Profiles
Phillippa Taberlay
Phillippa Taberlay
Senior Research Fellow in Epigenetics
Room 437A , Medical Sciences Precinct 2
03 6226 7771 (phone)
Associate Professor Phillippa Taberlay is a NHMRC Emerging Leadership Fellow and Senior Research Fellow in the Tasmanian School of Medicine, College of Health and Medicine. Her research centres on understanding two-dimensional and three-dimensional aspects of gene control, and uses cutting-edge methods to delineate mechanisms of epigenetic reprogramming in development, healthy ageing, cancer and neurodegenerative disorders.
Biography
Phillippa attained her Bachelor of Science majoring in Biochemistry, Microbiology and Immunology from the University of Tasmania in 2002, and graduated with a Bachelor of Science (First Class Honours) in Biochemistry and Molecular Biology in 2003. She then joined the laboratory of Dr Adele Holloway where she sought to understand how leukaemic fusion proteins disrupt epigenetic mechanisms in Acute Myeloid Leukaemia.
Phillippa undertook her post-doctoral research training in the laboratory of Professor Peter Jones at the University of Southern California, USA (2008-2011). Her discovery that enhancer epigenetic states underpin cell reprogramming (Taberlay, Cell 2011) was an advance for the field that has shaped new theories of epigenetic regulation. Her early-career research has also received two prestigious Faculty of 1000 recommendations, and was named as one of the Top Clinical Advances 2012 (American Society of Clinical Oncology). Phillippa co-developed the NOMe-Seq technique, described as an “impressive” and “ingenious innovation” and named as a Top 10 Innovation of 2013. In 2012, Phillippa established her research group within the Epigenetics Research Program of Professor Susan Clark at the Garvan Institute of Medical Research, where she developed several new projects, including cutting-edge technologies to map higher-order (3D) genome structures inside cells.
Phillippa returned to the University of Tasmania as a National Health and medical Research Council (NHMRC) Career Development Fellow in 2016. She established the ‘2D and 3D Epigenomic Remodelling’ Group under the umbrella of Medical Sciences in the Tasmanian School of Medicine and now mentors a number of research assistant, post-doctoral researchers, Ph.D. candidates and Honours students. She has published her work in prominent international journals including Cell, Genome Research, Cancer Cell and PNAS.
Career summary
Qualifications
- BSc, University of Tasmania, Australia, 2002
- BSc (1st Class Hons), University of Tasmania, Australia, 2003
- PhD, Regulation of Gene Expression by the RUNX1 Transcription Factor, University of Tasmania, Australia, 2008
Memberships
Professional practice
- Australian Epigenetics Alliance (AEpiA; National Scientific Advisory Board and National Conference Committee)
- American Association of Cancer Research (AACR)
- Australasian Genome Technologies Association (AGTA)
- Australasian Neuroscience Society (ANS)
- Australian Bioinformatics & Computational Biology Society (ABACBS)
- Australian Society for Medical Research (ASMR; Co-Convenor, Tasmania)
Administrative expertise
Phillippa has >18 years’ experience in a diverse range of epigenetic and molecular biology assays with emphasis on sequencing-based technologies including ChIP-seq, NOMe-seq, BS-seq, RNA-seq, HiC-seq, Capture-seq; analysis and biological interpretation of genome-scale data and epigenetic mechanisms.
Teaching
Phillippa supervises research projects for the Undergraduate Research Oportunity Program (UROP) and CBA344 Research Project in Health and Disease.
View more on AssocProf Phillippa Taberlay in WARP
Expertise
- Epigenomics
- Epigenetics
- Epigenetic Mechanisms
- Chromatin
- Molecular Biology
- Next-Generation Sequencing
- Assay Development
- Genomics
- Computational Biology
- Development
- Cancer
- Alzheimer’s Disease
Research Themes
Phillippa’s research is aligns to the University’s research theme of Better Health, including the core strengths of genetics, neuroscience and applied mathematics. Phillippa’s research focuses on understanding how the epigenetic machinery controls fundamental biological processes; molecular circuits, fate, memory and the functionality of cells. She employs a systematic approach using a combination of molecular techniques as well as computational and mathematical modelling to answer her biological questions, which also aligns to the research theme Data, Knowledge & Decisions.
Collaboration
Phillippa is currently involved in projects involving researchers from Switzerland, U.S.A and Australia. With Dr Adele Woodhouse, Phillippa co-established an international collaboration with A/Prof Mark Robinson (IMLS, Switzerland), A/Prof Timothy Mercer (Garvan Institute of Medical Research and Altius Institute of Biomedical Sciences, Seattle, Washington) and Prof James Vickers (UTAS) to investigate the epigenomic mechanisms of ageing, and underlying onset and development of sporadic Alzheimer’s disease. She also co-leads a project with A/Prof Tony Cesare and Dr Katherine Giles (Children’s Medical Research Institute, NSW) to investigate chromatin remodeling and epigenomic mechanisms of genomic instability and DNA repair, and Prof Peter Jones (Van Andel Research Institute, Michigan, USA) to study manipulation of chromatin remodeling by epigenome editing and novel therapeutics.
At UTAS, Phillippa works closely with A/Prof Adele Holloway, Prof Alex Hewitt, A/Prof Tony Cook, A/Prof Guei-Sheung (Rick) Liu, Prof Joanne Dickinson, Dr Raj Eri, Dr Kate Brettingham-Moore and Dr Liesel FitzGerald in several exciting projects across the School of Medicine, Wicking Dementia Research and Education Centre, School of Health Sciences and the Menzies Research Institute for Medical Research.
