A/Prof Clare Stirzaker

A/Prof Clare Stirzaker

Clare completed her Bachelor of Science majoring in Biochemistry and Microbiology, and her Bachelor of Science with First Class Honours in Molecular Biology,  at the University of Cape Town, South Africa,  before completing  her PhD at Macquarie University, Sydney, graduating in 1990.  Clare became

Biography

Clare completed her Bachelor of Science majoring in Biochemistry and Microbiology, and her Bachelor of Science with First Class Honours in Molecular Biology,  at the University of Cape Town, South Africa,  before completing  her PhD at Macquarie University, Sydney, graduating in 1990. 

Clare became fascinated by the field of Epigenetics and joined the group of Prof Susan Clark as a post-doc at the Kanematsu Laboratories, Royal Prince Alfred Hospital, in Sydney and later, at the Sydney Cancer Centre at Sydney University. The group moved to the Garvan Institute of Medical Research in 2004, where an Epigenetics Group was established within the Cancer Program.  Clare has since established her own group, which is interested in understanding "Epigenetic Deregulation in Cancer."

Clare has played a major role in delivery of many of the milestones in epigenetic research.  She has made highly significant contributions to the field of DNA methylation and epigenetic deregulation in cancer and has also played an integral role in developing new epigenetic technologies that have underpinned many of the seminal findings of the group.

Clare is involved in a number of collaborative projects which include an NBCF project grant  ‘Enabling Clinical Epigenetic Diagnostics:  The Next Generation of Personalised Breast Cancer Care’ and an NHMRC project grant  with Monash University ‘Defining Epigenetic Changes in Prostate Cancer Stroma.’

Clare completed her Bachelor of Science majoring in Biochemistry and Microbiology, and her Bachelor of Science with First Class Honours in Molecular Biology,  at the University of Cape Town, South Africa,  before completing  her PhD at Macquarie University, Sydney, graduating in 1990. 

Clare became fascinated by the field of Epigenetics and joined the group of Prof Susan Clark as a post-doc at the Kanematsu Laboratories, Royal Prince Alfred Hospital, in Sydney and later, at the Sydney Cancer Centre at Sydney University. The group moved to the Garvan Institute of Medical Research in 2004, where an Epigenetics Group was established within the Cancer Program.  Clare has since established her own group, which is interested in understanding "Epigenetic Deregulation in Cancer."

Clare has played a major role in delivery of many of the milestones in epigenetic research.  She has made highly significant contributions to the field of DNA methylation and epigenetic deregulation in cancer and has also played an integral role in developing new epigenetic technologies that have underpinned many of the seminal findings of the group.

Clare is involved in a number of collaborative projects which include an NBCF project grant  ‘Enabling Clinical Epigenetic Diagnostics:  The Next Generation of Personalised Breast Cancer Care’ and an NHMRC project grant  with Monash University ‘Defining Epigenetic Changes in Prostate Cancer Stroma.’

Education

1990 - PhD, Macquarie University, Sydney - Australia
1982 - BSc First Class Honours (Major: Molecular Biology), University of Cape Town - South Africa
1981 - BSc (Majors: Biochemistry and Microbiology), University of Cape Town - South Africa

Selected Publications

2020

Joanna Achinger-Kawecka, Fatima Valdes-Mora, Phuc Luu, Katherine Giles, C Caldon, Wenjia Qu, Shalima Nair, Sebastian Soto, Warwick Locke, Nicole Yeo-Teh, Cathryn Gould, Qian Du, Grady Smith, Irene Ramos, Kristine Fernandez, Dave Hoon, Julia Gee, Clare Stirzaker, and Susan Clark (2020). Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer.  Nature Communications 11 (1), 320 2020 PMID: 31949157 PMCID: PMC6965612 DOI: 10.1038/s41467-019-14098-x

Amanda Khoury, Joanna Achinger-Kawecka, Saul Bert, Grady Smith, Hugh French, Phuc Luu, Timothy Peters, Qian Du, Aled Parry, Fatima Valdes-Mora, Phillippa Taberlay, Clare Stirzaker, Aaron Statham, and Susan Clark (2020) Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. Nature Communications 2020  11 (1), 1-13 PMID: 31911579  PMCID: PMC6946690 DOI: 10.1038/s41467-019-13753-7

2019

Ksenia Skvortsova, Etienne Masle-Farquhar, Phuc-Loi Luu, Jenny Z. Song, Wenjia Qu, Elena Zotenko, Cathryn M. Gould,  Qian Du, Timothy Peters,Yolanda Colino-Sanguino, Ruth Pidsley, Shalima, S. Nair, Amanda Khoury1, Grady C. Smith, Lisa A. Miosge, Joanne H. Reed, James G. Kench, Mark A. Rubin, Lisa Horvath, Ozren Bogdanovic, Sue Mei Lim, Jose M. Polo, Christopher C. Goodnow, Clare Stirzaker* & Susan J. Clark* (2019) DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 mono-methylation patterns. * equal senior Cancer Cell 35 (2), 297-314.e8 ; Feb 112019 PMID: 30753827 DOI: 10.1016/j.ccell.2019.01.004

Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ. (2019) Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer. Nat Commun. Jan 2019 PMID: 30679435 PMCID: PMC6345877 DOI: 10.1038/s41467-019-08302-1

Giles KA, Gould CM, Du Q, Skvortsova K, Song JZ, Maddugoda MP, Achinger-Kawecka J, Stirzaker C, Clark SJ, Taberlay PC.(2019)  Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups.  Epigenetics Chromatin. Feb 12 (1), 12 2019 PMID: 30755246 PMCID: PMC6371444 DOI: 10.1186/s13072-019-0258-9

Bradford ST, Nair SS, Statham AL, van Dijk SJ, Peters TJ, Anwar F, French HJ, von Martels JZH, Sutcliffe B, Maddugoda MP, Peranec M, Varinli H, Arnoldy R, Buckley M, Ross JP, Zotenko E, Song JZ, Stirzaker C, Bauer DC, Qu W, Swarbrick MM, Lutgers HL, Lord RV, Samaras K, Molloy PL, Clark SJ (2019). Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes. Scientific Reports. Jul 2019  PMID: 31266983 PMCID: PMC6606599  DOI: 10.1038/s41598-019-45777-w

Peters TJ, French HJ, Bradford ST, Pidsley R, Stirzaker C, Varinli H, Nair S, Qu W, Song J, Giles KA, Statham AL, Speirs H, Speed TP, Clark SJ. (2019) Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. Bioinformatics. 2019 Feb 15;35(4):560-570. doi: 10.1093/bioinformatics/bty675.

R Pidsley, C Stirzaker  (2019). Cancer Methylation Biomarkers in Circulating Cell-Free DNA. Clinical Epigenetics, 217-245. Publisher Springer, Singapore. Editors: Luke Hesson and Antonia Pritchard (review)

K Skvortsova, C Stirzaker, P Taberlay  (2019) The DNA methylation landscape in cancer. Essays in Biochemistry 63 (6), 797-811 (review) PMID: 31845735  PMCID: PMC6923322  DOI: 10.1042/EBC20190037

2018

Peters TJ, French HJ, Bradford ST, Pidsley R, Stirzaker C, Varinli H, Nair S, Qu W, Song J, Giles KA, Statham AL, Speirs H, Speed TP, Clark SJ. (2018) Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. Bioinformatics. 35 (4), 560-570 2019 Feb 152018 . PMID: 30084929 PMCID: PMC6378945 DOI: 10.1093/bioinformatics/bty675

Ruth Pidsley, Mitchell G Lawrence, Elena Zotenko, Birunthi Niranjan, Aaron Statham, Jenny Song, Roman M Chabanon, Wenjia Qu, Hong Wang, Michelle Richards, Shalima S Nair, Nicola J Armstrong, Hieu T Nim, Melissa Papargiris, Preetika Balanathan, Hugh French, Timothy Peters, Sam Norden, Andrew Ryan, John Pedersen, James Kench, Roger J Daly, Lisa G Horvath, Phillip Stricker, Mark Frydenberg, Renea A Taylor, Clare Stirzaker, Gail P Risbridger, Susan J Clark (2018) Enduring Epigenetic marks define the cancer microenvironment. Genome Research. April. PMID: 29650553  PMCID: PMC5932604 DOI: 10.1101/gr.229070.117

2017

Valdés-Mora F, Gould CM, Colino-Sanguino Y, Qu W, Song JZ, Taylor KM, Buske FA, Statham AL, Nair SS, Armstrong NJ, Kench JG, Lee KML, Horvath LG, Qiu M, Ilinykh A, Yeo-Teh NS, Gallego-Ortega D, Stirzaker C, Clark SJ (2017). Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer. Nature Communications 8:1346. doi: 10.1038/s41467-017-01393-8.

