Isoform-Specific Differences in the Effector Binding Regions
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Deregulated Gene Expression Pathways in Myelodysplastic Syndrome Hematopoietic Stem Cells
Leukemia (2010) 24, 756–764 & 2010 Macmillan Publishers Limited All rights reserved 0887-6924/10 $32.00 www.nature.com/leu ORIGINAL ARTICLE Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells A Pellagatti1, M Cazzola2, A Giagounidis3, J Perry1, L Malcovati2, MG Della Porta2,MJa¨dersten4, S Killick5, A Verma6, CJ Norbury7, E Hellstro¨m-Lindberg4, JS Wainscoat1 and J Boultwood1 1LRF Molecular Haematology Unit, NDCLS, John Radcliffe Hospital, Oxford, UK; 2Department of Hematology Oncology, University of Pavia Medical School, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 3Medizinische Klinik II, St Johannes Hospital, Duisburg, Germany; 4Division of Hematology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden; 5Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK; 6Albert Einstein College of Medicine, Bronx, NY, USA and 7Sir William Dunn School of Pathology, University of Oxford, Oxford, UK To gain insight into the molecular pathogenesis of the the World Health Organization.6,7 Patients with refractory myelodysplastic syndromes (MDS), we performed global gene anemia (RA) with or without ringed sideroblasts, according to expression profiling and pathway analysis on the hemato- poietic stem cells (HSC) of 183 MDS patients as compared with the the French–American–British classification, were subdivided HSC of 17 healthy controls. The most significantly deregulated based on the presence or absence of multilineage dysplasia. In pathways in MDS include interferon signaling, thrombopoietin addition, patients with RA with excess blasts (RAEB) were signaling and the Wnt pathways. Among the most signifi- subdivided into two categories, RAEB1 and RAEB2, based on the cantly deregulated gene pathways in early MDS are immuno- percentage of bone marrow blasts. -
Mouse Rras2 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Rras2 Knockout Project (CRISPR/Cas9) Objective: To create a Rras2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rras2 gene (NCBI Reference Sequence: NM_025846 ; Ensembl: ENSMUSG00000055723 ) is located on Mouse chromosome 7. 6 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 6 (Transcript: ENSMUST00000069449). Exon 3~5 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygote and heterozygote null mice are lymphopenic, resulting from diminished homeostatic proliferation and impaired T cell and B cell survival. Mice homozygous for a gene trap insertion exhibit retinal degeneration, and increased total body mass and total body fat. Exon 3 starts from about 32.19% of the coding region. Exon 3~5 covers 54.08% of the coding region. The size of effective KO region: ~8729 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 3 4 5 6 Legends Exon of mouse Rras2 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 1302 bp section upstream of Exon 3 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. -
COVID-19—The Potential Beneficial Therapeutic Effects of Spironolactone During SARS-Cov-2 Infection
pharmaceuticals Review COVID-19—The Potential Beneficial Therapeutic Effects of Spironolactone during SARS-CoV-2 Infection Katarzyna Kotfis 1,* , Kacper Lechowicz 1 , Sylwester Drozd˙ zal˙ 2 , Paulina Nied´zwiedzka-Rystwej 3 , Tomasz K. Wojdacz 4, Ewelina Grywalska 5 , Jowita Biernawska 6, Magda Wi´sniewska 7 and Miłosz Parczewski 8 1 Department of Anesthesiology, Intensive Therapy and Acute Intoxications, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; [email protected] 2 Department of Pharmacokinetics and Monitored Therapy, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] 3 Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland; [email protected] 4 Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, 71-252 Szczecin, Poland; [email protected] 5 Department of Clinical Immunology and Immunotherapy, Medical University of Lublin, 20-093 Lublin, Poland; [email protected] 6 Department of Anesthesiology and Intensive Therapy, Pomeranian Medical University in Szczecin, 71-252 Szczecin, Poland; [email protected] 7 Clinical Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] 8 Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, 71-455 Szczecin, Poland; [email protected] * Correspondence: katarzyna.kotfi[email protected]; Tel.: +48-91-466-11-44 Abstract: In March 2020, coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 was declared Citation: Kotfis, K.; Lechowicz, K.; a global pandemic by the World Health Organization (WHO). The clinical course of the disease is Drozd˙ zal,˙ S.; Nied´zwiedzka-Rystwej, unpredictable but may lead to severe acute respiratory infection (SARI) and pneumonia leading to P.; Wojdacz, T.K.; Grywalska, E.; acute respiratory distress syndrome (ARDS). -
Identification and Characterization of a Novel Human Testis-Specific
Biochemical and Biophysical Research Communications 285, 400–408 (2001) doi:10.1006/bbrc.2001.5165, available online at http://www.idealibrary.com on Identification and Characterization of a Novel Human Testis-Specific Kinase Substrate Gene Which Is Downregulated in Testicular Tumors Andreas Scorilas,*,† George M. Yousef,*,† Klaus Jung,‡ Ewa Rajpert-De Meyts,§ Stephan Carsten,‡ and Eleftherios P. Diamandis*,†,1 *Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; †Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada; ‡Department of Urology, University Hospital Charite, Humboldt University, Berlin, Germany; and §Department of Growth and Reproduction, Juliane Marie Centre, National University Hospital, Copenhagen, Denmark Received June 8, 2001 physiology, most probably in the process of spermato- By using the positional candidate gene approach, we genesis or spermiogenesis. © 2001 Academic Press identified a novel putative serine/threonine kinase Key Words: kinase substrates; testis-specific genes; substrate gene that maps to chromosome 19q13.3. gene mapping; gene characterization; TSKS; testis- Screening of expressed sequence tags and reverse specific kinase substrate; RRAS; IRF3; testicular transcription–polymerase chain reaction of total RNA cancer. from human tissues allowed us to establish the expres- sion of the gene and delineate its genomic organiza- tion (GenBank Accession No. AF200923). This gene (TSKS, for testis-specific kinase substrate) is com- Protein phosphorylation is the most common post- posed of 11 exons and 10 intervening introns and is translational protein modification in eukaryotes and a likely the human homolog of the mouse testis-specific fundamental mechanism for the direct or indirect con- serine kinase substrate gene. -
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid Leukemia Cells Supported Only by Exogenous Cytokines Is Associated with a Patient Subset with Adverse Outcome Annette K. Brenner, Elise Aasebø, Maria Hernandez-Valladares, Frode Selheim, Frode Berven, Ida-Sofie Grønningsæter, Sushma Bartaula-Brevik and Øystein Bruserud Supplementary Material S2 of S31 Table S1. Detailed information about the 68 AML patients included in the study. # of blasts Viability Proliferation Cytokine Viable cells Change in ID Gender Age Etiology FAB Cytogenetics Mutations CD34 Colonies (109/L) (%) 48 h (cpm) secretion (106) 5 weeks phenotype 1 M 42 de novo 241 M2 normal Flt3 pos 31.0 3848 low 0.24 7 yes 2 M 82 MF 12.4 M2 t(9;22) wt pos 81.6 74,686 low 1.43 969 yes 3 F 49 CML/relapse 149 M2 complex n.d. pos 26.2 3472 low 0.08 n.d. no 4 M 33 de novo 62.0 M2 normal wt pos 67.5 6206 low 0.08 6.5 no 5 M 71 relapse 91.0 M4 normal NPM1 pos 63.5 21,331 low 0.17 n.d. yes 6 M 83 de novo 109 M1 n.d. wt pos 19.1 8764 low 1.65 693 no 7 F 77 MDS 26.4 M1 normal wt pos 89.4 53,799 high 3.43 2746 no 8 M 46 de novo 26.9 M1 normal NPM1 n.d. n.d. 3472 low 1.56 n.d. no 9 M 68 MF 50.8 M4 normal D835 pos 69.4 1640 low 0.08 n.d. -
