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1دورية أكاديمية
المؤلفون: Megan R. Reed, A. Geoffrey Lyle, Annick De Loose, Leena Maddukuri, Katrina Learned, Holly C. Beale, Ellen T. Kephart, Allison Cheney, Anouk van den Bout, Madison P. Lee, Kelsey N. Hundley, Ashley M. Smith, Teresa M. DesRochers, Cecile Rose T. Vibat, Murat Gokden, Sofie Salama, Christopher P. Wardell, Robert L. Eoff, Olena M. Vaske, Analiz Rodriguez
المصدر: Cells, Vol 10, Iss 12, p 3400 (2021)
مصطلحات موضوعية: Li Fraumeni, glioblastoma, precision medicine, organoid, transcriptomics, Cytology, QH573-671
الوصف: Li Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in TP53. TP53 is the most common mutated gene in human cancer, occurring in 30–50% of glioblastomas (GBM). Here, we highlight a precision medicine platform to identify potential targets for a GBM patient with LFS. We used a comparative transcriptomics approach to identify genes that are uniquely overexpressed in the LFS GBM patient relative to a cancer compendium of 12,747 tumor RNA sequencing data sets, including 200 GBMs. STAT1 and STAT2 were identified as being significantly overexpressed in the LFS patient, indicating ruxolitinib, a Janus kinase 1 and 2 inhibitors, as a potential therapy. The LFS patient had the highest level of STAT1 and STAT2 expression in an institutional high-grade glioma cohort of 45 patients, further supporting the cancer compendium results. To empirically validate the comparative transcriptomics pipeline, we used a combination of adherent and organoid cell culture techniques, including ex vivo patient-derived organoids (PDOs) from four patient-derived cell lines, including the LFS patient. STAT1 and STAT2 expression levels in the four patient-derived cells correlated with levels identified in the respective parent tumors. In both adherent and organoid cultures, cells from the LFS patient were among the most sensitive to ruxolitinib compared to patient-derived cells with lower STAT1 and STAT2 expression levels. A spheroid-based drug screening assay (3D-PREDICT) was performed and used to identify further therapeutic targets. Two targeted therapies were selected for the patient of interest and resulted in radiographic disease stability. This manuscript supports the use of comparative transcriptomics to identify personalized therapeutic targets in a functional precision medicine platform for malignant brain tumors.
وصف الملف: electronic resource
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المؤلفون: Justin W.C. Leung, Jessica H. Hartman, Makayla Berry, Robert L. Eoff, Lane Smith, Alyssa Richey, Julie Gunderson, Leena Maddukuri, Callie Johnson, Megan R. Reed, Amit Ketkar
المصدر: Nucleic Acids Research
مصطلحات موضوعية: DNA Replication, Models, Molecular, AcademicSubjects/SCI00010, Mutant, Genes, myc, DNA-Directed DNA Polymerase, Biology, Genome Integrity, Repair and Replication, medicine.disease_cause, G-quadruplex, Cell Line, 03 medical and health sciences, chemistry.chemical_compound, Genetics, medicine, Humans, Mutation frequency, Nucleotide Motifs, 030304 developmental biology, Alanine, 0303 health sciences, Mutation, 030302 biochemistry & molecular biology, Mutagenesis, DNA, Nucleotidyltransferases, Cell biology, G-Quadruplexes, chemistry, REV1, Protein Binding
الوصف: We previously reported that human Rev1 (hRev1) bound to a parallel-stranded G-quadruplex (G4) from the c-MYC promoter with high affinity. We have extended those results to include other G4 motifs, finding that hRev1 exhibited stronger affinity for parallel-stranded G4 than either anti-parallel or hybrid folds. Amino acids in the αE helix of insert-2 were identified as being important for G4 binding. Mutating E466 and Y470 to alanine selectively perturbed G4 binding affinity. The E466K mutant restored wild-type G4 binding properties. Using a forward mutagenesis assay, we discovered that loss of hRev1 increased G4 mutation frequency >200-fold compared to the control sequence. Base substitutions and deletions occurred around and within the G4 motif. Pyridostatin (PDS) exacerbated this effect, as the mutation frequency increased >700-fold over control and deletions upstream of the G4 site more than doubled. Mutagenic replication of G4 DNA (±PDS) was partially rescued by wild-type and E466K hRev1. The E466A or Y470A mutants failed to suppress the PDS-induced increase in G4 mutation frequency. These findings have implications for the role of insert-2, a motif conserved in vertebrates but not yeast or plants, in Rev1-mediated suppression of mutagenesis during G4 replication.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3c08dd83219609f6a81157da30073a87Test
http://europepmc.org/articles/PMC7913688Test -
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المؤلفون: Robert L. Eoff, Justin W.C. Leung, Maroof K. Zafar, Amit Ketkar, Analiz Rodriguez, Megan R. Reed, Leena Maddukuri
المصدر: The FASEB Journal. 35
