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  1. Article ; Online: Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13.

    Prajapati, Subhash C / Dunham, Nicholas / Fan, Hao / Garrett-Bakelman, Francine E

    BioTechniques

    2022  Volume 72, Issue 3, Page(s) 81–84

    Abstract: Acute myeloid leukemia patients with FMS-like tyrosine kinase 3-internal tandem duplications and mixed lineage leukemia-protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these ... ...

    Abstract Acute myeloid leukemia patients with FMS-like tyrosine kinase 3-internal tandem duplications and mixed lineage leukemia-protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these abnormalities and is used in CRISPR experiments to identify disease drivers. However, experimental observations may be biased or inconclusive in the absence of experimentally validated positive control genes. We validated sgRNAs for knockdown of
    MeSH term(s) Cell Line ; Cell Line, Tumor ; Cell Proliferation/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Cytarabine/pharmacology ; Humans ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/genetics
    Chemical Substances Cytarabine (04079A1RDZ)
    Language English
    Publishing date 2022-02-04
    Publishing country England
    Document type Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 48453-2
    ISSN 1940-9818 ; 0736-6205
    ISSN (online) 1940-9818
    ISSN 0736-6205
    DOI 10.2144/btn-2021-0089
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  2. Article ; Online: Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13

    Subhash C Prajapati / Nicholas Dunham / Hao Fan / Francine E Garrett-Bakelman

    BioTechniques, Vol 72, Iss 3, Pp 81-

    2022  Volume 84

    Abstract: Acute myeloid leukemia patients with FMS-like tyrosine kinase 3–internal tandem duplications and mixed lineage leukemia–protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these ... ...

    Abstract Acute myeloid leukemia patients with FMS-like tyrosine kinase 3–internal tandem duplications and mixed lineage leukemia–protein AF9 fusion proteins suffer from poor clinical outcomes. The MOLM-13 acute myeloid leukemia cell line harbors both of these abnormalities and is used in CRISPR experiments to identify disease drivers. However, experimental observations may be biased or inconclusive in the absence of experimentally validated positive control genes. We validated sgRNAs for knockdown of TP53 for cell proliferation and for DCK knockdown and CDA upregulation for cytarabine resistance control genes in MOLM-13 cells. We have provided a detailed CRISPR protocol applicable to both gene knockdown or activation experiments and downstream leukemic phenotype analyses. Inclusion of these controls in CRISPR experiments will enhance the capacity to identify novel myeloid leukemia drivers in MOLM-13 cells.
    Keywords acute myeloid leukemia ; CDA ; CRISPR-Cas9 ; cytarabine ; DCK ; MOLM-13 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Future Science Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Depletion of

    Neelamraju, Yaseswini / Gjini, Evisa / Chhangawala, Sagar / Fan, Hao / He, Shuning / Jing, Chang-Bin / Nguyen, Ashley T / Prajapati, Subhash / Sheridan, Caroline / Houvras, Yariv / Melnick, Ari / Look, A Thomas / Garrett-Bakelman, Francine E

    Frontiers in hematology

    2023  Volume 2

    Abstract: Introduction: Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (: Methods: In the current ... ...

    Abstract Introduction: Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (
    Methods: In the current study, we collected progenitor cells from the kidney marrows of the adult
    Results and discussion: A global increase in DNA methylation of gene promoter regions and CpG islands was observed in
    Language English
    Publishing date 2023-09-14
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2813-3935
    ISSN (online) 2813-3935
    DOI 10.3389/frhem.2023.1235170
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  4. Article ; Online: Acute myeloid leukemia stratifies as 2 clinically relevant sphingolipidomic subtypes.

