DOCSLIB.ORG

Link to Dr. Hunter's Slides

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Link to Dr. Hunter's Slides Making Sense of the Science of WM Zachary Hunter Bing Center for WM Dana-Farber Cancer Institute Harvard Medical School Bing Center for WM Harvard Research at the Medical Dana-Farber School Cancer Institute e Bing Center for WM Research at the Dana-Farber Cancer Institute Understanding Genetics If you only had four letters to work with, what kind of story could you tell? Genomics is easy… ➢ Deoxyribonucleic Acid (DNA) is made of complex molecules called nucleotides. There are 4 types abbreviated A,T,C,G. ➢ Nucleotide bases form stables pairs: A-T and C-G. Two complimentary strands of these bases form DNA. ➢ DNA is broken into 23 long strands known as chromosomes. ➢ The sections of the DNA that contain instructions on how to build proteins are called genes. ➢ Genes in the DNA are transcribed into a single strand of similar nucleotides called Ribonucleic Acid (RNA) and this “message” is processed by the cell and turned into protein. Something easy with ~ 3,000,000,000 pieces can be really complicated… For context, computers operate with just two “bases” 0 and 1. With enough 0s and 1s it turns out you can make computer’s do some pretty impressive and complicated stuff. DNA has 4 bases, x 3 Billion with a lot more chemical and spatial annotation. This makes IBM’s Watson look simple by comparison, even if it does beat us at Jeopardy DNA – RNA – Protein • Transcribed • Stores Provides from DNA information structure, • Encodes signaling, • Used as a instructions and carries template to make out most for RNA protein cellular work • Genes are regions of the DNA that are transcribed into RNA • RNA carries the DNA code out into the rest of the cell where it can be used as instructions to make protein How to make it all fit… 3 billion base pairs strung end to end is about 40 inches in length. This quantity of DNA resides inside the nucleus of every cell in your body Needless to say, this is a tightly controlled process. Our apologies, the DNA you are looking for is temporarily unavailable… Laura, B. (2008) Epigenomics: The new tools in studying complex disease. Nature Education Introducing the “omes” The Genome The Transcriptome The Proteome • Transcribed • Stores Provides from DNA information structure, • Encodes signaling, • Used as a instructions and carries template to make out most for RNA protein cellular work The Epigenome The genome as the cell’s operating system The Environment The operating system of your Protein computer (Windows/Max OSX/Linux) provides a set of tools to allow programs to be loaded and run. Every laptop may have the same operating system, but no one uses their RNA DNA laptop in exactly the same way DNA to Protein… translation please? ➢ Proteins are folded chains of amino acids ➢ Just like there are 4 bases that make of DNA, there are 20 different amino acids ➢ Groups of 3 DNA base pairs, called codons, code code for specific amino acids for example: DNA:CTC -> RNA:CUC -> Leucine ➢ T (thymidine) in the DNA is transcribed as U (uracil) in the RNA. DNA to Protein… translation please? DNA Amino Acid Translation XGAT GAT TAC CTG DDYL ATG ATT ACC TGC MITC Frame-shift The Genomics of WM Understanding the WM “Operating System” Mutation and Cancer Cancer can be caused by accidental changes in the genome known as mutations As these