Awards
- 2020 NHMRC Research Excellence, Sandra Eades Investigator Grant Award
- 2020-2024 NHMRC Emerging Leadership Research Fellow
- 2019 Research Award, College of Health and Medicine Awards
- 2016-2020 NHMRC Career Development Fellow
- 2016 Top 750 Scientists List, released by Australia’s Chief Scientist, Alan Finkel
- 2013 Young Garvan Award (runner up, 1 of 2 awardees)
- 2013 Top 10 Innovation of 2013 (for NOMe-seq, The Scientist, USA)
- 2012 L’Oréal for Women in Science Fellowship (shortlisted finalist, 1 of 8 nationally)
- 2012 F1000 “Must Read” (for De Carvalho et al., Cancer Cell 2012)
- 2012 American Society of Oncology Clinical Advance of the Year Award
- 2011 F1000 “Must Read” (for You et al., PNAS 2011)
- 2010 Outstanding Merit Award for Research, Norris Comprehensive Cancer Center (USA)
- 2009 Australian Department of Innovation, Industry & Regional Development Award
- 2009 Aspen Cancer Conference Fellow (USA)
- 2009 Benjamin F. Trump Award (USA)
- 2008-current Several prizes for poster presentations at local and international conferences
Current projects
- Long-range interactions and temporal regulation of the epigenome
- The role of three-dimensional genome structures in normal and cancer cell biology
- Mapping epigenomic information in a three-dimensional cell environment
- Delineating epigenetic evolution in Alzheimer’s disease
- Alterations in epigenetic modifier complexes in Alzheimer’s disease
- Using environmental enrichment to understand epigenetic ageing
Fields of Research
- Epigenetics (incl. genome methylation and epigenomics) (310504)
- Bioinformatic methods development (310201)
- Genome structure and regulation (310508)
Research Objectives
- Clinical health (200199)
- Expanding knowledge in the agricultural, food and veterinary sciences (280101)
Publications
Phillippa has published her work in esteemed international journals such as Cell, PNAS, Cancer Cell and Genome Research. Her work has commanded considerable international attention.Her finding that so-called “junk DNA” allows cells to change phenotype was highlighted in “Cancer: New Insights for the Healthcare Professional 2012” and was selected by the editorial board of Cell as the sole video feature.Her research describing epigenetic “drivers” and “passengers” was named one of the Top Clinical Advances 2012 (ASCO) and was featured by Faculty of 1000, Nat. Rev. Cancer and specialist websites. Peers recognised her co-authored work on deciphering how stem cell factors control DNA and the 'order' of epigenetic events with a prestigious F1000 recommendation, while the development of NOMe-Seq (Nucleosome Occupancy and Methylation Sequencing), of which she performed assay establishment and optimisation, has been described as an “impressive” and “ingenious innovation”. NOMe-Seq was named as a Top 10 Innovation of 2013 and has since been commercialised.
Total publications
36
Highlighted publications
(7 outputs)| Year | Type | Citation | Altmetrics |
|---|---|---|---|
| 2019 | Journal Article | Giles KA, Gould CM, Du Q, Skvortsova K, Song JZ, et al., 'Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups', Epigenetics and Chromatin, 12, (1) Article 12. ISSN 1756-8935 (2019) [Refereed Article] DOI: 10.1186/s13072-019-0258-9 [eCite] [Details] Citations: Scopus - 12Web of Science - 13 | |
| 2016 | Journal Article | Taberlay PC, Achinger-Kawecka J, Lun ATL, Buske FA, Sabir K, et al., 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, 26 pp. 719-731. ISSN 1549-5469 (2016) [Refereed Article] DOI: 10.1101/gr.201517.115 [eCite] [Details] Citations: Scopus - 187Web of Science - 170 | |
| 2014 | Review | Stirzaker C, Taberlay PC, Satham AL, Clark SJ, 'Mining cancer methylomes: prospects and challenges', Trends in Genetics: Dna, Differentiation and Development, 30, (2) pp. 75-84. ISSN 0168-9525 (2014) [Substantial Review] DOI: 10.1016/j.tig.2013.11.004 [eCite] [Details] Citations: Scopus - 141Web of Science - 121 | |
| 2014 | Journal Article | Taberlay PC, Stratham AL, Kelly TK, Clark SJ, Jones PA, 'Reconfiguration of Nucleosome Depleted Regions at Distal Regulatory Elements Accompanies DNA Methylation of Enhancers and Insulators in Cancer', Genome Research, 24 pp. 1421-1432. ISSN 1088-9051 (2014) [Refereed Article] DOI: 10.1101/gr.163485.113 [eCite] [Details] Citations: Scopus - 141Web of Science - 135 | |
| 2012 | Journal Article | De Carvalho DD, Sharma S, You JS, Su S-F, Taberlay PC, et al., 'DNA Methylation Screening Identifies Driver Epigenetic Events of Cancer Cell Survival', Cancer Cell, 21 pp. 655-667. ISSN 1535-6108 (2012) [Refereed Article] DOI: 10.1016/j.ccr.2012.03.045 [eCite] [Details] Citations: Scopus - 201Web of Science - 193 | |
| 2011 | Journal Article | Taberlay PC, Kelly TK, Liu C-C, You JS, De Carvalho DD, et al., 'Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming', Cell, 147 pp. 1283-1294. ISSN 0092-8674 (2011) [Refereed Article] DOI: 10.1016/j.cell.2011.10.040 [eCite] [Details] Citations: Scopus - 142Web of Science - 137 | |