    Paudel, B Bishal / Tan, Su-Fern / Fox, Todd E / Ung, Johnson / Golla, Upendarrao / Shaw, Jeremy J P / Dunton, Wendy / Lee, Irene / Fares, Wisam A / Patel, Satyam / Sharma, Arati / Viny, Aaron D / Barth, Brian M / Tallman, Martin S / Cabot, Myles / Garrett-Bakelman, Francine E / Levine, Ross L / Kester, Mark / Feith, David J /
    Claxton, David / Janes, Kevin A / Loughran, Thomas P

    Blood advances

    2024  Volume 8, Issue 5, Page(s) 1137–1142

    MeSH term(s) Humans ; Leukemia, Myeloid, Acute/diagnosis ; Nucleophosmin
    Chemical Substances Nucleophosmin (117896-08-9)
    Language English
    Publishing date 2024-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2915908-8
    ISSN 2473-9537 ; 2473-9529
    ISSN (online) 2473-9537
    ISSN 2473-9529
    DOI 10.1182/bloodadvances.2023010535
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  5. Article ; Online: COCOA: coordinate covariation analysis of epigenetic heterogeneity.

    Lawson, John T / Smith, Jason P / Bekiranov, Stefan / Garrett-Bakelman, Francine E / Sheffield, Nathan C

    Genome biology

    2020  Volume 21, Issue 1, Page(s) 240

    Abstract: A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across ... ...

    Abstract A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA's utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor ( http://bioconductor.org/packages/COCOA ).
    MeSH term(s) Breast Neoplasms/genetics ; DNA Methylation ; Epigenesis, Genetic ; Epigenomics/methods ; Genetic Heterogeneity ; Humans ; Molecular Sequence Annotation ; Software
    Language English
    Publishing date 2020-09-07
    Publishing country England
    Document type Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-020-02139-4
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  6. Article ; Online: Mutant IDH: a targetable driver of leukemic phenotypes linking metabolism, epigenetics and transcriptional regulation.

    Garrett-Bakelman, Francine E / Melnick, Ari M

    Epigenomics

    2016  Volume 8, Issue 7, Page(s) 945–957

    Abstract: Aberrant epigenomic programming is a hallmark of acute myeloid leukemia. This is partially due to somatic mutations that perturb cytosine methylation, histone post-translational modifications and transcription factors. Remarkably, mutations in the IDH1 ... ...

    Abstract Aberrant epigenomic programming is a hallmark of acute myeloid leukemia. This is partially due to somatic mutations that perturb cytosine methylation, histone post-translational modifications and transcription factors. Remarkably, mutations in the IDH1 and IDH2 genes perturb the epigenome through all three of these mechanisms. Mutant IDH enzymes produce high levels of the oncometabolite (R)-2-hydroxyglutarate that competitively inhibits dioxygenase enzymes that modify methylcytosine to hydroxymethylcytosine and histone tail methylation. The development of IDH mutant specific inhibitors may now enable the therapeutic reprogramming of both layers of the epigenome spontaneously to revert the malignant phenotype of these leukemias and improve clinical outcome for acute myeloid leukemia patients with IDH mutations.
    MeSH term(s) Animals ; Epigenesis, Genetic ; Gene Expression Regulation, Leukemic ; Humans ; Isocitrate Dehydrogenase/genetics ; Mutation ; Phenotype ; Transcription, Genetic
    Chemical Substances IDH2 protein, human (EC 1.1.1.41) ; Isocitrate Dehydrogenase (EC 1.1.1.41) ; IDH1 protein, human (EC 1.1.1.42.)
    Language English
    Publishing date 2016-07-19
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2016-0008
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  7. Article: Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes.

    Paudel, B Bishal / Tan, Su-Fern / Fox, Todd E / Ung, Johnson / Shaw, Jeremy / Dunton, Wendy / Lee, Irene / Sharma, Arati / Viny, Aaron D / Barth, Brian M / Tallman, Martin S / Cabot, Myles / Garrett-Bakelman, Francine E / Levine, Ross L / Kester, Mark / Claxton, David / Feith, David J / Janes, Kevin A / Loughran, Thomas P

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the ...

    Abstract Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives.
    Language English
    Publishing date 2023-04-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.13.536805
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  8. Article ; Online: Harnessing the power of sphingolipids: Prospects for acute myeloid leukemia.