accumulate, genes start to gain new functions, or lose old ones At the point that the cells start to multiply in an uncontrolled way, we call it cancer A single base pair TLR4 IL1R mutation the gene MYD88 is found in over MYD88 Signaling Wait…95% of Didn’tWM I promise that T I R A thisNFKB would Nuclear Translocationbe easy? in P The BCWM.1 Cell Line MYD88 MYD88 BTK I RA 4 K AK 4 IR I RA 1 K AK 1 IR <- This doesn’t look easy! 2 TA B B TRAF6 A 1 T TAK1 NEMO Control MYD88 Inhibitor IKKα IKKβ Proteasomal IκBα Degrada on p50 p65 Nuclear Transloca on and Signaling Treon et al NEJM 2012 Don’t Sweat the details unless necessary… Simple Complex Ouch… TLRs TLR4 IL1R T I R MYD88 A P MYD88 MYD88 IRAK1/4 BTK BTK I RA 4 K AK 4 IR I RA 1 K AK 1 IR IkBα 2 TA p50 p65 B B TRAF6 A 1 T TAK1 NEMO IKKα IKKβ growth survival Proteasomal IκBα NFKBp50 p65 Degrada on p50 p65 Nuclear Transloca on and Signaling MYD88 L265P in WM/IGM MGUS METHOD TISSUE WM IGM MGUS Treon WGS/Sanger BM CD19+ 91% 10% Xu AS-PCR BM CD19+ 93% 54% Gachard PCR BM 70% Varettoni AS-PCR BM 100% 47% Landgren Sanger BM 54% Jiminez AS-PCR BM 86% 87% Poulain PCR BM CD19+ 80% Argentou PCR-RFLP BM 92% 1/1 MGUS Willenbacher Sanger BM 86% Mori AS-PCR/BSiE1 BM 80% Ondrejka AS-PCR BM 100% Ansell WES/AS-PCR BM 97% Patkar AS-PCR BM 85% Updated from Treon and Hunter. Blood. 2013;121(22):4434-6. 17 A single base pair TLR4 IL1R mutation the gene MYD88 is found in over MYD88 Signaling 90% of WM T I R A NFKB Nuclear Translocation in P The BCWM.1 Cell Line MYD88 MYD88 BTK I RA 4 K AK 4 IR I Ibrutinib RA 1 K AK 1 IR 2 TA B B TRAF6 A 1 T TAK1 NEMO Control MYD88 Inhibitor IKKα IKKβ Proteasomal IκBα Degrada on p50 p65 Nuclear Transloca on and Signaling Guang Yang, PhD Yang et al. Blood 2013 WHIM-like CXCR4 mutations in Waldenstrom’s Macroglobulinemia • 30-40% of WM patients CXCL12/SDF-1a • Occur in the C-terminal domain (same site as WHIM patients) • Nonsense and frameshift mutations Most common • Associated with high mutation is S338X IGM, hyperviscosity. • Multiple CXCR4 352 S338X mutations can be present within an individual patient. Hunter et al, Blood 2013; Rocarro et al, Blood 2014: Poulain et al, Blood 2016; Poulain et al, CCR 2016; Xu et al, BJH 2016; Varettoni et al, Haematologica 2017. Hunter et al, Blood 2013 WHIM Syndrome Like Mutations in CXCR4 Wu et al, Science, 2010 Using Mutation Status to Understand Responses to Ibrutinib Serum IgM Response Hemoglobin Response 5 5 . 1 1 8 8 . s l 1 1 s l e e v v e e L L e e n i n l i l e e s s a 6 6 a . B B 1 1 0 0 o o . t t 1 1 e e v v a a l l e e R R 4 4 . e e minor response s 1 1 s n n o o p p s s e e 5 5 R . R 0 0 par al response n i M b g 2 2 o I . l 1 1 g m o u m r e e S H t t s s e e B B very good 0 0 0 0 . par al response 1 1 0 0 L265P WT L265P WHIM WT WT MYD88L265PCXCR4 MYD88 WHIMCXCR4 MYD88 WTCXCR4 MYD88L265PL265PCXCR4WT MYD88L2WHIM65PCXCR4WHIM MYD88WWTTCXCR4WT Treon et al, NEJM 2015 Hunter et al, Blood Advances 2018 Mutations in MYD88WT WM Hunter et al, Blood Advances 2018 Ibrutinib in MYD88WT WM Serum IgM Response Somatic Deletions on Chromosome 6q Whole GenomeSequencing Deletions on Chromosome 6q Chromosome on Deletions 0 1 s t PLEKHG1 9 n e i t a HIVEP2 8 P d signaling and BCL2CXCR4 MYD88, for genesregulatory target Macroglobulinemia in common deletionsare 6q Chromosome Luisa Maria e HLA-DQA/B BCLAF1 ARID1B t 7 c e f f COL19A1 BACH2 FOXO3 A 6 f o r CD83 EEF1A1 PRDM1 MAN1A1 TNFAIP3 CCR6 5 e b m Detection Threshold IBTK u 4 N 3 Guerrera Waldenström’s 1 1 3 3 2 1 3 1 3 1 2 1 3 1 2 1 3 1 3 1 2 3 1 2 3 1 2 3 . 