Periodic Reporting for period 2 - CombaTCancer (Rational combination therapies for metastatic cancer)
Reporting period: 2019-09-01 to 2021-02-28
To better understand the emergence of resistant cells within the framework of ""CombaTCancer"", we developed a novel functional lineage tracing tool that acts as a molecular time-machine termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations) (Umkehrer et al., Nature Biotechnology, 2020). CaTCH combines precise mapping of the lineage history of millions of cells with the ability to isolate any given clone alive from a complex population based on genetic barcodes. Thus, CaTCH enables the retrospective isolation and analysis of founding clones from heterogeneous cell populations before evolutionary selection with a remarkable resolution of 1:50.000 (0.002%) and purity (98%, ~20,000-fold enrichment). In first applications, we used CaTCH to provide insights into resistance to targeted cancer therapies in vivo. In our model, we find that most clones can acquire resistance to combined RAF/MEK inhibitor therapy, indicating that resistance to this clinically relevant regimen is a universally achievable state. We found a de novo KrasG12R mutation in a resistant clone, but not in its treatment-naïve counterpart. Our results provide experimental evidence that mutations are acquired during drug treatment, which is difficult to prove using prior methods, and challenges the current notion that mutations conferring drug-resistance generally pre-exist before therapy. We and several other collaborators are currently exploiting the technology in a wide range of topic related to cancer therapy, metastasis and stem cell behaviour.
To functionally dissect tumors and their microenvironment at different stages of cancer progression, including an active therapy-response and therapy-resistance, we have established novel clinically relevant human and murine model systems that recapitulate key stages of disease progression (Haas et al. in revision). Moreover, we are utilizing genome-wide CRISPR screens to assess mechanisms of immune evasion and sensitization to immunotherapies (Holstein et al. in preparation). For cancer types with no known genetic vulnerabilities, we are investigating whether lineage-specific dependencies could be used for treatment, in particular epigenetic regulators, which govern cell fate, provide unexplored therapeutic entry points. We have recently identified Lysine-specific histone demethylase 1A (LSD1, also known as KDM1A) as a new therapeutic target in MCC in vitro and in vivo (Leiendecker, Jung et al., EMBO MM, 2020)."