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Dharmadhikari AV, Abad MA, Khan S, Maroofian R, Sands TT, Ullah F, Samejima I, Wear MA, Moore KE, Kondakova E, Mitina N, Schaub T, Lee GK, Umandap CH, Berger SM, Iglesias AD, Popp B, Jamra RA, Gabriel H, Rentas S, Rippert AL, Izumi K, Conlin LK, Koboldt DC, Mosher TM, Hickey SE, Albert DVF, Norwood H, Lewanda AF, Dai H, Liu P, Mitani T, Marafi D, Pehlivan D, Posey JE, Lippa N, Vena N, Heinzen EL, Goldstein DB, Mignot C, de Sainte Agathe JM, Al-Sannaa NA, Zamani M, Sadeghian S, Azizimalamiri R, Seifia T, Zaki MS, Abdel-Salam GMH, Abdel-Hamid M, Alabdi L, Alkuraya FS, Dawoud H, Lofty A, Bauer P, Zifarelli G, Afzal E, Zafar F, Efthymiou S, Gossett D, Towne MC, Yeneabat R, Wontakal SN, Aggarwal VS, Rosenfeld JA, Tarabykin V, Ohta S, Lupski JR, Houlden H, Earnshaw WC, Davis EE, Jeyaprakash AA, Liao J. RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS. medRxiv 2024:2024.01.09.23300329. [PMID: 38260255 PMCID: PMC10802637 DOI: 10.1101/2024.01.09.23300329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, we identified 24 individuals with neurodevelopmental delays from 18 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants showed reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicated that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 revealed that most disease-associated missense variants mapped to the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants had reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS ( SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.
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O’Donnell MR, Grinsztejn B, Cummings MJ, Justman JE, Lamb MR, Eckhardt CM, Philip NM, Cheung YK, Gupta V, João E, Pilotto JH, Diniz MP, Cardoso SW, Abrams D, Rajagopalan KN, Borden SE, Wolf A, Sidi LC, Vizzoni A, Veloso VG, Bitan ZC, Scotto DE, Meyer BJ, Jacobson SD, Kantor A, Mishra N, Chauhan LV, Stone EF, Dei Zotti F, La Carpia F, Hudson KE, Ferrara SA, Schwartz J, Stotler BA, Lin WHW, Wontakal SN, Shaz B, Briese T, Hod EA, Spitalnik SL, Eisenberger A, Lipkin WI. A randomized double-blind controlled trial of convalescent plasma in adults with severe COVID-19. J Clin Invest 2021; 131:150646. [PMID: 33974559 PMCID: PMC8245169 DOI: 10.1172/jci150646] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUNDAlthough convalescent plasma has been widely used to treat severe coronavirus disease 2019 (COVID-19), data from randomized controlled trials that support its efficacy are limited.METHODSWe conducted a randomized, double-blind, controlled trial among adults hospitalized with severe and critical COVID-19 at 5 sites in New York City (USA) and Rio de Janeiro (Brazil). Patients were randomized 2:1 to receive a single transfusion of either convalescent plasma or normal control plasma. The primary outcome was clinical status at 28 days following randomization, measured using an ordinal scale and analyzed using a proportional odds model in the intention-to-treat population.RESULTSOf 223 participants enrolled, 150 were randomized to receive convalescent plasma and 73 to receive normal control plasma. At 28 days, no significant improvement in the clinical scale was observed in participants randomized to convalescent plasma (OR 1.50, 95% confidence interval [CI] 0.83-2.68, P = 0.180). However, 28-day mortality was significantly lower in participants randomized to convalescent plasma versus control plasma (19/150 [12.6%] versus 18/73 [24.6%], OR 0.44, 95% CI 0.22-0.91, P = 0.034). The median titer of anti-SARS-CoV-2 neutralizing antibody in infused convalescent plasma units was 1:160 (IQR 1:80-1:320). In a subset of nasopharyngeal swab samples from Brazil that underwent genomic sequencing, no evidence of neutralization-escape mutants was detected.CONCLUSIONIn adults hospitalized with severe COVID-19, use of convalescent plasma was not associated with significant improvement in day 28 clinical status. However, convalescent plasma was associated with significantly improved survival. A possible explanation is that survivors remained hospitalized at their baseline clinical status.TRIAL REGISTRATIONClinicalTrials.gov, NCT04359810.FUNDINGAmazon Foundation, Skoll Foundation.
