Katarina Mišura

Epigenetics of ALCL Drug Resistance

Medizinische Universität Wien

Supervisor: Gerda EGGER

Research objectives:

Our lab has previously identified DNA methylation signatures of primary human ALCL that reflect biological tumour characteristics and provide some insight into the potential origin of ALCL. We could further demonstrate that inhibition of DNA methylation via genetic or pharmacological means resulted in loss of transformation of T cells and reduced tumour growth in mouse models. Thus, we hypothesize that epigenetic mechanisms might also be implicated in drug response/resistance in ALCL and that epigenetic therapies might be suitable for combination drug treatment of patients.

Within this project, we aim to develop more suitable models for drug testing of ALCL based on innovative 3D organoid models and to investigate the epigenetic mechanisms related to drug resistance:

  1. Generate lymphoid organoids from patient samples (primary/therapy refractory). Currently, only a few cell lines established from human ALCL patient samples are available, which only partially reflect in vivo tumours. Thus, we will generate organoid models from primary patient material(ascites, blood, tumour samples) together with clinical partners in the consortium and patient-derived xenograft models (PDX) that have been established by B#1 and 3. To establish the model and to test for its feasibility, we will also include tumours from the NPM-ALK transgenic mouse model;
  2. Perform phenotypic and molecular characterization (scRNA-seq, RNA-seq, WES, epigenomic profiling). Organoid models will be characterized in comparison to the original tumours for their morphology using histological analyses and for their (epi)genetic signatures using WES and DNA methylation profiling;
  3. Perform drug testing and induce therapy resistance by long-term treatment. By using chemotherapy and ALK-specific targeted therapy (e.g., Crizotinib) we will compare in vitro drug response to drug response in the patient. Further, we will induce therapy resistance in those models using long-term treatment with sub-lethal drug doses;
  4. Investigate the mechanisms of drug resistance based on (epi)genomic alterations. Organoid lines resistant to chemotherapy or ALK inhibitor treatment, will be analysed for their (epi)genetic adaptations and gene expression signatures using WES, DNA methylation profiling and RNA-Seq;

Resensitize resistant lines with epigenetic drugs. We will use epigenetic drugs including inhibitors of DNA methylation, chromatin modification (e.g., HDAC) or chromatin reader proteins (e.g., BRD4) on sensitive and resistant lines and test for their efficacy in combinatorial treatments with approved drugs.

Expected results:

Our work will provide novel models to study ALCL biology and will be made available for the whole consortium. Using these models, we expect to get a deeper insight into drug response/resistance mechanisms and to explore additional (epi)genetic vulnerabilities of ALCL.

Planned secondments:

Year 1: THT Biomaterials GmbH: Development of organoids together with the experts at the company who have significant experience of this technology (3  months)

Year 2: Masters Chancellors and Scholars of the university of Cambridge: Creation of organoids from PDX which are uniquely available in the host lab, also facilitating training in organoid development in the host lab to local students (2 months)