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  1. Article ; Online: Patient-derived glioblastoma cultures as a tool for small-molecule drug discovery.

    Ye, Ling F / Reznik, Eduard / Korn, Joshua M / Lin, Fallon / Yang, Guizhi / Malesky, Kimberly / Gao, Hui / Loo, Alice / Pagliarini, Raymond / Mikkelsen, Tom / Lo, Donald C / deCarvalho, Ana C / Stockwell, Brent R

    Oncotarget

    2020  Volume 11, Issue 4, Page(s) 443–451

    Abstract: There is a compelling need for new therapeutic strategies for glioblastoma multiforme (GBM). Preclinical target and therapeutic discovery for GBMs is primarily conducted using cell lines grown in serum-containing media, such as U-87 MG, which do not ... ...

    Abstract There is a compelling need for new therapeutic strategies for glioblastoma multiforme (GBM). Preclinical target and therapeutic discovery for GBMs is primarily conducted using cell lines grown in serum-containing media, such as U-87 MG, which do not reflect the gene expression profiles of tumors found in GBM patients. To address this lack of representative models, we sought to develop a panel of patient-derived GBM models and characterize their genomic features, using RNA sequencing (RNA-seq) and growth characteristics, both when grown as neurospheres in culture, and grown orthotopically as xenografts in mice. When we compared these with commonly used GBM cell lines in the Cancer Cell Line Encyclopedia (CCLE), we found these patient-derived models to have greater diversity in gene expression and to better correspond to GBMs directly sequenced from patient tumor samples. We also evaluated the potential of these models for targeted therapy, by using the genomic characterization to identify small molecules that inhibit the growth of distinct subsets of GBMs, paving the way for precision medicines for GBM.
    Language English
    Publishing date 2020-01-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2560162-3
    ISSN 1949-2553 ; 1949-2553
    ISSN (online) 1949-2553
    ISSN 1949-2553
    DOI 10.18632/oncotarget.27457
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity.

    Xie, Xiaoling / Baird, Daniel / Bowen, Kimberly / Capka, Vladimir / Chen, Jinyun / Chenail, Gregg / Cho, YoungShin / Dooley, Julia / Farsidjani, Ali / Fortin, Pascal / Kohls, Darcy / Kulathila, Raviraj / Lin, Fallon / McKay, Daniel / Rodrigues, Lindsey / Sage, David / Touré, B Barry / van der Plas, Simon / Wright, Kirk /
    Xu, Ming / Yin, Hong / Levell, Julian / Pagliarini, Raymond A

    Structure (London, England : 1993)

    2017  Volume 25, Issue 3, Page(s) 506–513

    Abstract: Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric ... ...

    Abstract Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric pocket on IDH1, yet shape it differently, highlighting the plasticity of this site. Oncogenic IDH1
    MeSH term(s) Allosteric Regulation ; Allosteric Site ; Crystallography, X-Ray ; Enzyme Inhibitors/pharmacology ; Glutarates/metabolism ; Humans ; Isocitrate Dehydrogenase/antagonists & inhibitors ; Isocitrate Dehydrogenase/chemistry ; Isocitrate Dehydrogenase/genetics ; Neoplasms/genetics ; Protein Binding ; Protein Conformation ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Small Molecule Libraries/pharmacology
    Chemical Substances Enzyme Inhibitors ; Glutarates ; Protein Isoforms ; Small Molecule Libraries ; alpha-hydroxyglutarate (2889-31-8) ; Isocitrate Dehydrogenase (EC 1.1.1.41) ; IDH1 protein, human (EC 1.1.1.42.)
    Language English
    Publishing date 2017-03-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2016.12.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Isocitrate dehydrogenase (IDH) mutations promote a reversible ZEB1/microRNA (miR)-200-dependent epithelial-mesenchymal transition (EMT).

    Grassian, Alexandra R / Lin, Fallon / Barrett, Rosemary / Liu, Yue / Jiang, Wei / Korpal, Manav / Astley, Holly / Gitterman, Daniel / Henley, Thomas / Howes, Rob / Levell, Julian / Korn, Joshua M / Pagliarini, Raymond

    The Journal of biological chemistry

    2012  Volume 287, Issue 50, Page(s) 42180–42194

    Abstract: Mutations in the genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in a variety of tumor types, resulting in production of the proposed oncometabolite, 2-hydroxyglutarate (2-HG). How mutant IDH and 2-HG alter signaling pathways to promote ... ...

