Our lab does what you may call integrative systems proteomics. We leverage methods such as high-end proteomics, sequencing, and statistical and computational analysis with molecular biology techniques to understand different aspects of protein expression regulation in response to environmental stimuli. We aim to understand the connections between synthesis and degradation, and the interactions and modifications that affect their function.

Our favorite biological systems are

  1. protein expression regulation during misfolding stress and
  2. the host response to viral infection.

Within these projects, we discovered new roles for the proteasome in neuronal cells that might help combat Amyotrophic Lateral Sclerosis, new translation regulatory elements that affect the cellular stress response, and protein markers that help us distinguish between Zika and dengue infections!

The Biochemist lists a nice article summarizing our views. And so does this interview in PLoS Computational Biology.We also published a recent review of current developments here.

In more detail…

We continue our efforts in method development, both computationally and experimentally. We have developed the first tools to systematically explore the dynamic relationships between sequencing, ribosome footprinting, and proteomics data, and experimental methods to parse small protein samples from as few as 1,000 cells.

We quantify and compare transcription, translation, and protein stability of cells responding to protein misfolding stress. We discovered new links between small molecule metabolism and the stress response, roles of alternative splicing, and new translation regulatory elements.

We apply these quantitative methods to disease relevant systems:  using the stem-cell derived system developed in Esteban Mazzoni’s lab, we explore expression differences between induced cranial and spinal motor neurons in response to protein misfolding stress to understand the molecular underpinnings of Amyotrophic Lateral Sclerosis, a major neurodegenerative disease.

We collaborate with various groups at NYU: with Andreas Hochwagen to map protein modification during meiosis, with Lionel Christiaen to understand post-transcriptional regulation of heart development, with Richard Bonneau on integration of transcriptional and post-transcriptional processes, and with Elodie Ghedin to map the host response to virus infections and vaccines and identify new biomarkers of infection, e.g. in Zika.

We have a long-standing collaboration with  Hyungwon Choi (NU Singapore) to move towards what we think is the future: integrative systems proteomics approaches to better understand human disease, such as cancer.

A great summary of our research can be found in this talk as part of the Proteostasis Consortium Seminar Series.