Biology subjects

Liang, J. R.

Publications and source records attributed to Liang, J. R..

5 recordsLinked to original sources

bioRxiv2026

Epithelial-Mesenchymal Transition Induces FAM134A-mediated ER-phagy to Regulate Procollagen Secretion

EMT is accompanied by extensive remodeling of the secretory pathway, yet how cancer cells maintain endoplasmic reticulum (ER) homeostasis during this transition remains unclear. Here we show that EMT activates ER-phagy as an adaptive mechanism to constrain secretory output. A genome-wide CRISPR activation screen unexpectedly identified EMT- and MET-associated transcription factors as opposing regulators of ER-phagy, and TGF{beta}-induced EMT robustly stimulated this pathway. Proteomic analysis revealed that ER-phagy regulates EMT-induced secretory protein degradation, including procollagens. Among FAM134 ER-phagy receptors, FAM134A uniquely mediated procollagen degradation through a non-canonical, LC3-independent mechanism. Loss of FAM134A diverted procollagen from degradation to secretion, resulting in a pro-invasive secretome, as conditioned media from FAM134A-deficient cells enhanced matrix invasion. These findings identify ER-phagy as a regulatory node that buffers EMT-associated secretory remodeling and reveal FAM134A as a context-specific suppressor of pro-invasive secretion.

cell biology↗

bioRxiv2026

A Functional Genetic Atlas of Parkin Resolves Variants of Uncertain Significance and Predicts Parkinson's Disease Age at Onset

Autosomal recessive mutations in the Parkin gene (PRKN) cause early-onset Parkinsons disease (PD). Parkin functions as a ubiquitin E3 ligase acting downstream of the PINK1 kinase to promote phosphorylated ubiquitin at sites of mitochondrial damage. Yet the functional effects of most PRKN gene variants remain unknown. Here we use a pooled cellular assay measuring phosphorylated ubiquitin accumulation to quantify the activity of [~]9,200 PRKN missense and nonsense variants. Our screen identifies thousands of loss- and gain-of-function variants, including activating variants mainly residing at autoinhibitory interfaces. Functional scores accurately distinguish known PD pathogenic and benign variants, and enable reclassification of 173/184 variants of uncertain significance (VUS). When combined into biallelic genotype scores, these data predict the age at disease onset in patients, revealing a quantitative link between Parkin activity and clinical manifestation. Our results provide a comprehensive functional genetic map of Parkin and demonstrate the power of multiplexed assays of variant effects (MAVEs) for variant interpretation and precision medicine in PD.

genetics↗

bioRxiv2022

Human ATG3 contains a non-canonical LIR motif crucial for its enzymatic activity in autophagy

Macroautophagy is one of two major degradation systems in eukaryotic cells. Regulation and control of autophagy is often achieved through the presence of short peptide sequences called LC3 interacting regions (LIR) in autophagy-involved proteins. Using a combination of new protein-derived activity-based probes, protein modelling and X-ray crystallography, we identified a non-canonical LIR motif in the human E2 enzyme responsible for LC3 lipidation, ATG3. The LIR motif is present in the flexible region of ATG3 and adopts an uncommon {beta}-sheet structure binding to the backside of LC3. We show that the {beta}-sheet conformation is crucial for its interaction with LC3. In cellulo studies provide evidence that LIRATG3 is required for LC3 lipidation and ATG3[~]LC3 thioester formation. Removal of LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/502437v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@f952e4org.highwire.dtl.DTLVardef@b0fe6aorg.highwire.dtl.DTLVardef@eeabcorg.highwire.dtl.DTLVardef@154ee1c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

A genome-wide screen for ER autophagy highlights key roles of mitochondrial metabolism and ER- resident UFMylation

Selective degradation of organelles via autophagy is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few specialized autophagosomal receptors and remodelers. Using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence factors involved in human ER-phagy. We mechanistically investigated two pathways unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which reverses the logic of general autophagy. Mitochondrial crosstalk with ER-phagy bypasses the energy sensor AMPK, instead directly impacting ULK1. Second, ER-localized UFMylation is required for ER-phagy that represses the unfolded protein response. The UFL1 ligase is brought to the ER surface by DDRGK1, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the unique cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.

cell biology↗

bioRxiv2018

Double Stranded DNA Damage and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown

DNA damage activates a robust transcriptional stress response, but much less is known about how DNA impacts translation. The advent of genome editing via a Cas9-induced DNA double-strand break has intensified interest in understanding cellular responses to DNA damage. Here we find that DNA double-strand breaks (DSBs) induced by Cas9 or other damaging agents lead to a reduction of core ribosomal proteins, RPS27A and RPL40, and that the loss of these proteins is post-transcriptional and p53-independent. DSBs furthermore lead to the shutdown of translation through phosphorylation of eukaryotic initiation factor 2 alpha, and altering these signals affects genome editing outcomes. This DSB translational response is widespread and precedes the transcriptional response. Our results demonstrate that even a single double-strand break can lead to ribosome remodeling and reduced translational output, and suggest caution in interpreting cellular phenotypes measured immediately after genome editing.

molecular biology↗