| 2011 | Journal Article | You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, et al., 'OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes', Proceedings of the National Academy of Sciences, 108, (35) pp. 14497-14502. ISSN 0027-8424 (2011) [Refereed Article] DOI: 10.1073/pnas.1111309108 [eCite] [Details] Citations: Scopus - 100Web of Science - 96 |
Journal Article
(23 outputs)| Year | Citation | Altmetrics |
|---|---|---|
| 2021 | Giles KA, Gould CM, Achinge-Kawecka J, Page SG, Kafer GR, et al., 'BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer', Clinical Epigenetics, 13, (1) pp. 1-18. ISSN 1868-7075 (2021) [Refereed Article] DOI: 10.1186/s13148-021-01023-7 [eCite] [Details] Citations: Scopus - 7Web of Science - 6 Co-authors: Giles KA | |
| 2021 | Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, et al., 'Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition', Molecular Cell, 81, (10) pp. 2183-2200.e13. ISSN 1097-2765 (2021) [Refereed Article] DOI: 10.1016/j.molcel.2021.04.015 [eCite] [Details] Citations: Scopus - 19Web of Science - 25 Co-authors: Huskins SN | |
| 2020 | Khoury A, Achinger-Kawecka J, Bert SA, Smith GC, French HJ, et al., 'Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains', Nature Communications, 11, (1) Article 54. ISSN 2041-1723 (2020) [Refereed Article] DOI: 10.1038/s41467-019-13753-7 [eCite] [Details] Citations: Scopus - 43Web of Science - 43 | |
| 2019 | Dyer M, Phipps AJ, Mitew S, Taberlay PC, Woodhouse A, 'Age, but not amyloidosis, induced changes in global levels of histone modifications in susceptible and disease-resistant neurons in Alzheimer's disease model mice', Frontiers in Aging Neuroscience, 11 Article 68. ISSN 1663-4365 (2019) [Refereed Article] DOI: 10.3389/fnagi.2019.00068 [eCite] [Details] Citations: Scopus - 6Web of Science - 5 Co-authors: Dyer M; Phipps AJ; Woodhouse A | |
| 2019 | Giles KA, Gould CM, Du Q, Skvortsova K, Song JZ, et al., 'Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups', Epigenetics and Chromatin, 12, (1) Article 12. ISSN 1756-8935 (2019) [Refereed Article] DOI: 10.1186/s13072-019-0258-9 [eCite] [Details] Citations: Scopus - 12Web of Science - 13 | |
| 2019 | Skvortsova K, Stirzaker C, Taberlay P, 'The DNA methylation landscape in cancer', Essays in Biochemistry, 63, (6) pp. 797-811. ISSN 0071-1365 (2019) [Refereed Article] DOI: 10.1042/EBC20190037 [eCite] [Details] Citations: Scopus - 96Web of Science - 90 | |
| 2019 | Sutton LP, Jeffreys SA, Phillips JL, Taberlay PC, Holloway AF, et al., 'DNA methylation changes following DNA damage in prostate cancer cells', Epigenetics, 14, (10) pp. 989-1002. ISSN 1559-2294 (2019) [Refereed Article] DOI: 10.1080/15592294.2019.1629231 [eCite] [Details] Citations: Scopus - 16Web of Science - 13 Co-authors: Sutton LP; Jeffreys SA; Phillips JL; Holloway AF; Ambrose M; Young A; Berry R; Brettingham-Moore KH | |
| 2018 | Phillips JL, Taberlay PC, Woodworth AM, Hardy K, Brettingham-Moore KH, et al., 'Distinct mechanisms of regulation of the ITGA6 and ITGB4 genes by RUNX1 in myeloid cells', Journal of Cellular Physiology, 233, (4) pp. 3439-3453. ISSN 0021-9541 (2018) [Refereed Article] DOI: 10.1002/jcp.26197 [eCite] [Details] Citations: Scopus - 10Web of Science - 10 Co-authors: Phillips JL; Woodworth AM; Brettingham-Moore KH; Dickinson JL; Holloway AF | |
| 2016 | Achinger-Kawecka J, Taberlay PC, Clark SJ, 'Alterations in three-dimensional organization of the cancer genome and epigenome', Cold Spring Harbor Symposia on Quantitative Biology, 81 pp. 41-51. ISSN 0091-7451 (2016) [Refereed Article] DOI: 10.1101/sqb.2016.81.031013 [eCite] [Details] Citations: Scopus - 20Web of Science - 19 | |
| 2016 | Phipps AJ, Vickers JC, Taberlay PC, Woodhouse A, 'Neurofilament-labeled pyramidal neurons and astrocytes are deficient in DNA methylation marks in Alzheimer's disease', Neurobiology of Aging, 45 pp. 30-42. ISSN 0197-4580 (2016) [Refereed Article] DOI: 10.1016/j.neurobiolaging.2016.05.003 [eCite] [Details] Citations: Scopus - 24Web of Science - 23 Co-authors: Phipps AJ; Vickers JC; Woodhouse A | |
| 2016 | Skortsova K, Taberlay P, Clark SJ, Stirzaker C, 'Role of 5-Hydroxymethylation and TET enzymes in remodelling the epigenome', Experimental Medicine, 34, (10) pp. 1-9. ISSN 1791-9967 (2016) [Non Refereed Article] | |
| 2016 | Taberlay PC, Achinger-Kawecka J, Lun ATL, Buske FA, Sabir K, et al., 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, 26 pp. 719-731. ISSN 1549-5469 (2016) [Refereed Article] DOI: 10.1101/gr.201517.115 [eCite] [Details] Citations: Scopus - 187Web of Science - 170 | |
| 2015 | Brettingham-Moore KH, Taberlay PC, Holloway AF, 'Interplay between transcription factors and the epigenome: insight from the role of RUNX1 in leukemia', Frontiers in Immunology, 6 Article 499. ISSN 1664-3224 (2015) [Refereed Article] DOI: 10.3389/fimmu.2015.00499 [eCite] [Details] Citations: Scopus - 23Web of Science - 22 Co-authors: Brettingham-Moore KH; Holloway AF | |
