IGH Rearrangement in Myeloid Neoplasms Sion and Activation
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MECOM Permits Pancreatic Acinar Cell Dedifferentiation Avoiding Cell Death Under Stress Conditions
Cell Death & Differentiation (2021) 28:2601–2615 https://doi.org/10.1038/s41418-021-00771-6 ARTICLE MECOM permits pancreatic acinar cell dedifferentiation avoiding cell death under stress conditions 1 2 2 1 1 1,3 Elyne Backx ● Elke Wauters ● Jonathan Baldan ● Mathias Van Bulck ● Ellis Michiels ● Yves Heremans ● 4 5 5 2 6 Diedert Luc De Paep ● Mineo Kurokawa ● Susumu Goyama ● Luc Bouwens ● Patrick Jacquemin ● 1,2 1 Isabelle Houbracken ● Ilse Rooman Received: 20 July 2020 / Revised: 3 March 2021 / Accepted: 4 March 2021 / Published online: 24 March 2021 © The Author(s) 2021. This article is published with open access Abstract Maintenance of the pancreatic acinar cell phenotype suppresses tumor formation. Hence, repetitive acute or chronic pancreatitis, stress conditions in which the acinar cells dedifferentiate, predispose for cancer formation in the pancreas. Dedifferentiated acinar cells acquire a large panel of duct cell-specific markers. However, it remains unclear to what extent dedifferentiated acini differ from native duct cells and which genes are uniquely regulating acinar cell dedifferentiation. Moreover, most studies have been performed on mice since the availability of human cells is scarce. Here, we applied a non- fi 1234567890();,: 1234567890();,: genetic lineage tracing method of human pancreatic exocrine acinar and duct cells that allowed cell-type-speci c gene expression profiling by RNA sequencing. Subsequent to this discovery analysis, one transcription factor that was unique for dedifferentiated acinar cells was functionally characterized. RNA sequencing analysis showed that human dedifferentiated acinar cells expressed genes in “Pathways of cancer” with a prominence of MECOM (EVI-1), a transcription factor that was not expressed by duct cells. -
Chromosomal Aberrations in Head and Neck Squamous Cell Carcinomas in Norwegian and Sudanese Populations by Array Comparative Genomic Hybridization
825-843 12/9/08 15:31 Page 825 ONCOLOGY REPORTS 20: 825-843, 2008 825 Chromosomal aberrations in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization ERIC ROMAN1,2, LEONARDO A. MEZA-ZEPEDA3, STINE H. KRESSE3, OLA MYKLEBOST3,4, ENDRE N. VASSTRAND2 and SALAH O. IBRAHIM1,2 1Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91; 2Department of Oral Sciences - Periodontology, Faculty of Medicine and Dentistry, University of Bergen, Årstadveien 17, 5009 Bergen; 3Department of Tumor Biology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Montebello, 0310 Oslo; 4Department of Molecular Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway Received January 30, 2008; Accepted April 29, 2008 DOI: 10.3892/or_00000080 Abstract. We used microarray-based comparative genomic logical parameters showed little correlation, suggesting an hybridization to explore genome-wide profiles of chromosomal occurrence of gains/losses regardless of ethnic differences and aberrations in 26 samples of head and neck cancers compared clinicopathological status between the patients from the two to their pair-wise normal controls. The samples were obtained countries. Our findings indicate the existence of common from Sudanese (n=11) and Norwegian (n=15) patients. The gene-specific amplifications/deletions in these tumors, findings were correlated with clinicopathological variables. regardless of the source of the samples or attributed We identified the amplification of 41 common chromosomal carcinogenic risk factors. regions (harboring 149 candidate genes) and the deletion of 22 (28 candidate genes). Predominant chromosomal alterations Introduction that were observed included high-level amplification at 1q21 (harboring the S100A gene family) and 11q22 (including Head and neck squamous cell carcinoma (HNSCC), including several MMP family members). -
Prospective Isolation of NKX2-1–Expressing Human Lung Progenitors Derived from Pluripotent Stem Cells