Skvortsova K, Zotenko E, Luu PL, Gould CM, Nair SS, Clark SJ, Stirzaker C. Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA. Epigenetics Chromatin. 2017 Apr 20;10:16. PMID: 28428825

Clare Stirzaker1,2, Jenny Z. Song1, Wendy Ng1, Qian Du1, Nicola Armstrong3, Warwick Locke1, Aaron Statham1, Hugh French1, Ruth Pidsley1, Fatima Valdes-Mora1, Elena Zotenko1 & Susan J. Clark1,2 Methyl-CpG-Binding Protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene. 2017 Mar;36(10):1328-1338. PMID:27593931

Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, Van Djik S, Muhlhausler B, Stirzaker C*, Clark SJ*. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling .*equal senior authors Genome Biol. 2016 Oct 7;17(1):208 PMID:27717381

2016

BLUEPRINT consortium. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; epub ahead of print

Taberlay PC, Achinger-Kawecka J, Lun AT, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O'Donoghue SI, Clark SJ. Three-dimensional disorganisation of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res 2016; 26:719-31

2015 and prior

Stirzaker C*, Zotenko E*, Song JZ, Qu W, Nair SS, Locke WJ, Stone A, Armstong NJ, Robinson MD, Dobrovic A, Avery-Kiejda KA, Peters KM, French JD, Stein S, Korbie DJ, Trau M, Forbes JF, Scott RJ, Brown MA, Francis GD, Clark SJ. Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.  Nature Communications. 2015; Feb 2;6: 5899 Equal *first authors

Stone A, Zotenko E, Locke WJ, Korbie D, Millar EK, Pidsley R, Stirzaker C, Graham P, Trau M, Musgrove EA, Nicholson RI, Gee JM, Clark SJ. DNA methylation of oestrgen-regulated enhancers defines endocrine sensitivity in breast cancer. Nat Commun 2015; 6:7758

Stirzaker C, Zotenko E, Clark SJ. Genome-wide DNA methylation profiling in triple-negative breast cancer reveals epigenetic signatures with important clinical value. Mol Cell Oncol 2015; 3:e1038424

Locke WJ, Zotenko E, Stirzaker C, Robinson MD, Hinshelwood RA, Stone A, Reddel RR, Huschtscha LI, Clark SJ. Coordinated epigenetic remodelling of transcriptional networks occurs durng early breast carcinogenesis. Clin Epigenetics 2015; 7:52

Du Q, Luu PL, Stirzaker C, Clark SJ. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 2015; 7:1051-73

Korbie D, Lin E, Wall D, Nair SS, Stirzaker C, Clark SJ, Trau M. Multiplex bisulfate PCR resequencing of clinical FFPE DNA. Clin Epigenetics 2015; 7:28

Stirzaker C*, Taberlay PC*, Statham AL, Clark SJ. Mining Cancer Methylomes: Prospects and Challenges. Trends Genet 2013; 30:75-84 *authors contributed equally to the work.

Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C, Clark SJ. Regional Activation of the Cancer Genome by Long Range Epigenetic Remodelling. Cancer Cell 2013; 23:9-22

Hulf T, Sibbritt T, Wiklund ED, Patterson K, Song JZ, Stirzaker C, Qu W, Nair S, Horvath LG, Armstrong NJ, Kench JG, Sutherland RL, Clark SJ. Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer. Oncogene. 2012; 32:2891-9

Statham AL*, Robinson MD*, Song JZ, Coolen MW, Stirzaker C#, Clark SJ#. Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.  Genome Res 2012; 22:1120-7 Equal *first authors and #last authors

Valdés-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C, Clark SJ.  Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodelling in cancer. Genome Res 2012; 22:307-21

Devaney J*, Stirzaker C*, Qu W, Song JZ, Statham AL, Patterson KI, Horvath LG, Tabor B, Coolen MW, Kench JG, Henshall SM,  Pe Benito R, Haynes A-M, Mayor R, Peinado M, Sutherland RL, Clark SJ. Epigenetic deregulation across chromosome 2q14.2 differentiates normal cells from prostate cancer cells and provides a regional panel of DNA methylation prostate cancer biomarkers. Cancer Epidemiol Biomarkers Prev 2011; 20:148-59 *authors contributed equally to the work.

Nair S*, Coolen MW*, Stirzaker C*, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ. Comparison of Methyl-DNA Immunopreciptation (MeDIP) and Methyl-CpG Binding Domain (MBD) Protein Capture for Genome-wide DNA methylation Analysis Reveal CpG Sequence Coverage Bias.  Epigenetics 2011; 6:34-44   *authors contributed equally to the work

Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair S, Strbenac D, Speed TP, Clark SJ. Evaluation of enrichment-based genome-wide DNA methylation data: effects of CpG density, amplification bias and copy number variation.  Genome Res 2010; 20:1719-29

Coolen MW*, Stirzaker C*, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD, Clark SJ. Consolidation of the cancer genome into domains of repressive chromatin by long range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 2010; 12:235-46. *authors contributed equally to the work

Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. DNA methylation: bisulphite modification and analysis.  Nat Protoc 2006; 1:2353-64

Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ.  Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.  Nat Genet. 2006; 38(5):540-9.

Stirzaker C, Song JZ, Davidson B, Clark SJ. Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.  Cancer Res 2004; 64:3871-7