In our previous work, we were able to show that a repetitive RNA, the satellite RNA SATIII, induces resistance to the chemotherapeutic agent etoposide. We were able to show that the SATIII RNA recruits topoisomerase, the target of etoposide, to nuclear stress bodies and thereby leads to a redistribution of topoisomerase. Our working hypothesis is that this makes etoposide less efficient at attacking the enzyme, resulting in resistance to therapy (Hussong M. et al. 2017; Kanne J. et al. 2021). Since SATIII RNA plays an important role in the stress response, we believe that the sensitivity of other chemotherapeutic agents, such as platinum derivatives, is also regulated by SATIII. Furthermore, we find a strong deregulation of SATIII RNA in advanced tumors. To better understand the mechanisms of therapy resistance in lung cancer, we perform different functional experiments, e.g. cell cycle experiments, proliferation and apoptosis assays as well as immunofluorescence analysis of SATIII RNA foci, in the absence or presence of stress. SATIII RNA is encoded in the pericentromeric region of chromosome 9 in particular. This region is normally organized as heterochromatin. We were able to show that this region is demethylated under stress, resulting in transcriptional activation. The SATIII RNA is then synthesized and leads to the formation of nuclear stress bodies at the site of its expression. In a research focus of the institute, we are interested in the effects of hypomethylation of repetitive DNA on transcription and carcinogenesis. Together with the Summerer group (Prof. Dr. Daniel Summerer, Dortmund), we have developed site-specific TALEs ('transcription activator-like effectors') (Munoz-Lopez A. et al. 2020, Wolffgramm J. et al. 2021, Witte A. et al. 2020), which are linked to DNA methyltransferases. Using these epigenetic tools, we were able to show that an increase in DNA methylation leads to reduced SATIII transcription and ultimately to a restoration of therapy sensitivity (Kanne J. et al. 2021). To broaden our insight into the functions of SATIII, we are also investigating SATIII mechanisms in the context of head and neck squamous cell carcinoma (HNSCC), a work we are doing together with the Department of Otorhinolaryngology (Prof. Dr. Jens Klußmann) and the Poepsel lab (Dr. Simon Poepsel). In addition, we are pursuing our epigenetic drug screening functionally in order to understand the regulatory mechanisms at repetitive genomic sites. Since we have shown that SATIII is overexpressed in many tumors, and also causes etoposide therapy resistance, we are developing tools to disrupt SATIII expression. In particular, we are trying to reduce the expression of SATIII RNAs using nanocarriers that are chemically synthesized and optimized for our purposes. Here we are collaborating with the Department of Pathology (Prof. Dr. Reinhard Büttner, Prof. Dr. Margarete Odenthal) and the Institutes of Inorganic Chemistry, Organic Chemistry and Biochemistry (Prof. Dr. Sanjay Mathur, Prof. Dr. Stephanie Kath-Schorr, Prof. Dr. Ines Neundorf). With these approaches we hope to develop new strategies for the manipulation of repetitive DNA, which could be particularly useful in lung and head and neck tumors. We are convinced that in the long term these approaches will also be transferable to other cancers and diseases with pathological regulation of repetitive regions.

More information about the Nanocarriers project here: https://nanocarriers.uni-koeln.de/

Epigenetic processes play an important role in the development and (de)differentiation of tumor cells as well as in the drug resistance of tumors. This applies in particular to small cell lung tumors (SCLC), which exhibit mutations in histone lysine methyltransferases (HLMTs, such as KMT2D) and histone lysine acetyltransferases (HLATs, such as CREBBP/CBP, EP300) in up to 77 % of all SCLC patients. Physiological functions in the regulation of transcription, genome stability and chromatin compaction have been described for most of these epigenetic modifiers. In a mouse model, the loss of CREBBP (CREB binding protein) function can be at least partially compensated by histone deacetylase inhibitors. Proteins that modify or detect DNA methylation or the modification of histones are also involved in the regulation of stress-associated genes. However, it is largely unclear exactly how cancer mutations impair protein function, what consequences this has for the cells and how malignant transformation is achieved. To better understand the effects of the mutations on the epigenome, we are performing functional analyses of epigenetic modifiers (mainly KMT2D, CREBBP, EP300). If we know how the mutations affect the function of the protein, we can develop targeted treatments to specifically attack these subgroups of SCLC. The work is embedded in the SFB1399 (Mechanisms of Drug Sensitivity and Resistance in Small Cell Lung Cancer), in which we collaborate with numerous other groups to decipher epigenetic mechanisms in SCLC. There is a close collaboration with the laboratory of Prof. Dr. Stefan Knapp (Institute of Pharmaceutical Chemistry, Frankfurt) to identify epigenetic agents for the treatment of SCLC.

More information on the SCLC project here: https://www.sfb1399.de/about-us/collaborative-research-center-1399

In recent years, very effective therapies have been developed in the treatment of CLL. However, treatment resistance and disease progression are still inevitable and most patients die from their disease or from treatment-related complications. There are a number of genomic traits associated with unfavorable prognostic impact, such as del(17p), TP53mut, SF3B1mut, ATMmut, RPS15mut, NOTCH1mut, KRASmut and IGHV mutation status (Thomalla D. et al 2022). In addition, epigenetic prognostic biomarkers have been developed that interrogate the DNA methylation level of specific regions such as SATalpha regions and promoters of BCL2, MDR1, TCL1, hTERT and TWIST2, to name a few. Epigenetic signatures can even be used to subclassify IGHV-mutated patients with poor prognosis. Due to their large number and stable covalent DNA methylation binding, epigenetic markers are strong biomarker candidates for the subclassification of CLL patients (Grimm C. et al. 2022). In addition, several epigenetic therapies have already been approved by the FDA, e.g. DNMT inhibitors (decitabine) for myelodysplastic syndrome or pan-HDAC inhibitors (vorinostat) for cutaneous T-cell lymphoma. Many other substances are currently undergoing preclinical testing or are already included in clinical trials. Furthermore, epigenetic changes affect transcription and RNA splicing processes. Both are severely impaired in cancer, and several drugs targeting the splicing machinery have been shown to be effective in in vitro models. Our previous studies have shown that mutations in the splicing factor SF3B1 decreased intron retention rates in CLL and increased expression levels of perfectly spliced genes. We have also shown that the DNA methylomes of SF3B1mut and wt CLL patients differ, which is independent of the developmental stage of CLL (Pacholewska A. et al. 2021). For our investigations, we rely on state-of-the-art next-generation sequencing technologies already established in our laboratory and combine these with targeted functional studies of SF3B1 to gain an understanding of epigenetically driven splicing processes in refractory high-risk CLL. Again, we focus on the stress response and DNA repair and ask how this is modified by epigenetic and splicing changes.

The knowledge gained will also be examined for its usability as epigenetic biomarkers and tested in selected mouse models as new therapy options for advanced CLL. The projects are and have been supported by the DFG (KFO286, GOLONG sequencing projects), the Center for Molecular Medicine (CMMC) and the EU (CLL-CLUE) and are part of the new SFB1530 Lymphoma.

More information here:

    https://gepris.dfg.de/gepris/projekt/321184791?context=projekt&task=showDetail&id=321184791&
    https://cll-clue.eu/