| 2015 | Qadi A, Taberlay PC, Phillips JL, Young A, West AC, et al., 'The leukemia inhibitory factor receptor gene is a direct target of RUNX1', Journal of Cellular Biochemistry, 117, (1) pp. 49-58. ISSN 0730-2312 (2015) [Refereed Article] DOI: 10.1002/jcb.25246 [eCite] [Details] Citations: Scopus - 6Web of Science - 5 Co-authors: Phillips JL; Young A; West AC; Brettingham-Moore KH; Dickinson JL; Holloway AF | |
| 2015 | Statham AL, Taberlay PC, Kelly TC, Jones PA, Clark SJ, 'Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines', Genomics Data, 3 pp. 94-96. ISSN 2213-5960 (2015) [Refereed Article] DOI: 10.1016/j.gdata.2014.11.012 [eCite] [Details] Citations: Scopus - 10 | |
| 2014 | Taberlay PC, Stratham AL, Kelly TK, Clark SJ, Jones PA, 'Reconfiguration of Nucleosome Depleted Regions at Distal Regulatory Elements Accompanies DNA Methylation of Enhancers and Insulators in Cancer', Genome Research, 24 pp. 1421-1432. ISSN 1088-9051 (2014) [Refereed Article] DOI: 10.1101/gr.163485.113 [eCite] [Details] Citations: Scopus - 141Web of Science - 135 | |
| 2012 | De Carvalho DD, Sharma S, You JS, Su S-F, Taberlay PC, et al., 'DNA Methylation Screening Identifies Driver Epigenetic Events of Cancer Cell Survival', Cancer Cell, 21 pp. 655-667. ISSN 1535-6108 (2012) [Refereed Article] DOI: 10.1016/j.ccr.2012.03.045 [eCite] [Details] Citations: Scopus - 201Web of Science - 193 | |
| 2011 | Taberlay PC, Jones PA, 'DNA methylation and cancer', Progress in drug research pp. 1-23. ISSN 0071-786X (2011) [Refereed Article] DOI: 10.1007/978-3-7643-8989-5_1 [eCite] [Details] Citations: Scopus - 94 | |
| 2011 | Taberlay PC, Kelly TK, Liu C-C, You JS, De Carvalho DD, et al., 'Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming', Cell, 147 pp. 1283-1294. ISSN 0092-8674 (2011) [Refereed Article] DOI: 10.1016/j.cell.2011.10.040 [eCite] [Details] Citations: Scopus - 142Web of Science - 137 | |
| 2011 | You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, et al., 'OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes', Proceedings of the National Academy of Sciences, 108, (35) pp. 14497-14502. ISSN 0027-8424 (2011) [Refereed Article] DOI: 10.1073/pnas.1111309108 [eCite] [Details] Citations: Scopus - 100Web of Science - 96 | |
| 2010 | Oakford PC, James SR, Qadi A, West AC, Ray SN, et al., 'Transcriptional and epigenetic regulation of the GM-CSF promoter by RUNX1', Leukemia Research, 34, (9) pp. 1203-1213. ISSN 0145-2126 (2010) [Refereed Article] DOI: 10.1016/j.leukres.2010.03.029 [eCite] [Details] Citations: Scopus - 14Web of Science - 15 Co-authors: West AC; Ray SN; Holloway AF | |
| 2008 | Brettingham-Moore KH, Sprod OR, Chen X, Oakford PC, Shannon MF, et al., 'Determinants of a transcriptionally competent environment at the GM-CSF promoter', Nucleic Acids Research, 36, (8) pp. 2639-2653. ISSN 0305-1048 (2008) [Refereed Article] DOI: 10.1093/nar/gkn117 [eCite] [Details] Citations: Scopus - 17Web of Science - 14 Co-authors: Brettingham-Moore KH; Sprod OR; Holloway AF | |
| 2007 | Holloway AF, Oakford PC, 'Targeting Epigentic Modifiers in Cancer', Current Medicinal Chemistry, 14, (24) pp. 2540-2547. ISSN 0929-8673 (2007) [Refereed Article] DOI: 10.2174/092986707782023271 [eCite] [Details] Citations: Scopus - 16Web of Science - 13 Co-authors: Holloway AF |
Chapter in Book
(3 outputs)| Year | Citation | Altmetrics |
|---|---|---|
| 2019 | Giles KA, Taberlay PC, 'The Role of Nucleosomes in Epigenetic Gene Regulation', Clinical Epigenetics, Springer, Singapore, LB Hesson and AL Pritchard (ed), Singapore, pp. 87-117. ISBN 978-981-13-8957-3 (2019) [Research Book Chapter] DOI: 10.1007/978-981-13-8958-0_4 [eCite] [Details] Citations: Scopus - 1 | |
| 2018 | Giles KA, Taberlay PC, 'Mutations in Chromatin Remodeling Factors', Encyclopedia of Cancer 3rd Edition, Elsevier, G Pfeifer (ed), United States ISBN 9780128124840 (2018) [Other Book Chapter] DOI: 10.1016/B978-0-12-801238-3.65225-X [eCite] [Details] Citations: Scopus - 2 | |
| 2015 | Brettingham-Moore KH, Taberlay PC, 'Cancer Epigenetics', Drug Discovery in Cancer Epigenetics, Academic Press, G Egger & P Arimondo (ed), United Kingdom, pp. 41-62. ISBN 978-0128022085 (2015) [Research Book Chapter] Co-authors: Brettingham-Moore KH |
Review
(2 outputs)| Year | Citation | Altmetrics |
|---|---|---|
| 2014 | Skulte KA, Phan L, Clark SJ, Taberlay PC, 'Chromatin remodeler mutations in human cancers: epigenetic implications', Epigenomics, 6, (4) pp. 397-414. ISSN 1750-1911 (2014) [Substantial Review] DOI: 10.2217/epi.14.37 [eCite] [Details] Citations: Scopus - 29Web of Science - 26 | |
| 2014 | Stirzaker C, Taberlay PC, Satham AL, Clark SJ, 'Mining cancer methylomes: prospects and challenges', Trends in Genetics: Dna, Differentiation and Development, 30, (2) pp. 75-84. ISSN 0168-9525 (2014) [Substantial Review] DOI: 10.1016/j.tig.2013.11.004 [eCite] [Details] Citations: Scopus - 141Web of Science - 121 |
Conference Publication
(8 outputs)| Year | Citation | Altmetrics |
|---|---|---|
| 2019 | Phipps A, Giles K, Mercer T, Vickers J, Robinson M, et al., 'id #12216 - Dysregulation of the neuronal epigenome occurs prior to pathology-onset and alters with progressive amyloidosis', Australasian Neuroscience Society (ANS) 2019 Conference, 2-5 December, Adelaide Convention Centre (2019) [Conference Extract] Co-authors: Phipps A; Vickers J; Woodhouse A | |