    Abstract Mutations in the genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in a variety of tumor types, resulting in production of the proposed oncometabolite, 2-hydroxyglutarate (2-HG). How mutant IDH and 2-HG alter signaling pathways to promote cancer, however, remains unclear. Additionally, there exist relatively few cell lines with IDH mutations. To examine the effect of endogenous IDH mutations and 2-HG, we created a panel of isogenic epithelial cell lines with either wild-type IDH1/2 or clinically relevant IDH1/2 mutations. Differences were noted in the ability of IDH mutations to cause robust 2-HG accumulation. IDH1/2 mutants that produce high levels of 2-HG cause an epithelial-mesenchymal transition (EMT)-like phenotype, characterized by changes in EMT-related gene expression and cellular morphology. 2-HG is sufficient to recapitulate aspects of this phenotype in the absence of an IDH mutation. In the cells types examined, mutant IDH-induced EMT is dependent on up-regulation of the transcription factor ZEB1 and down-regulation of the miR-200 family of microRNAs. Furthermore, sustained knockdown of IDH1 in IDH1 R132H mutant cells is sufficient to reverse many characteristics of EMT, demonstrating that continued expression of mutant IDH is required to maintain this phenotype. These results suggest mutant IDH proteins can reversibly deregulate discrete signaling pathways that contribute to tumorigenesis.
    MeSH term(s) Amino Acid Substitution ; Cell Line, Tumor ; Epithelial-Mesenchymal Transition ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Neoplastic ; Glutarates/metabolism ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Humans ; Isocitrate Dehydrogenase/biosynthesis ; Isocitrate Dehydrogenase/genetics ; MicroRNAs/biosynthesis ; MicroRNAs/genetics ; Mutation, Missense ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; RNA, Neoplasm/biosynthesis ; RNA, Neoplasm/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Up-Regulation/genetics ; Zinc Finger E-box-Binding Homeobox 1
    Chemical Substances Glutarates ; Homeodomain Proteins ; MIRN200 microRNA, human ; MicroRNAs ; Neoplasm Proteins ; RNA, Neoplasm ; Transcription Factors ; ZEB1 protein, human ; Zinc Finger E-box-Binding Homeobox 1 ; alpha-hydroxyglutarate (2889-31-8) ; 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 2012-10-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M112.417832
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A small molecule that binds and inhibits the ETV1 transcription factor oncoprotein.

    Pop, Marius S / Stransky, Nicolas / Garvie, Colin W / Theurillat, Jean-Philippe / Hartman, Emily C / Lewis, Timothy A / Zhong, Cheng / Culyba, Elizabeth K / Lin, Fallon / Daniels, Douglas S / Pagliarini, Raymond / Ronco, Lucienne / Koehler, Angela N / Garraway, Levi A

    Molecular cancer therapeutics

    2014  Volume 13, Issue 6, Page(s) 1492–1502

    Abstract: Members of the ETS transcription factor family have been implicated in several cancers, where they are often dysregulated by genomic derangement. ETS variant 1 (ETV1) is an ETS factor gene that undergoes chromosomal translocation in prostate cancers and ... ...

    Abstract Members of the ETS transcription factor family have been implicated in several cancers, where they are often dysregulated by genomic derangement. ETS variant 1 (ETV1) is an ETS factor gene that undergoes chromosomal translocation in prostate cancers and Ewing sarcomas, amplification in melanomas, and lineage dysregulation in gastrointestinal stromal tumors. Pharmacologic perturbation of ETV1 would be appealing in these cancers; however, oncogenic transcription factors are often deemed "undruggable" by conventional methods. Here, we used small-molecule microarray screens to identify and characterize drug-like compounds that modulate the biologic function of ETV1. We identified the 1,3,5-triazine small molecule BRD32048 as a top candidate ETV1 perturbagen. BRD32048 binds ETV1 directly, modulating both ETV1-mediated transcriptional activity and invasion of ETV1-driven cancer cells. Moreover, BRD32048 inhibits p300-dependent acetylation of ETV1, thereby promoting its degradation. These results point to a new avenue for pharmacologic ETV1 inhibition and may inform a general means to discover small molecule perturbagens of transcription factor oncoproteins.
    MeSH term(s) Aniline Compounds/administration & dosage ; Cell Line, Tumor ; DNA-Binding Proteins/antagonists & inhibitors ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Male ; Molecular Targeted Therapy ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Promoter Regions, Genetic ; Prostatic Neoplasms/drug therapy ; Prostatic Neoplasms/pathology ; Small Molecule Libraries ; Surface Plasmon Resonance ; Transcription Factors/antagonists & inhibitors ; Transcription Factors/metabolism ; Triazines/administration & dosage
    Chemical Substances Aniline Compounds ; BRD32048 ; DNA-Binding Proteins ; ETV1 protein, human ; Small Molecule Libraries ; Transcription Factors ; Triazines
    Language English
    Publishing date 2014-04-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2063563-1
    ISSN 1538-8514 ; 1535-7163
    ISSN (online) 1538-8514
    ISSN 1535-7163
    DOI 10.1158/1535-7163.MCT-13-0689
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: ERG signaling in prostate cancer is driven through PRMT5-dependent methylation of the Androgen Receptor.

