Joseph F Costello

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Restriction landmark genome scanning
    Joseph F Costello
    University of California San Francisco, San Francisco, CA 94115 0875, USA
    Methods 27:144-9. 2002
  2. pmc Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific
    Peter Jun
    Department of Neurological Surgery, University of California, San Francisco, Cancer Center, Room N225, 2340 Sutter St, San Francisco, CA 94143, USA
    Neuro Oncol 11:414-22. 2009
  3. pmc Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma
    Bruno M Costa
    The Brain Tumor Research Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, California 94158 9001, USA
    Cancer Res 70:453-62. 2010
  4. ncbi request reprint Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells
    Paul A Reynolds
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143 0511, USA
    J Biol Chem 281:24790-802. 2006
  5. doi request reprint Epigenetic mechanisms in glioblastoma multiforme
    Raman P Nagarajan
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
    Semin Cancer Biol 19:188-97. 2009
  6. pmc Conserved role of intragenic DNA methylation in regulating alternative promoters
    Alika K Maunakea
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Nature 466:253-7. 2010
  7. doi request reprint Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis
    Joseph F Costello
    Department of Neurological Surgery, University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
    Methods Mol Biol 507:131-48. 2009
  8. ncbi request reprint Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8
    Chibo Hong
    Department of Neurological Surgery, Brain Tumor Research Center, University of California San Francisco, San Francisco, California 94143 0875, USA
    Cancer Res 65:3617-23. 2005
  9. pmc Molecular signatures define two main classes of meningiomas
    Lucia Helena Carvalho
    Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
    Mol Cancer 6:64. 2007
  10. ncbi request reprint Meningioma transcript profiles reveal deregulated Notch signaling pathway
    Ileana C Cuevas
    Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, California 94143, USA
    Cancer Res 65:5070-5. 2005

Detail Information

Publications47

  1. ncbi request reprint Restriction landmark genome scanning
    Joseph F Costello
    University of California San Francisco, San Francisco, CA 94115 0875, USA
    Methods 27:144-9. 2002
    ..RLGS is also a useful method for integrating methylation analyses with high-resolution gene copy number analyses...
  2. pmc Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific
    Peter Jun
    Department of Neurological Surgery, University of California, San Francisco, Cancer Center, Room N225, 2340 Sutter St, San Francisco, CA 94143, USA
    Neuro Oncol 11:414-22. 2009
    ..These findings indicate that epigenetic mechanisms are common across meningiomas of all grades and that for specific genes such as WNK2, epigenetic alteration may be the dominant, grade-specific mechanism of gene inactivation...
  3. pmc Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma
    Bruno M Costa
    The Brain Tumor Research Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, California 94158 9001, USA
    Cancer Res 70:453-62. 2010
    ..Our findings suggest a transcriptional pathway through which PI3K activates oncogenic HOXA expression with implications for mTOR or PI3K targeted therapies...
  4. ncbi request reprint Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells
    Paul A Reynolds
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143 0511, USA
    J Biol Chem 281:24790-802. 2006
    ....
  5. doi request reprint Epigenetic mechanisms in glioblastoma multiforme
    Raman P Nagarajan
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
    Semin Cancer Biol 19:188-97. 2009
    ..Ultimately, genomic and epigenomic data should provide new predictive markers of response and lead to more effective therapies for GBM...
  6. pmc Conserved role of intragenic DNA methylation in regulating alternative promoters
    Alika K Maunakea
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Nature 466:253-7. 2010
    ..These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies...
  7. doi request reprint Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis
    Joseph F Costello
    Department of Neurological Surgery, University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
    Methods Mol Biol 507:131-48. 2009
    ..These profiles are highly reproducible and are therefore amenable to inter- and intraindividual DNA sample comparisons. RLGS was the first of many technologies to allow large-scale DNA methylation analysis of CpG islands...
  8. ncbi request reprint Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8
    Chibo Hong
    Department of Neurological Surgery, Brain Tumor Research Center, University of California San Francisco, San Francisco, California 94143 0875, USA
    Cancer Res 65:3617-23. 2005
    ..The shared epigenetic inactivation of mSLC5A8 in mouse gliomas indicates an additional degree of commonality in the origin and/or pathway to tumorigenesis between primary human tumors and these mouse models of gliomas...
  9. pmc Molecular signatures define two main classes of meningiomas
    Lucia Helena Carvalho
    Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
    Mol Cancer 6:64. 2007
    ..The purpose of this study was identify molecular signatures unique to the different grades of meningiomas and to unravel underlying molecular mechanisms driving meningioma tumorigenesis...
  10. ncbi request reprint Meningioma transcript profiles reveal deregulated Notch signaling pathway
    Ileana C Cuevas
    Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, California 94143, USA
    Cancer Res 65:5070-5. 2005
    ....
  11. pmc Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma
    Brett E Johnson
    Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
    Science 343:189-93. 2014
    ..At recurrence, these tumors were hypermutated and harbored driver mutations in the RB (retinoblastoma) and Akt-mTOR (mammalian target of rapamycin) pathways that bore the signature of TMZ-induced mutagenesis. ..
