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  1. Article ; Online: A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

    Goodacre, Norman / Aljanahi, Aisha / Nandakumar, Subhiksha / Mikailov, Mike / Khan, Arifa S

    mSphere

    2018  Volume 3, Issue 2

    Abstract: Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure ...

    Abstract Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank.
    Language English
    Publishing date 2018-03
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/mSphereDirect.00069-18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection.

    Khan, Arifa S / Ng, Siemon H S / Vandeputte, Olivier / Aljanahi, Aisha / Deyati, Avisek / Cassart, Jean-Pol / Charlebois, Robert L / Taliaferro, Lanyn P

    mSphere

    2017  Volume 2, Issue 5

    Abstract: The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological ... ...

    Abstract The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics. Four model viruses were selected based upon different physical and biochemical properties and commercial availability: human respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO). Additionally, porcine circovirus (PCV) was tested by one laboratory. Independent samples were prepared for HTS by spiking intact viruses or extracted viral nucleic acids, singly or mixed, into different HeLa cell matrices (resuspended whole cells, cell lysate, or total cellular RNA). Data were obtained using different sequencing platforms (Roche 454, Illumina HiSeq1500 or HiSeq2500). Bioinformatic analyses were performed independently by each laboratory using available tools, pipelines, and databases. The results showed that comparable virus detection was obtained in the three laboratories regardless of sample processing, library preparation, sequencing platform, and bioinformatic analysis: between 0.1 and 3 viral genome copies per cell were detected for all of the model viruses used. This study highlights the potential for using HTS for sensitive detection of adventitious viruses in complex biological samples containing cellular background.
    Language English
    Publishing date 2017-09
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5042
    ISSN 2379-5042
    DOI 10.1128/mSphere.00307-17
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A macaque clonal hematopoiesis model demonstrates expansion of TET2-disrupted clones and utility for testing interventions.

    Shin, Tae-Hoon / Zhou, Yifan / Chen, Shirley / Cordes, Stefan / Grice, Max Z / Fan, Xing / Lee, Byung-Chul / Aljanahi, Aisha A / Hong, So Gun / Vaughan, Kelli L / Mattison, Julie A / Kohama, Steven G / Fabre, Margarete A / Uchida, Naoya / Demirci, Selami / Corat, Marcus A F / Métais, Jean-Yves / Calvo, Katherine R / Buscarlet, Manuel /
    Natanson, Hannah / McGraw, Kathy L / List, Alan F / Busque, Lambert / Tisdale, John F / Vassiliou, George S / Yu, Kyung-Rok / Dunbar, Cynthia E

    Blood

    2022  Volume 140, Issue 16, Page(s) 1774–1789

    Abstract: Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error- ... ...

    Abstract Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error-corrected sequencing of 56 human CH/myeloid malignancy genes, we identified natural CH driver mutations in aged rhesus macaques matching genes somatically mutated in human CH, with DNMT3A mutations being the most frequent. A CH model in young adult macaques was generated via autologous transplantation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated gene-edited hematopoietic stem and progenitor cells (HSPCs), targeting the top human CH genes with loss-of-function (LOF) mutations. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 LOF mutations, compared with minimal expansion of clones bearing other mutations. Although the blood counts of these CH macaques were normal, their bone marrows were hypercellular and myeloid-predominant. TET2-disrupted myeloid colony-forming units isolated from these animals showed a distinct hyperinflammatory gene expression profile compared with wild type. In addition, mature macrophages purified from the CH macaques showed elevated NLRP3 inflammasome activity and increased interleukin-1β (IL-1β) and IL-6 production. The model was used to test the impact of IL-6 blockage by tocilizumab, documenting a slowing of TET2-mutated expansion, suggesting that interruption of the IL-6 axis may remove the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and give insights into potential therapeutic interventions.
    MeSH term(s) Humans ; Young Adult ; Animals ; Aged ; Clonal Hematopoiesis/genetics ; Hematopoiesis/genetics ; Interleukin-1beta/genetics ; Inflammasomes ; NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; Macaca mulatta ; CRISPR-Associated Protein 9 ; Interleukin-6/genetics ; Clone Cells ; DNA-Binding Proteins/genetics ; Dioxygenases/genetics
    Chemical Substances Interleukin-1beta ; Inflammasomes ; NLR Family, Pyrin Domain-Containing 3 Protein ; CRISPR-Associated Protein 9 (EC 3.1.-) ; Interleukin-6 ; TET2 protein, human (EC 1.13.11.-) ; DNA-Binding Proteins ; Dioxygenases (EC 1.13.11.-)
    Language English
    Publishing date 2022-06-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood.2021014875
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Uh III Zs.140: Show issues Location:
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    Zs.MO 364: Show issues

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  4. Article: Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia

    Kim, Miriam Y / Yu, Kyung-Rok / Kenderian, Saad S / Ruella, Marco / Chen, Shirley / Shin, Tae-Hoon / Aljanahi, Aisha A / Schreeder, Daniel / Klichinsky, Michael / Shestova, Olga / Kozlowski, Miroslaw S / Cummins, Katherine D / Shan, Xinhe / Shestov, Maksim / Bagg, Adam / Morrissette, Jennifer J.D / Sekhri, Palak / Lazzarotto, Cicera R / Calvo, Katherine R /
    Kuhns, Douglas B / Donahue, Robert E / Behbehani, Gregory K / Tsai, Shengdar Q / Dunbar, Cynthia E / Gill, Saar

    Elsevier Inc. Cell. 2018 May 31, v. 173, no. 6

    2018  

    Abstract: The absence of cancer-restricted surface markers is a major impediment to antigen-specific immunotherapy using chimeric antigen receptor (CAR) T cells. For example, targeting the canonical myeloid marker CD33 in acute myeloid leukemia (AML) results in ... ...

