Joanna Achinger-Kawecka

Group Leader
Conjoint Senior Lecturer

Dr Joanna Achinger-Kawecka is a Group Leader of the 3D Epigenome in Cancer group at the Garvan Institute of Medical Research and Conjoint Senior Lecturer at St Vincent's Clinical School, UNSW Sydney. Joanna completed her PhD in 2014 at the University of Tuebingen, Germany supported by prestigious Marie Sklodowska-Curie Fellowship, studying epigenetic biomarkers in breast cancer.


Following her PhD, Joanna joined the Epigenetics Research laboratory of Prof Susan Clark at the Garvan Institute, where she established cutting-edge experimental and computational approaches to study the 3D genome organization. Dr Achinger-Kawecka has made significant contributions to the field, publishing in high-impact journals such as Nature Communications, Nature Structural & Molecular Biology and Genome Research. She has been awarded competitive research funding from NHMRC, CCNSW and NBCF and established her own research group at the Garvan Institute in 2023.


The main goal of the group’s research is to understand the role of 3D genome architecture in cancer, including its cell-to-cell and temporal variability. For that, they combine and integrate cutting-edge genomics technology, single-cell epigenome profiling, genome editing and pre-clinical models to study the interplay of the 3D genome and epigenome in cancer and how these 3D epigenome changes can be targeted with epigenetic therapy. Beyond fundamental discoveries, their main goal is to uncover new therapeutic targets and biomarkers for the treatment of metastatic disease.

Journal articles
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Peters TJ; Meyer B; Ryan L; Achinger-Kawecka J; Song J; Campbell EM; Qu W; Nair S; Loi-Luu P; Stricker P; Lim E; Stirzaker C; Clark SJ; Pidsley R, 2024, 'Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling', BMC Genomics, 25, http://dx.doi.org/10.1186/s12864-024-10027-5
2024
Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia KM; Du Q; Laven-Law G; Nair SS; Yong A; Wilkinson A; Clifton S; Milioli HH; Alexandrou S; Caldon CE; Song J; Khoury A; Meyer B; Chen W; Pidsley R; Qu W; Gee JMW; Schmitt A; Wong ES; Hickey TE; Lim E; Clark SJ, 2024, 'The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer', Nature Structural and Molecular Biology, 31, pp. 498 - 512, http://dx.doi.org/10.1038/s41594-023-01181-7
2024
Hastings JF; Latham SL; Kamili A; Wheatley MS; Han JZR; Wong-Erasmus M; Phimmachanh M; Nobis M; Pantarelli C; Cadell AL; O’Donnell YEI; Leong KH; Lynn S; Geng FS; Cui L; Yan S; Achinger-Kawecka J; Stirzaker C; Norris MD; Haber M; Trahair TN; Speleman F; De Preter K; Cowley MJ; Bogdanovic O; Timpson P; Cox TR; Kolch W; Fletcher JI; Fey D; Croucher DR, 2023, 'Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma', Science Advances, 9, pp. eabp8314, http://dx.doi.org/10.1126/sciadv.abp8314
2023
Brown LJ; Achinger-Kawecka J; Portman N; Clark S; Stirzaker C; Lim E, 2022, 'Epigenetic Therapies and Biomarkers in Breast Cancer', Cancers, 14, http://dx.doi.org/10.3390/cancers14030474
2022
Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell EM; Nair SS; Zotenko E; Gould CM; Buckley M; Chia KM; Portman N; Lim E; Kaczorowski D; Chan CL; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 2021, 'DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109722
2021
Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia K-M; Du Q; Laven-Law G; Nair SS; Yong A; Wilkinson A; Clifton S; Milioli HH; Alexandrou S; Caldon CE; Song J; Khoury A; Meyer B; Gee JMW; Schmitt A; Wong ES; Hickey TE; Lim E; Clark SJ, 2021, 'Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer', , http://dx.doi.org/10.1101/2021.06.21.449340
2021
Giles KA; Gould CM; Achinger-Kawecka J; Page SG; Kafer GR; Rogers S; Luu PL; Cesare AJ; Clark SJ; Taberlay PC, 2021, 'BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer', Clinical Epigenetics, 13, http://dx.doi.org/10.1186/s13148-021-01023-7
2021
Du Q; Smith G; Luu PL; Ferguson J; Armstrong N; Caldon E; Campbell E; Nair S; Zotenko E; Gould C; Buckley M; Kaczorowski D; Barton K; Deveson I; Smith M; Powell J; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark S, 2020, 'DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity', , http://dx.doi.org/10.1101/2020.10.15.338855
2020
Achinger-Kawecka J; Valdes-Mora F; Luu PL; Giles KA; Caldon CE; Qu W; Nair S; Soto S; Locke WJ; Yeo-Teh NS; Gould CM; Du Q; Smith GC; Ramos IR; Fernandez KF; Hoon DS; Gee JMW; Stirzaker C; Clark SJ, 2020, 'Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-14098-x
2020
Khoury A; Achinger-Kawecka J; Bert SA; Smith GC; French HJ; Luu PL; Peters TJ; Du Q; Parry AJ; Valdes-Mora F; Taberlay PC; Stirzaker C; Statham AL; Clark SJ, 2020, 'Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-13753-7
2020
Giles KA; Gould CM; Achinger-Kawecka J; Page SG; Kafer G; Luu P-L; Cesare AJ; Clark SJ; Taberlay PC, 2020, 'BRG1 promotes transcriptional patterns that are permissive to proliferation in cancer cells', , http://dx.doi.org/10.1101/2020.07.03.187385
2020
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 and Chromatin, 12, pp. 12, http://dx.doi.org/10.1186/s13072-019-0258-9
2019
Fuksiewicz M; Kotowicz B; Rutkowski A; Achinger-Kawecka J; Wagrodzki M; Kowalska MM, 2018, 'The assessment of clinical usage and prognostic value of YKL-40 serum levels in patients with rectal cancer without distant metastasis', Technology in Cancer Research and Treatment, 17, http://dx.doi.org/10.1177/1533033818765209
2018
Achinger-Kawecka J; Clark SJ, 2017, 'Disruption of the 3D cancer genome blueprint', Epigenomics, 9, pp. 47 - 55, http://dx.doi.org/10.2217/epi-2016-0111
2017
Achinger-Kawecka J; Taberlay PC; Clark SJ, 2016, 'Alterations in three-dimensional organization of the cancer genome and epigenome', Cold Spring Harbor Symposia on Quantitative Biology, 81, pp. 41 - 51, http://dx.doi.org/10.1101/sqb.2016.81.031013
2016
Taberlay PC; Achinger-Kawecka J; Lun ATL; Buske FA; Sabir KS; Gould CM; Zotenko E; Bert SA; Giles KA; Bauer D; Smyth GK; Stirzaker C; O Donoghue SI; Clark SJ, 2016, 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, 26, pp. 719 - 731, http://dx.doi.org/10.1101/gr.201517.115
2016
Hoppe R; Achinger-Kawecka J; Winter S; Fritz P; Lo WY; Schroth W; Brauch H, 2013, 'Increased expression of miR-126 and miR-10a predict prolonged relapse-free time of primary oestrogen receptor-positive breast cancer following tamoxifen treatment', European Journal of Cancer, 49, pp. 3598 - 3608, http://dx.doi.org/10.1016/j.ejca.2013.07.145
2013
Conference Abstracts
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Stirzaker C; Chia KM; Portman N; Milioli HH; Clifton S; Achinger-Kawecka J; Nair S; Lim E; Clark S, 2019, 'DNA demethylation agents as a therapeutic approach in endocrine-resistant breast cancer', in Oncolabs, presented at 7th PacRim Breast & Prostate Cancer Meeting, http://dx.doi.org/10.1530/oncolabs.1.P049
2019
Conference Papers
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Hoppe R; Achinger-Kawecka J; Winter S; Fritz P; Lo W-Y; Schroth W; Brauch H, 2013, 'Abstract 1938: Increased miR-126 and miR-375 expression in primary ER-positive breast cancer predict longer relapse-free time following treatment with tamoxifen.', in Cancer Research, American Association for Cancer Research (AACR), pp. 1938 - 1938, presented at Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC, http://dx.doi.org/10.1158/1538-7445.am2013-1938
2013