  12. pmc Phase II and pharmacogenomics study of enzastaurin plus temozolomide during and following radiation therapy in patients with newly diagnosed glioblastoma multiforme and gliosarcoma
    Nicholas Butowski
    Neuro Oncology Service, Department of Neurological Surgery, University of California, San Francisco, 400 Parnassus Avenue, A808, San Francisco, CA 94143 0350, USA
    Neuro Oncol 13:1331-8. 2011
    ..Adjusting for age and KPS, no other biomarker was associated with survival outcome. Correlation of relevant biomarkers with OS may be useful in future trials...
  13. pmc miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells
    Joachim Silber
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
    BMC Med 6:14. 2008
    ..In this study, we investigated the role of microRNAs in regulating the differentiation and proliferation of neural stem cells and glioblastoma-multiforme tumor cells...
  14. ncbi request reprint Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3
    Tsui Ting Ching
    The Brain Tumor Research Center, Department of Neurological Surgery and the Biomedical Sciences Program, University of California San Francisco, San Franciso, California 94143, USA
    Nat Genet 37:645-51. 2005
    ..Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats...
  15. ncbi request reprint The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas
    Chibo Hong
    Department of Neurological Surgery, The Brain Tumor Research Center, Department of Pathology, Comprehensive Cancer Center, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
    Cancer Res 63:7600-5. 2003
    ..This initial integrated approach identifies novel targets of gene silencing, and provides a more comprehensive view of the genes and mechanisms underlying oligodendrogliomas...
  16. ncbi request reprint Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation
    Benoit Cadieux
    The Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, CA 94143 0875, USA
    Cancer Res 66:8469-76. 2006
    ....
  17. pmc Molecular epigenetics and genetics in neuro-oncology
    Raman P Nagarajan
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
    Neurotherapeutics 6:436-46. 2009
    ..Next-generation sequencing technology is now the method of choice for genomic and epigenome profiling, allowing more comprehensive understanding of genetic and epigenetic contributions to tumorigenesis in the brain...
  18. doi request reprint A hierarchy of self-renewing tumor-initiating cell types in glioblastoma
    Ruihuan Chen
    Department of Tumor Biology and Angiogenesis, Genentech Inc, San Francisco, CA 94080, USA
    Cancer Cell 17:362-75. 2010
    ....
  19. pmc Genome-scale DNA methylation analysis
    Shaun D Fouse
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA 94158, USA
    Epigenomics 2:105-17. 2010
    ....
  20. pmc Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment
    Hinke F van Thuijl
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
    Acta Neuropathol 129:597-607. 2015
    ..These results suggest that tumor cells with methylated MGMT may undergo positive selection during TMZ treatment in the context of MMR deficiency...
  21. pmc Intratumoral Heterogeneity of the Epigenome
    Tali Mazor
    Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
    Cancer Cell 29:440-51. 2016
    ..This perspective presents these current concepts and clinical implications of epigenetic ITH, and the experimental and computational techniques at the forefront of ITH exploration. ..
  22. pmc DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors
    Tali Mazor
    Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
    Cancer Cell 28:307-17. 2015
    ..Moreover, phyloepigenetic relationships robustly recapitulated phylogenetic patterns inferred from somatic mutations. These findings highlight widespread co-dependency of genetic and epigenetic events throughout brain tumor evolution. ..
  23. pmc Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
    Robert J A Bell
    Department of Neurological Surgery, University of California, San Francisco, CA Department of Biostatistics and Epidemiology, University of California, San Francisco, CA
    Science 348:1036-9. 2015
    ..GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers. ..
  24. pmc Recurrent epimutations activate gene body promoters in primary glioblastoma
    Raman P Nagarajan
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, California 94143, USA
    Genome Res 24:761-74. 2014
    ....
  25. pmc Methods for cancer epigenome analysis
    Raman P Nagarajan
    University of California, San Francisco, CA, USA
    Adv Exp Med Biol 754:313-38. 2013
    ..Computational tools have been developed apace with these epigenome methods to better enable accurate interpretation of the profiling data...
  26. pmc Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells
    Yuki Ohi
    Department of Ob Gyn and Center for Reproductive Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA
    Nat Cell Biol 13:541-9. 2011
    ..Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming...
  27. pmc SOCS-3 is frequently silenced by hypermethylation and suppresses cell growth in human lung cancer
    Biao He
    Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, CA 94115, USA
    Proc Natl Acad Sci U S A 100:14133-8. 2003
    ..The data also suggest that SOCS-3 therapy may be useful in the treatment of cancer...
  28. pmc Mutant IDH1 expression is associated with down-regulation of monocarboxylate transporters
    Pavithra Viswanath
    Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA 94143, USA
    Oncotarget 7:34942-55. 2016
    ..Taken together, our study shows that reduced MCT expression is part of the metabolic reprogramming of mutant IDH1 gliomas. This finding could impact treatment and has important implications for metabolic imaging of mutant IDH1 gliomas. ..
