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Yihong Ye, Ph.D.

Photo of Yihong Ye
Scientific Focus Areas: Cell Biology, Chemical Biology, Molecular Biology and Biochemistry, Neuroscience

Professional Experience

  • Postdoctoral Fellow, Harvard Medical School, 2000-2005
  • Ph.D., University of Pennsylvania, 2000
  • Bachelors in Medicine, Peking University, 1995

Research Goal

The ultimate goal of our reseach is to understand how cells use various protein quality control (PQC) strategies to maintain protein homeostasis. Protein homeostasis is extremely important for the fitness of all multicellular organisms. Accordingly, PQC defects often disturb protein homeostasis, leading to accumulation of misfolded proteins and neurodegeneration. We wish to understand several key pathways that are crucial for protein homeostasis maintenance in higher eukaryotic cells including misfolding-associated protein secretion (MAPS), cell-to-cell transfer of misfolded neurotoxic proteins, endoplasmic reticulum-associated ribosome quality control, and quality control of large protein assembly.

Current Research

Role of misfolding-associated protein secretion (MAPS) in neurodegeneration

Many neurodegenerative disease-associated proteins are known to accumulate in extracellular space in the brain. The cause of their release from neurons is largely unclear, neither is the underlying molecular mechanism known. However, what has been clear is that these proteins need to be exported via an unconventional protein secretion (UPS) mechanism since they do not possess any leader sequences for entry into the endoplasmic reticulum. My laboratory recently uncovered an UPS pathway termed MAPS, which uses chaperones such as USP19 and DNAJC5 to concentrate misfolded proteins in late endosomes. These proteins are subsequently released into extracellular space. During MAPS, cargos need to be translocated from the cytoplasm into the lumen of late endosomes. A major ongoing effort is to elucidate the mechanism by which these proteins are moved across late endosome membrane.

Another area of research is to examine the link between MAPS and neurodegeneration. We are currently studying the fate of neurotoxic proteins released via the MAPS pathway, the interaction between secreted proteins and target cells (e.g. astrocyte and microglial cells), and the functional consequence associated with deregulation of the MAPS pathway. We apply a varity of modern cell biology and molecular biology tools to tissue culture cells, primary neurons, and animal models to address these questions.

Cell-to-cell transmission of misfolded neurotoxic proteins

Many neurotoxic proteins released into cell exterior can undergo cell-to-cell transmission. These proteins are usually aggregation-prone. Therefore, their transfer from cell to cell is thought to facilitate the spreading of protein aggregates in diseases such as Alzheimer’s disease and Parkinson’s disease. One sensible model in analogous to the prion hypothesis suggests that misfolded proteins upon entering recipient neurons may serve as seeds to amplify protein misfolding and aggregation.

The process of intercellular transmission of misfolded proteins is comprised of two steps: release of misfolded proteins from a donor neuron and their uptake by a recipient neuron. In addition to address whether the MAPS pathway contribute to cell-to-cell spearding of neurotoxic proteins, my laborotary also study the mechanism by which misfolded protein aggregates sush as preformed α-Synuclein fibril enter cells, and how they eventually reach the cytoplasm where they could serve as a misfolded protein seed.

Mechanism of endoplasmic reticulum-associated ribosome quality control

A major PQC mechanism in eukaryotic cells is to degrade misfolded proteins by the ubiquitin proteasome system as soon as they are generated. By doing so, cells can minimize the risk of protein aggregation. Protein misfolding can occur at every step during biogenesis, starting from translation at the ribosome. Therefore, protein synthesis in eukaryotic cells is also monitored by a PQC pathway that eliminates partially translated products due to ribosome stalling or prolonged pausing. Recent studies have revealed many important aspects of this ribosome quality control pathway, particularly for ribosomes translating cytosolic proteins. However, little is known about how cells deal with stalled ribosomes that are synthesizing ER-targeted proteins, which constitute approximately one third of the total human proteom. We are currently using a combination of biochemical and genetic tools to dissect the molecular mechanism of ER-associated ribosome quality control. Specifically, we focus on the role of a small ubiquitin modifier named Ufm1 in this process.

Protein quality control during protein assembly

Most proteins function in protein complex that consists of two or more subunits. During biogenesis of protein complexes, cells need to coordinate the expression and translation of distinct subunits to minimize over-production of individual ones. Otherwise, the over-producted subutnit cannot be properly assembled and could become misfolded. In addition, cells are also equipped with a PQC program that can effectively degrade protein subunits that are not incorporated into native compelx. Current efforts are focused on identification of cellular regulators of this PQC process.

Applying our Research

Intercellular transfer of misfolded proteins such as a-Synuclein and Tau contributes to the pathogenesis of many  neurodegenerative diseases including Parkinson’s and Alzheimer’s disease, but the underlying mechanism is unclear. Defects in ER ribosome quality control have been linked to anemia and abnormal neuronal development. We envision that a thorough characterization of these protein quality control systems may one day improve both diagnosis and treatment of these diseases.

Need for Further Study

In addition to studying the cellular mechanisms of various PQC pathways, we also need to conduct more animal-based studies to better evaluate the physiological roles of these PQC systems. We also need to develop more in vitro assays for small molecule inhibitor screens.

Select Publications

Unconventional secretion of misfolded proteins promotes adaptation to proteasome dysfunction in mammalian cells.
Lee JG, Takahama S, Zhang G, Tomarev SI, Ye Y.
Nat Cell Biol (2016 Jul) 18:765-76. Abstract/Full Text
Reversible inactivation of deubiquitinases by reactive oxygen species in vitro and in cells.
Lee JG, Baek K, Soetandyo N, Ye Y.
Nat Commun (2013) 4:1568. Abstract/Full Text
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Research in Plain Language

Protein misfolding in cells creats a stress condition that leads to cell death. Such protein-associated toxicity could be due to either loss of protein function when a misfolded protein forms aggregate, or be caused by a gain of toxic function when protein aggregates recruit and inactivate essential cellular factors. Protein aggregation has been linked to many human diseases including neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease etc. Currently, there is no effective cure to treat these diseases or even alleviate disease symptoms, revealing the need to better understand how cells cope with misfolded proteins using various protein quality control programs.

Our research group has made substantial progress toward the understanding of several PQC pathways. Our long term goal is to develop small molecules or macromolecules to curtail the production of misfolded proteins in cells, which may benefit patients suffering from protein misfolding-associated diseases.

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