Supplemental Table 1. Complete Gene Lists and GO Terms from Figure 3C
Supplemental Table 1. Complete gene lists and GO terms from Figure 3C. Path 1 Genes: RP11-34P13.15, RP4-758J18.10, VWA1, CHD5, AZIN2, FOXO6, RP11-403I13.8, ARHGAP30, RGS4, LRRN2, RASSF5, SERTAD4, GJC2, RHOU, REEP1, FOXI3, SH3RF3, COL4A4, ZDHHC23, FGFR3, PPP2R2C, CTD-2031P19.4, RNF182, GRM4, PRR15, DGKI, CHMP4C, CALB1, SPAG1, KLF4, ENG, RET, GDF10, ADAMTS14, SPOCK2, MBL1P, ADAM8, LRP4-AS1, CARNS1, DGAT2, CRYAB, AP000783.1, OPCML, PLEKHG6, GDF3, EMP1, RASSF9, FAM101A, STON2, GREM1, ACTC1, CORO2B, FURIN, WFIKKN1, BAIAP3, TMC5, HS3ST4, ZFHX3, NLRP1, RASD1, CACNG4, EMILIN2, L3MBTL4, KLHL14, HMSD, RP11-849I19.1, SALL3, GADD45B, KANK3, CTC- 526N19.1, ZNF888, MMP9, BMP7, PIK3IP1, MCHR1, SYTL5, CAMK2N1, PINK1, ID3, PTPRU, MANEAL, MCOLN3, LRRC8C, NTNG1, KCNC4, RP11, 430C7.5, C1orf95, ID2-AS1, ID2, GDF7, KCNG3, RGPD8, PSD4, CCDC74B, BMPR2, KAT2B, LINC00693, ZNF654, FILIP1L, SH3TC1, CPEB2, NPFFR2, TRPC3, RP11-752L20.3, FAM198B, TLL1, CDH9, PDZD2, CHSY3, GALNT10, FOXQ1, ATXN1, ID4, COL11A2, CNR1, GTF2IP4, FZD1, PAX5, RP11-35N6.1, UNC5B, NKX1-2, FAM196A, EBF3, PRRG4, LRP4, SYT7, PLBD1, GRASP, ALX1, HIP1R, LPAR6, SLITRK6, C16orf89, RP11-491F9.1, MMP2, B3GNT9, NXPH3, TNRC6C-AS1, LDLRAD4, NOL4, SMAD7, HCN2, PDE4A, KANK2, SAMD1, EXOC3L2, IL11, EMILIN3, KCNB1, DOK5, EEF1A2, A4GALT, ADGRG2, ELF4, ABCD1 Term Count % PValue Genes regulation of pathway-restricted GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, SMAD protein phosphorylation 9 6.34 1.31E-08 ENG pathway-restricted SMAD protein GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, phosphorylation -
Deciphering the Nature of Trp73 Isoforms in Mouse
cancers Article Deciphering the Nature of Trp73 Isoforms in Mouse Embryonic Stem Cell Models: Generation of Isoform-Specific Deficient Cell Lines Using the CRISPR/Cas9 Gene Editing System Lorena López-Ferreras 1,2,†, Nicole Martínez-García 1,3,†, Laura Maeso-Alonso 1,2,‡, Marta Martín-López 1,4,‡, Ángela Díez-Matilla 1,‡ , Javier Villoch-Fernandez 1,2, Hugo Alonso-Olivares 1,2, Margarita M. Marques 3,5,* and Maria C. Marin 1,2,* 1 Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain; [email protected] (L.L.-F.); [email protected] (N.M.-G.); [email protected] (L.M.-A.); [email protected] (M.M.-L.); [email protected] (Á.D.-M.); [email protected] (J.V.-F.); [email protected] (H.A.-O.) 2 Departamento de Biología Molecular, Universidad de León, 24071 León, Spain 3 Departamento de Producción Animal, Universidad de León, 24071 León, Spain 4 Biomar Microbial Technologies, Parque Tecnológico de León, Armunia, 24009 León, Spain 5 Instituto de Desarrollo Ganadero y Sanidad Animal (INDEGSAL), Universidad de León, 24071 León, Spain * Correspondence: [email protected] (M.M.M.); [email protected] (M.C.M.); Tel.: +34-987-291757 Citation: López-Ferreras, L.; (M.M.M.); +34-987-291490 (M.C.M.) Martínez-García, N.; Maeso-Alonso, † Equal contribution. ‡ Equal contribution. L.; Martín-López, M.; Díez-Matilla, Á.; Villoch-Fernandez, J.; Simple Summary: The Trp73 gene is involved in the regulation of multiple biological processes Alonso-Olivares, H.; Marques, M.M.; Marin, M.C. Deciphering the Nature such as response to stress, differentiation and tissue architecture. -
Nck Adaptor Proteins Link Nephrin at the Podocyte Slit Diaphragm to the Hippo Regulator WTIP