  29. pmc The genetics of splicing in neuroblastoma
    Justin Chen
    Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California Department of Neurology, University of California, San Francisco, San Francisco, California Department of Neurosurgery, University of California, San Francisco, San Francisco, California
    Cancer Discov 5:380-95. 2015
    ..Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma...
  30. pmc Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype
    Shaun D Fouse
    Department of Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, San Francisco, California S D F, C D J, S C, J F C Department of Radiation Oncology, University of California, San Francisco, California J L N
    Neuro Oncol 16:361-71. 2014
    ..Glioblastoma multiforme (GBM) contains a population of cells that exhibit stem cell phenotypes. These cancer stem cells (CSCs) may be a source of therapeutic resistance, although support for this important concept is limited...
  31. pmc Cancer Stem Cells Activate STAT3 the EZ Way
    Shaun D Fouse
    Brain Tumor Research Center, Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94158, USA
    Cancer Cell 23:711-3. 2013
    ..In this issue of Cancer Cell, Kim and colleagues discover that EZH2 enhances STAT3 activation by trimethylating lysine180 in STAT3 and does so preferentially in glioma stem-like cells...
  32. pmc Epigenetics of neurological cancers
    Shaun D Fouse
    Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
    Future Oncol 5:1615-29. 2009
    ..These methods are being applied to brain tumors, and will better define the contribution of epigenetic defects to tumorigenesis...
  33. ncbi request reprint Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer
    Ying Chen
    Department of Neurological Surgery, UCSF Comprehensive Cancer Center, San Francisco, California 9443 0875, USA
    Genet Test 10:281-4. 2006
    ..Thus, epimutation is an unlikely explanation for hereditary breast cancer in women who test negative for BRCA mutations...
  34. ncbi request reprint DNA methylation in brain development and gliomagenesis
    Joseph F Costello
    The Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, 2340 Sutter, San Francisco, CA 94115, USA
    Front Biosci 8:s175-84. 2003
    ....
  35. ncbi request reprint Restriction landmark genome scanning
    Joseph F Costello
    Department of Neurological Surgery, UCSF Brain Tumor Research Center, San Francisco, CA, USA
    Methods Mol Biol 200:53-70. 2002
  36. pmc methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser
    Xin Zhou
    Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA and Department of Neurosurgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
    Bioinformatics 30:2206-7. 2014
    ..Investigators can access and integrate these information visually at specific locus or at the genome-wide level on the WashU EpiGenome Browser in the context of other rich epigenomic datasets...
  37. pmc Phosphatase and tensin homologue growth suppression without phosphatase
    David Stokoe
    Cancer Research Institute and Brain Tumor Research Center, Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 102:2677-8. 2005
  38. ncbi request reprint Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors
    Giuseppe Zardo
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94115, USA
    Nat Genet 32:453-8. 2002
    ..Our results show that most aberrant methylation events are focal and independent of deletions, and the rare convergence of these mechanisms can pinpoint biallelic gene inactivation without the use of positional cloning...
  39. pmc Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth
    Chibo Hong
    Department of Neurological Surgery and the Comprehensive Cancer Center, University of California, San Francisco, CA 94143
    Proc Natl Acad Sci U S A 104:10974-9. 2007
    ..Thus, our integrated genetic and epigenetic approach might be useful to identify genes that are widely relevant to cancer, even when genetic alterations of the locus are infrequent...
  40. ncbi request reprint Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer
    Joseph F Smith
    Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, USA
    Epigenetics 2:161-72. 2007
    ....
  41. ncbi request reprint DNA motifs associated with aberrant CpG island methylation
    F Alex Feltus
    Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, 1365 C Clifton Road NE, Atlanta, GA 30322, USA
    Genomics 87:572-9. 2006
    ..The motifs identified here are candidate methylation-targeting or methylation-protection DNA sequences...
  42. ncbi request reprint Comparative epigenomics of leukemia
    Joseph F Costello
    Nat Genet 37:211-2. 2005
  43. ncbi request reprint Methylation matters: a new spin on maspin
    Joseph F Costello
    Nat Genet 31:123-4. 2002
  44. ncbi request reprint Genome-epigenome interactions in cancer
    Romulo M Brena
    Department of Molecular Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
    Hum Mol Genet 16:R96-105. 2007
    ..We discuss the knowledge gained from these large-scale analyses in the context of gene discovery, therapeutic application and building a more widely applicable mechanism-based model of human tumorigenesis...
  45. ncbi request reprint A broad band of silence
    Justin S Smith
    Nat Genet 38:504-6. 2006
  46. pmc Mining methylation for early detection of common cancers
    Romulo M Brena
    Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
    PLoS Med 3:e479. 2006
  47. doi request reprint Stem cells: Tips for priming potency
    Joseph F Costello
    Nature 454:45-6. 2008