Koppstein Group

Cancer Bioinformatics und Multiomics

Dr. David Koppstein

Dysregulation of fundamental transcriptional processes such as splicing is a widespread phenomenon in cancer, affecting diverse malignancies from medulloblastomas to leukemias. These profound perturbations remain a poorly characterized but important phenomenon whose study may yield several benefits, including improved cancer classification, detection of neoantigens for precision cancer therapy, and the possibility to correct misspliced transcripts with oligonucleotide therapy. Our group aims to comprehensively characterize the transcriptional landscape of these cancers using single-cell and third-generation sequencing technologies, yielding insight into the specific molecular pathways affected by these far-reaching mutations.

We also aim to understand the unique mutational signatures arising from driver mutations in specific cancers. Using single-cell multiomic approaches to characterize structural variants, SNVs, and transcription, we hope to comprehensively reconstruct the clonal evolution of cancers with unique "fingerprints" such as recombination signal sequence breakpoints or hyperdiploidy in different types of ALL. These analyses will yield a better understanding of the order of events leading to transformation. In order to pursue our studies we take a holistic approach, working at the interface of bioinformatics and multiomic assay development and collaborating closely with our clinical and experimental colleagues at DKTK/DKFZ and Uniklinik Düsseldorf.