Genomic and other molecular analyses in different cancer types have revealed a striking diversity of genomic aberrations, altered signaling pathways and oncogenic processes. We hypothesize that this diversity arises from endogenous factors, including developmental programs and epigenetic states of the originating cells, in conjunction with exogenous factors. A precise definition of the cell-of-origin and differentiation/developmental states during key events is of utmost importance. The aim of this research focus is to identify resurrected developmental programs in individual tumor cells by comparison to normal human embryonic/fetal cells.

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A key question is how driver mutations subvert the normal development of the tissue of origin. Preliminary analyses indicate that neuroblastomas across the entire clinical spectrum begin to develop via aberrant mitoses in early sympathetic neurogenesis probably already during pregnancy. However, when neuroblastomas exactly originate in development and how high-risk and low-risk cases evolve genetically is not known. By using bulk whole genome sequencing (WGS) data, we exploited the frequent copy number gains in neuroblastomas, together with characterization of somatic single-nucleotide variants (SSNVs) at high (>80x) coverage, to infer the evolutionary dynamics of neuroblastomas across the clinical spectrum of this cancer. We have defined when driver events occurred during neuroblastoma evolution, using neutral SSNVs as a molecular clock. We further used the mutation rate in normal neuroendocrine progenitors to calibrate the SSNV molecular clock against real time to define at which time during pregnancy the first transforming event (e.g., the initial mitotic failure resulting in aneuploid tumor cells) is placed.

 

 

 

 

 

The pathogenic role of many cancer-related point mutations, gene fusions, copy number aberrations and deregulated epigenetic marks affecting protein-coding sequences and promoters can be explained by their effects on gene function or gene dosage. In contrast, it is difficult to predict the functional consequence of (epi-)genetic changes affecting enhancers, which are cis-regulatory elements that may control the activity of a single or multiple gene(s) from a distance of up to 1 Mb. Alterations in non-coding regions can stably induce complex pathogenic alterations of gene expression by changing the activity of enhancers. However, the lack of a comprehensive understanding of the large-scale functional organization of the regulatory enhancer landscape is a major limitation in linking enhancer (epi-)mutations to cancer and exploiting them as drug targets.

We are currently testing in various projects the hypothesis that (structural) DNA mutations in concert with epigenetic alterations in non-coding loci deregulate enhancer function and - superimposed on a background of protein-coding mutations – are drivers of tumorigenesis. To this end, we are functionally dissecting prototypic mechanisms of enhancer deregulation that we have recently described for neuroblastoma and derive a conceptual framework for understanding how the corresponding (epi-)mutations in non-coding regulatory regions contribute to tumorigenesis.

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Cancer cells need to extend their telomere repeats for unlimited proliferation as critically short telomeres can induce senescence or cell death. The enzyme telomerase (TERT) is an oncogenic driver that prevents telomere attrition by synthesis of telomeric DNA in ~90% of cancers. The remaining ~10% fraction use the less-characterized alternative lengthening of telomeres (ALT) pathway. It is based on aberrant DNA repair and recombination and has been studied in our group. Notably, ALT is active in tumors like neuroblastoma, leiomyosarcoma, pancreatic neuroendocrine tumors and pediatric glioblastoma. In neuroblastoma, ALT is associated with a poor outcome and is enriched in relapsed disease. However, the current risk stratification schemes underestimate the poor prognosis of ALT cases in about 30% of ALT-positive neuroblastoma, as ALT activity is currently not evaluated in clinical diagnostics. Furthermore, drug treatments that specifically target ALT are not available, and ALT-positive neuroblastoma are not optimally treated using the standard of care chemotherapies highlighting the large clinical need for ALT-specific therapy concepts.

 

 

 

 

 

Furthermore, we contribute to the recently successfully implemented DFG SPP – 2306/1 on “Ferroptosis: From Molecular Basics to Clinical Applications”. Ferroptosis is a cellular vulnerability that is elicited when regulatory systems fail to block the chemical interaction between oxygen, iron, and polyunsaturated fatty acids leading to the accumulation of lethal levels of lipid hydroperoxides. It is thought to contribute to various pathological cell death scenarios, including (neuro-)degenerative diseases, brain injury, ischemia-reperfusion injury, and likely has a tumor-suppressor function in cancer. Despite its importance for various diseases, a comprehensive, systems-oriented, and disease-overarching exploration of this novel regulated cell death type is currently not available, which has yet obstructed a systems-level understanding and prohibited a targeted modulation of this vulnerability as a therapeutic option. Our task within the DFG SPP is to develop quantitative network models that allow to defining ferroptosis sensitivity/resistance states of cells and tissues. We will use these models to (i) functionally explore vulnerable nodes of the ferroptosis-regulating molecular network, and (ii) analyse the crosstalk between the key regulatory pathways controlling the metabolism of iron, oxygen, amino acids and unsaturated lipids.

 

 

 

 

In a DKFZ-Bayer collaborative project, we have focused on developing drug molecules that target proteins essential for the survival of MYC-driven cancer cells. Based on a MYCN synthetic lethal screen in neuroblastoma cells, we have identified the inhibition of CDK12/13/CCNK as a synthetic lethal interaction with high MYC(N) states. Based on a drug screen conducted at Bayer, we have isolated lead compounds that specifically target the CDK12/13/CCNK complex. Further analysis revealed that we have identified a novel class of proteolysis targeting molecular glue degraders. Molecular glue degraders, similar to PROTACs, achieve degradation through "hijacking" the cell's ubiquitin–proteasome system.

More specifically, PROTACs are heterobifunctional molecules that form a ternary complex with the target protein and an E3-ligase by making two distinct small molecule-protein interactions, whereas molecular glue degraders function by converting the target protein into a “neo-substrate” for an E3 ligase. Because molecular glue degraders/PROTACs need only to bind their targets with high selectivity (rather than inhibit the target protein's enzymatic activity), there are currently many efforts to retool previously ineffective inhibitor molecules as molecular glue degraders/PROTACs for next-generation drugs. We will further explore the clinical potential of our patented CDK12/13/CCNK inhibitory compounds that have favorable pharmacodynamic and -kinetic properties. In addition, we will further use the molecular glue degrader/PROTAC approach to target other previously undruggable targets such as MYC oncoproteins.