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 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
    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 Scopus5 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 Scopus4 Europe PMC3
    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 Scopus6 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 Scopus23 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 Scopus30 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 Scopus15 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 Scopus94 Europe PMC80
    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 Scopus58 Europe PMC52
    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 Scopus33 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 Scopus222 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 Scopus68 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

NHMRC Ideas Grant (2024 - 2026): Assessing the role of the tumour ecosystem in epigenetic therapy response in endocrine resistant breast cancer. CIA: Joanna Achinger-Kawecka, CIB: Timothy J. Peters (Garvan Institute, Australia), CIC: Anthony Schmitt (Arima Genomics, USA)

National Computing Infrastructure (NCI) NCMAS Adapter Grant: Targeting 3D Epigenome in Metastatic Prostate Cancer PI: Joanna Achinger-Kawecka

Prostate Cancer Foundation of Australia (PCFA) Young Investigator Award (2024 - 2025): Targeting epigenetic hallmarks in neuroendocrine-like prostate cancer PI: Joanna Achinger-Kawecka, Co-I: Anthony Joshua (Garvan Institute), Co-I: Mitch Lawrence (Monash University)

UNSW Cancer Theme EMCR Seed Grant (2023 - 2024): Targeting enhancers to overcome breast cancer resistance to CDK4/6 inhibition. PI: Joanna Achinger-Kawecka

NBCF Investigator Initiated Research Scheme and NBCF Mavis Robertson Fellowship (2021 - 2024): 3D Epigenome as a Target for Epigenetic Therapies in Endocrine-Resistant Breast Cancer. PI: Joanna Achinger-Kawecka, Co-I: Elgene Lim (Garvan Institute), Co-I: Anthony Schmitt (Arima Genomics)

Cancer Council NSW Project Grant (2020 - 2023): Using Epigenetic Therapies to Overcome Endocrine Resistance in Breast Cancer. CIA: Joanna Achinger-Kawecka

UNSW Cellular Genomics Futures Institute Seed Grant (2020 - 2021): Decoding 3D genome architecture in individual single-cells to establish molecular mechanisms of gene regulation in cancer. PI: Joanna Achinger-Kawecka, Co-I: Hamid Rokny (UNSW), Co-I: Anthony Schmitt (Arima Genomics)

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