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  1. Article ; Online: Oncohistone mutations enhance chromatin remodeling and alter cell fates.

    Bagert, John D / Mitchener, Michelle M / Patriotis, Agata L / Dul, Barbara E / Wojcik, Felix / Nacev, Benjamin A / Feng, Lijuan / Allis, C David / Muir, Tom W

    Nature chemical biology

    2021  Volume 17, Issue 4, Page(s) 403–411

    Abstract: Whole-genome sequencing data mining efforts have revealed numerous histone mutations in a wide range of cancer types. These occur in all four core histones in both the tail and globular domains and remain largely uncharacterized. Here we used two high- ... ...

    Abstract Whole-genome sequencing data mining efforts have revealed numerous histone mutations in a wide range of cancer types. These occur in all four core histones in both the tail and globular domains and remain largely uncharacterized. Here we used two high-throughput approaches, a DNA-barcoded mononucleosome library and a humanized yeast library, to profile the biochemical and cellular effects of these mutations. We identified cancer-associated mutations in the histone globular domains that enhance fundamental chromatin remodeling processes, histone exchange and nucleosome sliding, and are lethal in yeast. In mammalian cells, these mutations upregulate cancer-associated gene pathways and inhibit cellular differentiation by altering expression of lineage-specific transcription factors. This work represents a comprehensive functional analysis of the histone mutational landscape in human cancers and leads to a model in which histone mutations that perturb nucleosome remodeling may contribute to disease development and/or progression.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; Chromatin Assembly and Disassembly/physiology ; Gene Library ; Histones/genetics ; Humans ; Mutation/genetics ; Neoplasms/genetics ; Nucleosomes/genetics ; Protein Binding ; Protein Domains ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcriptional Activation
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; Transcription Factors
    Language English
    Publishing date 2021-03-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-021-00738-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: DRUL for school: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2.

    Frank, Mayu O / Blachere, Nathalie E / Parveen, Salina / Hacisuleyman, Ezgi / Fak, John / Luna, Joseph M / Michailidis, Eleftherios / Wright, Samara / Stark, Pamela / Campbell, Ann / Foo, Ashley / Sakmar, Thomas P / Huffman, Virginia / Bergh, Marissa / Goldfarb, Audrey / Mansisidor, Andres / Patriotis, Agata L / Palmquist, Karl H / Poulton, Nicolas /
    Leicher, Rachel / Vargas, César D M / Duba, Irene / Hurley, Arlene / Colagreco, Joseph / Pagane, Nicole / Orange, Dana E / Mora, Kevin / Rakeman, Jennifer L / Fowler, Randal C / Fernandes, Helen / Lamendola-Essel, Michelle F / Didkovsky, Nicholas / Silvera, Leopolda / Masci, Joseph / Allen, Machelle / Rice, Charles M / Darnell, Robert B

    PloS one

    2021  Volume 16, Issue 6, Page(s) e0252949

    Abstract: To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller ... ...

    Abstract To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/μl in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Nucleic Acid Testing ; Child ; Female ; Humans ; Male ; SARS-CoV-2 ; Saliva/virology ; Schools ; Specimen Handling
    Language English
    Publishing date 2021-06-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0252949
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: DRUL for School: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2

    Frank, Mayu / Blachere, Nathalie E / Parveen, Salina / Hacisuleyman, Ezgi / Fak, John / Luna, Joseph M / Michailidis, Eleftherios / Wright, Samara / Stark, Pamela / Campbell, Ann H / Foo, Ashley / Sakmar, Thomas P / Huffman, Virginia / Bergh, Marissa / Goldfarb, Audrey / Mansisidor, Andrew / Patriotis, Agata L / Palmquist, Karl H / Poulton, Nicolas /
    Leicher, Rachel / Vargas, Cesar D / Duba, Irene / Hurley, Arlene / Colagreco, Joseph P / Pagane, Nicole / Orange, Dana E / Mora, Kevin / Rakeman, Jennifer L / Fowler, Randal C / Fernandes, Helen / Lamendola-Essel, Michelle F / Didkovsky, Nick / Silvera, Leopolda / Masci, Joseph / Allen, Machelle / Rice, Charles M / Darnell, Robert B

    medRxiv

    Abstract: To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 ul saliva in vials containing Darnell Rockefeller ... ...

    Abstract To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 ul saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/ul in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
    Keywords covid19
    Language English
    Publishing date 2021-04-06
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.04.03.21254873
    Database COVID19

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