Susan J Clark

Summary

Affiliation: Garvan Institute of Medical Research
Country: Australia

Publications

  1. ncbi Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells
    Jenny Z Song
    Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
    Oncogene 21:1048-61. 2002
  2. ncbi Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events
    Kate M Peters
    School of Chemistry and Molecular Biosciences, The University of Queensland, St, Lucia 4072 Queensland, Australia
    BMC Cancer 12:132. 2012
  3. ncbi Epigenetic and phenotypic changes result from a continuous pre and post natal dietary exposure to phytoestrogens in an experimental population of mice
    Carlos M Guerrero-Bosagna
    Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA, 99164 4231, USA
    BMC Physiol 8:17. 2008
  4. ncbi Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis
    Susan J Clark
    Cancer Program, Garvan Institute of Medical Research, Darlinghurst Sydney, 2010 NSW, Australia
    Hum Mol Genet 16:R88-95. 2007
  5. ncbi DNA methylation: bisulphite modification and analysis
    Susan J Clark
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
    Nat Protoc 1:2353-64. 2006
  6. ncbi Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells
    Clare Stirzaker
    Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
    Cancer Res 64:3871-7. 2004
  7. ncbi Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
    Marcel W Coolen
    Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Nat Cell Biol 12:235-46. 2010
  8. ncbi Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
    Fatima Valdes-Mora
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:307-21. 2012
  9. ncbi Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning
    Rebecca A Hinshelwood
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
    Hum Mol Genet 18:3098-109. 2009
  10. ncbi Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    Aaron L Statham
    Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:1120-7. 2012