The Journal of Clinical Investigation RESEARCH ARTICLE Prospective isolation of NKX2-1–expressing human lung progenitors derived from pluripotent stem cells Finn Hawkins,1,2 Philipp Kramer,3 Anjali Jacob,1,2 Ian Driver,4 Dylan C. Thomas,1 Katherine B. McCauley,1,2 Nicholas Skvir,1 Ana M. Crane,3 Anita A. Kurmann,1,5 Anthony N. Hollenberg,5 Sinead Nguyen,1 Brandon G. Wong,6 Ahmad S. Khalil,6,7 Sarah X.L. Huang,3,8 Susan Guttentag,9 Jason R. Rock,4 John M. Shannon,10 Brian R. Davis,3 and Darrell N. Kotton1,2 2 1Center for Regenerative Medicine, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA. 3Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA. 4Department of Anatomy, UCSF, San Francisco, California, USA. 5Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA. 6Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA. 7Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. 8Columbia Center for Translational Immunology & Columbia Center for Human Development, Columbia University Medical Center, New York, New York, USA. 9Department of Pediatrics, Monroe Carell Jr. Children’s Hospital, Vanderbilt University, Nashville, Tennessee, USA. 10Division of Pulmonary Biology, Cincinnati Children’s Hospital, Cincinnati, Ohio, USA. It has been postulated that during human fetal development, all cells of the lung epithelium derive from embryonic, endodermal, NK2 homeobox 1–expressing (NKX2-1+) precursor cells. -
Genome-Wide Approach to Identify Risk Factors for Therapy-Related Myeloid Leukemia
Leukemia (2006) 20, 239–246 & 2006 Nature Publishing Group All rights reserved 0887-6924/06 $30.00 www.nature.com/leu ORIGINAL ARTICLE Genome-wide approach to identify risk factors for therapy-related myeloid leukemia A Bogni1, C Cheng2, W Liu2, W Yang1, J Pfeffer1, S Mukatira3, D French1, JR Downing4, C-H Pui4,5,6 and MV Relling1,6 1Department of Pharmaceutical Sciences, The University of Tennessee, Memphis, TN, USA; 2Department of Biostatistics, The University of Tennessee, Memphis, TN, USA; 3Hartwell Center, The University of Tennessee, Memphis, TN, USA; 4Department of Pathology, The University of Tennessee, Memphis, TN, USA; 5Department of Hematology/Oncology St Jude Children’s Research Hospital, The University of Tennessee, Memphis, TN, USA; and 6Colleges of Medicine and Pharmacy, The University of Tennessee, Memphis, TN, USA Using a target gene approach, only a few host genetic risk therapy increases, the importance of identifying host factors for factors for treatment-related myeloid leukemia (t-ML) have been secondary neoplasms increases. defined. Gene expression microarrays allow for a more 4 genome-wide approach to assess possible genetic risk factors Because DNA microarrays interrogate multiple ( 10 000) for t-ML. We assessed gene expression profiles (n ¼ 12 625 genes in one experiment, they allow for a ‘genome-wide’ probe sets) in diagnostic acute lymphoblastic leukemic cells assessment of genes that may predispose to leukemogenesis. from 228 children treated on protocols that included leukemo- DNA microarray analysis of gene expression has been used to genic agents such as etoposide, 13 of whom developed t-ML. identify distinct expression profiles that are characteristic of Expression of 68 probes, corresponding to 63 genes, was different leukemia subtypes.13,14 Studies using this method have significantly related to risk of t-ML. -
Factsheet XL T3;3 GATA2MECOM DF D-5124.Cdt
XL t(3;3) GATA2/ MECOM DF Translocation/Dual Fusion Order No.: Probe D-5124-100-OG Description XL t(3;3) GATA2/MECOM DF is designed as a dual fusion probe. The orange labeled probe spans the breakpoint at 3q26 (MECOM), the green labeled probe spans the breakpoint at 3q21 (GATA2 and RPN1). Clinical Details The chromosomal aberrations inv(3)(q21q26.2) and t(3;3)(q21;q26.2) characterize a distinct entity within patients with acute myeloid leukemia (AML). Their incidence in AML is about 1%-2.5% and patients have an unfavorable prognosis and low response to chemotherapy. Inv(3)/t(3;3) juxtapose the GATA2 enhancer with the MECOM locus which results in overexpression of EVI1. The EVI1 gene is located in 3q26 and is involved in hematopoietic stem cell maintenance. EVI1 is together with MDS located in the ´MDS1 and EVI1 complex locus´ (MECOM) and is the major player in this subtype XL t(3;3) GATA2/MECOM DF hybridized to lymphocytes. of AML. Furthermore, structural rearrangements caused by inv(3)/t(3;3) result in One normal interphase and two chromosomes 3 are reduced GATA2 expression which may contribute to the oncogenic potential of this shown. The expected normal signal pattern of XL t(3;3) GATA2/MECOM DF is two orange and two green aberration. GATA2 is located in chromosomal region 3q21 and is involved in develop- signals, representing the two normal MECOM and ment and proliferation of hematopoietic stem cells. Several other recurrent 3q26 G ATA 2 l o c i . B o t h , i n v ( 3 ) ( q 2 1 q 2 6 . -