Nck Adaptor Proteins Link Nephrin at the Podocyte Slit Diaphragm to the Hippo Regulator WTIP by Ava Keyvani Chahi A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Molecular and Cellular Biology Guelph, Ontario, Canada © Ava Keyvani Chahi, December, 2014 ABSTRACT NCK ADAPTOR PROTEINS LINK NEPHRIN AT THE PODOCYTE SLIT DIAPHRAGM TO THE HIPPO REGULATOR WTIP Ava Keyvani Chahi Advisor: University of Guelph, 2014 Dr. Nina Jones Podocytes are specialized epithelial cells that contribute to the kidney blood filtration barrier. Their unique cytoskeletal architecture and other complex biological signals are largely maintained by a modified adherens junction known as the slit diaphragm (SD). A major component of the SD is the transmembrane protein nephrin, which upon tyrosine phosphorylation of the intracellular domain regulates actin remodeling and cell survival. Nck adaptor proteins are a critical component of the filtration barrier and connect nephrin to actin-remodeling proteins by binding phosphotyrosine residues and proline-rich motifs. Herein we identify a novel Nck binding partner, Wilm’s tumor interacting protein (WTIP). WTIP is a transcription regulator in podocytes, though Nck is not nuclear localized under conditions known to induce WTIP nuclear accumulation. However, we demonstrate that WTIP is recruited to nephrin, upon nephrin tyrosine phosphorylation by Src Family Kinases, in an Nck-dependent manner. WTIP is an evolutionarily conserved negative regulator of the Hippo kinase pathway, which inhibits the transcription factor Yap. Yap activity promotes podocyte survival. We show in mice that cannot recruit Nck to nephrin, and by extension WTIP, that Yap protein levels are downregulated. -
RRAS2 Rabbit Polyclonal Antibody – TA308124 | Origene
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 TA308124 RRAS2 Rabbit Polyclonal Antibody Product data: Product Type: Primary Antibodies Applications: IHC, WB Recommended Dilution: IHC:1:100-1:1000; WB:1:1000-1:10000 Reactivity: Human, Mouse (Predicted: Bovine, Rhesus Monkey, Rat) Host: Rabbit Isotype: IgG Clonality: Polyclonal Immunogen: Recombinant fragment corresponding to a region within amino acids 1 and 204 of TC21 (Uniprot ID#P62070) Formulation: 0.1M Tris, 0.1M Glycine, 10% Glycerol (pH7). 0.01% Thimerosal was added as a preservative. Concentration: lot specific Purification: Purified by antigen-affinity chromatography. Conjugation: Unconjugated Storage: Store at -20°C as received. Stability: Stable for 12 months from date of receipt. Predicted Protein Size: 23 kDa Gene Name: related RAS viral (r-ras) oncogene homolog 2 Database Link: NP_001096139 Entrez Gene 66922 MouseEntrez Gene 365355 RatEntrez Gene 22800 Human P62070 Synonyms: TC21 Note: Seq homology of immunogen across species: Rat (100%), Rhesus Monkey (100%), Bovine (100%) Protein Families: Druggable Genome Protein Pathways: MAPK signaling pathway, Regulation of actin cytoskeleton, Tight junction 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 / 3 RRAS2 Rabbit Polyclonal Antibody – TA308124 Product images: Sample (50 ug of whole cell lysate). A: mouse brain. 12% SDS PAGE. TA308124 diluted at 1:5000. Sample (30 ug of whole cell lysate). -
RAP2 Mediates Mechanoresponses of the Hippo Pathway Zhipeng Meng1, Yunjiang Qiu2,3, Kimberly C
LETTER https://doi.org/10.1038/s41586-018-0444-0 RAP2 mediates mechanoresponses of the Hippo pathway Zhipeng Meng1, Yunjiang Qiu2,3, Kimberly C. Lin1, Aditya Kumar4, Jesse K. Placone4, Cao Fang1, Kuei-Chun Wang4,5, Shicong Lu1, Margaret Pan1, Audrey W. Hong1, Toshiro Moroishi1,6,7, Min Luo1,8, Steven W. Plouffe1, Yarui Diao2, Zhen Ye2, Hyun Woo Park1,9, Xiaoqiong Wang10, Fa-Xing Yu11, Shu Chien4,5, Cun-Yu Wang12, Bing Ren2,13, Adam J. Engler4 & Kun-Liang Guan1* Mammalian cells are surrounded by neighbouring cells and Extended Data Fig. 1b). Expression of the YAP and TAZ target extracellular matrix (ECM), which provide cells with structural genes CTGF, CYR61, and ANKRD1 was repressed by low stiffness in support and mechanical cues that influence diverse biological wild-type cells, but not in RAP2-KO cells (Fig. 1f). Similar results were