3 . 3 3 . 3 2 3 5 1 6 7 . 5 5 5 4 4 2 2 1 1 2 2 1 4 4 6 6 2 3 3 4 4 4 5 5 5 2 1 1 1 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 p q q q q q q 2 2 2 p p p p p p p p p p p p q q q q q q q q q q q q q p q q Chromosome 6 , and and , : MYD88Mutant WM MYD88WT WM Guererra et al, Haematologica 2018 Guererra et al, Haematologica 2018 Overlapping signatures between deletion 6q and CXCR4WHIM Gene Chrom Start End LogFC Del6q LogFC CXCR4mut FAM110C chr2 38813 41627 -3.61 -3.29 WNK2 chr9 95947211 95947892 -1.88 -4.92 SGCD chr5 155135062 155135118 -1.87 -3.26 CCDC141 chr2 179694483 179699167 -1.67 -1.30 PKHD1L1 chr8 110374705 110374882 -1.56 -1.47 EML6 chr2 54952148 54952395 -1.49 -1.03 ZNF214 chr11 7020548 7022786 -1.39 -1.85 SYTL2 chr11 85405264 85406383 -1.32 -1.30 C11orf92 chr11 111164113 111169391 -1.31 -0.91 IL17RB chr3 53880576 53880675 -1.26 -2.04 ZNF215 chr11 6947653 6947916 -1.19 -1.29 ZNF804A chr2 185463092 185463797 -1.12 -0.69 LINC00271 chr6 135818938 135819138 -0.99 -0.69 CDK14 chr7 90095737 90095827 -0.76 -0.57 FOXO3 chr6 108881025 108881218 -0.75 -0.54 CYP4V2 chr4 187112673 187113191 -0.69 -0.53 IGF2R chr6 160390130 160390427 -0.53 -0.43 EPS15 chr1 51819934 51822518 -0.39 -0.37 HRK chr12 117299026 117299271 1.84 2.02 Putting it all together : Signaling Networks in WM How we can use machine learning and bid data to better understand WM Negative Feedback Loops: Self Regulating Biological Networks A centrifugal governor is a mechanical analog to biological negative feedback loops.
Load more

Recommended publications
  • (BCLAF1) ELISA Kit Catalogue No.:Abx503645
    Datasheet Version: 1.0.0 Revision date: 14 Jan 2021 Human Bcl-2-associated transcription factor 1 (BCLAF1) ELISA Kit Catalogue No.:abx503645 Human Bcl-2-associated transcription factor 1 (BCLAF1) ELISA Kit is an ELISA Kit for the in vitro quantitative measurement of Human Bcl-2-associated transcription factor 1 (BCLAF1) concentrations in tissue homogenates, cell lysates and other biological fluids. Target: Bcl-2-associated transcription factor 1 (BCLAF1) Reactivity: Human Tested Applications: ELISA Recommended dilutions: Optimal dilutions/concentrations should be determined by the end user. Storage: Shipped at 4 °C. Upon receipt, store the kit according to the storage instruction in the kit's manual. Validity: The validity for this kit is 6 months. Stability: The stability of the kit is determined by the rate of activity loss. The loss rate is less than 5% within the expiration date under appropriate storage conditions. To minimize performance fluctuations, operation procedures and lab conditions should be strictly controlled. It is also strongly suggested that the whole assay is performed by the same user throughout. UniProt Primary AC: Q9NYF8 (UniProt, ExPASy) Gene Symbol: ForBCLAF1 Reference Only KEGG: hsa:9774 Test Range: 0.156 ng/ml - 10 ng/ml Standard Form: Lyophilized ELISA Detection: Colorimetric v1.0.0 Abbexa Ltd, Cambridge, UK · Phone: +44 1223 755950 · Fax: +44 1223 755951 1 Abbexa LLC, Houston, TX, USA · Phone: +1 832 327 7413 www.abbexa.com · Email: [email protected] Datasheet Version: 1.0.0 Revision date: 14 Jan 2021 ELISA Data: Quantitative Sample Type: Tissue homogenates, cell lysates and other biological fluids. Note: This product is for research use only.
