INPP5F Translocates Into Cytoplasm and Interacts with ASPH to Promote Tumor Growth in Hepatocellular Carcinoma
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Analyses of Allele-Specific Gene Expression in Highly Divergent
ARTICLES Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance James J Crowley1,10, Vasyl Zhabotynsky1,10, Wei Sun1,2,10, Shunping Huang3, Isa Kemal Pakatci3, Yunjung Kim1, Jeremy R Wang3, Andrew P Morgan1,4,5, John D Calaway1,4,5, David L Aylor1,9, Zaining Yun1, Timothy A Bell1,4,5, Ryan J Buus1,4,5, Mark E Calaway1,4,5, John P Didion1,4,5, Terry J Gooch1,4,5, Stephanie D Hansen1,4,5, Nashiya N Robinson1,4,5, Ginger D Shaw1,4,5, Jason S Spence1, Corey R Quackenbush1, Cordelia J Barrick1, Randal J Nonneman1, Kyungsu Kim2, James Xenakis2, Yuying Xie1, William Valdar1,4, Alan B Lenarcic1, Wei Wang3,9, Catherine E Welsh3, Chen-Ping Fu3, Zhaojun Zhang3, James Holt3, Zhishan Guo3, David W Threadgill6, Lisa M Tarantino7, Darla R Miller1,4,5, Fei Zou2,11, Leonard McMillan3,11, Patrick F Sullivan1,5,7,8,11 & Fernando Pardo-Manuel de Villena1,4,5,11 Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. -
ASPH-Notch Axis Guided Exosomal Delivery of Prometastatic Secretome
Lin et al. Molecular Cancer (2019) 18:156 https://doi.org/10.1186/s12943-019-1077-0 RESEARCH Open Access ASPH-notch Axis guided Exosomal delivery of Prometastatic Secretome renders breast Cancer multi-organ metastasis Qiushi Lin1†, Xuesong Chen2†, Fanzheng Meng3†, Kosuke Ogawa4†, Min Li5, Ruipeng Song3, Shugeng Zhang3, Ziran Zhang3, Xianglu Kong3, Qinggang Xu1,6, Fuliang He1,7, Xuewei Bai8, Bei Sun8, Mien-Chie Hung9,10, Lianxin Liu3,11*, Jack Wands4* and Xiaoqun Dong12,1* Abstract Background: Aspartate β-hydroxylase (ASPH) is silent in normal adult tissues only to re-emerge during oncogenesis where its function is required for generation and maintenance of malignant phenotypes. Exosomes enable prooncogenic secretome delivering and trafficking for long-distance cell-to-cell communication. This study aims to explore molecular mechanisms underlying how ASPH network regulates designated exosomes to program development and progression of breast cancer. Methods: Stable cell lines overexpressing or knocking-out of ASPH were established using lentivirus transfection or CRISPR-CAS9 systems. Western blot, MTT, immunofluorescence, luciferase reporter, co-immunoprecipitation, 2D/3-D invasion, tube formation, mammosphere formation, immunohistochemistry and newly developed in vitro metastasis were applied. Results: Through physical interactions with Notch receptors, ligands (JAGs) and regulators (ADAM10/17), ASPH activates Notch cascade to provide raw materials (especially MMPs/ADAMs) for synthesis/release of pro-metastatic exosomes. Exosomes orchestrate EMT, 2-D/3-D invasion, stemness, angiogenesis, and premetastatic niche formation. Small molecule inhibitors (SMIs) of ASPH’s β-hydroxylase specifically/efficiently abrogated in vitro metastasis, which mimics basement membrane invasion at primary site, intravasation/extravasation (transendothelial migration), and colonization/outgrowth at distant sites. -
Mutant IDH, (R)-2-Hydroxyglutarate, and Cancer
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer Julie-Aurore Losman1 and William G. Kaelin Jr.1,2,3 1Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA; 2Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Mutations in metabolic enzymes, including isocitrate whether altered cellular metabolism is a cause of cancer dehydrogenase 1 (IDH1) and IDH2, in cancer strongly or merely an adaptive response of cancer cells in the face implicate altered metabolism in tumorigenesis. IDH1 of accelerated cell proliferation is still a topic of some and IDH2 catalyze the interconversion of isocitrate and debate. 2-oxoglutarate (2OG). 