    Mounir, Zineb / Korn, Joshua M / Westerling, Thomas / Lin, Fallon / Kirby, Christina A / Schirle, Markus / McAllister, Gregg / Hoffman, Greg / Ramadan, Nadire / Hartung, Anke / Feng, Yan / Kipp, David Randal / Quinn, Christopher / Fodor, Michelle / Baird, Jason / Schoumacher, Marie / Meyer, Ronald / Deeds, James / Buchwalter, Gilles /
    Stams, Travis / Keen, Nicholas / Sellers, William R / Brown, Myles / Pagliarini, Raymond A

    eLife

    2016  Volume 5

    Abstract: The TMPRSS2:ERG gene fusion is common in androgen receptor (AR) positive prostate cancers, yet its function remains poorly understood. From a screen for functionally relevant ERG interactors, we identify the arginine methyltransferase PRMT5. ERG recruits ...

    Abstract The TMPRSS2:ERG gene fusion is common in androgen receptor (AR) positive prostate cancers, yet its function remains poorly understood. From a screen for functionally relevant ERG interactors, we identify the arginine methyltransferase PRMT5. ERG recruits PRMT5 to AR-target genes, where PRMT5 methylates AR on arginine 761. This attenuates AR recruitment and transcription of genes expressed in differentiated prostate epithelium. The AR-inhibitory function of PRMT5 is restricted to TMPRSS2:ERG-positive prostate cancer cells. Mutation of this methylation site on AR results in a transcriptionally hyperactive AR, suggesting that the proliferative effects of ERG and PRMT5 are mediated through attenuating AR's ability to induce genes normally involved in lineage differentiation. This provides a rationale for targeting PRMT5 in TMPRSS2:ERG positive prostate cancers. Moreover, methylation of AR at arginine 761 highlights a mechanism for how the ERG oncogene may coax AR towards inducing proliferation versus differentiation.
    Language English
    Publishing date 2016-05-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.13964
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism.

    Grassian, Alexandra R / Parker, Seth J / Davidson, Shawn M / Divakaruni, Ajit S / Green, Courtney R / Zhang, Xiamei / Slocum, Kelly L / Pu, Minying / Lin, Fallon / Vickers, Chad / Joud-Caldwell, Carol / Chung, Franklin / Yin, Hong / Handly, Erika D / Straub, Christopher / Growney, Joseph D / Vander Heiden, Matthew G / Murphy, Anne N / Pagliarini, Raymond /
    Metallo, Christian M

    Cancer research

    2014  Volume 74, Issue 12, Page(s) 3317–3331

    Abstract: Oncogenic mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in several types of cancer, but the metabolic consequences of these genetic changes are not fully understood. In this study, we performed (13)C metabolic flux analysis on a panel of ... ...

    Abstract Oncogenic mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in several types of cancer, but the metabolic consequences of these genetic changes are not fully understood. In this study, we performed (13)C metabolic flux analysis on a panel of isogenic cell lines containing heterozygous IDH1/2 mutations. We observed that under hypoxic conditions, IDH1-mutant cells exhibited increased oxidative tricarboxylic acid metabolism along with decreased reductive glutamine metabolism, but not IDH2-mutant cells. However, selective inhibition of mutant IDH1 enzyme function could not reverse the defect in reductive carboxylation activity. Furthermore, this metabolic reprogramming increased the sensitivity of IDH1-mutant cells to hypoxia or electron transport chain inhibition in vitro. Lastly, IDH1-mutant cells also grew poorly as subcutaneous xenografts within a hypoxic in vivo microenvironment. Together, our results suggest therapeutic opportunities to exploit the metabolic vulnerabilities specific to IDH1 mutation.
    MeSH term(s) Animals ; Antineoplastic Agents/pharmacology ; Cell Hypoxia ; Citric Acid Cycle ; Enzyme Inhibitors/pharmacology ; Glutamine/metabolism ; HCT116 Cells ; Humans ; Isocitrate Dehydrogenase/antagonists & inhibitors ; Isocitrate Dehydrogenase/genetics ; Isocitrate Dehydrogenase/metabolism ; Mice ; Mitochondria/metabolism ; Mutation, Missense ; Oxidation-Reduction ; Stress, Physiological ; Xenograft Model Antitumor Assays
    Chemical Substances Antineoplastic Agents ; Enzyme Inhibitors ; Glutamine (0RH81L854J) ; 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 2014-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-14-0772-T
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1.

