Cells carefully regulate the destruction of bulk internal components through processes that include proteasome-mediated degradation and lysosomal autophagy. It has recently been appreciated that large structures are also subject to active autophagic destruction, including damaged or stressed organelles such as mitochondria (mitophagy), peroxisomes (pexophagy), and the endoplasmic reticulum (ER-phagy). But little is known about the molecular mechanisms behind the autophagy of these large cargoes, from sensing of organelle stress, to marking of target organelles, to delivery to the core autophagic machinery, and how these processes are distinct from the autophagy of bulk cytosol. Working in human cells, my lab will use next- generation CRISPR-Cas9 genome editing and regulation technologies, combined with cellular biochemistry and imaging, to discover the pathways that signal for the remodeling and lysosomal degradation of multiple organelles. We will determine factors that promote and repress organelle autophagy, the pathways required to execute organelle autophagy programs, build real-time detection systems to measure the timing of organelle autophagy in living cells, and determine the general and organelle-specific signals that regulate organelle autophagy. Starting with autophagy of the endoplasmic reticulum (ER-phagy), we have used specialized CRISPR libraries to discover several novel, ubiquitin-related factors that are required for the proper completion of ER-phagy. Systematic CRISPR knockout, endogenous editing, and gene re-expression studies will allow us to dissect the molecular mechanisms by which these factors regulate ER-phagy, as well as identify the adapters that connect ubiquitination/deubiquitination cascades to the autophagy machinery. We will extend these studies to investigate how cells regulate the autophagy of multiple organelles, with the goal of discovering general signaling principles that underlie the marking of damaged organelles and delivery to the lysosome. We hypothesize that these signaling pathways may be analogous to (though chemically or structurally distinct from) ubiquitin-based signals that mark individual proteins for delivery to the proteasome, with refinements for each type of organelle. Our work will reveal the mechanisms by which cells maintain organelle homeostasis and respond to organelle damage or stress, as well as provide new insight into diseases linked to organelle dysfunction, including Parkinson?s Disease, lysosomal storage disorders, and cancer.

Public Health Relevance

Human cells can destroy their own contents in a tightly regulated process called autophagy, and it has recently been appreciated that entire organelles are subject to autophagic degradation. Dysfunction in organelle autophagy has been implicated in diverse diseases, including neurodegeneration, lysosomal storage disorders, and cancer. We will use a combination of next-generation genome editing, cellular biochemistry, and imaging to uncover the players involved in initiating and executing organelle autophagy programs, which could suggest new strategies to treat diseases associated with improper organelle autophagy.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
NIH Director’s New Innovator Awards (DP2)
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Special Emphasis Panel (ZRG1)
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Yang, Yu-Chung
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University of California Berkeley
Schools of Arts and Sciences
United States
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Liang, Jin Rui; Lingeman, Emily; Ahmed, Saba et al. (2018) Atlastins remodel the endoplasmic reticulum for selective autophagy. J Cell Biol 217:3354-3367