Cancer Research | Universitätsklinikum Freiburg

Division of Cancer Research

Department of Thoracic Surgery

Cancer Mutomics - Exploring the Dark Matter of the Cancer Genome

In the past decade, deep sequencing approaches have revolutionized cancer genome sequencing has identified millions of somatic mutations that a tumor has acquired, but which are not present in healthy cells of same individual. However, the functional relevance of the vast majority of these mutations is unknown. We investigate the impact of mutations in cancer with an emphasis on discovering novel types of relevant mutations which we collectively refer to as "non-canonical mutations". Beyond missense and nonsense mutations altering the protein sequence, we are convinced that many other alterations can significantly effect tumorigenesis (EMBO Mol Med 2019).

Nonstop extension mutations convert a stop codon into a sense codon and thereby extending a protein at its C-terminus - and had never been studied in cancer before. We systematically compiled nonstop mutations in human cancer and provide a comprehensive database (NonStopDB). For the tumor suppressor gene SMAD4, nonstop mutations in pancreatic and colon cancer abrogate protein expression by inducing proteasomal degradation via a novel degron of ten amino acids in the added extension (Nat Cell Biol 2020).

Synonymous mutations alter the gene and its mRNA sequence but not the protein due to the degeneracy of the genetic code. Traditionally, they have thus been viewed as "silent" mutations without a functional relavance. In a pan-cancer analysis, we have cataloged 659194 synonymous mutations in cancer at SynMICdb. Importantly, we identified relevant functions for synonymous in the strong oncogene KRAS affecting its expression and mRNA secondary structure (Nat Commun 2019).

In summary, our research thus uncovered that also so far neglected types of non-canonical mutations can have fundamental impact on cancer genes. The pioneering characterization of novel types of mutations in cancer will hence be the focus of our future research - with one main aim to dramatically increase the throughput, with which we can systematically characterize mutations in human tumor cells as endogenous model systems - to go from cancer genomics to mutomics.

More than 70% of the human Genome (blue) is transcribed into RNA forming the Transcriptome (red), while only less than 2% of the genome are needed to produce all proteins in a human cell constituting the Proteome (yellow).

RNA Biology

A particular emphasis of our research in our Heidelberg lab lies on the molecular biology of RNA, its ribonucleoprotein complexes and its function in cancer.

Recent insights into RNA biology induced a paradigm shift towards the recognition of RNAs as functionally important molecules - beyond serving as messengers for protein-encoding genes. A large fraction of the human genome is transcribed into RNA (more than 70%), while only 2% are protein-encoding. Non-protein-coding RNAs execute important functions in the cell. Very short non-coding RNAs, the microRNAs, play important roles in gene regulation. The tumor-suppressive or oncogenic role of many microRNAs and their frequent deregulation in tumors allow a first glimpse of the striking role that non-coding RNAs could play in cancer. Novel long non-coding RNAs (ncRNA, lncRNA, lincRNA) fulfill important functions in epigenetic regulation, chromatin remodeling or splicing. Taken together, the human cell contains many more RNAs than previously anticipated and many of them might just await their discovery as functionally important molecules in cancer.

Our research focuses on long non-coding RNAs (lncRNAs) and their role in cancer. Based on expression profiling using microarrays as well as deep RNA sequencing of the whole transcriptome, we elucidate the cellular and molecular functions of differentially regulated ncRNAs in cancer using innovative techniques like the CRISPR/Cas9 system (Nucleic Acids Res 2017), in vivo RNA Affinity Purification and our own customized siRNA and CRISPR libraries targeting specifically lung cancer-associated lncRNAs. Our RNAi & CRISPRi screens have uncovered numerous lncRNAs controlling several hallmarks of cancer including cancer cell viability, proliferation, migration and nucleotide metabolism (Nucleic Acids Res 2017, Hepatology 2018, Nat Commun 2020).

An emerging topic of particular importance are RNA-Protein complexes. We recently proposed the concept of RNA Dependence and the affiliated method as R-DeeP (Mol Cell 2019, Nat Protoc 2020).

Molecular Biology of Lung Cancer & Metastasis

Lung cancer is the leading cause of cancer-associated death world-wide. While its etiology based on smoking is well established, the molecular changes leading to this malignant disease are often not understood. This lack of molecular insight into tumorigenesis also frequently precludes the development of innovative and highly specific new drugs.

Metastasis - the development of new tumor nodules in distant organs - is the most frequent cause of death of all solid tumor entities. One of the distant sites most often affected by metastasis is the lung.

In our Division for Cancer Research in the Department of Thoracic Surgery, we hence investigate the mechanisms and networks, the regulation and function of the molecules involved in these essential processes to understand the processes and pathways leading to the development of lung cancer and metastasis to enable the future development of novel therapy approaches based on these mechanisms.

Division of RNA Biology & Cancer - German Cancer Research Center (DKFZ)

Our Division of Cancer Research at the Depatment of Thoracic Surgery in Freiburg closely cooperates with the Division of RNA Biology & Cancer at the German Cancer Research Center (DKFZ) in Heidelberg also headed by Prof. Dr. Sven Diederichs.