    [Show full text]
  • Downloaded with Ma- Disease D D
    bioRxiv preprint doi: https://doi.org/10.1101/483065; this version posted November 29, 2018. 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. F1000Research 2016 - DRAFT ARTICLE (PRE-SUBMISSION) Bioinformatics Approach to Identify Diseasome and Co- morbidities Effect of Mitochondrial Dysfunctions on the Progression of Neurological Disorders Md. Shahriare Satu1, Koushik Chandra Howlader2, Tajim Md. Niamat Ullah Akhund3, Fazlul Huq4, Julian M.W. Quinn5, and Mohammad Ali Moni4,5 1Dept. of CSE, Gono Bishwabidyalay, Dhaka, Bangladesh 2Dept. of CSTE, Noakhali Science and Technology University, Noakhali, Bangladesh 3Institute of Information Technology, Jahangirnagar University, Dhaka, Bangladesh 4School of Biomedical Science, Faculty of Medicine and Health, The University of Sydney, Australia 5Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia Abstract Mitochondrial dysfunction can cause various neurological diseases. We therefore developed a quantitative framework to explore how mitochondrial dysfunction may influence the progression of Alzheimer’s, Parkinson’s, Hunting- ton’s and Lou Gehrig’s diseases and cerebral palsy through analysis of genes showing altered expression in these conditions. We sought insights about the gene profiles of mitochondrial and associated neurological diseases by investigating gene-disease networks, KEGG pathways, gene ontologies and protein-protein interaction network. Gene disease networks were constructed to connect shared genes which are commonly found between the neurological diseases and Mito- chondrial Dysfunction. We also generated KEGG pathways and gene ontologies to explore functional enrichment among them, and protein-protein interaction networks to identify the shared protein groups of these diseases.
    [Show full text]
  • Anti-BCLAF1 / BTF Antibody (ARG11032)
    Product datasheet [email protected] ARG11032 Package: 100 μg anti-BCLAF1 / BTF antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes BCLAF1 / BTF Tested Reactivity Hu Tested Application IP, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name BCLAF1 / BTF Antigen Species Human Immunogen Recombinant His-tagged protein fragment of Human BCLAF1 / BTF. Conjugation Un-conjugated Alternate Names Bcl-2-associated transcription factor 1; Btf; BTF; bK211L9.1 Application Instructions Application table Application Dilution IP Assay-dependent WB 1:1000 - 1:3000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 106 kDa Properties Form Liquid Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol BCLAF1 Gene Full Name BCL2-associated transcription factor 1 Background This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of www.arigobio.com 1/2 proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins. The protein localizes to dot-like structures throughout the nucleus, and redistributes to a zone near the nuclear envelope in cells undergoing apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene.
    [Show full text]
  • Unbiased Phosphoproteomic Method Identifies the Initial Effects of a Methacrylic Acid Copolymer on Macrophages
    Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages Michael Dean Chamberlaina,1, Laura A. Wellsa,1,2, Alexandra Lisovskya, Hongbo Guob, Ruth Isserlinb, Ilana Talior-Volodarskya, Redouan Mahoua, Andrew Emilib, and Michael V. Seftona,c,3 aInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada M5S 3G9; bDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3G9; and cDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada M5S 3G9 Edited by Robert Langer, Massachusetts Institute of Technology, Cambridge, MA, and approved July 21, 2015 (received for review May 5, 2015) An unbiased phosphoproteomic method was used to identify the potential to develop “rules of engagement” between cells and biomaterial-associated changes in the phosphorylation patterns of biomaterials. macrophage-like cells. The phosphorylation differences between This study investigated the effects of a methacrylic acid differentiated THP1 (dTHP1) cells treated for 10, 20, or 30 min with (MAA) copolymer on cells because these polymers have been a vascular regenerative methacrylic acid (MAA) copolymer or a shown to promote vascular regenerative responses in vivo (9, 10), control methyl methacrylate (MM) copolymer were determined by but the mechanism behind this response is unknown (11–13). MS. There were 1,470 peptides (corresponding to 729 proteins) Previous studies showed that 45% poly(MAA-co-methyl meth- that were differentially phosphorylated in dTHP1 cells treated acrylate [MM]) copolymer beads promoted vascularization and with the two materials with a greater cellular response to MAA improved wound healing in diabetic mice (10) or with skin grafts treatment.
