DOCSLIB.ORG

A Sleeping Beauty Transposon-Mediated Screen Identifies Murine Susceptibility Genes for Adenomatous Polyposis Coli (Apc)-Dependent Intestinal Tumorigenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Sleeping Beauty Transposon-Mediated Screen Identifies Murine Susceptibility Genes for Adenomatous Polyposis Coli (Apc)-Dependent Intestinal Tumorigenesis A Sleeping Beauty transposon-mediated screen identifies murine susceptibility genes for adenomatous polyposis coli (Apc)-dependent intestinal tumorigenesis Timothy K. Starra,1, Patricia M. Scottb, Benjamin M. Marshb, Lei Zhaob, Bich L. N. Thanb, M. Gerard O’Sullivana,c, Aaron L. Sarverd, Adam J. Dupuye, David A. Largaespadaa, and Robert T. Cormierb,1 aDepartment of Genetics, Cell Biology and Development, Center for Genome Engineering, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455; bDepartment of Biochemistry and Molecular Biology, University of Minnesota Medical School, Duluth, MN 55812; cDepartment of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108; dDepartment of Biostatistics and Informatics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455; and eDepartment of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242 Edited* by William F. Dove, University of Wisconsin, Madison, WI, and approved March 2, 2011 (received for review December 1, 2010) Min Min It is proposed that a progressive series of mutations and epigenetic conducted the screen in mice carrying the Apc allele. Apc events leads to human colorectal cancer (CRC) and metastasis. mice harbor a T→A nonsense mutation in the Apc gene (4, 5) Furthermore, data from resequencing of the coding regions of that results in a truncated protein product that is unable to bind human CRC suggests that a relatively large number of mutations β-catenin and promote its degradation, thus leading to abnormal occur in individual human CRC, most at low frequency. The levels of β-catenin protein and up-regulation of β-catenin target functional role of these low-frequency mutations in CRC, and genes such as cyclin D1 (Ccnd1) and myelocytomatosis oncogene specifically how they may cooperate with high-frequency muta- (C-Myc). The Min mutation corresponds to a mutational hotspot tions, is not well understood. One of the most common rate- in the human APC ortholog, and these mutations similarly result limiting mutations in human CRC occurs in the adenomatous in dysregulation of the Wnt/β-catenin signaling pathway. There is polyposis coli (APC) gene. To identify mutations that cooperate strong evidence that β-catenin dysregulation is a common trans- Min with mutant APC, we performed a forward genetic screen in mice formative event in tumorigenesis in the Apc mouse and in both Min carrying a mutant allele of Apc (Apc ) using Sleeping Beauty (SB) the inherited form of APC-deficient CRC (familial adenomatous Min Min MEDICAL SCIENCES transposon-mediated mutagenesis. Apc SB-mutagenized mice polyposis, FAP) and in sporadic CRC (6). Thus, the Apc mouse developed three times as many polyps as mice with the ApcMin is an informative genetic model for APC-deficient intestinal Min allele alone. Analysis of transposon common insertion sites (CIS) cancer. Apc mice on the C57BL/6J background strain rarely identified the Apc locus as a major target of SB-induced mutagen- survive beyond 120 d and can develop >100 tumors throughout esis, suggesting that SB insertions provide an efficient route to the small and large intestine, with the phenotype dependent on biallelic Apc inactivation. We also identified an additional 32 CIS diet, mouse strain, and other environmental factors (7, 8). Min genes/loci that may represent modifiers of the Apc phenotype. As in human CRC patients, loss of heterozygosity (LOH) Five CIS genes tested for their role in proliferation caused a signif- leading to inactivation of both alleles of Apc is necessary for Min icant change in cell viability when message levels were reduced in tumorigenesis to commence in Apc mice (9, 10). However, in Min human CRC cells. These findings demonstrate the utility of using contrast to LOH events in many human CRC, LOH in Apc transposon mutagenesis to identify low-frequency and cooperat- tumors occurs predominantly by homologous somatic recom- ing cancer genes; this approach will aid in the development of bination (11). In this study we screened for mutations that co- Min combinatorial therapies targeting this deadly disease. operate with the Apc mutation by randomly mutating genes through selective activation of SB transposition in intestinal cells Min cancer gene discovery | transgenic mice of Apc mice. The results of our screen support the importance of the loss of the second allele of Apc, because the great major- uman colorectal cancers (CRC) generally can be divided into ity of tumors analyzed contained a transposon insertion in Apc, Htwo classes based on whether they display