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Affiliation(s)
- Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Department of Epidemiology, and
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Jessica E. Justman
- Department of Epidemiology, and
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew R. Lamb
- Department of Epidemiology, and
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Christina M. Eckhardt
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Neena M. Philip
- ICAP, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Ying Kuen Cheung
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Vinay Gupta
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, USA
| | - Esau João
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Jose Henrique Pilotto
- Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil and Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz – Fiocruz, Rio de Janeiro, Brazil
| | - Maria Pia Diniz
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | | | - Darryl Abrams
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Kartik N. Rajagopalan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarah E. Borden
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Leon Claude Sidi
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
| | - Alexandre Vizzoni
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Valdilea G. Veloso
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Zachary C. Bitan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Dawn E. Scotto
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Benjamin J. Meyer
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Samuel D. Jacobson
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Alex Kantor
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Elizabeth F. Stone
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Flavia Dei Zotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Francesca La Carpia
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Krystalyn E. Hudson
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Stephen A. Ferrara
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Joseph Schwartz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Brie A. Stotler
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Wen-Hsuan W. Lin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Sandeep N. Wontakal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Beth Shaz
- New York Blood Center, New York, New York, USA
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Eldad A. Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Steven L. Spitalnik
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrew Eisenberger
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Walter I. Lipkin
- Department of Epidemiology, and
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
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Wontakal SN, Bortz RH, Lin WHW, Gendlina I, Fox AS, Hod EA, Chandran K, Prystowsky MB, Weiss LM, Spitalnik SL. Approaching the Interpretation of Discordances in SARS-CoV-2 Testing. Open Forum Infect Dis 2021; 8:ofab144. [PMID: 34316498 PMCID: PMC8083692 DOI: 10.1093/ofid/ofab144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
The coronavirus disease 2019 pandemic has upended life throughout the globe. Appropriate emphasis has been placed on developing effective therapies and vaccines to curb the pandemic. While awaiting such countermeasures, mitigation efforts coupled with robust testing remain essential to controlling spread of the disease. In particular, serological testing plays a critical role in providing important diagnostic, prognostic, and therapeutic information. However, this information is only useful if the results can be accurately interpreted. This pandemic placed clinical testing laboratories and requesting physicians in a precarious position because we are actively learning about the disease and how to interpret serological results. Having developed robust assays to detect antibodies generated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and serving the hardest-hit areas within the New York City epicenter, we found 3 types of discordances in SARS-CoV-2 test results that challenge interpretation. Using representative clinical vignettes, these interpretation dilemmas are highlighted, along with suggested approaches to resolve such cases.
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Affiliation(s)
- Sandeep N Wontakal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Robert H Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Wen-Hsuan W Lin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Inessa Gendlina
- Department of Medicine (Infectious Disease), Albert Einstein College of Medicine, Bronx, New York, USA
| | - Amy S Fox
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Eldad A Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Michael B Prystowsky
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis M Weiss
- Department of Medicine (Infectious Disease), Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven L Spitalnik
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
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Lyashchenko AK, Wontakal SN, Reynafarje GM, Hod E, Kratz A. 18 Trust but Verify: Repeat CBC Sample Measurements Help Identify Automated Hematology Analyzer Errors. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx149.387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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DeSimone RA, Wontakal SN, Lyashchenko AK, Schwartz J. Acute mechanical hemolysis as a complication of extracorporeal photopheresis in a low-weight child. J Clin Apher 2016; 32:571-573. [DOI: 10.1002/jca.21520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 10/29/2016] [Accepted: 11/13/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | - Joseph Schwartz
- New York-Presbyterian Hospital; New York New York
- Department of Pathology and Cell Biology; Columbia University Medical Center; New York New York
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Hooven TA, Hooper EM, Wontakal SN, Francis RO, Sahni R, Lee MT. Diagnosis of a rare fetal haemoglobinopathy in the age of next-generation sequencing. BMJ Case Rep 2016; 2016:10.1136/bcr-2016-215193. [PMID: 27095814 DOI: 10.1136/bcr-2016-215193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Neonatal cyanosis resulting from a fetal methaemoglobin variant is rare. Most such variants are only described in a few published case reports. We present the case of a newborn with unexplained persistent cyanosis, ultimately determined to have a γ-chain mutation causing Hb FM-Fort Ripley. This neonatal haemoglobinopathy can be challenging to diagnose, as significant oxygen desaturation may result from barely detectable levels of the mutant haemoglobin and co-oximetry studies may show a falsely normal methaemoglobin level. Our analysis of the infant's haemoglobin included high-performance liquid chromatography, cellulose acetate electrophoresis and citrate agar electrophoresis, which showed trace amounts of a suspected variant. Ultimately, the diagnosis was made through a novel application of next-generation sequencing (NGS). NGS-based diagnostic approaches are becoming increasingly available to clinicians, and our case provides a framework and evidence for the utilisation of such testing paradigms in the diagnosis of a rare cause of neonatal cyanosis.