    [Show full text]
  • Restoration of Mir-517A Expression Induces Cell Apoptosis in Bladder Cancer Cell Lines
    ONCOLOGY REPORTS 25: 1661-1668, 2011 Restoration of miR-517a expression induces cell apoptosis in bladder cancer cell lines TAKAYUKI YOSHITOMI1, KAZUMORI KAWAKAMI1, HIDEKI ENOKIDA1, TAKESHI CHIYOMARU1, ICHIRO KAGARA1, SHUICHI TATARANO1, HIROFUMI YOSHINO1, HIROSHI ARIMURA1, KENRYU NISHIYAMA1, NAOHIKO SEKI2 and MASAYUKI NAKAGAWA1 1Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima; 2Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba, Japan Received December 13, 2010; Accepted January 31, 2011 DOI: 10.3892/or.2011.1253 Abstract. The aim of this study was to find novel tumor in patients with urological malignancy (1). Although the exact suppressor microRNAs through screening genes epigenetically mechanism of bladder carcinogenesis is still unclear, some silenced by methylation in bladder cancer (BC) cell lines oncogenes and tumor suppressor genes have been suggested using microRNA microarrays. Since miR-517a and miR-520g, to play important roles in bladder tumorigenesis (2). Recently, both located on chromosome 19q13.42, were found to highly it has been reported that microRNAs may act as oncogenes or up-regulated genes after treatment with a demethylating agent, tumor suppressors in BC (3). 5-aza-2'-deoxycytidine (5-Aza-dc), we hypothesized that they microRNAs are small non-coding RNAs of 20-22 nucle- are tumor-suppressor microRNAs and performed a gain-of- otides and involved in crucial biological processes, including function study using these mature microRNAs. The miR-517a development, differentiation, apoptosis and proliferation restoration showed significant inhibition of cell proliferation (4-6) through imperfect pairing with target messenger RNAs in the transfectants compared to miR-control-transfected cells (mRNAs) of protein-coding genes and the transcriptional or (p<0.0001 both in BOY and T24 cells).
    [Show full text]
  • Involvement of Bcl-2-Associated Transcription Factor 1 in the Differentiation of Early-Born Retinal Cells
    1530 • The Journal of Neuroscience, January 22, 2014 • 34(4):1530–1541 Development/Plasticity/Repair Involvement of Bcl-2-Associated Transcription Factor 1 in the Differentiation of Early-Born Retinal Cells Gae¨l Orieux,1* Laura Picault,1* Ame´lie Slembrouck,1 Je´roˆme E. Roger,1 Xavier Guillonneau,1 Jose´-Alain Sahel,1,2 Simon Saule,3 J. Peter McPherson,4 and Olivier Goureau1 1Institut de la Vision, INSERM UMR_S968, CNRS UMR 7210, Sorbonne Universite´s, UPMC Univ Paris 06, 75012 Paris, France, 2Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503, 75 571 PARIS Cedex 12, France, 3CNRS-UMR 3347, INSERM U1021, Universite´ Paris-sud11, Centre Universitaire, 91405 Orsay, France, and 4Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada Retinal progenitor proliferation and differentiation are tightly controlled by extrinsic cues and distinctive combinations of transcription factors leading to the generation of retinal cell type diversity. In this context, we have characterized Bcl-2-associated transcription factor (Bclaf1) during rodent retinogenesis. Bclaf1 expression is restricted to early-born cell types, such as ganglion, amacrine, and horizontal cells. Analysis of developing retinas in Bclaf1-deficient mice revealed a reduction in the numbers of retinal ganglion cells, amacrine cells and horizontal cells and an increase in the numbers of cone photoreceptor precursors. Silencing of Bclaf1expression by in vitro electro- poration of shRNA in embryonic retina confirmed that Bclaf1 serves to promote amacrine and horizontal cell differentiation. Misexpres- sion of Bclaf1 in late retinal progenitors was not sufficient to directly induce the generation of amacrine and horizontal cells.