    Levell, Julian R / Caferro, Thomas / Chenail, Gregg / Dix, Ina / Dooley, Julia / Firestone, Brant / Fortin, Pascal D / Giraldes, John / Gould, Ty / Growney, Joseph D / Jones, Michael D / Kulathila, Raviraj / Lin, Fallon / Liu, Gang / Mueller, Arne / van der Plas, Simon / Slocum, Kelly / Smith, Troy / Terranova, Remi /
    Touré, B Barry / Tyagi, Viraj / Wagner, Trixie / Xie, Xiaoling / Xu, Ming / Yang, Fan S / Zhou, Liping X / Pagliarini, Raymond / Cho, Young Shin

    ACS medicinal chemistry letters

    2016  Volume 8, Issue 2, Page(s) 151–156

    Abstract: High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of ... ...

    Abstract High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1
    Language English
    Publishing date 2016-12-16
    Publishing country United States
    Document type Journal Article
    ISSN 1948-5875
    ISSN 1948-5875
    DOI 10.1021/acsmedchemlett.6b00334
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5.

    Mavrakis, Konstantinos J / McDonald, E Robert / Schlabach, Michael R / Billy, Eric / Hoffman, Gregory R / deWeck, Antoine / Ruddy, David A / Venkatesan, Kavitha / Yu, Jianjun / McAllister, Gregg / Stump, Mark / deBeaumont, Rosalie / Ho, Samuel / Yue, Yingzi / Liu, Yue / Yan-Neale, Yan / Yang, Guizhi / Lin, Fallon / Yin, Hong /
    Gao, Hui / Kipp, D Randal / Zhao, Songping / McNamara, Joshua T / Sprague, Elizabeth R / Zheng, Bing / Lin, Ying / Cho, Young Shin / Gu, Justin / Crawford, Kenneth / Ciccone, David / Vitari, Alberto C / Lai, Albert / Capka, Vladimir / Hurov, Kristen / Porter, Jeffery A / Tallarico, John / Mickanin, Craig / Lees, Emma / Pagliarini, Raymond / Keen, Nicholas / Schmelzle, Tobias / Hofmann, Francesco / Stegmeier, Frank / Sellers, William R

    Science (New York, N.Y.)

    2016  Volume 351, Issue 6278, Page(s) 1208–1213

    Abstract: 5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a ... ...

    Abstract 5-Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway. The MTAP gene is frequently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. By interrogating data from a large-scale short hairpin RNA-mediated screen across 390 cancer cell line models, we found that the viability of MTAP-deficient cancer cells is impaired by depletion of the protein arginine methyltransferase PRMT5. MTAP-deleted cells accumulate the metabolite methylthioadenosine (MTA), which we found to inhibit PRMT5 methyltransferase activity. Deletion of MTAP in MTAP-proficient cells rendered them sensitive to PRMT5 depletion. Conversely, reconstitution of MTAP in an MTAP-deficient cell line rescued PRMT5 dependence. Thus, MTA accumulation in MTAP-deleted cancers creates a hypomorphic PRMT5 state that is selectively sensitized toward further PRMT5 inhibition. Inhibitors of PRMT5 that leverage this dysregulated metabolic state merit further investigation as a potential therapy for MTAP/CDKN2A-deleted tumors.
    MeSH term(s) Cell Line, Tumor ; Cell Survival ; Cyclin-Dependent Kinase Inhibitor p16/genetics ; Cyclin-Dependent Kinase Inhibitor p16/metabolism ; Deoxyadenosines/metabolism ; Gene Deletion ; Humans ; Methionine/metabolism ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; Purine-Nucleoside Phosphorylase/genetics ; Purine-Nucleoside Phosphorylase/metabolism ; RNA, Small Interfering/genetics ; Thionucleosides/metabolism
    Chemical Substances Cyclin-Dependent Kinase Inhibitor p16 ; Deoxyadenosines ; RNA, Small Interfering ; Thionucleosides ; 5'-methylthioadenosine (634Z2VK3UQ) ; Methionine (AE28F7PNPL) ; PRMT5 protein, human (EC 2.1.1.319) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; Purine-Nucleoside Phosphorylase (EC 2.4.2.1) ; 5'-methylthioadenosine phosphorylase (EC 2.4.2.28)
    Language English
    Publishing date 2016-03-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aad5944
    Database MEDical Literature Analysis and Retrieval System OnLINE

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