Research

Virtually every form of human disease is shaped by the individual or concerted action of genes. Incredibly successful work in model organisms – most importantly in yeast – has paved the way to build genetic wiring diagrams of the eukaryotic cell (for a recent example see Costanzo et al., Science, 2016). Mapping genetic interactions through knock-out genetics is not only a remarkably useful tool in the mechanistic dissection of complex cellular phenomena, but can also aid the annotation of orphan genes and potentially reveal new strategies to therapeutically combat disease states. However, strategies for comparable experiments in a human system have long been hindered by the diploid nature of the human genome, which buffers against individual genetic insults. With the advent of haploid mutagenesis in human cells (Carette et al., Science, 2009) and repurposing of CRISPR-Cas (Jinek et al., Science, 2012) we can finally embark on similar genetic expeditions in the human system. 

Examples of genetic interactions. Adapted from van Leeuwen*, Pons* et al., Science 2016.

 

Genetic interactions.

The observation that the nature and principles of genetic interactions appear to be conserved between yeast and man (Costanzo et al, Science, 2016; Blomen*, Májek*, Jae* et al., Science, 2015) implies that the majority of human genes should engage in genetic co-dependencies. This suggests that different types of human disease with a genetic component may be susceptible to secondary genetic insults in trans as a result of their wiring. In cancer it has been historically difficult to drug the absence of tumor suppressors given the lack of a target in most cases. The search for synthetic lethal relationships of tumor genes has lagged behind expectations (Nijman and Friend, Science, 2013) but with improved possibilities for loss-of-function genetics approaches this might change (see e.g. Steinhart et al., Nature Medicine, 2017). Similarly, we are only just beginning to appreciate the scope and qualities of genetic suppression (van Leeuwen*, Pons* et al., Science, 2016). We are interested in studying both genetic phenomena and exploit them to manipulate cellular states based on genome-wide loss-of-function surveys in defined CRISPR-generated mutants. We hope to identify cancer cell vulnerabilities and genetic suppressors of disease phenotypes elicited by dysfunctional alleles.

Synthetic lethality network of the human secretory pathway mapped through ultra-deep haploid mutagenesis in CRISPR-generated query mutants. Adapted from Blomen*, Májek*, Jae* et al., Science, 2015.

 

Mitochondria.

Endosymbionts by origin, over time mitochondria have earned a central role in the functioning of eukaryotic cells, including those of man. Mitochondria are the site of respiration, various metabolic programs and the mitochondrial surface has emerged as a hub for signaling processes, such as the detection of foreign genomic material in innate immunity, calcium flux or the nucleation of autophagic membranes. This creates a tight link between mitochondrial fidelity and overall cellular health and may contribute to the fact that mitochondrial dysfunction is linked to a number of neurodegenerative diseases such as Parkinsonism, Charcot-Marie-Tooth disease, optic atrophy disorders and others. It has become particularly clear that damaged mitochondria are a source of trouble the cell needs to mitigate. Proteins at the mitochondrial surface such as mitofusins are multiply involved in this challenge, as they not only control mitotic fusion events which can rejuvenate wounded organelles but can also themselves be turned into beacons that signal for the catabolic removal of mitochondria in a process termed mitophagy. Despite extensive research in recent times, mitochondrial dynamics remain poorly understood. We want to dissect the complex regulation of mitochondrial turnover and signaling events under different conditions using loss-of-function genetic approaches coupled to fluorescent readouts and deep sequencing. This includes the search for genetic suppressors of mutant phenotypes associated with mitochondrial dysfunction as well as unbiased surveys for hitherto unknown factors in signal transduction at the surface of the organelle.

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