2022 - St Vincent’s Campus Rising Star Award

2022 - Franklin Women 2022 Teresa Anderson Award

2019 - Best Selected Speaker Prize, 2019 Post-Doc Symposium, Garvan Institute


2018 - CASS Foundation Travel Grant


2017 - The Ian Potter Foundation Travel Grant


2016 - Best Postdoc Prize, 24th St Vincent’s Campus Research Symposium


2016 - Heliflite Young Explorer Award


2015 - Best Oral Presentation Prize, 23rd St Vincent’s Campus Research Symposium


2011 – EU FP7 Marie Curie Initial Training Network “Fighting Drug Failure” Fellowship

 

 

Title of Project Role in Project Funding Organisation Start Date Duration Total Grant Amount

Assessing the role of the tumour ecosystem in epigenetic therapy response in ER+ endocrine-resistant breast cancer

 

CIA NHMRC Ideas 2024 3 years $1,090,079

Targeting epigenetic hallmarks in neuroendocrine-like prostate cancer

 

PI Prostate Cancer Foundation of Australia 2023 2 years $100,000

Targeting enhancers to overcome breast cancer resistance to CDK4/6 inhibition

 

PI UNSW Cancer Research EMCR Seed Grant 2023 1 year $50,000

3D EPIGENOME AS A TARGET FOR EPIGENETIC THERAPIES IN ENDOCRINE-RESISTANT BREAST CANCER

 

PI National Breast Cancer Foundation Investigator Grant (IIRS) 2021 3 years $366,000

Targeting the Three-Dimensional Epigenome in Endocrine Resistant Breast Cancer

 

CIA Cancer Council NSW Project Grant 2020 3 years $434,000

Decoding 3D genome architecture in individual single-cells to establish molecular mechanisms of gene regulation in cancer

 

PI UNSW Cellular Genomics Futures Institute Seed Grant 2020 1 year $99,000

Single-Cell Hi-C: A Novel Tool to Identify Key Epigenetic Drivers of Endocrine Resistant Breast Cancer

 

PI Estee Lauder Companies Breast Cancer Campaign 2019 1 year

$15,000

Genetic perturbations to the 3D genome architecture: Implications for endocrine resistance in breast cancer (Clark S, Achinger-Kawecka J)

Co-I National Breast Cancer Foundation 2017 1 year

$200,000

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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