2OG is a TCA cycle intermediate The recent identification of cancer-associated muta- and an essential cofactor for many enzymes, including tions in three metabolic enzymes suggests that altered JmjC domain-containing histone demethylases, TET cellular metabolism can indeed be a cause of some 5-methylcytosine hydroxylases, and EglN prolyl-4-hydrox- cancers (Pollard et al. 2003; King et al. 2006; Raimundo ylases. Cancer-associated IDH mutations alter the enzymes et al. 2011). Two of these enzymes, fumarate hydratase such that they reduce 2OG to the structurally similar (FH) and succinate dehydrogenase (SDH), are bone fide metabolite (R)-2-hydroxyglutarate [(R)-2HG]. Here we tumor suppressors, and loss-of-function mutations in FH review what is known about the molecular mechanisms and SDH have been identified in various cancers, in- of transformation by mutant IDH and discuss their im- cluding renal cell carcinomas and paragangliomas. -
Allele-Specific Demethylation at an Imprinted Mammalian Promoter Andrew J
Published online 16 October 2007 Nucleic Acids Research, 2007, Vol. 35, No. 20 7031–7039 doi:10.1093/nar/gkm742 Allele-specific demethylation at an imprinted mammalian promoter Andrew J. Wood1,De´ borah Bourc’his2, Timothy H. Bestor3 and Rebecca J. Oakey1,* 1Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, SE1 9RT, UK, 2INSERM U741, Institut Jacques Monod, 2 Place Jussieu, 75251 Paris, CEDEX 05, France and 3Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY10032, USA Received July 4, 2007; Revised August 24, 2007; Accepted September 6, 2007 ABSTRACT Mutations in members of the de novo methyltransferase gene family lead to disruptions in imprinted gene A screen for imprinted genes on mouse expression and to retrotransposon animation (3,4), Chromosome 7 recently identified Inpp5f_v2, suggesting that the two processes are controlled by a a paternally expressed retrogene lying within an common mechanism (5). Dnmt3l encodes a regulatory intron of Inpp5f. Here, we identify a novel paternally protein that stimulates de novo methylation by Dnmt3a expressed variant of the Inpp5f gene (Inpp5f_v3) that and Dnmt3b, but lacks the catalytic motifs necessary for shows a number of unusual features. Inpp5f_v3 methyltransferase activity. Male mice lacking functional initiates from a CpG-rich repeat region adjoining copies of the Dnmt3l gene are sterile due to meiotic arrest, two B1 elements, despite previous reports that which is associated with the upregulation of endogenous SINEs are generally excluded from imprinted pro- retrotransposons (3). Females carrying null mutations in moters. Accordingly, we find that the Inpp5f_v3 the Dnmt3l gene fail to establish imprinted methylation promoter acquires methylation around the time of marks during oogenesis, but show no obvious effects on implantation, when many repeat families undergo de retrotransposon activity (6). -
Genetic Variant in 3' Untranslated Region of the Mouse Pycard Gene
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.437184; this version posted March 26, 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 4.0 International license. 1 2 3 Title: 4 Genetic Variant in 3’ Untranslated Region of the Mouse Pycard Gene Regulates Inflammasome 5 Activity 6 Running Title: 7 3’UTR SNP in Pycard regulates inflammasome activity 8 Authors: 9 Brian Ritchey1*, Qimin Hai1*, Juying Han1, John Barnard2, Jonathan D. Smith1,3 10 1Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 11 Cleveland, OH 44195 12 2Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 13 44195 14 3Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western 15 Reserve University, Cleveland, OH 44195 16 *, These authors contributed equally to this study. 17 Address correspondence to Jonathan D. Smith: email [email protected]; ORCID ID 0000-0002-0415-386X; 18 mailing address: Cleveland Clinic, Box NC-10, 9500 Euclid Avenue, Cleveland, OH 44195, USA. 19 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.437184; this version posted March 26, 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 4.0 International license. 