Research Topics
Species | Joseph CostelloSummaryAffiliation: University of California Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
A sequence-based survey of the complex structural organization of tumor genomesBenjamin 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...- Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinationsDominic 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.".. 
Aberrant CpG-island methylation has non-random and tumour-type-specific patternsJ 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...- DNA methylation in brain development and gliomagenesisJoseph 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.... - Methylation mattersJ 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... - Aberrant methylation of genes in low-grade astrocytomasJ 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... - miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cellsJoachim 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... - Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8Chibo 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... - The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomasChibo 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... - Restriction landmark genome scanningJoseph 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... - Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumorsGiuseppe 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... - Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specificPeter 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... 
Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresisJoseph 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...- A hierarchy of self-renewing tumor-initiating cell types in glioblastomaRuihuan Chen
Department of Tumor Biology and Angiogenesis, Genentech Inc, San Francisco, CA 94080, USA
Cancer Cell 17:362-75. 2010.... - Epigenetic mechanisms in glioblastoma multiformeRaman 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... - Molecular epigenetics and genetics in neuro-oncologyRaman 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... - Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growthChibo 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... - Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferationBenoit 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.... - Conserved role of intragenic DNA methylation in regulating alternative promotersAlika 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... - Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3Tsui 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... - Restriction landmark genome scanningJoseph F Costello
Department of Neurological Surgery, UCSF Brain Tumor Research Center, San Francisco, CA, USA
Methods Mol Biol 200:53-70. 2002 - Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastomaBruno 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... - SOCS-3 is frequently silenced by hypermethylation and suppresses cell growth in human lung cancerBiao 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... - Epigenetics of neurological cancersShaun 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... - Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cellsPaul A Reynolds
Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143 0511, USA
J Biol Chem 281:24790-802. 2006.... - Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancerYing 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... - Phosphatase and tensin homologue growth suppression without phosphataseDavid 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 - Methylation matters: a new spin on maspinJoseph F Costello
Nat Genet 31:123-4. 2002 - Comparative epigenomics of leukemiaJoseph F Costello
Nat Genet 37:211-2. 2005 - Mining methylation for early detection of common cancersRomulo M Brena
Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
PLoS Med 3:e479. 2006 - DNA motifs associated with aberrant CpG island methylationF 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... - A broad band of silenceJustin S Smith
Nat Genet 38:504-6. 2006 - Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancerJoseph F Smith
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, USA
Epigenetics 2:161-72. 2007.... - Genome-epigenome interactions in cancerRomulo 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... - Stem cells: Tips for priming potencyJoseph F Costello
Nature 454:45-6. 2008
Research Grants
- CONVERGENT MECHANISMS CONTRIBUTING TO CANCERJoseph Costello; Fiscal Year: 2006....