| 2019 | Phipps A, Giles K, Mercer T, Vickers JC, Robinson M, et al., 'Recapitulation of juvenile-like histone landscape in aged neurons', Australian Dementia Forum 2019, 13-14 June 2019, Hobart, Tasmania (2019) [Conference Extract] Co-authors: Phipps A; Vickers JC; Woodhouse A | |
| 2018 | Taberlay PC, Singh V, Lu V, Chen J, Hung SSC, et al., 'A genome-wide CRISPR/CAS9 screen to identify novel therapeutic targents for uveal melanoma', The Royal Australian and New Zealand College of Ophthalmologists 50th Annual Scientific Congress, 17-21 November 2018, Adelaide, Australia (2018) [Conference Extract] | |
| 2016 | Phipps A, Vickers J, Mercer G, Woodhouse A, Taberlay P, 'Poster 299 - Epigenetic dysregulation of critical gene regulatory elements in AD mice', Australasian Neuroscience Society Annual Scientific Meeting 2016, 4-7 December, Hobart, Tasmania (2016) [Conference Extract] Co-authors: Phipps A; Vickers J; Woodhouse A | |
| 2016 | Phipps A, Woodhouse A, Taberlay P, 'Poster 341 - Simultaneous alterations in nucleosome positions and DNA methylation predict epigenome-wide changes in Alzheimer's disease', Australasian Neuroscience Society Annual Scientific Meeting 2016, 4-7 December, Hobart, Tasmania (2016) [Conference Extract] Co-authors: Phipps A; Woodhouse A | |
| 2015 | Phipps AJ, Vickers JC, Taberlay PC, Woodhouse A, 'No difference in DNA methylation and hydroxymethylation marks in cortical pyramidal neurons, interneurons and microglia in control, early- and late-stage sporadic AD cases', 9th Alzheimer's + Parkinson's Disease (A+PD) Symposium, 23-24 April, Queensland Brain Institute (St Lucia) (2015) [Conference Extract] Co-authors: Phipps AJ; Vickers JC; Woodhouse A | |
| 2015 | Phipps AJ, Vickers JC, Taberlay PC, Woodhouse A, 'Neurofilament-labelled pyramidal neurons and astrocytes are deficient in DNA methylation marks in Alzheimer's disease', Epigenetics 2015 - Australian Scientific Conference, 12-14 November, Hobart, Tasmania (2015) [Conference Extract] Co-authors: Phipps AJ; Vickers JC; Woodhouse A | |
| 2005 | Oakford PC, Holloway AF, 'Regulation of gene expression by the RUNX-1 transcription factor', The Genome Conference, 13-17 Feb 2005, Victoria, pp. 108. (2005) [Conference Extract] Co-authors: Holloway AF |
Grants & Funding
Phillippa has secured a broad range of competitive funding including fellowships from Cancer Institute NSW (1 of 6 awarded) and NHMRC (x2 consecutive fellowships) as well as research funding from Cancer Australia (Priority Driven Collaborative Cancer Research; 1 of 16 awarded), NHMRC Project and ARC Indigenous Discovery Scheme grants. In addition, she is recipient of competitive funding from Brain Foundation, Rebecca L Cooper Medical Research Foundation, Cancer Council Tasmania, Judith Jane Mason & Harold Stannett Williams, University of Tasmania Foundation Inc. and Royal Hobart Hospital Research Foundation, and has received additional peer-reviewed seed funding for innovative research.
Funding Summary
Number of grants
26
Total funding
Projects
- Description
- To map the genetic and epigenetic changes that drive brain tumour development.
- Funding
- Walter and Eliza Hall Institute of Medical Research ($97,812)
- Scheme
- Contract Research
- Administered By
- University of Tasmania
- Research Team
- Dickinson JL; Marshall O; Taberlay PC; Young K; Dickson TC
- Year
- 2024
- Description
- The University of Tasmania operates the only research-based Flow Cytometry Facility in the state, which is accessed by researchers spanning neurosciences, ecology, evolutionary biology, oceanography, marine sciences, epi/genomics and immunology. Our research endeavours are cross-disciplinary and aimed at increasing and translating knowledge through the commercial application of discoveries. Investment in a new Flow sorter will provide a vital resource that underpins internationally relevant research that is important to our Tasmanian identity: our ageing population and our environment (Tasmanian Devil Facial Tumour Disease, Antarctic and climate science, Southern oceanography
- Funding
- Australian Research Council ($500,000)
- Scheme
- Grant-Linkage Infrastructure
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Woodhouse A; Wapstra E; Bolch CJS; Flies AS
- Year
- 2024
- Grant Reference
- LE240100080
- Description
- Radiotherapy is frequently used in treating brain cancers such as medulloblastoma. Unfortunately, outcomes are poor for many patients. This study will investigate the potential of targeting DNA hydroxymethylation to sensitise medulloblastoma cells to radiotherapy. Aim 1 will profile levels of hydroxymethylation while Aim 2 will assess the impact of TET inhibition on response to radiotherapy.
- Funding
- Cancer Council of Tasmania ($11,000)
- Scheme
- Grant-Small
- Administered By
- University of Tasmania
- Research Team
- Brettingham-Moore KH; Taberlay PC; Holloway AF
- Year
- 2021
- Description
- Molecular analysis of prostate cancer tumour specimen to identify new molecular targets for therapy.