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Affiliation(s)
- Thomas A Hooven
- Department of Pediatrics, New York University Langone Medical Center, New York, New York, USA Department of Pediatrics, Columbia University, New York, New York, USA
| | - Ellen M Hooper
- Department of Pediatrics, Columbia University, New York, New York, USA
| | | | - Richard O Francis
- Department of Pathology, Columbia University, New York, New York, USA
| | - Rakesh Sahni
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Margaret T Lee
- Department of Pediatrics, Columbia University, New York, New York, USA
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Lu X, Wontakal SN, Kavi H, Kim BJ, Guzzardo PM, Emelyanov AV, Xu N, Hannon GJ, Zavadil J, Fyodorov DV, Skoultchi AI. Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3-9. Science 2013; 340:78-81. [PMID: 23559249 DOI: 10.1126/science.1234654] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Eukaryotic genomes harbor transposable elements and other repetitive sequences that must be silenced. Small RNA interference pathways play a major role in their repression. Here, we reveal another mechanism for silencing these sequences in Drosophila. Depleting the linker histone H1 in vivo leads to strong activation of these elements. H1-mediated silencing occurs in combination with the heterochromatin-specific histone H3 lysine 9 methyltransferase Su(var)3-9. H1 physically interacts with Su(var)3-9 and recruits it to chromatin in vitro, which promotes H3 methylation. We propose that H1 plays a key role in silencing by tethering Su(var)3-9 to heterochromatin. The tethering function of H1 adds to its established role as a regulator of chromatin compaction and accessibility.
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Affiliation(s)
- Xingwu Lu
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. PLoS Genet 2011; 7:e1001392. [PMID: 21695229 PMCID: PMC3111485 DOI: 10.1371/journal.pgen.1001392] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 05/10/2011] [Indexed: 01/17/2023] Open
Abstract
PU.1 is a hematopoietic transcription factor that is required for the development of myeloid and B cells. PU.1 is also expressed in erythroid progenitors, where it blocks erythroid differentiation by binding to and inhibiting the main erythroid promoting factor, GATA-1. However, other mechanisms by which PU.1 affects the fate of erythroid progenitors have not been thoroughly explored. Here, we used ChIP-Seq analysis for PU.1 and gene expression profiling in erythroid cells to show that PU.1 regulates an extensive network of genes that constitute major pathways for controlling growth and survival of immature erythroid cells. By analyzing fetal liver erythroid progenitors from mice with low PU.1 expression, we also show that the earliest erythroid committed cells are dramatically reduced in vivo. Furthermore, we find that PU.1 also regulates many of the same genes and pathways in other blood cells, leading us to propose that PU.1 is a multifaceted factor with overlapping, as well as distinct, functions in several hematopoietic lineages.
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Affiliation(s)
- Sandeep N. Wontakal
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Xingyi Guo
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Minyi Shi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Debasish Raha
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Milind C. Mahajan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Sherman Weissman
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Michael Snyder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deyou Zheng
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (AI Skoultchi); (D Zheng)
| | - Arthur I. Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (AI Skoultchi); (D Zheng)
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Maxson ME, Volpi SA, Wontakal SN. From Bio 101 to Pillars of Biology: A Pedagogical Experiment. Einstein J Biol Med 2011; 27:86-93. [PMID: 22468141 PMCID: PMC3315383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Michelle E. Maxson
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Volpi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
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Chahwan R, Wontakal SN, Roa S. The multidimensional nature of epigenetic information and its role in disease. Discov Med 2011; 11:233-243. [PMID: 21447282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This year marks the 10th anniversary of the publications that reported the initial human genome sequence. In the historic press conference that announced this landmark accomplishment, it was proclaimed that the genome sequence would "revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases." However, subsequent work over the past decade has revealed that "complex diseases" are much more intricate than originally thought. Even with the advent of several new powerful technologies, our understanding of the underlying genetic etiologies of most complex and non-Mendelian diseases is far from complete. These results have raised the possibility that the DNA sequence, i.e., genetic information, may not be the only relevant source of information in order to understand the molecular basis of disease. In this review, we assemble evidence that information encoded beyond the DNA sequence, i.e., epigenetic information, may hold the key to a better understanding of various pathological conditions. Unlike the genetic information encoded within the DNA sequence, epigenetic information can be stored in multiple dimensions, such as in the form of DNA modifications, RNA, or protein. Ideas presented here support the view that to better understand the molecular etiology of diseases, we need to gain a better understanding of both the genetic and epigenetic components of biological information. We hence believe that the fast development of genome-wide technologies will facilitate a better understanding of both genetic and epigenetic dimensions of disease.
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Affiliation(s)
- Richard Chahwan
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, USA.
