Kramer1, Sami Cheong2, Rhonda Geoffrey1, Mark F. Roethle1, Jeffrey E. Woodliff3, Carla J. Greenbaum4, Xujing Wang5, and Martin J. Hessner1 1The Max McGee National Research Center for Juvenile Diabetes, Children's Research Institute of Children's Hospital of Wisconsin, and Department of Pediatrics at the Medical College of Wisconsin Milwaukee, WI 53226, USA. 2The Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. 3Flow Cytometry & Cell Separation Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA. 4Diabetes Research Program, Benaroya Research Institute, Seattle, WA, 98101, USA. 5Systems Biology Center, the National Heart, Lung, and Blood Institute, the National Institutes of Health, Bethesda, MD 20824, USA. Corresponding author: Martin J. Hessner, Ph.D., The Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI 53226, USA Tel: 011-1-414-955-4496; Fax: 011-1-414-955-6663; E-mail: [email protected]. Running title: Innate Inflammation in T1D Families Word count: 3999 Number of Tables: 1 Number of Figures: 7 1 For Peer Review Only Diabetes Publish Ahead of Print, published online April 23, 2014 Diabetes Page 2 of 65 ABSTRACT Mechanisms associated with Type 1 diabetes (T1D) development remain incompletely defined. Employing a sensitive array-based bioassay where patient plasma is used to induce transcriptional responses in healthy leukocytes, we previously reported disease-specific, partially IL-1 dependent, signatures associated with pre and recent onset (RO) T1D relative to unrelated healthy controls (uHC). -
Original Article Associations of Novel Variants in PIK3C3, INSR and MAP3K4 of the ATM Pathway Genes with Pancreatic Cancer Risk
Am J Cancer Res 2020;10(7):2128-2144 www.ajcr.us /ISSN:2156-6976/ajcr0116403 Original Article Associations of novel variants in PIK3C3, INSR and MAP3K4 of the ATM pathway genes with pancreatic cancer risk Ling-Ling Zhao1,2,3, Hong-Liang Liu2,3, Sheng Luo4, Kyle M Walsh2,5, Wei Li1, Qingyi Wei2,3,6 1Cancer Center, The First Hospital of Jilin University, Changchun, China; 2Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA; Departments of 3Medicine, 4Biostatistics and Bioinformatics, 5Neurosurgery, 6Population Health Sciences, Duke University School of Medicine, Durham, NC, USA Received June 16, 2020; Accepted June 21, 2020; Epub July 1, 2020; Published July 15, 2020 Abstract: The ATM serine/threonine kinase (ATM) pathway plays important roles in pancreatic cancer (PanC) de- velopment and progression, but the roles of genetic variants of the genes in this pathway in the etiology of PanC are unknown. In the present study, we assessed associations between 31,499 single nucleotide polymorphisms (SNPs) in 198 ATM pathway-related genes and PanC risk using genotyping data from two previously published PanC genome-wide association studies (GWASs) of 15,423 subjects of European ancestry. In multivariable logis- tic regression analysis, we identified three novel independent SNPs to be significantly associated with PanC risk [PIK3C3 rs76692125 G>A: odds ratio (OR)=1.26, 95% confidence interval (CI)=1.12-1.43 and P=2.07×10-4, INSR rs11668724 G>A: OR=0.89, 95% CI=0.84-0.94 and P=4.21×10-5 and MAP3K4 rs13207108 C>T: OR=0.83, 95% CI=0.75-0.92, P=2.26×10-4]. -
Approx. Size Peak Max (Nm) Scattered Light Intensity (Average, Kcps)
Electronic Supplementary Material (ESI) for Nanoscale Advances. This journal is © The Royal Society of Chemistry 2020 Suppl. Table S1. Characterization of Ag nanoparticles. Time point Approx. size peak Scattered light Zeta-potential (h) max (nm) intensity (average, (average, mV) kcps) Ag10 0 h 10, 1000 730 -0.587 24 h 10, 100, 1000 63 N.D. Ag75 0 h 3.5, 40, 400 2790 -7.78 24 h 5, 100, 1000 1100 N.D. Ag nanoparticles (primary particle size: 10 nm and 75 nm) were dispersed in bronchial epithelial growth medium (BEGM) and hydro- dynamic size distribution and zeta potential values were determined. The data are reproduced from Gliga et al. Sci. Reports. 2018 (8):6668 [Creative Commons licence]. Suppl. Table S2. Canonical pathways enriched after long-term exposure of BEAS-2B cells to Ag nanoparticles. Ingenuity Canonical Pathways p-value z-score n Gene symbols TIMP3, FGFR2, FGFR3, CXCR4, VAV3, ITGA1, F11R, EDIL3, MAP3K4, FER, PIK3C3, PIK3R3, MAPK14, AFDN, Leukocyte Extravasation Signaling 0.001 0.39 28 TIMP4, ITGA5, TEC, WIPF1, CLDN15, MMP19, THY1, MMP11, ITGB2, JAM2, FGFR4, CYBA, ITGA4, MMP2 FGFR2, FGFR3, HLA-DQB1, IL1A, IL1B, IL18, MYD88, PIK3C3, CREB1, PIK3R3, ATF2, MAPK14, Dendritic Cell Maturation 0.002 0.20 26 CD83, PLCE1, PLCH1, COL1A1, HLA-DMA, PLCL2, PLCD4, LY75, CREB5, FGFR4, COL18A1, TNFRSF1B, COL1A2, DDR2 FGG, IL1A, IL1B, SAA2, FGA, IL18, SOCS2, MAP3K5, MAP3K1, IL6ST, MYD88, SOD2, SOCS5, PIK3R3, SOCS6, MAPK14, Acute Phase Response Signaling 0.002 -0.94 24 FTL, RBP7, RBP1, CRABP2, ITIH3, TNFRSF1B, MRAS, SERPINF1 IL1B, IL18, NEK7, -
