Joseph Costello

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    Mingchao Xie
    Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
    Nat Genet 45:836-41. 2013
  2. pmc Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R Alan Harris
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1097-105. 2010
  3. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
  4. pmc Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
    Dominic J Smiraglia
    Department of Cancer Genetics, and Comprehensive Cancer Center, Roswell Park Cancer Institute, Buffalo, NY, USA
    BMC Genomics 8:446. 2007
  5. ncbi request reprint Aberrant CpG-island methylation has non-random and tumour-type-specific patterns
    J F Costello
    1 Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California, USA
    Nat Genet 24:132-8. 2000
  6. 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
  7. ncbi request reprint Aberrant methylation of genes in low-grade astrocytomas
    J F Costello
    University of California San Francisco, The Brain Tumor Research Center, USA
    Brain Tumor Pathol 17:49-56. 2000
  8. pmc Methylation matters
    J F Costello
    The Brain Tumor Research Center and the Department of Neurological Surgery, University of California, 2340 Sutter, Room N261, San Francisco, San Francisco, CA 94143 0875, USA
    J Med Genet 38:285-303. 2001
  9. 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
  10. 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

Research Grants

  1. CONVERGENT MECHANISMS CONTRIBUTING TO CANCER
    Joseph Costello; Fiscal Year: 2006

Collaborators

Detail Information

Publications37

  1. pmc DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    Mingchao Xie
    Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
    Nat Genet 45:836-41. 2013
    ..These data suggest that sequences derived from TEs may be responsible for wiring tissue type-specific regulatory networks and may have acquired tissue-specific epigenetic regulation. ..
  2. pmc Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    R Alan Harris
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
    Nat Biotechnol 28:1097-105. 2010
    ....
  3. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
    ..The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes...
  4. pmc Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations
    Dominic J Smiraglia
    Department of Cancer Genetics, and Comprehensive Cancer Center, Roswell Park Cancer Institute, Buffalo, NY, USA
    BMC Genomics 8:446. 2007
    ..However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning."..
  5. ncbi request reprint Aberrant CpG-island methylation has non-random and tumour-type-specific patterns
    J F Costello
    1 Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California, USA
    Nat Genet 24:132-8. 2000
    ..The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types...
  6. 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
    ....
  7. ncbi request reprint Aberrant methylation of genes in low-grade astrocytomas
    J F Costello
    University of California San Francisco, The Brain Tumor Research Center, USA
    Brain Tumor Pathol 17:49-56. 2000
    ..The data suggest that aberrant methylation of genes is more prevalent than genetic alterations and may have consequences for the development of low-grade astrocytomas...
  8. pmc Methylation matters
    J F Costello
    The Brain Tumor Research Center and the Department of Neurological Surgery, University of California, 2340 Sutter, Room N261, San Francisco, San Francisco, CA 94143 0875, USA
    J Med Genet 38:285-303. 2001
    ..Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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
    ....
  17. 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
    ....
  18. 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...
  19. doi request reprint 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...
  20. 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...
  21. 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...
  22. 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
  23. 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...
  24. doi request reprint 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...
  25. 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...
  26. doi request reprint 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...
  27. 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
  28. 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...
  29. 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
    ....
  30. 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
    ....
  31. 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...
  32. ncbi request reprint Methylation matters: a new spin on maspin
    Joseph F Costello
    Nat Genet 31:123-4. 2002
  33. ncbi request reprint A broad band of silence
    Justin S Smith
    Nat Genet 38:504-6. 2006
  34. 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...
  35. ncbi request reprint Comparative epigenomics of leukemia
    Joseph F Costello
    Nat Genet 37:211-2. 2005
  36. 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
  37. doi request reprint Stem cells: Tips for priming potency
    Joseph F Costello
    Nature 454:45-6. 2008

Research Grants6

  1. CONVERGENT MECHANISMS CONTRIBUTING TO CANCER
    Joseph Costello; Fiscal Year: 2006
    ....