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Chahwan R, Wontakal SN, Roa S. Crosstalk between genetic and epigenetic information through cytosine deamination. Trends Genet 2010; 26:443-8. [DOI: 10.1016/j.tig.2010.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/16/2010] [Accepted: 07/19/2010] [Indexed: 01/25/2023]
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Papetti M, Wontakal SN, Stopka T, Skoultchi AI. GATA-1 directly regulates p21 gene expression during erythroid differentiation. Cell Cycle 2010; 9:1972-80. [PMID: 20495378 DOI: 10.4161/cc.9.10.11602] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Lineage-determination transcription factors coordinate cell differentiation and proliferation by controlling the synthesis of lineage-specific gene products as well as cell cycle regulators. GATA-1 is a master regulator of erythropoiesis. Its role in regulating erythroid-specific genes has been extensively studied, whereas its role in controlling genes that regulate cell proliferation is less understood. Ectopic expression of GATA-1 in erythroleukemia cells releases the block to their differentiation and leads to terminal cell division. An early event in reprogramming the erythroleukemia cells is induction of the cyclin-dependent kinase inhibitor p21. Remarkably, ectopic expression of p21 also induces the erythroleukemia cells to differentiate. We now report that GATA-1 directly regulates transcription of the p21 gene in both erythroleukemia cells and normal erythroid progenitors. Using reporter, electrophoretic mobility shift, and chromatin immunoprecipitation assays, we show that GATA-1 stimulates p21 gene transcription by binding to consensus binding sites in the upstream region of the p21 gene promoter. This activity is also dependent on a binding site for Sp1/KLF-like factors near the transcription start site. Our findings indicate that p21 is a crucial downstream gene target and effector of GATA-1 during red blood cell terminal differentiation.
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Affiliation(s)
- Michael Papetti
- 1Department of Cell Biology, Montefiore Medical Center, Bronx, NY, USA
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Choe KS, Ujhelly O, Wontakal SN, Skoultchi AI. PU.1 directly regulates cdk6 gene expression, linking the cell proliferation and differentiation programs in erythroid cells. J Biol Chem 2009; 285:3044-52. [PMID: 19955566 DOI: 10.1074/jbc.m109.077727] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cell proliferation and differentiation are highly coordinated processes during normal development. Most leukemia cells are blocked from undergoing terminal differentiation and also exhibit uncontrolled proliferation. Dysregulated expression of transcription factor PU.1 is strongly associated with Friend virus-induced erythroleukemia. PU.1 inhibits erythroid differentiation by binding to and inhibiting GATA-1. PU.1 also may be involved in controlling proliferation of erythroid cells. We reported previously that the G(1) phase-specific cyclin-dependent kinase 6 (CDK6) also blocks erythroid differentiation. We now report that PU.1 directly stimulates transcription of the cdk6 gene in both normal erythroid progenitors and erythroleukemia cells, as well as in macrophages. We propose that PU.1 coordinates proliferation and differentiation in immature erythroid cells by inhibiting the GATA-1-mediated gene expression program and also by regulating expression of genes that control progression through the G(1) phase of the cell cycle, the period during which the decision to differentiate is made.
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Affiliation(s)
- Kevin S Choe
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Lu X, Wontakal SN, Emelyanov AV, Morcillo P, Konev AY, Fyodorov DV, Skoultchi AI. Linker histone H1 is essential for Drosophila development, the establishment of pericentric heterochromatin, and a normal polytene chromosome structure. Genes Dev 2009; 23:452-65. [PMID: 19196654 PMCID: PMC2648648 DOI: 10.1101/gad.1749309] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 01/05/2009] [Indexed: 01/22/2023]
Abstract
We generated mutant alleles of Drosophila melanogaster in which expression of the linker histone H1 can be down-regulated over a wide range by RNAi. When the H1 protein level is reduced to approximately 20% of the level in wild-type larvae, lethality occurs in the late larval - pupal stages of development. Here we show that H1 has an important function in gene regulation within or near heterochromatin. It is a strong dominant suppressor of position effect variegation (PEV). Similar to other suppressors of PEV, H1 is simultaneously involved in both the repression of euchromatic genes brought to the vicinity of pericentric heterochromatin and the activation of heterochromatic genes that depend on their pericentric localization for maximal transcriptional activity. Studies of H1-depleted salivary gland polytene chromosomes show that H1 participates in several fundamental aspects of chromosome structure and function. First, H1 is required for heterochromatin structural integrity and the deposition or maintenance of major pericentric heterochromatin-associated histone marks, including H3K9Me(2) and H4K20Me(2). Second, H1 also plays an unexpected role in the alignment of endoreplicated sister chromatids. Finally, H1 is essential for organization of pericentric regions of all polytene chromosomes into a single chromocenter. Thus, linker histone H1 is essential in Drosophila and plays a fundamental role in the architecture and activity of chromosomes in vivo.
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Affiliation(s)
- Xingwu Lu
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Sandeep N. Wontakal
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Alexander V. Emelyanov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Patrick Morcillo
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Alexander Y. Konev
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Dmitry V. Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Arthur I. Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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