مصطلحات موضوعية: Replication (statistics), Genetics, medicine, DNA Polymerase Kappa, Biology, medicine.disease, Molecular Biology, Biochemistry, Molecular biology, Biotechnology, Glioblastoma
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::5135b1063f38eb6806bfcdb84747814bTest
https://doi.org/10.1096/fasebj.2021.35.s1.03041Test -
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المؤلفون: Robert L. Eoff, Megan R. Reed, Justin W.C. Leung, Amit Ketkar, Leena Maddukuri
المصدر: The FASEB Journal. 35
مصطلحات موضوعية: Genome instability, Replication stress, Biology, medicine.disease, Biochemistry, Cell biology, chemistry.chemical_compound, chemistry, Genetics, medicine, Xenobiotic, Molecular Biology, Biotechnology, Glioblastoma
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::e8495ef04b8f98f1e24ce8e13d8e872bTest
https://doi.org/10.1096/fasebj.2021.35.s1.02971Test -
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المؤلفون: Jessica Hartman, Amit Ketkar, Alyssa Richey, Megan Reed, Lane Smith, Julie Gunderson, Leena Maddukuri, Robert L. Eoff, Makayla Berry, Justin W.C. Leung, Callie Johnson
المصدر: The FASEB Journal. 35
مصطلحات موضوعية: chemistry.chemical_compound, chemistry, Biochemistry, Genetics, REV1, G-quadruplex, Molecular Biology, DNA, Biotechnology
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::43eb87c39b0362f5a2d575e0f28c9b93Test
https://doi.org/10.1096/fasebj.2021.35.s1.02319Test -
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المؤلفون: Narsimha Reddy Penthala, Amit Ketkar, Peter A. Crooks, Maroof K. Zafar, Leena Maddukuri, Robert L. Eoff, Megan R. Reed
المصدر: ACS Chem Biol
مصطلحات موضوعية: 0301 basic medicine, Indoles, Alkylation, DNA damage, DNA-Directed DNA Polymerase, 01 natural sciences, Biochemistry, Article, Inhibitory Concentration 50, 03 medical and health sciences, chemistry.chemical_compound, Humans, Nucleotide, Enzyme Inhibitors, Ternary complex, Polymerase, chemistry.chemical_classification, biology, DNA synthesis, 010405 organic chemistry, General Medicine, Molecular biology, Footprinting, 0104 chemical sciences, 030104 developmental biology, Enzyme, chemistry, biology.protein, Molecular Medicine, DNA, DNA Damage
الوصف: Overexpression of human DNA polymerase kappa (hpol κ) in glioblastoma is associated with shorter survival time and resistance to the alkylating agent temozolomide (TMZ), making it an attractive target for the development of small-molecule inhibitors. We previously reported on the development and characterization of indole barbituric acid-derived (IBA) inhibitors of translesion DNA synthesis polymerases (TLS pols). We have now identified a potent and selective inhibitor of hpol κ based on the indole-aminoguanidine (IAG) chemical scaffold. The most promising IAG analogue, IAG-10, exhibited greater inhibitory action against hpol κ than any other human Y-family member, as well as pols from the A-, B-, and X-families. Inhibition of hpol κ by IAG analogues appears to proceed through a mechanism that is distinct from inhibition of hpol η based on changes in DNA binding affinity and nucleotide insertion kinetics. By way of comparison, both IAG and IBA analogues inhibited binary complex formation by hpol κ and ternary complex formation by hpol η. Decreasing the concentration of enzyme and DNA in the reaction mixture lowered the IC(50) value of IAG-10 to submicromolar values, consistent with inhibition of binary complex formation for hpol κ. Chemical footprinting experiments revealed that IAG-10 binds to a cleft between the finger, little finger, and N-clasp domains on hpol κ and that this likely disrupts the interaction between the N-clasp and the TLS pol core. Ln cell culture, IAG-10 potentiated the antiproliferative activity and DNA damaging effects of TMZ in hpol κ-proficient cells but not in hpol κ-deficient cells, indicative of a target-dependent effect. Mutagenic replication across alkylation damage increased in hpol κ-proficient cells treated with IAG-10, while no change in mutation frequency was observed for hpol κ-deficient cells. Ln summary, we developed a potent and selective small-molecule inhibitor of hpol κ that takes advantage of structural features unique to this TLS enzyme to potentiate TMZ, a standard-of-care drug used in the treatment of malignant brain tumors. Furthermore, the IAG scaffold represents a new chemical space for the exploration of TLS pol inhibitors, which could prove useful as a strategy for improving patient response to genotoxic drugs.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::26018f3e9d3838c0e9c18de7d9702ef6Test
https://doi.org/10.1021/acschembio.9b00304Test -
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المؤلفون: Christopher P. Wardell, Robert L. Eoff, Annick De Loose, Sofie R. Salama, Anouk van den Bout, Teresa M. DesRochers, A. Geoffrey Lyle, Murat Gokden, Madison P Lee, Kelsey Hundley, Analiz Rodriguez, Allison Cheney, Katrina Learned, Leena Maddukuri, Olena M. Vaske, Megan R. Reed, Holly C. Beale, Cecile Rose T. Vibat, Ashley M. Smith, Ellen Kephart