    [Show full text]
  • Bclaf1 Critically Regulates the Type I Interferon Response and Is Degraded By
    bioRxiv preprint doi: https://doi.org/10.1101/392555; this version posted August 16, 2018. 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. 1 Bclaf1 critically regulates the type I interferon response and is degraded by 2 alphaherpesvirus US3 3 4 Chao Qin1, Rui Zhang1, Yue Lang1, Anwen Shao2, Aotian Xu1, Wenhai Feng2, Jun Han1, 5 Mengdong Wang1, Wanwei He1, Cuilian Yu1, and Jun Tang1,* 6 1State Key Laboratory of Agrobiotechnology and College of Veterinary Medicine, China 7 Agricultural University, Beijing 100193, China 8 2Department of Microbiology and Immunology, College of Biological Sciences, China 9 Agricultural University, Beijing 100193, China 10 *Correspondence: [email protected] (J.T.) 11 bioRxiv preprint doi: https://doi.org/10.1101/392555; this version posted August 16, 2018. 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. 12 Abstract 13 14 Type I interferon response plays a prominent role against viral infection, which is frequently 15 disrupted by viruses. Here, we report Bcl-2 associated transcription factor 1 (Bclaf1) is 16 degraded during the alphaherpesvirus Pseudorabies virus (PRV) and Herpes simplex virus 17 type 1 (HSV-1) infections through the viral protein US3. We further reveal that Bclaf1 functions 18 critically in type I interferon signaling. Knockdown or knockout of Bclaf1 in cells significantly 19 impairs interferon-α (IFNα) -mediated gene transcription and viral inhibition against US3 20 deficient PRV and HSV-1.
    [Show full text]
  • Polyclonal Antibody to BCLAF1
    AP08266PU-N OriGene Technologies Inc. OriGene EU Acris Antibodies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-858-888-7900 Phone: +49-5221-34606-0 Fax: +1-858-888-7904 Fax: +49-5221-34606-11 [email protected] [email protected] Polyclonal Antibody to BCLAF1 / BTF (700-750) - Aff - Purified Alternate names: Aa2-041, Bcl-2-associated transcription factor 1, KIAA0164 Catalog No.: AP08266PU-N Quantity: 50 µg Concentration: 0.5 mg/ml Background: BTF is a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co- expression of BCL2 proteins. BTF localizes to dot-like structures throughout the nucleus, and redistributes to a zone near the nuclear envelope in cells undergoing apoptosis. Multiple transcript variants encoding different isoforms have been found for this protein. Uniprot ID: Q9NYF8 NCBI: NP_001070908.1 GeneID: 9774 Host / Isotype: Rabbit / IgG Immunogen: Synthetic peptide corresponding to a portion of the amino acids 700-750 of human BCLAF1 Format: State: Liquid purified Ig fraction Purification: Immunoaffinity Chromatography Buffer System: PBS containing 0.05% Sodium Azide as preservative and 0.2% Gelatin as stabilizer Applications: Immunohistochemistry on Paraffin Sections: 10 µg/ml; Heat induced antigen retrieval in pH 6.0 citrate buffer is recommended. Western blot: 0.5-2.0 µg/ml. Other applications not tested. Optimal dilutions are dependent on conditions and should be determined by the user. Specificity: This antibody recognizes BCL2-associated Transcription Factor 1 (BCLAF1) at aa 700-750.
    [Show full text]
  • Defining a Transcriptional Fingerprint of Murine Splenic B-Cell Development
    Genes and Immunity (2008) 9, 706–720 & 2008 Macmillan Publishers Limited All rights reserved 1466-4879/08 $32.00 www.nature.com/gene ORIGINAL ARTICLE Defining a transcriptional fingerprint of murine splenic B-cell development I Debnath1, KM Roundy1, DM Dunn2, RB Weiss2, JJ Weis1 and JH Weis1 1Division of Cell Biology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA and 2Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA B-cell development occurs in a stepwise fashion that can be followed by the expression of B cell-specific surface markers. In this study, we wished to identify proteins that could contribute to the changes in expression of such markers. By using RNA from freshly isolated B220 þ cells, we hoped to reduce the effect of artifacts that occur during the isolation and amplification steps necessary to use flow cytometry analysis-sorted subsets in microarray experiments. Analyses comparing expression patterns from B220 þ 2-week bone marrow (pro-B, pre-B, immature B cells), 2-week spleen (predominantly transitional cells) and 8-week spleen (mainly mature B cells) yielded hundreds of genes. We also examined the B cell-activating factor (BAFF)- dependent effects on immature splenic B cells by comparing expression patterns in the spleen between 2-week A/J vs 2-week A/WySnJ mice, which lack functional BAFF receptor signaling. Genes that showed the expression differences between spleen and bone marrow samples were then analyzed through quantitative PCR on B-cell subsets isolated using two different sorting protocols.