chromosomal in- in particular in tumors in which there was maintenance of het- stability (CIN) or microsatellite instability (MSI). The majority erozygosity (MOH) for the Min allele. In addition to Apc,we fi of CRC (∼80–90%) have a CIN phenotype; the remaining cases identi ed 32 other genes and loci that probably facilitate the ApcMin are characterized by MSI (1). CRC displaying CIN frequently development of intestinal cancer in an model. The func- harbor allelic losses or mutations in adenomatous polyposis coli tion of these additional mutations could be to remove the re- Apc (APC), v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog quirement for LOH, or they may function in some other (KRAS), SMAD family member 4 (SMAD4), and tumor protein manner. The majority of these genes have not been associated fi p53 (TP53), whereas MSI-type CRC usually have a mutation in with CRC previously. To con rm that these genes play a causal one of six DNA mismatch repair genes (2). In both CIN and MSI CRC complete functional loss of a gatekeeper tumor suppressor gene typically is the rate-limiting event in intestinal cell trans- Author contributions: T.K.S., P.M.S., D.A.L., and R.T.C. designed research; T.K.S., P.M.S., APC B.M.M., L.Z., B.L.N.T., M.G.O., and R.T.C. performed research; A.J.D. contributed new formation. For CIN CRC, plays the key gate-keeping role, reagents/analytic tools; T.K.S., P.M.S., B.M.M., L.Z., B.L.N.T., M.G.O., A.L.S., and R.T.C. and its loss underlies the great majority of CIN CRC and >80% analyzed data; and T.K.S. wrote the paper. of all CRC. Although both classes of CRC are characterized by Conflict of interest statement: D.A.L. is a cofounder of, and has an equity interest in, high-frequency mutations, such as those in APC, it is evident that Discovery Genomics Inc. (DGI), a biotechnology company that is pursuing SB technology many more low-frequency mutations are required for CRC de- for human gene therapy. No resources or personnel from DGI were involved in this work. The University of Minnesota has filed a patent related to the work described in this paper. velopment, and the majority of these low-frequency mutations All other authors state no conflict of interest. are unknown (3). *This Direct Submission article had a prearranged editor. To identify these low-frequency mutations, we performed 1To whom correspondence may be addressed. E-mail: [email protected] or rcormier@d. a forward genetic screen in mice using the Sleeping Beauty (SB) umn.edu. DNA transposon as a mutagen in intestinal epithelial cells. To This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. focus on mutations that contribute to the CIN phenotype, we 1073/pnas.1018012108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1018012108 PNAS Early Edition | 1of6 Downloaded by guest on October 1, 2021 role in tumor development, we used siRNA to knock down the Rosa-26-LsL-SB11 allele but not the complete combination message levels of nine of the candidate genes in human colon of alleles required for transposition. This control group de- cancer cell lines and demonstrated that five of these genes af- veloped an average of 182 polyps (control group 1, Table 1), a fected the growth rate of these cells. result that was unexpected based on previous screens. It is pos- sible that the increased polyp number in these animals is caused Results by one or more modifiers linked to the Rosa26-LsL-SB11 trans- Design of a Forward Genetic Screen for CRC Genes. In a previous gene, because strain-specific modifiers are known to exist (19). Min study we demonstrated that SB transposon-mediated mutagen- Control animals carrying the Apc allele, T2/Onc, and/or Vil- +/+ esis in the intestinal tract of C57BL/6J Apc mice resulted in Cre, but not Rosa26-LsL-SB11 (control group 2, Table 1) devel- polyp formation (12). By mapping transposon insertions in DNA oped the same number of polyps as the control mice carrying the Min extracted from these tumors, we were able to identify 77 genetic Apc allele alone. Although the Rosa26-LsL-SB11 allele alone loci which probably harbored genes that, when mutated, con- contributes to polyp formation, the effect of active SB trans- tributed to tumor development. Because APC loss is rate limiting position was much greater, resulting in twice as many polyps in the in the development of most human CRC (13), we reasoned that test mice. In addition, the tumor burden was so extensive that Min SB mutagenesis in a mouse already harboring a mutation in Apc Apc SB test mice became moribund earlier than any of the Min might generate more tumors with a shorter latency and reveal three control groups (Table 1). Indeed, in a subset of Apc SB mutations that cooperate with Apc during tumor development. test mice the tumor load was very severe, with some animals de- To identify these genes, we performed a forward genetic screen veloping as many as 700 tumors.