المصدر: Cells, Vol 10, Iss 3400, p 3400 (2021)
Cells
Cells; Volume 10; Issue 12; Pages: 3400مصطلحات موضوعية: Adult, Male, Ruxolitinib, Adolescent, QH301-705.5, precision medicine, organoid, Li Fraumeni, glioblastoma, transcriptomics, Article, Li-Fraumeni Syndrome, Transcriptome, Young Adult, Germline mutation, Glioma, Nitriles, medicine, Humans, RNA-Seq, Biology (General), Child, Germ-Line Mutation, Janus kinase 1, business.industry, Cancer, STAT2 Transcription Factor, Janus Kinase 1, General Medicine, Janus Kinase 2, Precision medicine, medicine.disease, Gene Expression Regulation, Neoplastic, Organoids, Pyrimidines, STAT1 Transcription Factor, Li–Fraumeni syndrome, Cancer research, Pyrazoles, Female, business, medicine.drug
الوصف: Li Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in TP53. TP53 is the most common mutated gene in human cancer, occurring in 30–50% of glioblastomas (GBM). Here, we highlight a precision medicine platform to identify potential targets for a GBM patient with LFS. We used a comparative transcriptomics approach to identify genes that are uniquely overexpressed in the LFS GBM patient relative to a cancer compendium of 12,747 tumor RNA sequencing data sets, including 200 GBMs. STAT1 and STAT2 were identified as being significantly overexpressed in the LFS patient, indicating ruxolitinib, a Janus kinase 1 and 2 inhibitors, as a potential therapy. The LFS patient had the highest level of STAT1 and STAT2 expression in an institutional high-grade glioma cohort of 45 patients, further supporting the cancer compendium results. To empirically validate the comparative transcriptomics pipeline, we used a combination of adherent and organoid cell culture techniques, including ex vivo patient-derived organoids (PDOs) from four patient-derived cell lines, including the LFS patient. STAT1 and STAT2 expression levels in the four patient-derived cells correlated with levels identified in the respective parent tumors. In both adherent and organoid cultures, cells from the LFS patient were among the most sensitive to ruxolitinib compared to patient-derived cells with lower STAT1 and STAT2 expression levels. A spheroid-based drug screening assay (3D-PREDICT) was performed and used to identify further therapeutic targets. Two targeted therapies were selected for the patient of interest and resulted in radiographic disease stability. This manuscript supports the use of comparative transcriptomics to identify personalized therapeutic targets in a functional precision medicine platform for malignant brain tumors.
وصف الملف: application/pdf
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f35e9765ca24ba4181d07b0b2ccd621Test
https://doi.org/10.3390/cells10123400Test -
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المؤلفون: Maroof K. Zafar, Leena Maddukuri, Robert L. Eoff, Amit Ketkar, Stephanie D. Byrum, Alan J. Tackett, April C.L. Bostian, Megan R. Reed
المصدر: Nar Cancer
مصطلحات موضوعية: AcademicSubjects/SCI01140, 0301 basic medicine, AcademicSubjects/SCI01060, DNA damage, DNA repair, AcademicSubjects/SCI00030, SIRT7, Standard Article, AcademicSubjects/SCI01180, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Replication protein A, biology, Chemistry, General Medicine, Aryl hydrocarbon receptor, Chromatin, Cell biology, 030104 developmental biology, Histone, Sirtuin, biology.protein, Phosphorylation, AcademicSubjects/SCI00980, Signal transduction, 030217 neurology & neurosurgery, Kynurenine
الوصف: Expression of tryptophan 2,3-dioxygenase (TDO) is a determinant of malignancy in gliomas through kynurenine (KYN) signaling. We report that inhibition of TDO activity attenuated recovery from replication stress and increased the genotoxic effects of bis-chloroethylnitrosourea (BCNU). Activation of the Chk1 arm of the replication stress response (RSR) was reduced when TDO activity was blocked prior to BCNU treatment, whereas phosphorylation of serine 33 (pS33) on replication protein A (RPA) was enhanced—indicative of increased fork collapse. Analysis of quantitative proteomic results revealed that TDO inhibition reduced nuclear 53BP1 and sirtuin levels. We confirmed that cells lacking TDO activity exhibited elevated gamma-H2AX signal and defective recruitment of 53BP1 to chromatin following BCNU treatment, which corresponded with delayed repair of DNA breaks. Addition of exogenous KYN increased the rate of break repair. TDO inhibition diminished SIRT7 deacetylase recruitment to chromatin, which increased histone H3K18 acetylation—a key mark involved in preventing 53BP1 recruitment to sites of DNA damage. TDO inhibition also sensitized cells to ionizing radiation (IR)-induced damage, but this effect did not involve altered 53BP1 recruitment. These experiments support a model where TDO-mediated KYN signaling helps fuel a robust response to replication stress and DNA damage.