20 Abstract 21 Quantitative trait locus mapping for interleukin-1 release after inflammasome priming and activation 22 was performed on bone marrow-derived macrophages (BMDM) from an AKRxDBA/2 strain intercross. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Synthesis of 2-Oxoglutarate Derivatives and Their Evaluation As Cosubstrates and Inhibitors of Human Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human Cite this: Chem. Sci.,2021,12,1327 b † All publication charges for this article aspartate/asparagine- -hydroxylase have been paid for by the Royal Society of Chemistry Lennart Brewitz, Yu Nakashima and Christopher J. Schofield * 2-Oxoglutarate (2OG) is involved in biological processes including oxidations catalyzed by 2OG oxygenases for which it is a cosubstrate. Eukaryotic 2OG oxygenases have roles in collagen biosynthesis, lipid metabolism, DNA/RNA modification, transcriptional regulation, and the hypoxic response. Aspartate/asparagine-b-hydroxylase (AspH) is a human 2OG oxygenase catalyzing post- translational hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs) in the endoplasmic reticulum. AspH is of chemical interest, because its Fe(II) cofactor is complexed by two rather than the typical three residues. AspH is upregulated in hypoxia and is a prognostic marker on the surface of cancer cells. We describe studies on how derivatives of its natural 2OG cosubstrate Creative Commons Attribution 3.0 Unported Licence. modulate AspH activity. An efficient synthesis of C3- and/or C4-substituted 2OG derivatives, proceeding via cyanosulfur ylid intermediates, is reported. Mass spectrometry-based AspH assays with >30 2OG derivatives reveal that some efficiently inhibit AspH via competing with 2OG as evidenced by crystallographic and solution analyses. Other 2OG derivatives can substitute for 2OG enabling substrate hydroxylation. The results show that subtle changes, e.g. methyl- to ethyl- substitution, can significantly alter the balance between catalysis and inhibition. -
The Abundance of Cis-Acting Loci Leading to Differential Allele
Yeo et al. BMC Genomics (2016) 17:620 DOI 10.1186/s12864-016-2922-9 RESEARCH ARTICLE Open Access The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits Seungeun Yeo1, Colin A. Hodgkinson1, Zhifeng Zhou1, Jeesun Jung2, Ming Leung1, Qiaoping Yuan1 and David Goldman1* Abstract Background: Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL’s for complex phenotypes. Results: We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/ 129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. -
Targeting the PI3K/AKT Pathway Overcomes Enzalutamide Resistance by Inhibiting
Author Manuscript Published OnlineFirst on May 5, 2020; DOI: 10.1158/1535-7163.MCT-19-0936 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Targeting the PI3K/AKT pathway overcomes enzalutamide resistance by inhibiting induction of the glucocorticoid receptor Remi Adelaiye-Ogala1, Berkley E. Gryder2, Yen Thi Minh Nguyen1, Aian Neil Alilin1, Adlai R. Grayson1, Wardah Bajwa1, Keith H. Jansson1, Michael L. Beshiri1, Supreet Agarwal1, Jose 1 1 1 1,3* Antonio Rodriguez-Nieves , Brian Capaldo , Kathleen Kelly and David J. VanderWeele 1Laboratory for Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH Bethesda, MD, 2Oncogenomics Section, Genetics Branch, National Cancer Institute, NIH Bethesda, MD, 3Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL. Running Title: Targeting the PI3K/AKT pathway and the glucocorticoid receptor Key Words: Prostate cancer, therapeutic resistance, AKT inhibition, androgen and glucocorticoid receptors Conflict of interest: The authors declare no conflict of interest. *Corresponding Author David J. VanderWeele, M.D., Ph.D. 676 N. St. Clair Suite 850 Chicago, IL . 60611 Phone: 312-926-2413 [email protected] Downloaded from mct.aacrjournals.org on October 1, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on May 5, 2020; DOI: 10.1158/1535-7163.MCT-19-0936 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. ABSTRACT The PI3K-AKT pathway has pleiotropic effects, and its inhibition has long been of interest in the management of prostate cancer, where a compensatory increase in PI3K signaling has been reported following Androgen Receptor (AR) blockade. -
