Overview of research directions

Current research directions (Updated 4/11/2022)

Specific lab research directions

What problems do we study?

Every protein-coding change compatible with life exists in humans, and we’ve already seen millions of changes using high throughput sequencing. Sequencing is being increasingly adopted in the clinic for precision diagnosis, but we often lack understanding of what the observed changes mean for disease. We characterize how changes to protein sequences affect their function(s), causing developmental abnormalities, cancer, immunosuppression, and / or autoimmunity. This work will be a crucial for empowering sequencing-based personalized medicine in the future.

Example work: PTEN tumor suppressor variants in PHTS and cancer, PTEN dominant negatives

Virus entry is a key step during viral infection, and oftentimes decides whether a cell gets infected or not. Compatibilities in the protein sequences between viral and host proteins can impact the likelihood of zoonosis, such as what has occurred with the SARS-CoV-2 pandemic. We use cell engineering and multiplex infection assays to better understand the molecular barriers (or lack thereof) that dictate potential routes of viral cross-species transmissions that can result in disease in people.

Example work: Mutants of human ACE2 impacting SARS-CoV and SARS-CoV-2 entry, Diverse SARS-like CoV in Africa and Europe use ACE2 for entry.

Bat_ACE2s_extended

Humans possess an arsenal of immune proteins that protect us from pathogenic viral infections, but viruses use their mutational prowess to evolve proteins that give them the upper hand. We will explore the mutational sequence landscapes available to our immune proteins to understand how they have adapted to viruses in the past, and learn how we may rationally engineer them to overcome pathogenic viruses in the future.

Example work: Mutational pathways for Tetherin / BST-2 escape from diverse viral immune evasion factors (ongoing).

How do we study them?

Massively parallel, single-cell assays can increase the throughput of traditional ensemble-based measurements by multiple orders of magnitude. We combine single cell variant assessment frameworks with high throughput sequencing to functionally characterize libraries of thousands of proteins variants within a single experiment. By combining comprehensive mutational maps of different functions / properties of the same protein to genetically separate roles of multi-functional proteins.

Example work: 1. “Landing Pad” single cell variant expression platform, 2. Characterizing protein variant intracellular abundance at high throughput using VAMP-seq. 3. Fluorescence MAPK intracellular signaling reporter (ongoing)

We combine cutting-edge recombinant DNA manipulation with human cell engineering to create biotechnologies capable of addressing previously inaccessible aspects of cell and protein biology. This includes the development of new single-cell transgenic expression systems, biological reporter assays, and mammalian continuous directed evolution frameworks. These technologies will be freely distributed to academic research groups to enable their work, and licensed to companies for commercialization.

Example work: 1. Synthetic nucleoporin – E3 ubiquitin ligase fusion to score an intracellular protein interactions with HIV. 2. Combinatorial transgene expression platform. 3. Mammalian directed evolution platforms (ongoing)

Project_components
Themes common to many of the projects in the lab

We are an interdisciplinary research group performing both hands-on benchwork and computational data analysis to perform cutting-edge biomedical research on human diseases:

Wet-lab: Recombinant DNA engineering (individual or library-based), human cell engineering, protein biochemistry, assay development.

Dry-lab: Data analysis, statistics and coding (Python, R, BASH). Pymol. Vector graphics (Inkscape or Adobe Illustrator).