Load more

Recommended publications
  • Discovery of the First Genome-Wide Significant Risk Loci for ADHD
    bioRxiv preprint doi: https://doi.org/10.1101/145581; this version posted June 3, 2017. 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. Discovery of the first genome-wide significant risk loci for ADHD Ditte Demontis,1,2,3† Raymond K. Walters,4,5† Joanna Martin,5,6,7 Manuel Mattheisen,1,2,3,8,9 Thomas D. Als,1,2,3 Esben Agerbo,1,10,11 Rich Belliveau,5 Jonas Bybjerg-Grauholm,1,12 Marie Bækvad-Hansen,1,12 Felecia Cerrato,5 Kimberly Chambert,5 Claire Churchhouse,4,5,13 Ashley Dumont,5 Nicholas Eriksson,14 Michael Gandal,15,16,17,18 Jacqueline Goldstein,4,5,13 Jakob Grove,1,2,3,19 Christine S. Hansen,1,12,20 Mads E. Hauberg,1,2,3 Mads V. Hollegaard,1,12 Daniel P. Howrigan,4,5 Hailiang Huang,4,5 Julian Maller,5,21 Alicia R. Martin,4,5,13 Jennifer Moran,5 Jonatan Pallesen,1,2,3 Duncan S. Palmer,4,5 Carsten B. Pedersen,1,10,11 Marianne G. Pedersen,1,10,11 Timothy Poterba,4,5,13 Jesper B. Poulsen,1,12 Stephan Ripke,4,5,13,22 Elise B. Robinson,4,23 Kyle F. Satterstrom,4,5,13 Christine Stevens,5 Patrick Turley,4,5 Hyejung Won,15,16 ADHD Working Group of the Psychiatric Genomics Consortium (PGC), Early Lifecourse & Genetic Epidemiology (EAGLE) Consortium, 23andMe Research Team, Ole A.
    [Show full text]
  • Farnesol-Induced Apoptosis in Human Lung Carcinoma Cells Is Coupled to the Endoplasmic Reticulum Stress Response
    Research Article Farnesol-Induced Apoptosis in Human Lung Carcinoma Cells Is Coupled to the Endoplasmic Reticulum Stress Response Joung Hyuck Joo,1 Grace Liao,1 Jennifer B. Collins,2 Sherry F. Grissom,2 and Anton M. Jetten1 1Cell Biology Section, LRB, and 2Microarray Group, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina Abstract range of fruits and vegetables (9, 10). Each isoprenoid has been Farnesol (FOH) and other isoprenoid alcohols induce apopto- shown to inhibit proliferation and induce apoptosis in a number of sis in various carcinoma cells and inhibit tumorigenesis in neoplastic cell lines from different origins (4, 11–14). In addition, in vivo these isoprenoids have been reported to be effective in chemo- several models. However, the mechanisms by which in vivo they mediate their effects are not yet fully understood. In this prevention and chemotherapy in various cancer models study, we show that FOH is an effective inducer of apoptosis in (10, 12, 15, 16). FOH has been reported to exhibit chemopreventive several lung carcinoma cells, including H460. This induction is effects in colon and pancreas carcinogenesis in rats (9, 17) whereas associated with activation of several caspases and cleavage of phase I and II clinical trials have indicated therapeutic potential poly(ADP-ribose) polymerase (PARP). To obtain insight into for POH (16, 18). The mechanisms by which these isoprenoids induce these effects are not yet fully understood. Isoprenoids have the mechanism involved in FOH-induced apoptosis, we compared the gene expression profiles of FOH-treated and been reported to inhibit posttranslational protein prenylation (19) control H460 cells by microarray analysis.