- Funding
- Royal Hobart Hospital Research Foundation ($24,925)
- Scheme
- Grant-Project
- Administered By
- University of Tasmania
- Research Team
- Dickinson JL; Holloway AF; Nott LM; Liu G; FitzGerald LM; Brettingham-Moore KH; Hewitt A; Taberlay PC
- Year
- 2020
- Description
- Ageing is the single greatest risk factor for both cancers and dementias, indicating that the things we are exposed to over a lifetime can alter our disease risk. The epigenome lies at this interface - it is dynamic and modifiable. For decades the field has sought to determine what epigenetic changes dysregulate gene promoters in cancer and how or why they occur. However, promoters do not act in isolation, DNA does not exist as a linear molecule inside cells and many questions remain. Foremost, it is increasingly apparent that epigenomic reprogramming is necessary during healthy aging and that deviations from this process underpin every disease affecting human health, including dementia and other non-cancerous pathologies. My research program will have an exceptional KNOWLEDGE impact by (1) defining the limits of epigenetic flexibility in healthy ageing and (2) understanding why and how the epigenome is reprogrammed, causing molecular damage that initiates and drives cancers and dementias. My complementary research themes address a deceptively simple question: How, why and what makes the epigenome so important? * BRG1-driven three-dimensional chromatin remodeling in cancer cells* Epigenetic evolution of neurons in sporadic Alzheimer's disease* Positively modulating the ageing epigenome with environmental enrichment* Manipulating chromatin modifiers to recreate cancer epigenomes* Higher-order neuronal chromatin maps in healthy ageing and Alzheimer's diseaseThese projects leverage my expertise in sophisticated epigenomic assays in combination with advanced cell biology approaches in 2D and 3D cancer models, mouse models of ageing and Alzheimer's disease, as well as human Alzheimer's disease cases and healthy, aged individuals. By challenging currently accepted paradigms we will make the greatest knowledge breakthroughs, towards understanding how we can purposefully modulate the epigenome for future health, economic and social benefit.
- Funding
- National Health & Medical Research Council ($1,241,554)
- Scheme
- Fellowship-Investigator Grant
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC
- Period
- 2020 - 2024
- Grant Reference
- 1176417
- Description
- Many cancer patients receive fractionated/recurrent dosages of DNA damaging agents and there is some evidence that this may drive future treatment resistance and metastasis. This project will profile prostate cancer cells after repeated DNA damage via RNA-seq and EPIC arrays
- Funding
- Royal Hobart Hospital Research Foundation ($23,295)
- Scheme
- Grant-Project
- Administered By
- University of Tasmania
- Research Team
- Brettingham-Moore KH; Black A; Taberlay PC; Holloway AF
- Year
- 2019
- Description
- Sporadic Alzheimer's disease (sAD) is not part of normal aging and we must determine how and why it occurs. The epigenome (meaning, 'above genes') ensures that our genes are expressed in the right cell type at the right time. Epigenetic defects are of great interest as they are reversible; but first, the epigenetic changes that characterise AD progression must be defined. Our overall aim is to identify how epigenetic programming is altered in the nerve cells that die in AD.
- Funding
- National Health & Medical Research Council ($826,102)
- Scheme
- Grant-Project
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Woodhouse A; Robinson M; Mercer T
- Period
- 2019 - 2021
- Grant Reference
- 1161768
- Description
- Our goal is to determine why DNA is packaged differently inside normal and cancer cells. We hypothesise that we can change the way DNA is packaged inside cancer cells so that we can force them to behave similarly to normal cells.
- Funding
- National Health & Medical Research Council ($969,187)
- Scheme
- Grant-Project
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Jones P; Robinson M
- Period
- 2019 - 2022
- Grant Reference
- 1161985
- Description
- We propose to build upon the clinically-focused Prostate Cancer Outcomes Registry, Tasmania (PCOR-TAS) and collect matched biological samples to create a valuable resource for both clinicians and scientists. The availability of clinical and genetic data will allow important biomarker research into predicting prostate cancer outcomes and improving treatment strategies.
- Funding
- Royal Hobart Hospital Research Foundation ($22,146)
- Scheme
- Grant-Minor Project
- Administered By
- University of Tasmania
- Research Team
- FitzGerald LM; Dickinson JL; Skala M; Stokes BC; Donovan S; Malley RC; Redwig F; Holloway AF; Taberlay PC
- Year
- 2018
- Description
- This proposal aims to determine the role of fundamental epigenetic mechanisms in the process of aging. It combines the fields of epigenetics, neurosciences and mathematics to delineate the dynamics of DNA methylation and histone modification marking on the transcriptome during normal, healthy aging. This project will uniquely apply environmental enrichment to determine whether modulation of the epigenome underpins an improvement in cognitive function. Thus, whether an adult, rather than aged, epigenome can be maintained in neurons duringaging.
- Funding
- Australian Research Council ($458,608)
- Scheme
- Grant-Discovery Indigenous
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Woodhouse A; Vickers JC
- Period
- 2018 - 2021
- Grant Reference
- IN180100005
- Description
- Aging causes our cells to decline in both integrity and function. As such, the incidence of disorders that affect nerve cells, including Alzheimer's disease (AD), increases with aging. In healthy cells, our genes are tightly regulated so that the correct combination of genes are switched on, or off, at the proper time to allow for learning and memory to occur. This is achieved by the addition or removal of small chemical residues associated with DNA, and the study of these processes is known as 'epigenetics'. Epigenetic marks can change during aging, and diseases occur when this happens too quickly or in an uncontrolled way. Proper epigenetic control must be maintained during aging and we raise the possibility that epigenetic dysregulation plays an important role in AD progression. Surprising though, existing knowledge of the epigenetic alterations in AD is extremely limited, highlighting that new knowledge in this area is critical and that the timing of our study is significant. We present striking preliminary data revealing that epigenetic changes are occurring in AD and that they are affecting important gene regulatory regions. Our overall aim is to investigate whether the proteins in charge of regulating epigenetic processes behave abnormally in AD. At completion we will understand whether certain epigenetic signatures are associated with different stages in sporadic AD, and whether they differ between sporadic and familial AD. Ours is the only study currently measuring epigenetic changes specifically in nerve cells. These findings will significantly advance our understanding of the role of epigenetic dysregulation in AD and ss epigenetic defects are reversible, this study could also identify new clinical targets to improve the outcomes for people living with AD.
