Joanna Achinger-Kawecka

Dr Joanna Achinger-Kawecka

Head, 3D Chromatin Organisation Laboratory

South Australian Immunogenomics Cancer Institute

Faculty of Health and Medical Sciences

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

Dr Joanna Achinger-Kawecka is a Group Leader at SAiGENCI, University of Adelaide, and an emerging leader in cancer epigenomics and 3D genome biology.

She completed her PhD at the University of Tübingen, Germany, supported by the prestigious Marie Curie Fellowship, and undertook postdoctoral training at the Garvan Institute of Medical Research, where she later established her research group. Her pioneering lead-author work has been published in high-impact journals, including Nature Communications, Nature Structural & Molecular Biology and Genome Research. She was subsequently awarded NBCF Mavis Robertson Fellowship and PCFA Young Investigator Award and was appointed as a Group Leader at the Garvan Institute.

Joanna has secured over $4 million in competitive funding as a chief investigator (>$3.3M as a CIA, including NHMRC Ideas) and has led multiple successful research programs in collaboration with clinician-researchers, resulting in novel pre-clinical discoveries. In partnership with Arima Genomics (USA), she co-developed a high-resolution Capture Hi-C method, now commercialised and widely adopted by the genomics research community. She is an internationally recognized emerging leader in the field, as evidenced by invitations to present at leading international (EACR 2025, EMBO 2022, Gordon Conference 2018) and national (Lorne Cancer 2025, ACBCC 2025, BMH 2024, ComBio 2022, Lorne Genome 2022, Oz Single Cell 2021) conferences

At SAiGENCI, she leads the 3D Chromatin Organisation Laboratory, integrating multi-omics, preclinical functional genomics, and translational research to investigate how genome folding and transposable elements drive gene deregulation and therapy resistance, with the goal of informing new therapeutic strategies in rare and hard-to-treat cancers.

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.

Current Research Projects:

  1. Exploring the contribution of transposable elements to gene deregulation in cancer

Transposable elements (TEs), known as “jumping genes”, are mobile DNA elements that have expanded within the genome throughout evolution and constitute over 50% of the human genome. 

Epigenetic dysregulations are hallmarks of cancer and that provides a particularly fertile ground for TE activation.  TEs reactivated in cancer can serve as regulatory elements, including promoters and enhancers, triggering oncogenic transcriptional response.  In contrast, induction of TEs through genome-wide epigenetic changes in cancer cells could also potentially trigger anti-tumour immune responses leading to the destruction of cancer cells via “viral mimicry".  

The primary objective of this research is to comprehensively delineate the molecular and cellular functions of TEs in the regulatory cancer genome and characterise the epigenetic mechanisms that define their diverse activities. The key aims are to:

  •  Identify and characterize regulatory TEs across all cancer sub-types in TCGA and determine their transcriptional effects
  •  Explore how these regulatory TEs contribute to cancer cellular phenotypes using models of TE activation in cancer
  •  Identify chromatin variants and transcription factors involved in TE regulation and assess their potential for targeting in cancer. 


  1. Targeting transposable elements in CDK4/6i resistant breast cancer

Inhibitors of cyclin-dependant kinases 4 and 6 (CDK4/6i) are now standard of care treatment of metastatic estrogen receptor-positive (ER+) breast cancer. It is expected that all patients with advanced ER+ breast cancer will receive CDK4/6i. However, eventual treatment failure is unfortunately inevitable. No clear second-line treatment strategy exists following the development of CDK4/6i resistance. The widespread emergence of resistance to CDK4/6i is therefore poised to become the major challenge for the management of metastatic ER+ breast cancer. 

The TP53 tumour suppressor gene, known as the “guardian of the genome”, is the most frequently altered gene in cancer. It encodes for a transcription factor p53 that triggers a transcriptional program to control cellular stress response. The control of TEs is an important component of p53's function as the guardian of the genome and p53 reactivation is a promising anticancer strategy.  

Using in vitro and in vivo pre-clinical models we are uncovering the molecular mechanisms of CDK4/6i resistance and testing if therapeutic targeting of TEs via p53 activation can restore sensitivity and prolong response to CDK4/6 inhibitors in our established cell line and PDX models. 


  1. Elucidating the role of 3D genome structure in lineage plasticity in cancer

Cell lineage plasticity is recognized as a novel mechanism of tumor progression and treatment resistance in cancer. It is mainly driven by dynamic transcriptional and epigenetic changes, however the role of 3D genome structure alterations in driving lineage plasticity is not yet fully understood. Understanding the key 3D genome structure, epigenetic and transcriptional regulators of cancer cell plasticity can yield new avenues for therapy.