    [Show full text]
  • Multi-Targeted Mechanisms Underlying the Endothelial Protective Effects of the Diabetic-Safe Sweetener Erythritol
    Multi-Targeted Mechanisms Underlying the Endothelial Protective Effects of the Diabetic-Safe Sweetener Erythritol Danie¨lle M. P. H. J. Boesten1*., Alvin Berger2.¤, Peter de Cock3, Hua Dong4, Bruce D. Hammock4, Gertjan J. M. den Hartog1, Aalt Bast1 1 Department of Toxicology, Maastricht University, Maastricht, The Netherlands, 2 Global Food Research, Cargill, Wayzata, Minnesota, United States of America, 3 Cargill RandD Center Europe, Vilvoorde, Belgium, 4 Department of Entomology and UCD Comprehensive Cancer Center, University of California Davis, Davis, California, United States of America Abstract Diabetes is characterized by hyperglycemia and development of vascular pathology. Endothelial cell dysfunction is a starting point for pathogenesis of vascular complications in diabetes. We previously showed the polyol erythritol to be a hydroxyl radical scavenger preventing endothelial cell dysfunction onset in diabetic rats. To unravel mechanisms, other than scavenging of radicals, by which erythritol mediates this protective effect, we evaluated effects of erythritol in endothelial cells exposed to normal (7 mM) and high glucose (30 mM) or diabetic stressors (e.g. SIN-1) using targeted and transcriptomic approaches. This study demonstrates that erythritol (i.e. under non-diabetic conditions) has minimal effects on endothelial cells. However, under hyperglycemic conditions erythritol protected endothelial cells against cell death induced by diabetic stressors (i.e. high glucose and peroxynitrite). Also a number of harmful effects caused by high glucose, e.g. increased nitric oxide release, are reversed. Additionally, total transcriptome analysis indicated that biological processes which are differentially regulated due to high glucose are corrected by erythritol. We conclude that erythritol protects endothelial cells during high glucose conditions via effects on multiple targets.
    [Show full text]
  • Long, Noncoding RNA Dysregulation in Glioblastoma
    cancers Review Long, Noncoding RNA Dysregulation in Glioblastoma Patrick A. DeSouza 1,2 , Xuan Qu 1, Hao Chen 1,3, Bhuvic Patel 1 , Christopher A. Maher 2,4,5,6 and Albert H. Kim 1,6,* 1 Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] (P.A.D.); [email protected] (X.Q.); [email protected] (H.C.); [email protected] (B.P.) 2 Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] 3 Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 4 Department of Biomedical Engineering, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 5 McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 6 Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA * Correspondence: [email protected] Simple Summary: Developing effective therapies for glioblastoma (GBM), the most common primary brain cancer, remains challenging due to the heterogeneity within tumors and therapeutic resistance that drives recurrence. Noncoding RNAs are transcribed from a large proportion of the genome and remain largely unexplored in their contribution to the evolution of GBM tumors. Here, we will review the general mechanisms of long, noncoding RNAs and the current knowledge of how these impact heterogeneity and therapeutic resistance in GBM. A better understanding of the molecular drivers required for these aggressive tumors is necessary to improve the management and outcomes Citation: DeSouza, P.A.; Qu, X.; of this challenging disease.
    [Show full text]
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Downloaded from URL: Δ Δ Nated ALG-2 GF122) and GST-ALG-2 GF122 Was Cium.Uhnres.Utoronto.Ca/Vgm
    Inuzuka et al. BMC Structural Biology 2010, 10:25 http://www.biomedcentral.com/1472-6807/10/25 RESEARCH ARTICLE Open Access Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2ΔGF122) and structural roles of F122 in target recognition Tatsutoshi Inuzuka1, Hironori Suzuki1,2, Masato Kawasaki2, Hideki Shibata1, Soichi Wakatsuki2, Masatoshi Maki1* Abstract Background: ALG-2 (a gene product of PDCD6) belongs to the penta-EF-hand (PEF) protein family and Ca2 +-dependently interacts with various intracellular proteins including mammalian Alix, an adaptor protein in the ESCRT system. Our previous X-ray crystal structural analyses revealed that binding of Ca2+ to EF3 enables the side chain of R125 to move enough to make a primary hydrophobic pocket (Pocket 1) accessible to a short fragment of Alix. The side chain of F122, facing a secondary hydrophobic pocket (Pocket 2), interacts with the Alix peptide. An alternatively spliced shorter isoform, designated ALG-2ΔGF122, lacks Gly121Phe122 and does not bind Alix, but the structural basis of the incompetence has remained to be elucidated. Results: We solved the X-ray crystal structure of the PEF domain of ALG-2ΔGF122 in the Ca2+-bound form and compared it with that of ALG-2. Deletion of the two residues shortened a-helix 5 (a5) and changed the configuration of the R125 side chain so that it partially blocked Pocket 1. A wall created by the main chain of 121- GFG-123 and facing the two pockets was destroyed. Surprisingly, however, substitution of F122 with Ala or Gly, but not with Trp, increased the Alix-binding capacity in binding assays.
