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Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine
Published OnlineFirst September 14, 2016; DOI: 10.1158/2159-8290.CD-16-0263 RESEARCH BRIEF Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine Kinase Inhibition Mary T. Scott 1 , 2 , Koorosh Korfi 1 , 2 , Peter Saffrey 1 , Lisa E.M. Hopcroft 2 , Ross Kinstrie 1 , Francesca Pellicano 2 , Carla Guenther 1 , 2 , Paolo Gallipoli 2 , Michelle Cruz 1 , Karen Dunn 2 , Heather G. Jorgensen 2 , Jennifer E. Cassels 2 , Ashley Hamilton 2 , Andrew Crossan 1 , Amy Sinclair 2 , Tessa L. Holyoake 2 , and David Vetrie 1 ABSTRACT A major obstacle to curing chronic myeloid leukemia (CML) is residual disease main- tained by tyrosine kinase inhibitor (TKI)–persistent leukemic stem cells (LSC). These are BCR–ABL1 kinase independent, refractory to apoptosis, and serve as a reservoir to drive relapse or TKI resistance. We demonstrate that Polycomb Repressive Complex 2 is misregulated in chronic phase CML LSCs. This is associated with extensive reprogramming of H3K27me3 targets in LSCs, thus sensi- tizing them to apoptosis upon treatment with an EZH2-specifi c inhibitor (EZH2i). EZH2i does not impair normal hematopoietic stem cell survival. Strikingly, treatment of primary CML cells with either EZH2i or TKI alone caused signifi cant upregulation of H3K27me3 targets, and combined treatment further potentiated these effects and resulted in signifi cant loss of LSCs compared to TKI alone, in vitro , and in long-term bone marrow murine xenografts. Our fi ndings point to a promising epigenetic-based thera- peutic strategy to more effectively target LSCs in patients with CML receiving TKIs. SIGNIFICANCE: In CML, TKI-persistent LSCs remain an obstacle to cure, and approaches to eradicate them remain a signifi cant unmet clinical need. -
Gene Essentiality Landscape and Druggable Oncogenic Dependencies in Herpesviral Primary Effusion Lymphoma
ARTICLE DOI: 10.1038/s41467-018-05506-9 OPEN Gene essentiality landscape and druggable oncogenic dependencies in herpesviral primary effusion lymphoma Mark Manzano1, Ajinkya Patil1, Alexander Waldrop2, Sandeep S. Dave2, Amir Behdad3 & Eva Gottwein1 Primary effusion lymphoma (PEL) is caused by Kaposi’s sarcoma-associated herpesvirus. Our understanding of PEL is poor and therefore treatment strategies are lacking. To address this 1234567890():,; need, we conducted genome-wide CRISPR/Cas9 knockout screens in eight PEL cell lines. Integration with data from unrelated cancers identifies 210 genes as PEL-specific oncogenic dependencies. Genetic requirements of PEL cell lines are largely independent of Epstein-Barr virus co-infection. Genes of the NF-κB pathway are individually non-essential. Instead, we demonstrate requirements for IRF4 and MDM2. PEL cell lines depend on cellular cyclin D2 and c-FLIP despite expression of viral homologs. Moreover, PEL cell lines are addicted to high levels of MCL1 expression, which are also evident in PEL tumors. Strong dependencies on cyclin D2 and MCL1 render PEL cell lines highly sensitive to palbociclib and S63845. In summary, this work comprehensively identifies genetic dependencies in PEL cell lines and identifies novel strategies for therapeutic intervention. 1 Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. 2 Duke Cancer Institute and Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA. 3 Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. Correspondence and requests for materials should be addressed to E.G. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:3263 | DOI: 10.1038/s41467-018-05506-9 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-05506-9 he human oncogenic γ-herpesvirus Kaposi’s sarcoma- (IRF4), a critical oncogene in multiple myeloma33. -
Identifying and Mapping Cell-Type-Specific Chromatin PNAS PLUS Programming of Gene Expression
Identifying and mapping cell-type-specific chromatin PNAS PLUS programming of gene expression Troels T. Marstranda and John D. Storeya,b,1 aLewis-Sigler Institute for Integrative Genomics, and bDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544 Edited by Wing Hung Wong, Stanford University, Stanford, CA, and approved January 2, 2014 (received for review July 2, 2013) A problem of substantial interest is to systematically map variation Relating DHS to gene-expression levels across multiple cell in chromatin structure to gene-expression regulation across con- types is challenging because the DHS represents a continuous ditions, environments, or differentiated cell types. We developed variable along the genome not bound to any specific region, and and applied a quantitative framework for determining the exis- the relationship between DHS and gene expression is largely tence, strength, and type of relationship between high-resolution uncharacterized. To exploit variation across cell types and test chromatin structure in terms of DNaseI hypersensitivity and genome- for cell-type-specific relationships between DHS and gene expres- wide gene-expression levels in 20 diverse human cell types. We sion, the measurement units must be placed on a common scale, show that ∼25% of genes show cell-type-specific expression ex- the continuous DHS measure associated to each gene in a well- plained by alterations in chromatin structure. We find that distal defined manner, and all measurements considered simultaneously. regions of chromatin structure (e.g., ±200 kb) capture more genes Moreover, the chromatin and gene-expression relationship may with this relationship than local regions (e.g., ±2.5 kb), yet the local only manifest in a single cell type, making standard measures of regions show a more pronounced effect. -