processes1. The Hippo pathway effectors YAP (also known as YAP1) observed in human mesenchymal stem cells (Extended Data Fig. 1c–e), and TAZ (also known as WWTR1) are regulated by mechanical in which RAP2 deletion suppressed differentiation into adipocytes cues and mediate cellular responses to ECM stiffness2,3. Here we (Extended Data Fig. 1f, g). In luminal breast cancer MCF7 cells, identified the Ras-related GTPase RAP2 as a key intracellular ECM stiffness modulated localization of YAP and TAZ in a RAP2- signal transducer that relays ECM rigidity signals to control dependent manner, whereas the basal type MDA-MB-468 cells showed mechanosensitive cellular activities through YAP and TAZ. constitutively cytoplasmic localization of YAP and TAZ regardless RAP2 is activated by low ECM stiffness, and deletion of RAP2 of stiffness (Extended Data Fig. -
SHOC2–MRAS–PP1 Complex Positively Regulates RAF Activity and Contributes to Noonan Syndrome Pathogenesis
SHOC2–MRAS–PP1 complex positively regulates RAF activity and contributes to Noonan syndrome pathogenesis Lucy C. Younga,1, Nicole Hartiga,2, Isabel Boned del Ríoa, Sibel Saria, Benjamin Ringham-Terrya, Joshua R. Wainwrighta, Greg G. Jonesa, Frank McCormickb,3, and Pablo Rodriguez-Vicianaa,3 aUniversity College London Cancer Institute, University College London, London WC1E 6DD, United Kingdom; and bHelen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158 Contributed by Frank McCormick, September 18, 2018 (sent for review November 22, 2017; reviewed by Deborah K. Morrison and Marc Therrien) Dephosphorylation of the inhibitory “S259” site on RAF kinases CRAF/RAF1 mutations are also frequently found in NS and (S259 on CRAF, S365 on BRAF) plays a key role in RAF activation. cluster around the S259 14-3-3 binding site, enhancing CRAF ac- The MRAS GTPase, a close relative of RAS oncoproteins, interacts tivity through disruption of 14-3-3 binding (8) and highlighting the with SHOC2 and protein phosphatase 1 (PP1) to form a heterotri- key role of this regulatory step in RAF–ERK pathway activation. meric holoenzyme that dephosphorylates this S259 RAF site. MRAS is a very close relative of the classical RAS oncoproteins MRAS and SHOC2 function as PP1 regulatory subunits providing (H-, N-, and KRAS, hereafter referred to collectively as “RAS”) the complex with striking specificity against RAF. MRAS also func- and shares most regulatory and effector interactions as well as tions as a targeting subunit as membrane localization is required transforming ability (9–11). However, MRAS also has specific for efficient RAF dephosphorylation and ERK pathway regulation functions of its own, and uniquely among RAS family GTPases, it in cells. -
The Tumor Suppressor SCRIB Is a Negative Modulator of the Wnt/-Catenin Signaling Pathway
The Tumor Suppressor SCRIB is a Negative Modulator of the Wnt/β-Catenin Signaling Pathway Avais Daulat, Mônica Silveira Wagner, Alexandra Walton, Emilie Baudelet, Stéphane Audebert, Luc Camoin, Jean-Paul Borg To cite this version: Avais Daulat, Mônica Silveira Wagner, Alexandra Walton, Emilie Baudelet, Stéphane Audebert, et al.. The Tumor Suppressor SCRIB is a Negative Modulator of the Wnt/β-Catenin Signaling Pathway. Pro- teomics, Wiley-VCH Verlag, 2019, 19 (21-22), pp.1800487. 10.1002/pmic.201800487. hal-02518664 HAL Id: hal-02518664 https://hal.archives-ouvertes.fr/hal-02518664 Submitted on 7 Apr 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. PROTEOMICS Page 2 of 35 1 2 3 1 The tumor suppressor SCRIB is a negative modulator of the Wnt/-catenin signaling 4 5 6 2 pathway 7 8 3 Avais M. Daulat1,§, Mônica Silveira Wagner1,§, Alexandra Walton1, Emilie Baudelet2, 9 10 4 Stéphane Audebert2, Luc Camoin2, #,*, Jean-Paul Borg1,2,#,* 11 12 13 5 14 15 6 16 17 7 18 19 8 20 21 For Peer Review 1 22 9 Centre de Recherche en Cancérologie de Marseille, Equipe