    [Show full text]
  • PDCD6 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50Ul [email protected] 100 Ul √ √ Web
    TD7978 PDCD6 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50ul [email protected] 100 uL √ √ Web www.ab-mart.com.cn Description: Calcium sensor that plays a key role in processes such as endoplasmic reticulum (ER)- Golgi vesicular transport, endosomal biogenesis or membrane repair. Acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium: calcium-binding triggers exposure of apolar surface, promoting interaction with different sets of proteins thanks to 3 different hydrophobic pockets, leading to translocation to membranes. Involved in ER-Golgi transport by promoting the association between PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes. Together with PEF1, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in ER-Golgi transport by regulating the size of COPII coats. In response to cytosolic calcium increase, the heterodimer formed with PEF1 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification. Involved in the regulation of the distribution and function of MCOLN1 in the endosomal pathway. Promotes localization and polymerization of TFG at endoplasmic reticulum exit site. Required for T-cell receptor-, Fas-, and glucocorticoid- induced apoptosis (By similarity). May mediate Ca(2+)-regulated signals along the death pathway: interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity. Its role in apoptosis may however be indirect, as suggested by knockout experiments (By similarity). May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphorylation of the Akt signaling pathway.
    [Show full text]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • (Q36.1;Q24) with a Concurrent Submicroscopic Del(4)(Q23q24) in an Adult with Polycythemia Vera
    cancers Case Report A Novel Acquired t(2;4)(q36.1;q24) with a Concurrent Submicroscopic del(4)(q23q24) in An Adult with Polycythemia Vera Eigil Kjeldsen Cancer Cytogenetic Section, HemoDiagnostic Laboratory, Department of Hematology, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 Aarhus C, Denmark; [email protected]; Tel.: +45-7846-7398; Fax: +45-7846-7399 Received: 6 June 2018; Accepted: 21 June 2018; Published: 25 June 2018 Abstract: Background: Polycythemia vera (PV) is a clonal myeloid stem cell disease characterized by a growth-factor independent erythroid proliferation with an inherent tendency to transform into overt acute myeloid malignancy. Approximately 95% of the PV patients harbor the JAK2V617F mutation while less than 35% of the patients harbor cytogenetic abnormalities at the time of diagnosis. Methods and Results: Here we present a JAK2V617F positive PV patient where G-banding revealed an apparently balanced t(2;4)(q35;q21), which was confirmed by 24-color karyotyping. Oligonucleotide array-based Comparative Genomic Hybridization (aCGH) analysis revealed an interstitial 5.4 Mb large deletion at 4q23q24. Locus-specific fluorescent in situ hybridization (FISH) analyses confirmed the mono-allelic 4q deletion and that it was located on der(4)t(2;4). Additional locus-specific bacterial artificial chromosome (BAC) probes and mBanding refined the breakpoint on chromosome 2. With these methods the karyotype was revised to 46,XX,t(2;4)(q36.1;q24)[18]/46,XX[7]. Conclusions: This is the first report on a PV patient associated with an acquired novel t(2;4)(q36.1;q24) and a concurrent submicroscopic deletion del(4)(q23q24).