Viewed Under 23 (B) Or 203 (C) fi M M Male Cko Mice, and Largely Unaffected Magni Cation; Scale Bars, 500 M (B) and 50 M (C)
BRIEF COMMUNICATION www.jasn.org Renal Fanconi Syndrome and Hypophosphatemic Rickets in the Absence of Xenotropic and Polytropic Retroviral Receptor in the Nephron Camille Ansermet,* Matthias B. Moor,* Gabriel Centeno,* Muriel Auberson,* † † ‡ Dorothy Zhang Hu, Roland Baron, Svetlana Nikolaeva,* Barbara Haenzi,* | Natalya Katanaeva,* Ivan Gautschi,* Vladimir Katanaev,*§ Samuel Rotman, Robert Koesters,¶ †† Laurent Schild,* Sylvain Pradervand,** Olivier Bonny,* and Dmitri Firsov* BRIEF COMMUNICATION *Department of Pharmacology and Toxicology and **Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland; †Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts; ‡Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia; §School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; |Services of Pathology and ††Nephrology, Department of Medicine, University Hospital of Lausanne, Lausanne, Switzerland; and ¶Université Pierre et Marie Curie, Paris, France ABSTRACT Tight control of extracellular and intracellular inorganic phosphate (Pi) levels is crit- leaves.4 Most recently, Legati et al. have ical to most biochemical and physiologic processes. Urinary Pi is freely filtered at the shown an association between genetic kidney glomerulus and is reabsorbed in the renal tubule by the action of the apical polymorphisms in Xpr1 and primary fa- sodium-dependent phosphate transporters, NaPi-IIa/NaPi-IIc/Pit2. However, the milial brain calcification disorder.5 How- molecular identity of the protein(s) participating in the basolateral Pi efflux remains ever, the role of XPR1 in the maintenance unknown. Evidence has suggested that xenotropic and polytropic retroviral recep- of Pi homeostasis remains unknown. Here, tor 1 (XPR1) might be involved in this process. Here, we show that conditional in- we addressed this issue in mice deficient for activation of Xpr1 in the renal tubule in mice resulted in impaired renal Pi Xpr1 in the nephron. -
PLEKHM2 Mutation Leads to Abnormal Localization of Lysosomes, Impaired
Human Molecular Genetics, 2015, Vol. 24, No. 25 7227–7240 doi: 10.1093/hmg/ddv423 Advance Access Publication Date: 12 October 2015 Original Article ORIGINAL ARTICLE PLEKHM2 mutation leads to abnormal localization Downloaded from of lysosomes, impaired autophagy flux and associates with recessive dilated cardiomyopathy and left ventricular noncompaction http://hmg.oxfordjournals.org/ Emad Muhammad1,†, Aviva Levitas2,†, Sonia R. Singh3,4, Alex Braiman1, Rivka Ofir5, Sharon Etzion5, Val C. Sheffield6, Yoram Etzion5,7, Lucie Carrier3,4 and Ruti Parvari1,8,* 1Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, 2Department of Pediatric Cardiology, Soroka University Medical Center and at Bibliothekssystem Universitaet Hamburg on December 2, 2015 Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel, 3Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany, 4DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany, 5Regenerative Medicine and Stem Cell Research Center, Beer-Sheva 84105, Israel, 6Department of Pediatrics, Division of Medical Genetics and Hughes Medical Institute, University of Iowa, Iowa City, IA 52242, USA, 7Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel and 8National Institute for Biotechnology in the Negev, Ben- Gurion University of the Negev, Beer-Sheva, Israel *To whom correspondence should be addressed. Tel: +972 86479967; Fax: +972 86472983; Email: [email protected] Abstract Gene mutations, mostly segregating with a dominant mode of inheritance, are important causes of dilated cardiomyopathy (DCM), a disease characterized by enlarged ventricular dimensions, impaired cardiac function, heart failure and high risk of death. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Vascular Homeostasis and Inflammation in Health and Disease