- Funding
- Brain Foundation ($33,000)
- Scheme
- Grant-Research
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Woodhouse A; Robinson M; Mercer T
- Year
- 2017
- Description
- Every cell in our body contains an identical genetic code; yet, for example, our heart and brain are very different. This is made possible by a process called 'epigenetics', which describes the addition and removal of small chemical marks above ('epi') our DNA ('genetics'). Epigenetic marks carefully build layers on top of each other and when this happens properly, the right genes are expressed in the right cells at the right time and allow them to function as they should. However, there are no techniques to measure more than two epigenetic marks at the same time. Our overall goal is to address this deficit by developing a new technique that measures three epigenetic marks simultaneously (DNA methylation, histone modifications, nucleosomes). The benefit will be unlimited because it will be applicable to all normal and disease states, and all organisms. Furthermore, we will use this capability to determine whether epigenetic mistakes could explain why certain cells in the brain (neurons) are dysfunctional and die in Alzheimer's disease, while other cells are resistant. This is a critical question in the field and our new data may unlock vital clues about the molecular etiology of this currently incurable disease.
- Funding
- Rebecca L Cooper Medical Research Foundation ($24,971)
- Scheme
- Grant
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Woodhouse A
- Year
- 2017
- Description
- We lack a model that better replicates in vivo tumour development to study epigenomic mechanisms of prostate cancer. To date, epigenetic changes in cancer have been investigated in homogenous cell lines from two-dimensional laboratory cultures or end-point tumour samples (static) from patients. Without doubt these studies have provided great insight into epigenetic differences that distinguish cancer cells from normal cells. However, there is a glaring lack of information about dynamic and temporal changes to the epigenome and cell behaviour as the cells acquire invasive potential. This is not possible using currently available two-dimensional models and clinical samples. We will address this deficit by establishing a three-dimensional model of prostate cancer that allows us to map how epigenomes and cell behaviours change during cancer development.
- Funding
- Cancer Council of Tasmania ($20,990)
- Scheme
- Grant-Cancer Research
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Brettingham-Moore KH; Holloway AF; Biro M
- Year
- 2017
- Description
- Our understanding of many cancers has improved dramatically over the past decade predominantly due to our ability to sequence entire genomes, at scale. Yet, we still require a better understanding of the underlying mechanisms that initiate and perpetuate cancers, as well as gene-based factors that initiate the transition from indolent to aggressive cancers with a propensity to metastasize. CRISPR/Cas is proving a robust, powerful and necessary tool in the laboratory that will undoubtedly underpin the next breakthrough in the field of cancer. As such, it is essential that we develop this capability at the University of Tasmania in a timely manner.The specific AIMS of this proposal are to:Aim 1: Establish CRISPR/Cas screening at the University of Tasmania as a tool to identify genesthat drive aggressive and metastatic cancers.Aim 2: Perform a genome-wide CRISPR/Cas negative selection (loss-of-function) screen toidentify genes essential for proliferation and survival, as well as metastatic behaviour.
- Funding
- University of Tasmania Foundation Inc ($63,845)
- Scheme
- Grant-Cancer Research
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC; Hewitt A; Holloway AF; Liu G; Dickinson JL; Brettingham-Moore KH; Fitzgerald L; Eri RD; Cook AL
- Year
- 2017
- Description
- This project will investigate the basal and post radiotherapy epigenetic changes in prostate cancer cells with divergent response to radiotherapy (RT). It will validate methylation data obtained from illumina Infinium 450 beadchip arrays, profile histone modifications post RT and investigate DNA damage post RT in cells treated with inhibitors of epigenetic enzymes (DNMT and HDAC).
- Funding
- Cancer Council of Tasmania ($33,000)
- Scheme
- Grant-Cancer Research
- Administered By
- University of Tasmania
- Research Team
- Brettingham-Moore KH; Ambrose M; Holloway AF; Skala M; Taberlay PC
- Year
- 2016
- Funding
- National Health & Medical Research Council ($419,180)
- Scheme
- Fellowship-Career Development
- Administered By
- University of Tasmania
- Research Team
- Taberlay PC
- Period
- 2016 - 2019
- Grant Reference
- 1109696
- Description
- Cancer initiation and progression is caused by a complex series of genetic and epigenetic changes. Such epigenetic changes drive atypical gene activity through altered patterns of DNA methylation, histone variants/modifications and the physical chromatin structure (eg. nucleosome positions). These epigenetic changes have been extensively characterised at gene promoters and are considered hallmarks of cancer cells. However, it is often overlooked that many promoters themselves are regulated by distal regulatory elements (eg. enhancers) that act by long-range looping mechanisms to facilitate communication across genome-scale distances. The extent or importance of the epigenetic changes that occur at enhancers in cancer cells has not been determined. Striking observations from my recent work 1 (Taberlay et al., Cell 2011)[CIA-P10911062] established the model on which this new proposal is based. Foremost, that enhancers with active epigenetic signatures regulate transcriptionally repressed promoters. We found that the purpose of this unexpected, divergent epigenetic combination at enhancer/promoter pairs was to ensure that epigenetic flexibility was retained, so that normal cells can respond to reprogramming signals. Importantly, we observed that cells are rendered resistant to reprogramming signals when an enhancer is abnormally epigenetically silenced in cancer cells. The underlying mechanisms, and the wider implications of enhancer epigenetic alterations in cancer is unknown.
- Funding
- Cancer Australia ($37,000)
- Scheme
- Grant-Priority-driven Collab. Cancer Research
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Taberlay PC
- Year
- 2016
- Description
- Chemical and physical modification of DNA enables phenotypic variation within individuals built from a single genome. Thestudy of epigenetics has the potential to span the spectrum of biology, but has been somewhat limited to some fields (e.g. cancerand aging) or by virtue of the methods currently available to map epigenomes. DNA methylation is a major component of theepigenome and underpins normal development and survival. It is measured by whole genome bisulfite sequencing (WGBS), whichprovides information on the methylation status of DNA loci from the entire pools of cells sampled as a population; thus,knowledge regarding the cell-to-cell variation in epigenetic signatures is severely lacking. Single-cell WGBS experiments are atthe cutting edge of epigenetics research (Smallwood et al., 2014, Nature Methods, Farlik et al., 2015, Cell Reports) and will allowus to ascertain the heterogeneity in DNA methylation patterns from cell to cell. Our study will address a substantial gap in knowledge in the field by generating the first single-cell WGBS data from individual aged neurons. Pyramidal neurons are postmitotic long-lived cells with the ability to accrue epigenetic differences over time, thus, providing an ideal model to assess the heterogeneity in the DNA methylomes of individual cells in healthy aging.