Leukaemia Section
Atlas of Genetics and Cytogenetics in Oncology and Haematology INIST -CNRS OPEN ACCESS JOURNAL Leukaemia Section Short Communication t(3;12)(q26;p13) ETV6/MECOM / t(3;12)(q26;p13) ETV6/EVI1 Etienne De Braekeleer, Nathalie Douet-Guilbert, Marc De Braekeleer Cytogenetics Laboratory, Faculty of Medicine, University of Brest, France (EDB, NDG, MDB) Published in Atlas Database: April 2014 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/t0312.html DOI: 10.4267/2042/54377 This article is an update of : Desangles F. t(3;12)(q26;p13). Atlas Genet Cytogenet Oncol Haematol 1997;1(1):21. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2014 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract M7. Short communication on t(3;12)(q26;p13) Epidemiology ETV6/MECOM, with data on clinics, and the genes 46 cases described so far; sex ratio: 29M/16F (1 implicated. unknown); age: 2.5-87 yrs (med: 49 yrs), unknown age for 10 cases. Identity Cytology Note Dysplasia of megakaryocytes, multilineage Only a few cases were shown to involve a involvement. ETV6/MECOM fusion by FISH or RT-PCR. In Prognosis other cases, only MECOM or ETV6 was shown to be rearranged by FISH. Over-expression of See survival curve above. MECOM/EVI1 was found in other cases. Finally, no cytogenetic or molecular analysis was performed Cytogenetics in a few cases. Cytogenetics molecular Heterogeneity of the EVI1 breakpoints, as evidenced by the Cytocell Aquarius EVI1 Breakapart probe. The EVI1 Breakapart probe contains three probes: a probe labeled in Aqua of 562 kb in size centromeric to the EVI1 gene, a probe labeled in Spectrum Green of 181 kb covering EVI1 and its flanking regions and a probe labeled in Spectrum Orange of 124 kb telomeric of the EVI1 gene (telomeric of t(3;12)(q26;p13) G-banding - Courtesy Jean-Luc Lai and Alain Vanderhaegen.Clinics and pathology MYNN and covering LRRC34). -
Molecular Phenotyping Using Networks, Diffusion, and Topology
www.nature.com/scientificreports OPEN Molecular phenotyping using networks, difusion, and topology: soft tissue sarcoma Received: 27 November 2018 James C. Mathews 1, Maryam Pouryahya1, Caroline Moosmüller 2, Yannis G. Kevrekidis2, Accepted: 6 September 2019 Joseph O. Deasy1 & Allen Tannenbaum3 Published: xx xx xxxx Many biological datasets are high-dimensional yet manifest an underlying order. In this paper, we describe an unsupervised data analysis methodology that operates in the setting of a multivariate dataset and a network which expresses infuence between the variables of the given set. The technique involves network geometry employing the Wasserstein distance, global spectral analysis in the form of difusion maps, and topological data analysis using the Mapper algorithm. The prototypical application is to gene expression profles obtained from RNA-Seq experiments on a collection of tissue samples, considering only genes whose protein products participate in a known pathway or network of interest. Employing the technique, we discern several coherent states or signatures displayed by the gene expression profles of the sarcomas in the Cancer Genome Atlas along the TP53 (p53) signaling network. The signatures substantially recover the leiomyosarcoma, dediferentiated liposarcoma (DDLPS), and synovial sarcoma histological subtype diagnoses, and they also include a new signature defned by activation and inactivation of about a dozen genes, including activation of serine endopeptidase inhibitor SERPINE1 and inactivation of TP53-family tumor suppressor gene TP73. Modern biological investigations ofen result in dense, high-dimensional datasets describing genes, proteins, mutations, or other variables. A near universal problem arises as the dimensionality of the data grows: how can the data be investigated in a relatively unbiased manner, to expose underlying clusters and relational structure? To date, there is a lack of robust techniques for exposing the structure of biological data in an unbiased, agnostic fashion. -
Exploiting Oncogenic Drivers Along the CCNG1 Pathway for Cancer