  1. Development and optimzation of new Hi-C technologies 

Cellular heterogeneity is a major problem in cancer therapy, as treatment-resistant cells can promote relapse. The advent of single-cell genomics techniques allows the determination of epigenetic and transcriptional profiles of these treatment-resistant populations. By developing new methods to study and integrate the 3D genome, epigenetic and transcriptomics datasets from single-cells, we aim to further understand the molecular mechanisms of treatment resistance and identify new avenues for therapy to target the entire tumour population, or in combination with existing therapies.

  • Appointments
    Date Position Institution name
    2025 - ongoing Head, 3D Chromatin Organisation Laboratory South Australian ImmunoGENomics Cancer Institute
    2025 - ongoing NBCF Fellow University of Adelaide
    2023 - 2024 PCFA Young Investigator Garvan Institute of Medical Research
    2021 - 2024 Head, 3D Epigenome in Cancer Group Garvan Institute of Medical Research
    2021 - 2024 NBCF Fellow Garvan Institute of Medical Research
    2014 - 2021 Senior Research Officer Garvan Institute of Medical Research
    2011 - 2014 Marie Curie ECR Fellow Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology

  • Awards and Achievements
    Date Type Title Institution Name Country Amount
    2025 Fellowship NBCF Elaine Henry Fellowship National Breast Cancer Foundation Australia -
    2023 Fellowship PCFA Young Investigator Award Prostate Cancer Foundation of Australia Australia -
    2023 Award EMBO Travel Award EMBO Germany -
    2022 Award Franklin Women 2022 Teresa Anderson Award Franklin Women Australia -
    2022 Award St Vincent’s Campus Rising Star Award Garvan Institute of Medical Research Australia -
    2021 Fellowship NBCF Mavis Robertson Fellowship National Breast Cancer Foundation Australia -
    2019 Research Award Estee Lauder Breast Cancer Research Award Garvan Institute of Medical Research Australia -
    2019 Award EMBO Travel Award EMBO Germany -
    2019 Award CASS Foundation Award CASS Foundation Australia -
    2018 Award Ian Potter Foundation Travel Award Ian Potter Foundation Australia -
    2017 Award Young Garvan Award (finalist) Garvan Institute of Medical Research Australia -
    2016 Award Heliflite Young Explorer Award Garvan Institute of Medical Research Australia -

  • Education
    Date Institution name Country Title
    2011 - 2014 University of Tubingen Germany PhD
    2005 - 2011 Warsaw University of Life Sciences Poland MSc

  • Research Interests
    Epigenetics Epigenetics (incl. genome methylation and epigenomics) Gene expression (incl. microarray and other genome-wide approaches) Cancer Cell Biology Gene and Molecular Therapy Biochemistry & Molecular Biology

  • 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 Scopus9 Europe PMC9
    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), 251-1-251-23.
    DOI Scopus7 Europe PMC6
    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 Europe PMC1
    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), eabp8314-1-eabp8314-23.
    DOI Scopus8 Europe PMC4
    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 Scopus28 Europe PMC21
    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 Scopus35 Europe PMC37
    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 Scopus18 Europe PMC15
    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 Scopus100 Europe PMC92
    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 Scopus61 Europe PMC62
    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 Scopus19 Europe PMC20
    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 Scopus15 Europe PMC10
    2017 Achinger-Kawecka, J., & Clark, S. J. (2017). Disruption of the 3D cancer genome blueprint. Epigenomics, 9(1), 47-55.
    DOI Scopus36 Europe PMC30
    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 Scopus25 Europe PMC21
    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 Scopus227 Europe PMC211
    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 Scopus71 Europe PMC62
    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

  • Preprint
    Year Citation
    2024 Campbell, E. M., Laven-Law, G., Smith, G., Peters, T. J., Colino-Sanguino, Y., Moulder, D., . . . Achinger-Kawecka, J. (2024). Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer.
    DOI
    2020 Giles, K. A., Gould, C. M., Achinger-Kawecka, J., Page, S. G., Kafer, G., Luu, P. -L., . . . Taberlay, P. C. (2020). BRG1 promotes transcriptional patterns that are permissive to proliferation in cancer cells.
    DOI
    2020 Du, Q., Smith, G. C., Luu, P. L., Ferguson, J. M., Armstrong, N. J., Caldon, C. E., . . . Clark, S. J. (2020). DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity.
    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 - 2026 Cancer Council NSW (CID, $450k): Resolving Prostate Cancer: Elucidating the epigenetics of tumour microenvironment cells to advance understanding of disease aetiology and improve patient diagnosis.

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.

2017 - 2018 National Breast Cancer Foundation (NBCF) Innovator Grant (Co-I, $192k): Genetic perturbations to the 3D genome architecture: Implications for endocrine resistance in breast cancer.