    [Show full text]
  • Transposon Mutagenesis Identifies Genetic Drivers of Brafv600e Melanoma
    ARTICLES Transposon mutagenesis identifies genetic drivers of BrafV600E melanoma Michael B Mann1,2, Michael A Black3, Devin J Jones1, Jerrold M Ward2,12, Christopher Chin Kuan Yew2,12, Justin Y Newberg1, Adam J Dupuy4, Alistair G Rust5,12, Marcus W Bosenberg6,7, Martin McMahon8,9, Cristin G Print10,11, Neal G Copeland1,2,13 & Nancy A Jenkins1,2,13 Although nearly half of human melanomas harbor oncogenic BRAFV600E mutations, the genetic events that cooperate with these mutations to drive melanogenesis are still largely unknown. Here we show that Sleeping Beauty (SB) transposon-mediated mutagenesis drives melanoma progression in BrafV600E mutant mice and identify 1,232 recurrently mutated candidate cancer genes (CCGs) from 70 SB-driven melanomas. CCGs are enriched in Wnt, PI3K, MAPK and netrin signaling pathway components and are more highly connected to one another than predicted by chance, indicating that SB targets cooperative genetic networks in melanoma. Human orthologs of >500 CCGs are enriched for mutations in human melanoma or showed statistically significant clinical associations between RNA abundance and survival of patients with metastatic melanoma. We also functionally validate CEP350 as a new tumor-suppressor gene in human melanoma. SB mutagenesis has thus helped to catalog the cooperative molecular mechanisms driving BRAFV600E melanoma and discover new genes with potential clinical importance in human melanoma. Substantial sun exposure and numerous genetic factors, including including BrafV600E, recapitulate the genetic and histological hallmarks skin type and family history, are the most important melanoma risk of human melanoma. In these models, increased MEK-ERK signaling factors. Familial melanoma, which accounts for <10% of cases, is asso- initiates clonal expansion of melanocytes, which is limited by oncogene- ciated with mutations in CDKN2A1, MITF2 and POT1 (refs.
    [Show full text]
  • The RNA Processing Factors THRAP3 and BCLAF1 Promote the DNA Damage Response Through Selective Mrna Splicing and Nuclear Export Vohhodina, J., Barros, E
    The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export Vohhodina, J., Barros, E. M., Savage, A. L., Liberante, F. G., Manti, L., Bankhead, P., Cosgrove, N., Madden, A. F., Harkin, D. P., & Savage, K. I. (2017). The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Nucleic Acids Research, 45(22), 1-18. [gkx1046]. https://doi.org/10.1093/nar/gkx1046 Published in: Nucleic Acids Research Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2017 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • In Search of a Function for BCLAF1
    Mini-Review TheScientificWorldJOURNAL (2010) 10, 1450–1461 ISSN 1537-744X; DOI 10.1100/tsw.2010.132 In Search of a Function for BCLAF1 Haya Sarras, Solmaz Alizadeh Azami, and J. Peter McPherson* Department of Pharmacology and Toxicology, University of Toronto, Canada E-mail: [email protected] Received March 30, 2010; Revised May 31, 2010; Accepted June 7, 2010; Published July 20, 2010 BCLAF1 was originally identified as a protein that interacts with antiapoptotic members of the Bcl2 family. Initial studies indicated a role for this protein as an inducer of apoptosis and repressor of transcription. Subsequent studies have shown that BCLAF1 plays criticals roles in a wide range of processes that are not normally associated with actions of Bcl2 family members, including lung development, T-cell activation, and control of the lytic infection program of Kaposi’s sarcoma–associated herpesvirus. Here, we provide an overview of findings from past studies that both support and challenge the role of BCLAF1 in cell death and transcriptional control. We also present recent findings from our laboratory and others indicating a role for BCLAF1 in post-transcriptional processes that impact mRNA metabolism, instead of a direct role for this protein in apoptosis or transcription. KEYWORDS: BCLAF1, apoptosis, transcription, RS domain, lung development, Kaposi’s sarcoma, ribonucleoprotein, TRAP150, RNA transport BCLAF1 DISCOVERY AS AN E1B 19K INTERACTING PROTEIN, PROAPOPTOTIC FACTOR, AND TRANSCRIPTIONAL REPRESSOR Our interest in BCLAF1 stems from initial studies by White and colleagues, who identified BCLAF1 (Bcl2 associated transcription factor; also known as BTF) in a screen for proteins that interact with the adenoviral E1B 19K protein[1].
    [Show full text]