Commentary the cyclical behavior of the so-called “canon- Exploiting Oncogenic Drivers ical cyclins” that agreeably and accordingly marked the major phase transitions of the along the CCNG1 Pathway for mammalian cell division cycle. Fortunately, what was hidden from the wise Cancer Therapy and Gene Therapy in terms of rigid canonical considerations was revealed to the experimentalists and Ahmad Al-Shihabi,1 Sant P. Chawla,1 Frederick L. Hall,2 physician-scientists who looked beyond the and Erlinda M. Gordon1,2,3 meager definitions to explore the actual structure and function relations of the cyclin https://doi.org/10.1016/j.omto.2018.11.002 G1 protein (by genetic engineering of CCNG1) in the context of cancer gene ther- The search for strategic molecular targets recognize specific structural features or apy, long before cyclin G1 was determined among a myriad of cell signaling pathways target sequences, characterized by Gordon to be the prime molecular driver of the has long been a cornerstone for both molec- et al.,1 arrayed along major cell-cycle and elusive cell competence factor, the pivotal ex- ular cancer research and gene therapy gene-regulatory proteins. Thus, a canonical ecutive component of the Cyclin G1/p53/ research, leading to the development of novel “cyclin” is thought of as an oscillating, posi- Mdm2 Axis governing cell cycle checkpoint cancer therapies that act at the level of the tive-acting “regulatory subunit” of an identi- control and, perhaps, a most strategic target genome (DNA), the transcriptome (RNA), fied CDK, which both “activates” the for new precision molecular and genetic can- and/or the proteome (protein). -
Viewed and Approved by the Quencing (RRBS) Kit (Diagenode) Following Manufacturer’S Institutional Animal Care and Use Committee of University Instruction
BASIC RESEARCH www.jasn.org DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development Szu-Yuan Li,1,2,3,4 Jihwan Park ,1,2 Yuting Guan,1,2 Kiwung Chung,1,2 Rojesh Shrestha,1,2 Matthew B. Palmer,5 and Katalin Susztak 1,2 1Renal-Electrolyte and Hypertension Division, Department of Medicine, 2Department of Genetics, and 5Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; 3Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; and 4School of Medicine, National Yang-Ming University, Taipei, Taiwan ABSTRACT Background Cytosine methylation of regulatory regions, such as promoters and enhancers, plays a key role in regulating gene expression, however, its role in kidney development has not been analyzed. Methods To identify functionally important epigenome-modifying enzymes and genome regions where methylation modifications are functionally important for kidney development, we performed genome- wide methylation analysis, expression profiling, and systematic genetic targeting of DNA methyltrans- ferases (Dnmt1, Dnmt3a,andDnmt3b) and Ten-eleven translocation methylcytosine hydroxylases (Tet2) in nephron progenitor cells (Six2Cre)inmice. Results Genome-wide methylome analysis indicated dynamic changes on promoters and enhancers dur- ing development. Six2CreDnmt3af/f, Six2CreDnmt3bf/f, and Six2CreTet2f/f mice showed no significant struc- tural or functional renal abnormalities. In contrast, Six2CreDnmt1f/f mice died within 24 hours of birth, from a severe kidney developmental defect. Genome-wide methylation analysis indicated a marked loss of methylation of transposable elements. RNA sequencing detected endogenous retroviral transcripts. Expression of intracellular viral sensing pathways (RIG-I), early embryonic, nonrenal lineage genes and increased cell death contributed to the phenotype development. -
Posttranslational Modifications of RUNX1 As Potential Anticancer
Oncogene (2015) 34, 3483–3492 © 2015 Macmillan Publishers Limited All rights reserved 0950-9232/15 www.nature.com/onc REVIEW Posttranslational modifications of RUNX1 as potential anticancer targets S Goyama1, G Huang1, M Kurokawa2 and JC Mulloy1 The transcription factor RUNX1 is a master regulator of hematopoiesis. Disruption of RUNX1 activity has been implicated in the development of hematopoietic neoplasms. Recent studies also highlight the importance of RUNX1 in solid tumors both as a tumor promoter and a suppressor. Given its central role in cancer development, RUNX1 is an excellent candidate for targeted therapy. A potential strategy to target RUNX1 is through modulation of its posttranslational modifications (PTMs). Numerous studies have shown that RUNX1 activity is regulated by PTMs, including phosphorylation, acetylation, methylation and ubiquitination. These PTMs regulate RUNX1 activity either positively or negatively by altering RUNX1-mediated transcription, promoting protein degradation and affecting protein interactions. In this review, we first summarize the