    Ung, Johnson / Tan, Su-Fern / Fox, Todd E / Shaw, Jeremy J P / Vass, Luke R / Costa-Pinheiro, Pedro / Garrett-Bakelman, Francine E / Keng, Michael K / Sharma, Arati / Claxton, David F / Levine, Ross L / Tallman, Martin S / Cabot, Myles C / Kester, Mark / Feith, David J / Loughran, Thomas P

    Blood reviews

    2022  Volume 55, Page(s) 100950

    Abstract: Acute myeloid leukemia (AML) is an aggressive, heterogenous malignancy characterized by clonal expansion of bone marrow-derived myeloid progenitor cells. While our current understanding of the molecular and genomic landscape of AML has evolved ... ...

    Abstract Acute myeloid leukemia (AML) is an aggressive, heterogenous malignancy characterized by clonal expansion of bone marrow-derived myeloid progenitor cells. While our current understanding of the molecular and genomic landscape of AML has evolved dramatically and opened avenues for molecularly targeted therapeutics to improve upon standard intensive induction chemotherapy, curative treatments are elusive, particularly in older patients. Responses to current AML treatments are transient and incomplete, necessitating the development of novel treatment strategies to improve outcomes. To this end, harnessing the power of bioactive sphingolipids to treat cancer shows great promise. Sphingolipids are involved in many hallmarks of cancer of paramount importance in AML. Leukemic blast survival is influenced by cellular levels of ceramide, a bona fide pro-death molecule, and its conversion to signaling molecules such as sphingosine-1-phosphate and glycosphingolipids. Preclinical studies demonstrate the efficacy of therapeutics that target dysregulated sphingolipid metabolism as well as their combinatorial synergy with clinically-relevant therapeutics. Thus, increased understanding of sphingolipid dysregulation may be exploited to improve AML patient care and outcomes. This review summarizes the current knowledge of dysregulated sphingolipid metabolism in AML, evaluates how pro-survival sphingolipids promote AML pathogenesis, and discusses the therapeutic potential of targeting these dysregulated sphingolipid pathways.
    MeSH term(s) Aged ; Ceramides/metabolism ; Ceramides/therapeutic use ; Humans ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/therapy ; Signal Transduction ; Sphingolipids/metabolism ; Sphingolipids/therapeutic use
    Chemical Substances Ceramides ; Sphingolipids
    Language English
    Publishing date 2022-04-09
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 639015-8
    ISSN 1532-1681 ; 0268-960X
    ISSN (online) 1532-1681
    ISSN 0268-960X
    DOI 10.1016/j.blre.2022.100950
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    Zs.A 2207: Show issues Location:
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  9. Article ; Online: Differentiation therapy for IDH1/2 mutant malignancies.

    Garrett-Bakelman, Francine E / Melnick, Ari M

    Cell research

    2013  Volume 23, Issue 8, Page(s) 975–977

    Abstract: Recently discovered recurrent somatic mutations in the key metabolic enzymes IDH1 and IDH2 produce the aberrant oncometabolite 2-HG and contribute to malignant transformation of hematopoietic and glial cells. Two recent reports in Science describe the ... ...

    Abstract Recently discovered recurrent somatic mutations in the key metabolic enzymes IDH1 and IDH2 produce the aberrant oncometabolite 2-HG and contribute to malignant transformation of hematopoietic and glial cells. Two recent reports in Science describe the first IDH1 and IDH2 mutant-specific small-molecule inhibitors, which induce cell differentiation of myeloid leukemias and malignant gliomas.
    Language English
    Publishing date 2013-06-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/cr.2013.73
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  10. Article ; Online: COCOA

    John T. Lawson / Jason P. Smith / Stefan Bekiranov / Francine E. Garrett-Bakelman / Nathan C. Sheffield

    Genome Biology, Vol 21, Iss 1, Pp 1-

    coordinate covariation analysis of epigenetic heterogeneity

    2020  Volume 23

    Abstract: Abstract A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals ... ...

    Abstract Abstract A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA’s utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor ( http://bioconductor.org/packages/COCOA ).
    Keywords Epigenetics ; DNA methylation ; Chromatin accessibility ; Principal component analysis ; Dimensionality reduction ; Data integration ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
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