Periodic Reporting for period 3 - CrispSCNAs (Dissecting the Functional and Therapeutic Impact of Somatic Copy Number Alterations (SCNAs))
Période du rapport: 2023-01-01 au 2024-06-30
In 1914 Theodor Boveri described abnormal chromosome counts in cancer cells and speculated that these alterations are the driving force of cancer. Almost 100 years later it became clear that somatic copy number alterations (SCNAs) are one of the most striking characteristics of cancer genomes. SCNAs comprise deletions and amplifications of whole chromosome arms and therefore alter the expression patterns of several hundred genes simultaneously. These alterations show defined patterns suggesting selective pressure, and thus likely contain multiple driver genes, which can shape several tumorigenic properties. Therefore, studying how these events contribute to tumor development will be fundamental to understand cancer biology and develop targeted cancer therapies. However, whereas the function of recurrently mutated driver genes can be readily assessed, studying SCNAs remains challenging so far. This project will overcome these limitations by combining our unique ability to model liver cancer in vivo and in vitro with innovative CRISPR-based genomic engineering technologies. First, we will generate large chromosomal deletions in murine livers and human-derived liver organoids by CRISPR technologies and assess their functional role in cancer development. Furthermore, synthetic lethal interactions generated by these deletions will be evaluated on their therapeutic potential. Additionally, driver genes and driver gene-combinations of amplified chromosomal regions will be investigated using a novel CRISPR/Cas9-based mouse model for endogenous gene activation and chromosome engineering. Finally, we will exploit a novel concept for targeting cancer cells with specific amplifications. Our unique approach will for the first time systematically investigate the functional role of SCNAs in tumor pathobiology, identify new therapeutic strategies specifically tailored for individual SCNAs, and will therefore have high impact for future efforts to understand and combat cancer.
In this period we made great progress in regard to finding specific therapeutic targets for chromosomal alterations. First, we concentrated on chromosomal deletions. Here we identified a gene, which when inhibited is detrimental specifically for chromosome 8p deleted cancer cells. We found that this gene is specifically required for chromosome 8p deleted cancer cells because when deletion of 8p occurs the paralog of our newly identified target gets deleted and thus the biological process this gene fullfills can only be executed by our target. We further characterized the biological consequences of inhibiting our target and have gained a lot of knowledge what happens to cancer cells upon inhibition. Moreover, we filed a patent for future inhibitors for this gene.
Additionally, we were investigating opportunities to target amplified chromosomal regions. We could identify a gene, which encodes a cell surface receptor on chromosome 1q, which is amplified in majority of solid cancers. We further could show that the protein product of this gene is specifically highly expressed in human cancers and not in normal tissue. Further, we generated antibodies targeting the extracellular part of this protein and could show high specificity of these antibodies. Finally, we generated CAR-T cells using the sequence of the antibody and showed their potent capabilities to eliminate cancer cells with high protein expression of the target.
Additionally, we were investigating opportunities to target amplified chromosomal regions. We could identify a gene, which encodes a cell surface receptor on chromosome 1q, which is amplified in majority of solid cancers. We further could show that the protein product of this gene is specifically highly expressed in human cancers and not in normal tissue. Further, we generated antibodies targeting the extracellular part of this protein and could show high specificity of these antibodies. Finally, we generated CAR-T cells using the sequence of the antibody and showed their potent capabilities to eliminate cancer cells with high protein expression of the target.
We expect that we will further be able to charcterize the inhibition of the target we identified for chrmosome 8p deletions by utilizing a preclinical mouse mode that can inhibit the target in a temporal and spatial manner. This will allow us to probe if inhibition of the target leads to off target toxicity in normal tissues and if we can see anti-tumor effects. This will be crucial to know because it would give us an idea if the inhibitors of this target would be worth to investing in.
We also expect to further benchmark the performance of the newly developed CAR-T cells. We plan to check their ability to target cancer cells in preclinical mouse models. Moreover, we will check their ability to kill cancer cells in explanted tumor tissue from human patients, which will also allow us to see if normal tissues are spared by the CAR-T cell therapy.
We also expect to further benchmark the performance of the newly developed CAR-T cells. We plan to check their ability to target cancer cells in preclinical mouse models. Moreover, we will check their ability to kill cancer cells in explanted tumor tissue from human patients, which will also allow us to see if normal tissues are spared by the CAR-T cell therapy.