International Journal of Molecular Sciences Review Vascular Homeostasis and Inflammation in Health and Disease—Lessons from Single Cell Technologies Olga Bondareva * and Bilal N. Sheikh * Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103 Leipzig, Germany * Correspondence: [email protected] (O.B.); [email protected] (B.N.S.); Tel.: +49-341-9722912 (B.N.S.) Received: 5 June 2020; Accepted: 30 June 2020; Published: 30 June 2020 Abstract: The vascular system is critical infrastructure that transports oxygen and nutrients around the body, and dynamically adapts its function to an array of environmental changes. To fulfil the demands of diverse organs, each with unique functions and requirements, the vascular system displays vast regional heterogeneity as well as specialized cell types. Our understanding of the heterogeneity of vascular cells and the molecular mechanisms that regulate their function is beginning to benefit greatly from the rapid development of single cell technologies. Recent studies have started to analyze and map vascular beds in a range of organs in healthy and diseased states at single cell resolution. The current review focuses on recent biological insights on the vascular system garnered from single cell analyses. We cover the themes of vascular heterogeneity, phenotypic plasticity of vascular cells in pathologies such as atherosclerosis and cardiovascular disease, as well as the contribution of defective microvasculature to the development of neurodegenerative disorders such as Alzheimer’s disease. Further adaptation of single cell technologies to study the vascular system will be pivotal in uncovering the mechanisms that drive the array of diseases underpinned by vascular dysfunction. -
Contributions of the Renin Angiotensin System to Fear Memory and Fear Conditioned Cardiovascular Responses
Contributions of the Renin Angiotensin System to Fear Memory and Fear Conditioned Cardiovascular Responses by Adam Swiercz B.S. in Biology, May 2006, The George Washington University M.P.S. in Molecular Biotechnology, May 2009, The George Washington University M.S. in Physiology, May 2011, Georgetown University A Dissertation submitted to The Faculty of The Columbian College of Arts & Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy January 10, 2020 Dissertation co-directed by Paul J. Marvar Associate Professor of Pharmacology and Physiology and David Mendelowitz Professor of Pharmacology & Physiology The Columbian College of Arts and Sciences of The George Washington University certifies that Adam Swiercz has passed the Final Examination for the degree of Doctor of Philosophy as of October 2nd, 2019. This is the final and approved form of the dissertation. Contributions of the Renin Angiotensin System to Fear Memory and Fear Conditioned Cardiovascular Responses Adam Swiercz Dissertation Research Committee: Paul J. Marvar, Associate Professor of Pharmacology & Physiology, Dissertation Co-Director David Mendelowitz, Professor of Pharmacology & Physiology, Dissertation Co-Director Abigail Polter, Assistant Professor of Pharmacology & Physiology, Committee Member Colin Young, Assistant Professor of Pharmacology & Physiology, Committee Member ii © Copyright 2020 by Adam Swiercz All rights reserved iii Acknowledgements I would like to thank and acknowledge Dr. Paul Marvar, whose mentorship has made this dissertation possible. It has been a pleasure working in your lab, and I am truly grateful for your support and encouragement throughout the years. Thanks to the current and former members of the Marvar lab who have made my time at GW a rewarding and enjoyable experience. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
C-Terminal Region (ARP58987 P050) Data Sheet
CASP3 antibody - C-terminal region (ARP58987_P050) Data Sheet Product Number ARP58987_P050 Product Name CASP3 antibody - C-terminal region (ARP58987_P050) Size 50ug Gene Symbol CASP3 Alias Symbols CPP32; CPP32B; SCA-1 Nucleotide Accession# NM_032991 Protein Size (# AA) 277 amino acids Molecular Weight 12kDa Product Format Lyophilized powder NCBI Gene Id 836 Host Rabbit Clonality Polyclonal Official Gene Full Name Caspase 3, apoptosis-related cysteine peptidase Gene Family CASP This is a rabbit polyclonal antibody against CASP3. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Peptide Sequence Synthetic peptide located within the following region: NLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFG CASP3 is a protein which is a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce two subunits, Description of Target large and small, that dimerize to form the active enzyme. This protein cleaves and activates caspases 6, 7 and 9, and the protein itself is processed by caspases 8, 9 and 10. It is the predominant caspase involved in the cleavage of amyloid-beta 4A precursor protein, which is associated with neuronal death in Alzheimer's disease. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
PLEKHM2 (NM 015164) Human Recombinant Protein – TP320299
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP320299 PLEKHM2 (NM_015164) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human pleckstrin homology domain containing, family M (with RUN domain) member 2 (PLEKHM2) Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 112.6 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_055979 Locus ID: 23207 UniProt ID: Q8IWE5 RefSeq Size: 4231 Cytogenetics: 1p36.21 RefSeq ORF: 3057 Synonyms: SKIP This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 PLEKHM2 (NM_015164) Human Recombinant Protein – TP320299 Summary: This gene encodes a protein that binds the plus-end directed microtubule motor protein kinesin, together with the lysosomal GTPase Arl8, and is required for lysosomes to distribute away from the microtubule-organizing center. The encoded protein belongs to the multisubunit BLOC-one-related complex that regulates lysosome positioning.