Our Aims

Cancer is an extremely heterogeneous disease that is characterized by the accumulation of mutations, altered expression of coding and non-coding genes but also genomic instability. Our group aims to provide new insights of tumor-formation and genomic instability by:

• Developing patient derived 3D cell models, so-called “tumor-organoids” to provide tools for precision cancer medicine
• Unravel the role of RNA:DNA hybrids causing instability of telomeres and the genome during cancer formation an progression
• Understand the role of miRNAs in controlling telomere function in cancer cells

CURRENT PROJECT

1. Generation of cell models for precision cancer medicine

Project website

PRECANMED movie into website in Italian

PRECANMED movie into website in German

Project description (English and German)

Website

The PI of the research group is coordinating the interregional PreCanMed project, a strategic project funded by the European Union, the European Regional Development Fund and the Interreg V-A Italia-Austria Program 2014-2020. The goal of the project is to carry out the interregional implementation of patient derived tumor organoid technology. This powerful and novel tool allows the investigation of normal and diseased cancer tissues for the personalized development of treatments for patients (Fig. 1). Patient derived tumor organoid technology consists of functional, 3D, ex vivo, culture systems of tumor cells from patients. Defined as effective patient avatars, these systems have emerged as one of the latest frontiers in disease modelling and they represent a very promising experimental tool to reproduce and study a tumor in the laboratory, in a nearly physiological state (Fig. 2).

Inside the PreCanMed project, the research group will develop lung cancer organoid technology

PreCanMed is expected:

• to accelerate the pace of our understanding of multiple facets of the disease,
• to unleash new cancer breakthroughs, and
• to help realize the full potential and promise of personalized medicine.

In 2019, the research group received a follow-up research grant from the Interreg V-A Italia-Austria Program 2014-2020. With the new research program entitled “P-CARE”, the Schoeftner group will address mechanisms of therapy to cancer resistance and reconstruct the tumor-microenvironment of patient tumors by co-cultivating tumor-organoids with patient derived autologous cells.

Fig. 1 - Precision cancer medicine using tumor-organoids. Cancer tissue derived cells will be grown to tumor-organoids. Genome analysis of tumor-organoids will provide cues to predict and test patient specific therapeutic strategies.

Fig. 2 - Tumor organoids generated in the laboratory show the same marker gene expression as the donor tissue.

2) Impact of RNA:DNA hybrids on telomere and genome stability in cancer cells

Human cancer cells are characterized by an accumulation of mutations and an instable genome. In our second line of research we focus on genome instability induced by persistent hybrids between RNA and DNA that block the passage of DNA polymerases and other enzymes (Fig. 3). This can lead to breaks in the DNA that leads to genomic instability. Telomeres are localized at chromosome ends, consist of TTAGGG repeats and are essential for the protection of chromosome ends.

The activation of processes that maintain telomere function are essential for the viability of cancer cells. Transcription of telomeres result telomeric UUAGGG repeat containing non-coding RNAs (TERRA) that frequently result RNA:DNA hybrid formation (Fig. 4). We successfully identified proteins that interact with TERRA and localize to telomeres but also at other positions in the genome. The lack of these proteins result in increased RNA:DNA hybrids at telomeres, DNA breaks and increased homologous recombination that ensures telomere length maintenance in telomerase in negative cancer cells. Funded by an AIRC – Investigator grant (2020-2025) we currently investigate the molecular mechanism of RNA:DNA hybrid depended genomic instability at the telomeres but also at the entire genome level. Results from epigenome and biochemical analysis will help to understand the clinical relevance of proteins regulating RNA:DNA hybrids in telomerase negative osteosarcoma.

Fig. 3 - A model showing the consequences of increased RNA:DNA hybrid load at telomeres

Fig. 4 - RNA-FISH to detect TERRA in interphase cells. A fluorescently labeled (CCCTAA)6 probe was used to visualize UUAGGG repeat containing TERRA at telomeres (red). Genomic DNA is shown in blue.

3) Regulation of telomere function by “telo-miRNAs” in human cancer

A screen has identified a panel of miRNAs that efficiently target central components of the telomere regulating protein complex “shelterin” and the telomerase complex. Altering endogenous “telo-miRNA” expression critically impacts on telomere function, telomere length, drives genomic instability and is linked to poor prognosis in human breast cancer (Dinami et al 2014). This identifies “telo-miRNAs” as new level of telomere regulation with clinical relevance in human cancer. Currently, we integrate multiple telo-miRNAs into central pathways that drive human cancer. This will highlight a role for miRNAs in linking telomere function to central events in cancer formation and progression.
In parallel we are studying a subset of telo-miRNAs in the context of telomere related senescence and aging.

Fig.5 - Schematic representation of the high-throughput luciferase reporter screen. miRNAs with predicted targeting specificity for the indicated 3’UTRs were functionally validated in high-throughput luciferase reporter assay. The impact of positive candidate telo-miRNAs on telomere function will be tested in the context of cancer and aging (screen in collaboration with  M. Giacca ICGEB, Trieste and R. Agami, NKI, Amsterdam).