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Cancer ResearchDepartment of Thoracic Surgery

Databases - AG Diederichs

From our different research projects, we provide comprehensive and easy-to-use databases to facilitate research and access to our research data for the scientific community. Please share your thoughts - and cite the respective original publications if you use any of our databases.

Databases on RNA - Protein Complexes

R-DeeP
R-DeeP provides the proteome-wide screening results for RNA-dependent protein complexes based on our paper in Molecular Cell 2019.

RBP2GO
RBP2GO provides a comprehensive database of RNA-binding or RNA-dependent proteins from all available proteome-wide studies in 13 different species. It includes the annotation of their functions as well as interaction partners - and allows also reverse searches for RNA-binding proteins with specific molecular functions, biological processes, cellular compartments or a known link to cancer.

circ2GO
... coming soon ...
This database will include also the circular RNA expression data derived from our comprehensive transcriptome profiling of human lung cancer cell lines using rRNA-depleted RNA published in Cancers 2020.

Databases on non-canonical Mutations in Cancer

SynMICdb
SynMICdb provides a comprehensive database on synonymous mutations in human cancer including their frequency, signature-normalized frequency and related tumor entities as well as orthogonal data like evolutionary conservation and impact on secondary RNA structure leading to the SynMICdb score to predict the likelihood of a functional impact of a given synonymous mutation. SynMICdb is based on our publication in Nature Communications 2019.

NonStopdb
NonStopdb is the first database devoted to nonstop mutations - a.k.a. stop-loss mutations and comprising nonstop extension and readthrough mutations - which extend a protein at its C-terminus. It is based on our research on nonstop mutations in human cancer and has been published in Nature Cell Biology 2020.

Division of Cancer Research

Department of Thoracic Surgery

Center for Translational Cell Research (ZTZ)
Breisacher Str. 115
D-79106 Freiburg

 

Prof. Dr. Sven Diederichs

Division Head

Phone:
+49 761 270-77571
E-Mail:
lung-cancer-research
@uniklinik-freiburg.de
 

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 lies on the Molecular Biology of RNA and its associated molecules.

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, in vivo RNA Affinity Purification and our own customized siRNA and CRISPR libraries targeting specifically lung cancer-associated lncRNAs. Our RNAi screens have uncovered numerous lncRNAs controlling several hallmarks of cancer including cancer cell viability, mitosis and Migration.

An emerging Topic of particular importance in our lab are RNA-Protein complexes, especially the new concept of RNA Dependence: R-DeeP (Mol Cell 2019).