Genetics and Cellular Engineering

 Our focus is on using genetic tools for pathway investigation and engineering synthetic cellular systems for drug discovery. In particular, we are interested in the new capabilities presented by the CRISPR/Cas9 mutagenesis system, both from a target discovery perspective, as well as from the potential usage in homology-directed repair applications (see Gratz et al., 2014, for example).

Using forward genetics to investigate pathways in somatic cells is a powerful new method in the CRISPR toolbox and we are using the sgRNA libraries combined with deep sequencing in order to investigate new players in apoptotic and programmed non-apoptotic cell death pathways. To support these efforts we have developed in-house software to rapidly identify significant new proteins which accelerates the usage of CRISPR-based screening in novel applications. Newly discovered members are expected to serve as a basis for pharmacological inhibition as well as to help elucidate cellular control mechanisms in cell physiology.

Concurrent efforts focus on customizing CRISPR technology for gene therapy applications. 

In addition to CRISPR technologies, we are currently engaged in the following projects:

Peptide Discovery

Biologics can serve as finely-controlled tools for the manipulation of cellular processes. By screening a phage-display library, we have discovered a new 7-amino acid cell-surface binding peptide that specifically binds to cell stimulated to undergo programmed non-apoptotic cell death but prior to overt membrane permeabilization. Thus, conjugating to fluorescent tags or antibody accessible versions enables its usage as a biomarker. The peptide is unique as it also confers survival to cells exposed to different challenges such as non-apoptotic cell death stimuli or UV light triggers but not stereotypical ligand-induced extrinsic apoptosis. Current efforts are focused on identifying the cognate receptor and characterizing the mechanism of survival in the broader context of specialized cell death.

Nonsense mediated decay

Nonsense mediated decay (NMD) is a process by which cells restrict the pool of expressed non-coding RNAs. As these RNAs comprise more than 95% of the genome but are relatively uncharacterized they are often referred to as the “dark matter” of the genome. We have identified key players in the regulation of NMD and are using a combination of genetics and deep sequencing to identify specific targets and to characterize their role in cell physiology.