ASPH (F-7): Sc-365012
SAN TA C RUZ BI OTEC HNOL OG Y, INC . ASPH (F-7): sc-365012 BACKGROUND APPLICATIONS Aspartyl/asparaginyl β-hydroxylase (ASPH) is a widely-expressed type II ASPH (F-7) is recommended for detection of ASPH of mouse, rat and human membrane protein involved in calcium homeostasis. Located in the endo - origin by Western Blotting (starting dilution 1:100, dilution range 1:100- plasmic reticulum, ASPH specifically hydroxylates an Asp or Asn residue in 1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml the epidermal growth factor-like (EGF) domains of several proteins, using of cell lysate)], immunofluorescence (starting dilution 1:50, dilution range iron as a cofactor. The ASPH gene encodes three proteins, ASPH, Junctin and 1:50-1:500), immunohistochemistry (including paraffin-embedded sections) Junctate (or Humbug), that differ significantly in their C-terminal domains. (starting dilution 1:50, dilution range 1:50-1:500) and solid phase ELISA These ASPH gene products are expressed as five transcript variants that dif - (starting dilution 1:30, dilution range 1:30-1:3000). fer by their roles in calcium storage and release, hydroxylation capabilities Suitable for use as control antibody for ASPH siRNA (h): sc-44989, ASPH and tissue specificity. While all ASPH variants are expressed in skeletal siRNA (m): sc-44990, ASPH shRNA Plasmid (h): sc-44989-SH, ASPH shRNA muscle, only some are detected in heart, brain, pancreas, placenta, lung, Plasmid (m): sc-44990-SH, ASPH shRNA (h) Lentiviral Particles: sc-44989-V liver and kidney tissues. In the lumen of the endoplasmic reticulum, ASPH and ASPH shRNA (m) Lentiviral Particles: sc-44990-V. -
Defining Endothelial Cell Functional Heterogeneity and Plasticity Using Single-Cell RNA-Sequencing
Defining endothelial cell functional heterogeneity and plasticity using single-cell RNA-sequencing The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Kalluri, Aditya Sreemadhav. 2019. Defining endothelial cell functional heterogeneity and plasticity using single-cell RNA- sequencing. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42013060 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 Title Pag e Defining endothelial cell functional heterogeneity and plasticity using single-cell RNA-sequencing A dissertation presented by Aditya Sreemadhav Kalluri to The Committee on Higher Degrees in Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biophysics Harvard University Cambridge, Massachusetts June 2019 i © 2019 – Aditya Sreemadhav Kalluri All rights reserved. Cop yrig ht ii Dissertation Advisor: Professor Elazer R. Edelman Aditya Sreemadhav Kalluri Defining endothelial cell functional heterogeneity and plasticity using single-cell RNA-sequencing Abstract The state of the endothelium defines vascular health – ensuring homeostasis when intact and driving pathology when dysfunctional. The endothelial cells (ECs) which comprise the endothelium are necessarily highly responsive and reflect their local mechanical, biological, and cellular context, making a concrete definition of endothelial state elusive. Heterogeneity is the hallmark of ECs and has long been studied in the context of structural and functional differences between organs and vascular beds. -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.