Unmasking epigenetic redundancies in cancer

• Applicant: Dr. Olaf Klingbeil
• Subject Area: Cell Biology
• Term: from 2018 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 404660516

Research over the last few decades has revealed a critical role for chromatin remodeling enzymes (epigenetic modifiers) in defining the identity of a cell by influencing and maintaining the chromatin landscape. This landscape is known to affect important cellular processes like replication, gene transcription and genome stability. Importantly, this also includes oncogene expression, which is strongly dependent on the epigenetic state, and makes epigenetic modifiers attractive targets for cancer therapy. However, so far single agent cancer therapies using epigenetic drugs have shown only limited success and resistance arises quickly. This could be due to the presence of homologous proteins that can serve as an enzymatic backup system, reducing or even reversing the effect of targeted therapies in the cancer. To fully understand the molecular mechanisms of epigenetic modulators in cancer, and to develop efficient epigenetic cancer therapies, it is essential to study homologous proteins, which have so far been understudied. This knowledge gap in the field is in part due to the lack of efficient means to genetically define the function and deviate the functional redundancy of homologous epigenetic regulators. To address this problem and to close the gap, I propose to establish and use a combinatory genetics screening approach utilizing recently identified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas nucleases. A comprehensive amino acid sequence similarity-based bioinformatic analysis will be carried out to guide the identification of candidate homolog gene pairs of the human genome.Using this information, the next aim will be to screen for functional redundancy in the group of epigenetic regulators. The functional read-out for this screen will be the proliferative fitness of the cancer cells, which will be compared between single and double homolog gene knockout. Next, this study aims to validate the uncovered gene pairs that show a fitness defect only in double-knockout cells. To functionally characterize the extend of functional redundancies between the identified gene pairs, the final aim will be to perform genome-wide analysis of the transcriptome and of the chromatin landscape in single- and double-knockout cells using RNA-seq and ChIP-seq (chromatin immunoprecipitation followed by sequencing) methodologies. Overall this study will aim to uncover functional homolog redundancies and thereby identify novel cancer targets using powerful genetic screening tools like CRISPR technologies, which will pave the way to the development of innovative cancer therapies.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor Dr. Christopher Vakoc