Inhibition of ERK 1/2 Kinases Prevents Tendon Matrix Breakdown Ulrich Blache1,2,3, Stefania L
www.nature.com/scientificreports OPEN Inhibition of ERK 1/2 kinases prevents tendon matrix breakdown Ulrich Blache1,2,3, Stefania L. Wunderli1,2,3, Amro A. Hussien1,2, Tino Stauber1,2, Gabriel Flückiger1,2, Maja Bollhalder1,2, Barbara Niederöst1,2, Sandro F. Fucentese1 & Jess G. Snedeker1,2* Tendon extracellular matrix (ECM) mechanical unloading results in tissue degradation and breakdown, with niche-dependent cellular stress directing proteolytic degradation of tendon. Here, we show that the extracellular-signal regulated kinase (ERK) pathway is central in tendon degradation of load-deprived tissue explants. We show that ERK 1/2 are highly phosphorylated in mechanically unloaded tendon fascicles in a vascular niche-dependent manner. Pharmacological inhibition of ERK 1/2 abolishes the induction of ECM catabolic gene expression (MMPs) and fully prevents loss of mechanical properties. Moreover, ERK 1/2 inhibition in unloaded tendon fascicles suppresses features of pathological tissue remodeling such as collagen type 3 matrix switch and the induction of the pro-fbrotic cytokine interleukin 11. This work demonstrates ERK signaling as a central checkpoint to trigger tendon matrix degradation and remodeling using load-deprived tissue explants. Tendon is a musculoskeletal tissue that transmits muscle force to bone. To accomplish its biomechanical function, tendon tissues adopt a specialized extracellular matrix (ECM) structure1. Te load-bearing tendon compart- ment consists of highly aligned collagen-rich fascicles that are interspersed with tendon stromal cells. Tendon is a mechanosensitive tissue whereby physiological mechanical loading is vital for maintaining tendon archi- tecture and homeostasis2. Mechanical unloading of the tissue, for instance following tendon rupture or more localized micro trauma, leads to proteolytic breakdown of the tissue with severe deterioration of both structural and mechanical properties3–5. -
Learning Chroma\N States from Chip-‐Seq Data
Learning Chroman States from ChIP-seq data Luca Pinello GC Yuan Lab Outline • Chroman structure, histone modificaons and combinatorial paerns • How to segment the genome in chroman states • How to use ChromHMM step by step • Further references 2 Epigene-cs and chroman structure • All (almost) the cells of our body share the same genome but have very different gene expression programs…. 3 h?p://jpkc.scu.edu.cn/ywwy/zbsw(E)/edetail12.htm The code over the code • The chroman structure and the accessibility are mainly controlled by: 1. Nucleosome posioning, 2. DNA methylaon, 3. Histone modificaons. 4 Histone Modificaons Specific histone modificaons or combinaons of modificaons confer unique biological func-ons to the region of the genome associated with them: • H3K4me3: promoters, gene acva.on • H3K27me3: promoters, poised enhancers, gene silencing • H2AZ: promoters • H3K4me1: enhancers • H3K36me3: transcribed regions • H3K9me3: gene silencing • H3k27ac: acve enhancers 5 Examples of *-Seq Measuring the genome genome fragmentation assembler DNA DNA reads “genome” ChIP-seq to measure histone data fragments Measuring the regulome (e.g., protein-binding of the genome) Chromatin Immunopreciptation genomic (ChIP) + intervals fragmentation Protein - peak caller bound by DNA bound DNA reads proteins REVIEWS fragments a also informative, as this ratio corresponds to the fraction ChIP–chip of nucleosomes with the particular modification at that location, averaged over all the cells assayed. One of the difficulties in conducting a ChIP–seq con- trol experiment is the large amount of sequencing that ChIP–seq may be necessary. For input DNA and bulk nucleosomes, many of the sequenced tags are spread evenly across the genome.