Collaborators

Detail Information

Publications42

  1. ncbi Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells
    Jenny Z Song
    Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
    Oncogene 21:1048-61. 2002
    ..We propose that the GSTP1 gene is initially silenced in the prostate cancer and random sites of methylation accumulate that result in subsequent hypermethylation and chromatin remodelling...
  2. ncbi Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events
    Kate M Peters
    School of Chemistry and Molecular Biosciences, The University of Queensland, St, Lucia 4072 Queensland, Australia
    BMC Cancer 12:132. 2012
    ..In this study, AR protein levels were determined in a cohort of 73 Grade III invasive breast ductal adenocarcinomas...
  3. ncbi Epigenetic and phenotypic changes result from a continuous pre and post natal dietary exposure to phytoestrogens in an experimental population of mice
    Carlos M Guerrero-Bosagna
    Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA, 99164 4231, USA
    BMC Physiol 8:17. 2008
    ....
  4. ncbi Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis
    Susan J Clark
    Cancer Program, Garvan Institute of Medical Research, Darlinghurst Sydney, 2010 NSW, Australia
    Hum Mol Genet 16:R88-95. 2007
    ....
  5. ncbi DNA methylation: bisulphite modification and analysis
    Susan J Clark
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
    Nat Protoc 1:2353-64. 2006
    ..Bisulphite conversion of DNA, in either single tubes or in a 96-well format, can be performed in a minimum of 8 h and a maximum of 18 h, depending on the amount and quality of starting DNA...
  6. ncbi Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells
    Clare Stirzaker
    Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
    Cancer Res 64:3871-7. 2004
    ..These findings have important implications for understanding the biochemical events underlying the mechanisms responsible for abnormal hypermethylation of CpG island-associated genes in cancer cells...
  7. ncbi Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
    Marcel W Coolen
    Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Nat Cell Biol 12:235-46. 2010
    ..We propose that consolidation or effective reduction of the cancer genome commonly occurs in domains through a combination of LRES and LOH or genomic deletion, resulting in reduced transcriptional plasticity within these regions...
  8. ncbi Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
    Fatima Valdes-Mora
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:307-21. 2012
    ..Z anti-correlates with promoter H3K27me3 and DNA methylation. We show for the first time, that acetylation of H2A.Z is a key modification associated with gene activity in normal cells and epigenetic gene deregulation in tumorigenesis...
  9. ncbi Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning
    Rebecca A Hinshelwood
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
    Hum Mol Genet 18:3098-109. 2009
    ....
  10. ncbi Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    Aaron L Statham
    Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:1120-7. 2012
    ..BisChIP-seq is a novel approach that can be widely applied to directly interrogate the genomic relationship between allele-specific DNA methylation, histone modification, or other important epigenetic regulators...
  11. ncbi Bisulfite methylation analysis of tumor suppressor genes in prostate cancer from fresh and archival tissue samples
    Susan J Clark
    Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, Australia
    Methods Mol Med 81:219-40. 2003
  12. ncbi Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers
    Brian S Gloss
    Cancer Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
    Cancer Lett 318:76-85. 2012
    ..05). We propose that this potential biomarker panel holds great promise as a diagnostic test for high-grade (Type II) serous ovarian cancer...
  13. ncbi Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
    Shalima S Nair
    Epigenetics Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
    Epigenetics 6:34-44. 2011
    ..Our study highlights the importance of understanding the nuances of the methods used for DNA genome-wide methylation analyses so that accurate interpretation of the biology is not overlooked...
  14. ncbi Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis
    Rebecca A Hinshelwood
    Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
    Cancer Res 67:11517-27. 2007
    ....
  15. ncbi Repitools: an R package for the analysis of enrichment-based epigenomic data
    Aaron L Statham
    Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Bioinformatics 26:1662-3. 2010
    ..We have created a toolbox of procedures to interrogate and visualize epigenomic data (both array- and sequencing-based) and make available a software package for the cross-platform R language...
  16. ncbi Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
    Mark D Robinson
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
    Genome Res 20:1719-29. 2010
    ....
  17. ncbi Prognostic and diagnostic significance of DNA methylation patterns in high grade serous ovarian cancer
    Celine Montavon
    Cancer Research Program, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
    Gynecol Oncol 124:582-8. 2012
    ....
  18. ncbi Protocol matters: which methylome are you actually studying?
    Mark D Robinson
    Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Epigenomics 2:587-98. 2010
    ..There is promise for this to change, as the third generation of sequencing technologies is expected to again 'revolutionize' the way that we study genomes and epigenomes...
  19. ncbi Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins
    Marcel W Coolen
    Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia
    PLoS ONE 6:e25590. 2011
    ....
  20. ncbi Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
    Toby Hulf
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    BMC Genomics 12:54. 2011
    ..Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically deregulated miRNAs in cancer...
  21. ncbi Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers
    James Devaney
    Epigenetics Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
    Cancer Epidemiol Biomarkers Prev 20:148-59. 2011
