Cellular identity is defined by proteins. The synthesis of proteins requires an extensive biological machinery and a large proportion of cellular resources is devoted to the translation of genetic information encoded in messenger RNAs (mRNAs). Protein synthesis is modulated quantitatively and in time and space by a large network of regulators, collectively referred to as translational control. Although efforts to globally monitor gene expression have historically focused on measuring mRNA levels, it has become clear that translational control is a key determinant of cellular protein abundance and has therefore a vast potential to impact cellular fate.
Our laboratory studies the role of translational control in stem cells and cancer to understand how intrinsic and extrinsic factors impose specific protein synthesis programs that ultimately govern stem cell function and drive tumor initiation and progression. Collectively, our long-term vision is to obtain a fundamental understanding of how translational regulation determines cell fate in homeostasis and disease.
Translational control in homeostasis and disease
Protein synthesis visualized in the mouse
1. The secret life of 5‘UTRs
Despite its definition, half of the mammalian mRNAs contain 5’ UnTranslated Regions (5‘UTRs) that are translated. We have recently uncovered an essential role for translational reprogramming in cancer initiation, which involves a genome-wide redirection towards increased 5’UTR translation (Sendoel et al., Nature, 2017). These observations suggest that 5’UTRs constitute an exciting new frontier in the field of gene expression. We aim to systematically document the role of translated 5’UTR loci in epidermal stem cells and cancer-initiating cells and decipher the molecular mechanisms by which translated 5’UTR loci exert their function. These studies will provide insights into the biology of 5’UTRs, unravel new paradigms in the control of gene expression and expose novel strategies for cancer diagnostics and treatment.
5‘UTR translation of an CUG uORF in the Npm1 gene
2. Translational reprogramming in cancer
Global changes in gene expression driven by transcription factors have been studied extensively and referred to as transcriptional reprogramming. In contrast, the notion that distinct protein synthesis programs exist that can be co-opted by cancer cells is relatively new.
We recently found that cancer-initiating cells depend on alternative initiation factors, resulting in preferential translation of oncogenic mRNAs. These findings point at a switch from conventional towards alternative translation programs and suggest that cells can selectively control the translational efficiency of its mRNA pool.
We are interested in systematically understanding the role of translational reprogramming in cancer. How is alternative translation controlled at the molecular level? Which initiation factors are involved, how do they interact with the ribosome to initiate translation? Which cofactors help to control these processes?
Answers to these questions may help to disentangle the enigmatic field of alternative translation, introduce new concepts in the regulation of gene expression and assess it as a potential new Achilles heel for cancer.
Transcriptional and translational changes during early stages of tumorigenesis
3. RNA-binding proteins in stem cells and cancer
The human genome contains more than 1500 RNA-binding proteins, which together coordinate virtually all aspects of the life cycle of mRNAs. We aim to systematically annotate the in vivo function of RNA-binding proteins in epidermal stem cells and upon oncogenic transformation. These studies will add to our understanding of how RNA-binding proteins control stem cell function and cancer initiation and will provide insight specifically into the role of RNA-binding proteins in alternative translation.
The subcellular localization of eIF2A (green) and PABP (red) upon stress.
Intra-amniotic microinjections of lentiviral libraries
Many of our projects leverage the in utero microinjection technique developed in Elaine Fuchs' lab. This method employs ultrasound-guided high-titer lentivirus injections into the amniotic sac of E9.5 mouse embryos at a stage when the epidermis exists as one layer of proliferating progenitors. When the lentivirus is introduced into the sac harboring an E9.5 embryo in utero, the surface ectoderm is selectively infected. Once integrated, the viral genome is stably propagated and expressed by all tissues that derive from the E9.5 K14+ progenitors. The systems greatly extend the available molecular and genetic toolbox for comprehensive functional examination and is a powerful tool - in combination with recent CRISPR/CAS9 advances - for in vivo functional genomics and multiplexed screens.
The ultrasound-guided in utero microinjection system, showing the microinjection needle (upper left), an ultrasound view with needle (upper right) and following injection of K14-actin-GFP (lower panel).
(Beronja and Fuchs, 2013 and Beronja et al, 2013)