Epigenetics in ALK driven cancers

Medical University Vienna

Dr. Gerda Egger


Publication Link ORCID Link

Epigenetics of ALK dependent cancers

Research Interest

Gerda Egger is lecturer on epigenetics and tumour biology since 2009. She directs a research group studying the impact of epigenetics in different diseases including cancer. Using mouse models we are trying to understand how epigenetic aberrations are generated and how they can be reversed and remodelled. We are using genome-scale analyses to define targets of differential DNA methylation in patient samples to define epigenetic biomarkers and to discover epigenetic drivers of different pathologies.

Karthik Natarajan

Research student


Research Interest

(Karthik)raj Natarajan is a PhD candidate working under the supervision of Dr. Gerda Egger at the Medical University of Vienna, Austria. His research interests are epigenetics and chromatin biology. His project focuses on Epigenetics of ALK (Anaplastic Lymphoma Kinase) dependent cancers. The study emphasizes on epigenetic alterations— such as DNA methylation, histone modifications and non-coding RNAs— in ALK driven cancer. Prior to beginning his PhD, he worked as Researcher at Beijing Genomics Institute, China for 2.5 years, where he acquired experience in cancer epigenomics, single cell analysis, transcriptomics and product development of NGS technologies. Karthik received his Master’s in Molecular Biotechnology from Uppsala University, Sweden and Bachelor’s in Biotechnology from SASTRA University, India. His academic and industrial experiences sparked his interest to specialize in cancer epigenetics. In the future, he will consider exploring epigenetic-based therapies to knock out tumors ‘effectively’. For further information, please refer to his LinkedIn profile here.

Research description

Changes in DNA methylation and miRNA expression are associated with a variety of cancers, are causally involved in tumorgenesis and provide options for sensitive biomarker development.We hypothesize that NSCLC that harbour an EML4-ALK translocation have characteristic epigenetic signatures. Using transgenic mouse models and primary tumour samples from patients with EML4-ALK positive NSCLC we aim to:

Define genome-wide DNA methylation and miRNA signatures of ALK dependent lung cancer; determine the biological and clinical relevance of these alterations using functional genetics and analysis of primary patient samples; investigate the biological role of the maintenance methyltransferase Dnmt1 in a mouse model of ALK dependent lung cancer for tumour development and progression using Cre mediated deletion of Dnmt1.

Expected Results:
To identify novel disease mechanisms and targets, which depend on epigenetic regulation in ALK dependent tumours; to identify novel epigenetic biomarkers based on DNA methylation and miRNA signatures in EML-ALK NSCLC; to provide a rationale for epigenetic therapy of EML4-ALK positive NSCLC; to establish the biolgical role of DNMT1 for ALK driven lung cancer 

Planned secondment(s):
Year 1: MU, Brno (B#4) – miRNA screen and analysis – 2 months;
Year 2: Varionostics GmbH (PO#6) – validation of epigenetic markers as potential biomarkers in ALK-related malignancies – 2 months.

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