    ..We now investigate whether LRES also occurs in prostate cancer across this 4-Mb region and whether differential DNA methylation of 2q14.2 genes could provide a regional panel of prostate cancer biomarkers...
  22. ncbi DNA methylation changes in leukaemia
    John R Melki
    Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
    Semin Cancer Biol 12:347-57. 2002
    ..This review will discuss the multitude of DNA methylation changes in haematopoietic malignancies and the implications they have for diagnosis and treatment...
  23. ncbi Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells
    Douglas S Millar
    Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia
    Methods 27:108-13. 2002
    ....
  24. ncbi DNA methylation and gene silencing in cancer: which is the guilty party?
    Susan J Clark
    Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
    Oncogene 21:5380-7. 2002
    ....
  25. ncbi Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
    Jordi Frigola
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney 2010, New South Wales, Australia
    Nat Genet 38:540-9. 2006
    ..We propose that loss of gene expression can occur through long-range epigenetic silencing, with similar implications as loss of heterozygosity in cancer...
  26. ncbi Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements
    Marcel W Coolen
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney 2010, New South Wales, Australia
    Nucleic Acids Res 35:e119. 2007
    ..The new protocol is ideally suitable for detailed DNA methylation analysis of multiple genomic regions and large sample cohorts that is critical for comprehensive profiling of normal and diseased human epigenomes...
  27. ncbi Lineage specific methylation of the Elf5 promoter in mammary epithelial cells
    Heather J Lee
    Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
    Stem Cells 29:1611-9. 2011
    ....
  28. ncbi Identification and resolution of artifacts in bisulfite sequencing
    Peter M Warnecke
    Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia
    Methods 27:101-7. 2002
    ..We also include a brief summary of the experimental protocol for bisulfite treatment and tips for designing polymerase chain reaction (PCR) primers to amplify from bisulfite-treated DNA...
  29. ncbi Epigenetic markers of ovarian cancer
    Caroline A Barton
    Ovarian Cancer Center, Garvan Institute, Sydney, NSW, Australia
    Adv Exp Med Biol 622:35-51. 2008
  30. ncbi Breast cancer epigenetics: normal human mammary epithelial cells as a model system
    Rebecca A Hinshelwood
    The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
    J Mol Med (Berl) 86:1315-28. 2008
    ..In particular, this model system has been used to investigate the relationship between gene silencing, DNA methylation, histone modifications, and polycomb association that may occur early in oncogenic transformation...
  31. ncbi Telomere-driven karyotypic complexity concurs with p16INK4a inactivation in TP53-competent immortal endothelial cells
    Victoria W Wen
    Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia
    Cancer Res 66:10691-700. 2006
    ..These investigations provide new insight to the role of p16(INK4a) as a tumor suppressor...
  32. ncbi ELF5 Suppresses Estrogen Sensitivity and Underpins the Acquisition of Antiestrogen Resistance in Luminal Breast Cancer
    Maria Kalyuga
    Cancer Research Program and The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
    PLoS Biol 10:e1001461. 2012
    ....
  33. ncbi DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment
    Caroline A Barton
    Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia
    Gynecol Oncol 109:129-39. 2008
    ..To review epigenetic changes identified in ovarian cancer, focusing on their potential as clinical markers for detection, monitoring of disease progression and as markers of therapeutic response...
  34. ncbi Low O6-methylguanine-DNA methyltransferase (MGMT) expression and response to temozolomide in aggressive pituitary tumours
    Ann I McCormack
    Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, NSW, Australia
    Clin Endocrinol (Oxf) 71:226-33. 2009
    ..Recent case reports detail the successful use of temozolomide in the management of aggressive pituitary tumours. O(6)-methylguanine-DNA methyltransferase (MGMT) is a DNA repair protein that counteracts the effect of temozolomide...
  35. ncbi Headloop suppression PCR and its application to selective amplification of methylated DNA sequences
    Keith N Rand
    CSIRO Molecular and Health Technologies PO Box 184, North Ryde, NSW 1670, Australia
    Nucleic Acids Res 33:e127. 2005
    ....
  36. ncbi Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation
    Nicholas C Wong
    Chromosome Research Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
    PLoS Genet 2:e17. 2006
    ....
  37. ncbi Bisulphite differential denaturation PCR for analysis of DNA methylation
    Keith N Rand
    Preventative Health Flagship, CSIRO Molecular and Health Technologies, North Ryde, Australia
    Epigenetics 1:94-100. 2006
    ....
  38. ncbi DNA methylation analysis in mammalian cells
    Susan J Clark
    Methods 27:99-100. 2002
  39. ncbi Moving AHEAD with an international human epigenome project
    Peter A Jones
    Nature 454:711-5. 2008
  40. ncbi Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives
    Keith Rand
    Sydney Laboratory, CSIRO Division of Molecular Science, P.O. Box 184, North Ryde, New South Wales 1670, Australia
    Methods 27:114-20. 2002
    ..We recommend that MSP detection always should include a step to detect unconverted DNA to avoid overestimation of the frequency or level of methylated DNA in the sample...
  41. ncbi Alterations in the p16(INK4a) and p53 tumor suppressor genes of hTERT-immortalized human fibroblasts
    Jane R Noble
    Children s Medical Research Institute, 214 Hawkesbury Rd, Westmead, Sydney NSW 2145, Australia
    Oncogene 23:3116-21. 2004
    ....
  42. ncbi Hypermethylation of the prostacyclin synthase (PTGIS) promoter is a frequent event in colorectal cancer and associated with aneuploidy
    Jordi Frigola
    Molecular Oncology, IDIBELL Institut de Recerca Oncologica, Gran Via Km 2 7, Hospital Duran i Reynals, L Hospitalet, Barcelona 08907, Spain
    Oncogene 24:7320-6. 2005
    ..In the adjusted model, PTGIS methylation, but not p53 mutation, maintained the association with aneuploidy. We conclude that epigenetic inactivation of the PTGIS gene is a recurrent alteration in colorectal carcinogenesis...