Functional Genomics – Michal Šmída

• Mechanisms of resistance to monoclonal antibody therapy in B-cell malignancies
• Identification of novel therapy targets through genome-wide knockout screens using CRISPR/Cas9 technology
• Repurposing of approved drugs for personalized therapy in hematological cancers (chronic lymphocytic leukemia, acute myeloid leukemia)
• Improvement of CAR-T cell therapy for chronic lymphocytic leukemia
• Mechanisms of resistance to Venetoclax and prediction of alternative therapies in acute myeloid leukemia

• Analysis of molecular mechanisms regulating CD20 expression as the prime target of immunotherapy, elucidation of potential therapy sensitizers and proposition of novel therapies that might be combined with anti-CD20 therapy
• Generation of diverse cell models gene edited via the CRISPR/Cas9 technology to analyze the functional consequences of mutated genes and suggest potential targets for therapy
• Implementation of different drug and loss-of-function screens (primarily genome-wide CRISPR/Cas9 knockout) to reveal synthetic lethality interactions and to predict targeted therapies specific for individual gene mutations present in solid and hematological cancers
• Optimization of tumor immunotherapy using T cells genetically engineered to carry chimeric antigen receptors (CAR-T cell therapy), identification of novel gene targets that might enhance the efficacy and/or safety of CAR-T cells
• Identification of molecular factors determining the response to Venetoclax in acute myeloid leukemia, description of the mechanisms responsible for Venetoclax failure and proposal of novel therapies alternative to Venetoclax or in combination with Venetoclax

The focus of modern cancer therapy is set on personalizing the therapy with major emphasis put on developing specific small-molecule compounds targeting key cellular components essential for tumorigenesis. We are in our lab predominantly aiming at identification of novel drug targets that might then be exploited in the clinic as innovative targeted therapies. We focus our efforts primarily on two common hematologic malignancies, namely chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML).

We use a plethora of molecular biology and cell biology techniques to elucidate the molecular mechanisms regulating expression of CD20 surface molecule, the prime target of immunotherapy in B cell malignancies that is often downregulated, hence leading to therapy resistance. Better insight into CD20 regulation may reveal novel targets to be pharmacologically exploited for enhancing CD20 expression and thereby improving therapy outcome.
Revolutionary CRISPR/Cas9 technology in conjunction with lentiviral infection is utilized to generate cell models carrying common mutations observed in cancer patients. Functional consequences of these aberrations onto cell signaling and behavior are thoroughly analyzed. Libraries of small-molecule compounds as well as genome-wide CRISPR/Cas9 knockout constructs are employed in order to reveal critical weak-points triggered by individual cell aberrations. The molecular mechanisms underlying observed synthetic lethality interactions are then investigated in detail.

In addition, we are screening libraries of already approved drugs against a variety of diverse patient samples ex vivo. This shall lead to an elegant drug repurposing, i.e. taking an approved drug and applying it onto a different disease or indication. This has proven to provide a smart way of producing fast and relatively cheap novel treatment options.

Another project is focused on the identification of factors that determine response to Venetoclax therapy in AML. We have access to AML primary samples as well as AML cell lines (of which we have generated Venetoclax-resistant variants) that we subject to a variety of molecular-biology techniques like targeted DNA sequencing, RNA sequencing, single-cell RNA sequencing, in order to reveal the mechanisms responsible for Venetoclax resistance. Drug screening with carefully selected drug library in combination with the genomic/transcriptomic data will reveal novel alternative therapies.

We have also established and optimized a breakthrough cancer immunotherapy that relies on administering a synthetic chimeric antigen receptor into the patient´s own T lymphocytes. These re-engineered cells (CAR-T cells) are then given back to the patient where they recognize malignant cells specifically through their newly introduced antigen receptor, leading to the tumor cell eradication. In spite of enormous success in some blood malignancies, CAR-T cells underperform in many others, like e.g. CLL. Using genome-wide CRISPR/Cas9 knockout screening, we aim to identify novel targets that might enhance the efficacy and safety of CAR-T cells.

Overall, all our projects aim to decipher the functional changes triggered in malignant cells and to reveal novel cellular vulnerabilities that might be translated into the clinic as unique personalized therapy available to stratified groups of patients.