    Abstract The absence of cancer-restricted surface markers is a major impediment to antigen-specific immunotherapy using chimeric antigen receptor (CAR) T cells. For example, targeting the canonical myeloid marker CD33 in acute myeloid leukemia (AML) results in toxicity from destruction of normal myeloid cells. We hypothesized that a leukemia-specific antigen could be created by deleting CD33 from normal hematopoietic stem and progenitor cells (HSPCs), thereby generating a hematopoietic system resistant to CD33-targeted therapy and enabling specific targeting of AML with CAR T cells. We generated CD33-deficient human HSPCs and demonstrated normal engraftment and differentiation in immunodeficient mice. Autologous CD33 KO HSPC transplantation in rhesus macaques demonstrated long-term multilineage engraftment of gene-edited cells with normal myeloid function. CD33-deficient cells were impervious to CD33-targeting CAR T cells, allowing for efficient elimination of leukemia without myelotoxicity. These studies illuminate a novel approach to antigen-specific immunotherapy by genetically engineering the host to avoid on-target, off-tumor toxicity.
    Keywords Macaca mulatta ; T-lymphocytes ; antigens ; genetic engineering ; hematopoietic stem cells ; humans ; immunotherapy ; mice ; myeloid leukemia ; toxicity
    Language English
    Dates of publication 2018-0531
    Size p. 1439-1453.e19.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.05.013
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia.

    Kim, Miriam Y / Yu, Kyung-Rok / Kenderian, Saad S / Ruella, Marco / Chen, Shirley / Shin, Tae-Hoon / Aljanahi, Aisha A / Schreeder, Daniel / Klichinsky, Michael / Shestova, Olga / Kozlowski, Miroslaw S / Cummins, Katherine D / Shan, Xinhe / Shestov, Maksim / Bagg, Adam / Morrissette, Jennifer J D / Sekhri, Palak / Lazzarotto, Cicera R / Calvo, Katherine R /
    Kuhns, Douglas B / Donahue, Robert E / Behbehani, Gregory K / Tsai, Shengdar Q / Dunbar, Cynthia E / Gill, Saar

    Cell

    2018  Volume 173, Issue 6, Page(s) 1439–1453.e19

    Abstract: The absence of cancer-restricted surface markers is a major impediment to antigen-specific immunotherapy using chimeric antigen receptor (CAR) T cells. For example, targeting the canonical myeloid marker CD33 in acute myeloid leukemia (AML) results in ... ...

    Abstract The absence of cancer-restricted surface markers is a major impediment to antigen-specific immunotherapy using chimeric antigen receptor (CAR) T cells. For example, targeting the canonical myeloid marker CD33 in acute myeloid leukemia (AML) results in toxicity from destruction of normal myeloid cells. We hypothesized that a leukemia-specific antigen could be created by deleting CD33 from normal hematopoietic stem and progenitor cells (HSPCs), thereby generating a hematopoietic system resistant to CD33-targeted therapy and enabling specific targeting of AML with CAR T cells. We generated CD33-deficient human HSPCs and demonstrated normal engraftment and differentiation in immunodeficient mice. Autologous CD33 KO HSPC transplantation in rhesus macaques demonstrated long-term multilineage engraftment of gene-edited cells with normal myeloid function. CD33-deficient cells were impervious to CD33-targeting CAR T cells, allowing for efficient elimination of leukemia without myelotoxicity. These studies illuminate a novel approach to antigen-specific immunotherapy by genetically engineering the host to avoid on-target, off-tumor toxicity.
    MeSH term(s) Animals ; Cell Differentiation ; Cell Line, Tumor ; Cell Lineage ; Electroporation ; Female ; Hematopoiesis ; Hematopoietic Stem Cells/cytology ; Humans ; Immunotherapy/methods ; Leukemia, Myeloid, Acute/immunology ; Leukemia, Myeloid, Acute/therapy ; Macaca mulatta ; Male ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; Neoplasm Transplantation ; RNA, Guide, CRISPR-Cas Systems/genetics ; Reactive Oxygen Species ; Sialic Acid Binding Ig-like Lectin 3/genetics ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology
    Chemical Substances CD33 protein, human ; RNA, Guide, CRISPR-Cas Systems ; Reactive Oxygen Species ; Sialic Acid Binding Ig-like Lectin 3
    Language English
    Publishing date 2018-05-31
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.05.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1167: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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