available data on the context- and dosage- dependent roles of RUNX1 in various types of neoplasms. We then provide a comprehensive overview of RUNX1 PTMs from biochemical and biologic perspectives. Finally, we discuss how aberrant PTMs of RUNX1 might contribute to tumorigenesis and also strategies to develop anticancer therapies targeting RUNX1 PTMs. Oncogene (2015) 34, 3483–3492; doi:10.1038/onc.2014.305; published online 29 September 2014 INTRODUCTION recent studies have revealed the important role of RUNX1 in solid 8 RUNX1 is an essential transcription factor for the generation of tumors. Given its central roles for cell fate decisions in definitive hematopoietic stem cells and for hematopoietic hematopoiesis and leukemogenesis, RUNX1 is an attractive target differentiation to myeloid and lymphoid lineages (reviewed in to develop curative therapies for leukemia patients. -
Cryptic Genomic Lesions in Adverse-Risk Acute Myeloid Leukemia Identified by Integrated Whole Genome and Transcriptome Sequencing
Leukemia (2020) 34:306–311 https://doi.org/10.1038/s41375-019-0546-1 LETTER Cytogenetics and molecular genetics Cryptic genomic lesions in adverse-risk acute myeloid leukemia identified by integrated whole genome and transcriptome sequencing 1,2,3 2 3 3,4 2 Jaeseung C. Kim ● Philip C. Zuzarte ● Tracy Murphy ● Michelle Chan-Seng-Yue ● Andrew M. K. Brown ● 2 5 1,3,4 1,3 1,2,6 Paul M. Krzyzanowski ● Adam C. Smith ● Faiyaz Notta ● Mark D. Minden ● John D. McPherson Received: 15 March 2019 / Revised: 23 April 2019 / Accepted: 17 June 2019 / Published online: 21 August 2019 © The Author(s) 2019. This article is published with open access To the Editor: treated accordingly [1]. In recent years, advancements in next-generation sequencing and efforts by large genomics Acute myeloid leukemia (AML) is a heterogeneous group studies have led to a classification of 11 AML subgroups of hematologic malignancies characterized by the pro- based on cytogenetic abnormalities as well as mutations in liferation of myeloid cells blocked in their ability to dif- genes, such as NPM1 or CEBPA [1]. 1234567890();,: 1234567890();,: ferentiate. Evaluation by G-banding and fluorescence in situ AML with a complex karyotype, defined by the presence hybridization is an essential aspect in the initial disease of three or more unrelated chromosomal aberrations and the characterization and even now is fundamental in identifying absence of favorable cytogenetic rearrangements, is asso- cytogenetic abnormalities that can inform disease diagnosis, ciated with TP53 mutations and strikingly poor outcome prognosis, and treatment decision [1, 2]. For instance, the [1, 3]. -
4-Phenylthiobutanoic Acid Inhibits Histone Deacetylase 8 to Enhance Post-Acute Kidney Injury Repair
Title Page Slow and Steady: 4-Phenylthiobutanoic Acid Inhibits Histone Deacetylase 8 to Enhance Post-Acute Kidney Injury Repair by Hwa In Han B.S., College of William & Mary, 2014 Submitted to the Graduate Faculty of the School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2020 Committee Page UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE This dissertation was presented by Hwa In Han It was defended on May 29, 2020 and approved by Jacqueline Ho, M.D., Department of Pediatric Nephrology Penelope Morel, M.D., Department of Immunology Kyle Orwig, Ph.D., Department of Obstetrics, Gynecology & Reproductive Services Michael Tsang, Ph.D., Department of Developmental Biology Dissertation Director: Neil Hukriede, Ph.D., Department of Developmental Biology ii Copyright © by Hwa In Han 2020 iii Abstract Slow and Steady: 4-Phenylthiobutanoic Acid Inhibits Histone Deacetylase 8 to Enhance Post-Acute Kidney Injury Repair Hwa In Han, PhD University of Pittsburgh, 2020 Acute kidney injury (AKI) is a rapid decline in kidney function that is associated with high mortality and morbidity rates, affecting 1 in 5 adults worldwide 1. While damaged renal tubular epithelial cells (RTECs) undergo reparative process to proliferate and replace the damaged epithelium, it is not a robust mechanism. The initial damage is followed by a cross-talk of innate immune system and RTECs resulting in exacerbation of inflammation, fibrosis, and sometimes irreversible damage. Despite the prevalence and severity of AKI, no FDA approved therapeutics exist to replace damaged or lost RTECS. Therefore, it is imperative to screen, identify, and understand mechanisms with which candidate therapeutics can enhance repair.