Graphical Abstract Graphical abstractThe replication stress and DNA damage responses in glioma cells are modulated by tryptophan 2,3-dioxygenase activity, a key factor controlling kynurenine signaling and de novo synthesis of NAD+.الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3b6a536ca8038d6c8cc55a6c11f9dbcTest
https://doi.org/10.1101/2020.05.28.110874Test -
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المؤلفون: Megan R. Reed, Robert L. Eoff, Narsimha Reddy Penthala, Leena Maddukuri, Peter A. Crooks, Maroof K. Zafar, Sarah Eddy, Amit Ketkar
المصدر: Biochemistry
مصطلحات موضوعية: 0301 basic medicine, Indoles, Stereochemistry, Antineoplastic Agents, DNA-Directed DNA Polymerase, Biochemistry, Article, Small Molecule Libraries, 03 medical and health sciences, chemistry.chemical_compound, Cell Line, Tumor, Neoplasms, medicine, Humans, Enzyme Inhibitors, Polymerase, Cisplatin, Indole test, Barbituric acid, DNA synthesis, biology, Thiobarbiturates, Small molecule, Footprinting, Molecular Docking Simulation, Pyrimidines, 030104 developmental biology, chemistry, biology.protein, DNA, medicine.drug
الوصف: Translesion DNA synthesis (TLS) performed by human DNA polymerase eta (hpol η) allows tolerance of damage from cis-diamminedichloroplatinum(II) (CDDP or cisplatin). We have developed hpol η inhibitors derived from N-aryl-substituted indole barbituric acid (IBA), indole thiobarbituric acid (ITBA), and indole quinuclidine scaffolds and identified 5-((5-chloro-1-(naphthalen-2-ylmethyl)-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6-(1H,5H)-dione (PNR-7-02), an ITBA derivative that inhibited hpol η activity with an IC(50) value of 8 μM and exhibited 5–10-fold specificity for hpol η over replicative pols. We conclude rom kinetic analyses, chemical footprinting assays, and molecular docking that PNR-7-02 binds to a site on the little finger domain and interferes with the proper orientation of template DNA to inhibit hpol η. A synergistic increase in CDDP toxicity was observed in hpol η-proficient cells co-treated with PNR-7-02 (combination index values = 0.4–0.6). Increased γH2AX formation accompanied treatment of hpol η-proficient cells with CDDP and PNR-7-02. Importantly, PNR-7-02 did not impact the effect of CDDP on cell viability or γH2AX in hpol η-deficient cells. In summary, we observed hpol η-dependent effects on DNA damage/replication stress and sensitivity to CDDP in cells treated with PNR-7-02. The ability to employ a small-molecule inhibitor of hpol η to improve the cytotoxic effect of CDDP may aid in the development of more effective chemotherapeutic strategies.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dd4734c01ca96f549f43ec9e06fdf89eTest
https://doi.org/10.1021/acs.biochem.7b01176Test -
10دورية أكاديمية
المؤلفون: Leena Maddukuri, Dominika Dudzińska, Barbara Tudek
المساهمون: The Pennsylvania State University CiteSeerX Archives
مصطلحات موضوعية: DNA damage, DNA repair, nucleotide excision repair, xeroderma pigmentosum, Cockayne syndrome
الوصف: DNA repair genes and their eukaryotic homologues: 4. The role of nucleotide excision DNA repair (NER) system in mammalian cells*
وصف الملف: application/pdf
النص الكامل