Joanna Achinger-Kawecka

Joanna Achinger-Kawecka

South Australian Immunogenomics Cancer Institute

Faculty of Health and Medical Sciences

Eligible to supervise Masters and PhD - email supervisor to discuss availability.

The 3D Chromatin Organisation Lab (PI Dr Joanna Achinger) is an experimental biology and bioinformatics laboratory studying the principles of 3D genome folding in cancer. The 3D genome architecture brings together genes and distant regulatory elements to orchestrate gene transcription, and has been implicated in many diseases, including cancer.

Our research focuses on understanding the role of 3D chromatin alterations in driving cancer development, progression and treatment resistance. We use cutting-edge methods (multi-omics, single-cell, genome editing as well as various pre-clinical model systems) to study the interplay of the 3D chromatin, epigenome and transcriptome in cancer.

We use hormone-dependent cancers as a model system for experimental design aimed at increasing our understanding of the cancer biology and to accelerate the development of new therapies.

  • Journals
    Year Citation
    2024 Achinger-Kawecka, J., Stirzaker, C., Portman, N., Campbell, E., Chia, K. -M., Du, Q., . . . Clark, S. J. (2024). The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer. Nature Structural and Molecular Biology, 31(3), 498-512.
    DOI Scopus6 Europe PMC4
    2024 Peters, T. J., Meyer, B., Ryan, L., Achinger-Kawecka, J., Song, J., Campbell, E. M., . . . Pidsley, R. (2024). Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics, 25(1), 251.
    DOI Scopus6 Europe PMC3
    2024 Chen, W., Zeng, Y. C., Achinger-Kawecka, J., Campbell, E., Jones, A. K., Stewart, A. G., . . . Clark, S. J. (2024). Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.. Nucleic acids research, 52(14), 8086-8099.
    DOI
    2023 Achinger-Kawecka, J., Correa, S., Hu, J., Li, G., Lindeboom, R. G. H., Misale, S., . . . Watson, C. J. (2023). The 2023 generation. Nature Cancer, 4(12), 1630-1635.
    DOI
    2023 Hastings, J. F., Latham, S. L., Kamili, A., Wheatley, M. S., Han, J. Z. R., Wong-Erasmus, M., . . . Croucher, D. R. (2023). Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma.. Science Advances, 9(9), 23 pages.
    DOI Scopus8 Europe PMC3
    2022 Brown, L. J., Achinger-Kawecka, J., Portman, N., Clark, S., Stirzaker, C., & Lim, E. (2022). Epigenetic Therapies and Biomarkers in Breast Cancer. Cancers, 14(3), 20 pages.
    DOI Scopus25 Europe PMC14
    2021 Du, Q., Smith, G. C., Luu, P. L., Ferguson, J. M., Armstrong, N. J., Caldon, C. E., . . . Clark, S. J. (2021). DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity. Cell Reports, 36(12), 26 pages.
    DOI Scopus32 Europe PMC28
    2021 Giles, K. A., Gould, C. M., Achinger-Kawecka, J., Page, S. G., Kafer, G. R., Rogers, S., . . . Taberlay, P. C. (2021). BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clinical Epigenetics, 13(1), 18 pages.
    DOI Scopus17 Europe PMC12
    2021 Achinger-Kawecka, J., Stirzaker, C., Portman, N., Campbell, E., Chia, K. -M., Du, Q., . . . Clark, S. J. (2021). Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer.
    DOI
    2020 Achinger-Kawecka, J., Valdes-Mora, F., Luu, P. L., Giles, K. A., Caldon, C. E., Qu, W., . . . Clark, S. J. (2020). Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Nature Communications, 11(1), 17 pages.
    DOI Scopus97 Europe PMC82
    2020 Khoury, A., Achinger-Kawecka, J., Bert, S. A., Smith, G. C., French, H. J., Luu, P. L., . . . Clark, S. J. (2020). Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. Nature Communications, 11(1), 13 pages.
    DOI Scopus60 Europe PMC55
    2019 Giles, K. A., Gould, C. M., Du, Q., Skvortsova, K., Song, J. Z., Maddugoda, M. P., . . . Taberlay, P. C. (2019). Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups. Epigenetics and Chromatin, 12(1), 19 pages.
    DOI Scopus18 Europe PMC16
    2018 Fuksiewicz, M., Kotowicz, B., Rutkowski, A., Achinger-Kawecka, J., Wagrodzki, M., & Kowalska, M. M. (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, 8 pages.
    DOI Scopus14 Europe PMC9
    2017 Achinger-Kawecka, J., & Clark, S. J. (2017). Disruption of the 3D cancer genome blueprint. Epigenomics, 9(1), 47-55.
    DOI Scopus35 Europe PMC24
    2016 Achinger-Kawecka, J., Taberlay, P. C., & Clark, S. J. (2016). Alterations in three-dimensional organization of the cancer genome and epigenome. Cold Spring Harbor Symposia on Quantitative Biology, 81(1), 41-51.
    DOI Scopus24 Europe PMC19
    2016 Taberlay, P. C., Achinger-Kawecka, J., Lun, A. T. L., Buske, F. A., Sabir, K., Gould, C. M., . . . Clark, S. J. (2016). Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Research, 26(6), 719-731.
    DOI Scopus224 Europe PMC179
    2013 Hoppe, R., Achinger-Kawecka, J., Winter, S., Fritz, P., Lo, W. Y., 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(17), 3598-3608.
    DOI Scopus70 Europe PMC56
    2013 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.. Cancer Research, 73(8_Supplement), 1938.
    DOI
    - Stirzaker, C., Chia, K. M., Portman, N., Milioli, H. H., Clifton, S., Achinger-Kawecka, J., . . . Clark, S. J. (n.d.). DNA demethylation agents as a therapeutic approach in endocrine-resistant breast cancer. Oncology Abstracts.
    DOI

  • Conference Papers
    Year Citation
    2024 Tian, L., Jiao, X., Wang, C., Ertel, A., Soccio, R., Chen, E. R., . . . Pestell, R. G. (2024). PPAR gamma acetylation governs mammary adenocarcinoma tumor growth via acetylated residues that determine DNA sequence-specific binding. In CANCER RESEARCH Vol. 84 (pp. 2 pages). CA, San Diego: AMER ASSOC CANCER RESEARCH.
    DOI

2025 - 2026 National Computing Infrastructure (NCI) NCMAS Grant (PI): Establishing the regulatory role of transposable elements in cancer.

2024 - 2026 NHMRC Ideas Grant (CIA, $1.09M): Assessing the role of the tumour ecosystem in epigenetic therapy response in endocrine resistant breast cancer. 

2024 - 2025 Prostate Cancer Foundation of Australia (PCFA) Young Investigator Award (PI, $100K): Targeting epigenetic hallmarks in neuroendocrine-like prostate cancer.

2023 - 2024 UNSW Cancer Theme EMCR Seed Grant (PI, $50k): Targeting enhancers to overcome breast cancer resistance to CDK4/6 inhibition.

2021 - 2024 National Breast Cancer Foundation (NBCF) Investigator Initiated Research Scheme and NBCF Mavis Robertson Fellowship (PI, $366k): 3D Epigenome as a Target for Epigenetic Therapies in Endocrine-Resistant Breast Cancer.

2020 - 2023 Cancer Council NSW Project Grant (CIA, $450k): Using Epigenetic Therapies to Overcome Endocrine Resistance in Breast Cancer.

2020 - 2021 UNSW Cellular Genomics Futures Institute Seed Grant (PI, $100k): Decoding 3D genome architecture in individual single-cells to establish molecular mechanisms of gene regulation in cancer.

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