    [Show full text]
  • PDCD6IP (Human) Recombinant Protein (P01)
    PDCD6IP (Human) Recombinant Preparation Method: in vitro wheat germ expression Protein (P01) system Purification: Glutathione Sepharose 4 Fast Flow Catalog Number: H00010015-P01 Storage Buffer: 50 mM Tris-HCI, 10 mM reduced Regulation Status: For research use only (RUO) Glutathione, pH=8.0 in the elution buffer. Product Description: Human PDCD6IP full-length ORF Storage Instruction: Store at -80°C. Aliquot to avoid ( AAH20066, 1 a.a. - 868 a.a.) recombinant protein with repeated freezing and thawing. GST-tag at N-terminal. Entrez GeneID: 10015 Sequence: MATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQ Gene Symbol: PDCD6IP YCRAAEELSKLRRAAVGRPLDKHEGALETLLRYYDQIC SIEPKFPFSENQICLTFTWKDAFDKGSLFGGSVKLALA Gene Alias: AIP1, Alix, DRIP4, HP95, MGC17003 SLGYEKSCVLFNCAALASQIAAEQNLDNDEGLKIAAKH YQFASGAFLHIKETVLSALSREPTVDISPDTVGTLSLIM Gene Summary: This gene encodes a protein thought LAQAQEVFFLKATRDKMKDAIIAKLANQAADYFGDAFK to participate in programmed cell death. Studies using QCQYKDTLPKEVFPVLAAKHCIMQANAEYHQSILAKQ mouse cells have shown that overexpression of this QKKFGEEIARLQHAAELIKTVASRYDEYVNVKDFSDKI protein can block apoptosis. In addition, the product of NRALAAAKKDNDFIYHDRVPDLKDLDPIGKATLVKSTP this gene binds to the product of the PDCD6 gene, a VNVPISQKFTDLFEKMVPVSVQQSLAAYNQRKADLVN protein required for apoptosis, in a calcium-dependent RSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSIL manner. This gene product also binds to endophilins, TKSRSVIEQGGIQTVDQLIKELPELLQRNREILDESLRLL proteins that regulate membrane shape during DEEEATDNDLRAKFKERWQRTPSNELYKPLRAEGTNF endocytosis.
    [Show full text]
  • Human Leucine-Rich Repeat Proteins: a Genome-Wide Bioinformatic Categorization and Functional Analysis in Innate Immunity
    Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity Aylwin C. Y. Nga,b,1, Jason M. Eisenberga,b,1, Robert J. W. Heatha, Alan Huetta, Cory M. Robinsonc, Gerard J. Nauc, and Ramnik J. Xaviera,b,2 aCenter for Computational and Integrative Biology, and Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; bThe Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142; and cMicrobiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved June 11, 2010 (received for review February 17, 2010) In innate immune sensing, the detection of pathogen-associated proteins have been implicated in human diseases to date, notably molecular patterns by recognition receptors typically involve polymorphisms in NOD2 in Crohn disease (8, 9), CIITA in leucine-rich repeats (LRRs). We provide a categorization of 375 rheumatoid arthritis and multiple sclerosis (10), and TLR5 in human LRR-containing proteins, almost half of which lack other Legionnaire disease (11). identifiable functional domains. We clustered human LRR proteins Most LRR domains consist of a chain of between 2 and 45 by first assigning LRRs to LRR classes and then grouping the proteins LRRs (12). Each repeat in turn is typically 20 to 30 residues long based on these class assignments, revealing several of the resulting and can be divided into a highly conserved segment (HCS) fol- protein groups containing a large number of proteins with certain lowed by a variable segment (VS).
    [Show full text]
  • GWAS Plus:'' General Cognitive Ability Is Substantially Heritable And
    Results of a ‘‘GWAS Plus:’’ General Cognitive Ability Is Substantially Heritable and Massively Polygenic Robert M. Kirkpatrick1*, Matt McGue1, William G. Iacono1, Michael B. Miller1, Saonli Basu2 1 University of Minnesota, Department of Psychology, Minneapolis, Minnesota, United States of America, 2 University of Minnesota, School of Public Health, Division of Biostatistics, Minneapolis, Minnesota, United States of America Abstract We carried out a genome-wide association study (GWAS) for general cognitive ability (GCA) plus three other analyses of GWAS data that aggregate the effects of multiple single-nucleotide polymorphisms (SNPs) in various ways. Our multigenerational sample comprised 7,100 Caucasian participants, drawn from two longitudinal family studies, who had been assessed with an age-appropriate IQ test and had provided DNA samples passing quality screens. We conducted the GWAS across ,2.5 million SNPs (both typed and imputed), using a generalized least-squares method appropriate for the different family structures present in our sample, and subsequently conducted gene-based association tests. We also conducted polygenic prediction analyses under five-fold cross-validation, using two different schemes of weighting SNPs. Using parametric bootstrapping, we assessed the performance of this prediction procedure under the null. Finally, we estimated the proportion of variance attributable to all genotyped SNPs as random effects with software GCTA. The study is limited chiefly by its power to detect realistic single-SNP or single-gene effects, none of which reached genome-wide significance, though some genomic inflation was evident from the GWAS. Unit SNP weights performed about as well as least-squares regression weights under cross-validation, but the performance of both increased as more SNPs were included in calculating the polygenic score.
    [Show full text]