Teaching, Mentoring and Supervision:

Postdoctoral Fellows (Present):

Dr Daniel Thomson

Dr Fiona Zhou

Dr Dayna Challis

Geraldine Laven Law (Research Manager)

 

Postdoctoral Fellows (Past):

Dr Qian Du (Now postdoc at University of Copenhagen)

Dr Kate Giles (Now postdoc at CMRI, Sydney)

 

Teaching:

2022 - 2024 Co-ordinator of TKCC Cancer Seminars, Garvan Institute

2022 - Guest Lecturer, School of Biotechnology and Biomolecular Sciences, UNSW

2022 - Guest Lecturer, St George and Sutherland Clinical School Research in Progress Meetings, University of Sydney

2019 - Guest Lecturer, Brain Sciences UNSW Colloquia: “Genetic and Epigenetic Contributions”, Black Dog Institute

  • Other Supervision Activities
    Date Role Research Topic Location Program Supervision Type Student Load Student Name
    2023 - ongoing Principal Supervisor Targeting epigenetic hallmarks in advanced prostate cancer UNSW Sydney Doctor of Philosophy Doctorate Full Time Anthony Rodrigues
    2022 - ongoing Principal Supervisor Targeting the 3D epigenome to overcome treatment resistance in cancer UNSW Sydney Doctor of Philosophy Doctorate Full Time Elyssa Campbell
    2021 - ongoing Co-Supervisor Chromatin architecture and epigenomic regulation of cardiomyocyte regeneration UNSW Sydney Doctor of Philosophy Doctorate Full Time Gabrielle Smith
    2015 - 2019 Co-Supervisor BRG1 ATP-Dependent Chromatin Remodelling in Prostate Cancer: Epigenetic Consequences UNSW Sydney Doctor of Philosophy Doctorate Full Time Kate Giles

  • Committee Memberships
    Date Role Committee Institution Country
    2025 - ongoing Co-Chair High Performance Computing Committee SAiGENCI Australia
    2025 - ongoing Member Australian Bioinformatics and Computational Biology Society ABACBS Australia
    2024 - ongoing Member Chair and Programme Co-organizer, Biomolecular Horizons 2024 ComBio Australia
    2024 - 2024 Member UNSW Cancer Theme Strategic Advisory Committee UNSW Australia
    2024 - ongoing Member Australian Academy of Science, Science at the Shine Dome EMCR Committee Australian Academy of Science Australia
    2021 - 2024 Member Higher Research Degree Committee Garvan Institute of Medical Research Australia
    2020 - 2023 Member Garvan Engagement Committee Garvan Institute of Medical Research Australia
    2017 - 2018 Co-Chair ASMR NSW Annual Scientific Meeting Committee ASMR Australia
    2015 - 2016 Co-Chair Garvan Postdoctoral Developmental Committee Garvan Institute of Medical Research Australia

  • Memberships
    Date Role Membership Country
    2024 - ongoing Member Australian Bioinformatics and Computational Biology Society Australia
    2014 - ongoing Member Australian Society for Medical Research Australia
    2014 - ongoing Member Australasian Epigenetics Alliance Australia
    2011 - ongoing Member American Association for Cancer Research United States

  • Community Engagement
    Date Title Engagement Type Institution Country
    2024 - ongoing Researcher Showcase (video) Public Community Engagement Cancer Council NSW and Box Rallies -
    2024 - 2024 New hope for breast cancer patients Public Community Engagement The Australian (newspaper) -
    2023 - 2023 Interview, NBCF 30th Anniversary Public Community Engagement National Breast Cancer Foundation -
    2020 - ongoing Researcher Showcase Discussion Panel (Public Event) Public Community Engagement Garvan Institute of Medical Research -

  • Review, Assessment, Editorial and Advice
    Date Title Type Institution Country
    2025 - ongoing DFG - Deutsche Forschungsgemeinschaft Grant Assessment DFG Germany
    2025 - ongoing Worldwide Cancer Research Foundation Peer Review Worldwide Cancer Research Foundation -
    2024 - ongoing Fondation pour la Recherche Médicale (France) Grant Assessment Fondation pour la Recherche Médicale (France) France
    2024 - ongoing Neurological Foundation of New Zealand Grant Assessment Neurological Foundation of New Zealand New Zealand
    2024 - ongoing Diabetes Australia Grant Assessment Diabetes Australia Australia
    2023 - ongoing Garvan-Estée Lauder Award Grant Assessment Garvan Institute of Medical Research -
    2023 - ongoing Young TAD Award Peer Review Genome Organisation Australia -
    2023 - ongoing Harry Perkins Institute of Medical Research Grant Assessment Harry Perkins Institute of Medical Research Australia
    2021 - ongoing NHMRC Ideas Grants Peer Review NHMRC -
    2020 - ongoing European Research Council MSCA Horizon Grant Assessment European Research Council -
    2020 - ongoing NCN Poland Grant Assessment NCN Poland Poland
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