- Funding
- University of Tasmania ($14,407)
- Scheme
- Grant-Research Enhancement (REGS)
- Administered By
- University of Tasmania
- Research Team
- Woodhouse A; Taberlay PC; Vickers JC
- Year
- 2016
- Description
- Aging constitutes a time-dependent decline in cellular integrity and function. As we age, the incidence of neurodegenerative disorders, including Alzheimer's disease (AD) increase. Ordinarily, the genome remains under exquisite control; epigenetic plasticity in neurons isimportant for continued learning and memory1,2 and is retained across lifespan3. Epigenetic mechanisms such as DNA methylation, and histone modifications are absolutely necessary for proper transcriptional output that underpins these normal cellular processes. Indeed, theimportance of epigenetics has now been well established in cancer field, yet other diseases have been largely overlooked.We hypothesize that epigenetic changes are hallmarks of Alzheimer's disease.Here, we emphasize that proper epigenetic control must be maintained during aging and raise the possibility that epigenetic dysregulation plays an important role in AD progression. Striking observations from our preliminary study forms the basis of this new proposal. Foremost, epigenetic marks defining both enhancers (H3K4me1, H3K27Ac) and promoters (H3K4me3, H3K27me3) are lost from gene regulatory regions, revealing that epigenetic reprogramming does occur in AD. Existing knowledge of the epigenetic alterations in AD is extremely limited, highlighting that new knowledge in this area is critical and the timing of this work is highly significant.Our OVERALL AIM is to determine the repertoire of epigenetic aberrations associated with Alzheimer's disease and to test whether the development of disease is underpinned by an abnormal epigenetic program.Our Overall Aim will be addressed by:1) Generating maps of activating and repressive epigenetic marks across a time course that encompasses pre-disease, disease onset and late disease stages in a mouse model of AD.2) Identifing the spatial epigenetic changes that occur in distinct cell types across a time course of disease progression in AD mice.At completion we will understand whether distinct epigenetic signatures are associated with different stages in disease progression in AD, and if epigenetic alterations are cell typespecific or dependent on proximity to AD pathology. These findings will significantly advance our understanding of the role of pigenetic dysregulation in AD and could identifying new clinical targets to improve the outcomes for AD patients.
- Funding
- The Mason Foundation ($50,020)
- Scheme
- Grant-Judith Jane Mason & Harold Stannett Williams
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Taberlay PC; Woodhouse A; Mercer T; Phipps AJ
- Year
- 2015
- Funding
- University of New South Wales ($106,176)
- Scheme
- Australian Postgraduate Award (APA)
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Giles Katherine A; Taberlay Phillippa C; Clark Susan J
- Period
- 2014 - 2017
- Funding
- Cancer Australia (Cure Cancer Australia Foundation) ($199,298)
- Scheme
- Project Grant
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Taberlay Phillippa
- Period
- 2014 - 2015
- Funding
- Young Garvan Foundation ($693,374)
- Scheme
- Special Initiative Grant
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Taberlay Phillippa
- Year
- 2013
- Funding
- NHMRC ($693,374)
- Scheme
- Project Grant
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Clark Susan J; Taberlay Phillippa C
- Period
- 2013 - 2015
- Funding
- Cancer Institute NSW ($582,876)
- Scheme
- Fellowship
- Administered By
- Garvan Institute of Medical Research
- Research Team
- Taberlay Phillippa
- Period
- 2013 - 2015
- Funding
- Cancer Council of Tasmania ($1,200)
- Scheme
- Grant-Travel
- Administered By
- University of Tasmania
- Research Team
- Holloway AF; Taberlay PC
- Year
- 2007
- Funding
- David Collins Leukaemia Foundation ($400)
- Scheme
- Award-Professional Development
- Administered By
- University of Tasmania
- Research Team
- Holloway AF; Taberlay PC
- Year
- 2007
Research Supervision
Phillippa has supervised four First Class Honours, two Masters and three PhD students to completion. Her students have gone on to graduate from Cambridge University and attained post-doctoral positions at Oxford University, Children’s Medical Research Institute and Garvan Institute of Medical Research. They have published a number of papers and received a number of research awards including Dean’s Award for Outstanding PhD Thesis (UNSW), AAAS/Science Award (USA), University Medal (Western Sydney University), Yulgilbar Alzheimer’s Research Scholarships (2x), poster prizes (4x) and competitive travel grants (3x). Phillippa is also involved in formal mentoring programs for students (e.g. “Life after a PhD”) and postdocs (e.g. “Effective Networking”).
Current
6
Completed
4
Current
| Degree | Title | Commenced |
|---|---|---|
| PhD | Investigating Neuronal Epigenome Ageing in an Enriched Environment | 2020 |
| PhD | Epigenetic Evolution During Cancer Treatment | 2020 |
| PhD | The Role of Pericytes in Vascular Recovery Following Stroke and Ageing | 2021 |
| PhD | BRG1-Dependent Evolution of the Cancer Epigenome | 2021 |
| PhD | Identification of Genes Causing Inherited Paediatric Cataract | 2021 |
| PhD | Investigating the Epigenetic Remodelling Events that Produce Glia and Glioma | 2023 |
Completed
| Degree | Title | Completed |
|---|---|---|
| PhD | DNA Methylation and Nucleosome Occupancy Landscapes of Excitatory Neurons in Human Sporadic Alzheimer's Disease Candidate: Thalia Gabriela Perez Suarez | 2022 |
| PhD | Identifying Genetic Causes of Paediatric Cataract Onset and Severity: Validation of candidate gene HTR1F and mapping of modifier genes Candidate: Duran Zhao | 2022 |
| PhD | Transcriptomic and DNA Methylation Alterations in Prostate Cancer Metastasis Candidate: Aparna Shree Raina | 2021 |
| PhD | DNA Methylation and Histone Modification Dynamics in Neurons in Aging and Alzheimer's Disease Candidate: Andrew James Phipps | 2019 |