Biology subjects

Yu, C.-J.

Publications and source records attributed to Yu, C.-J..

7 recordsLinked to original sources

bioRxiv2025

A Single-Aliquot, Enrichment-Free Workflow for High-Throughput Plasma Proteome and N-Glycoproteome Profiling

High cancer mortality rates highlight an urgent need for early detection. Plasma proteomics and glycoproteomics provide minimally invasive routes for biomarker discovery, yet achieving an optimal balance among profiling depth, throughput, and longitudinal reproducibility remains a major challenge for clinical application and translation. To overcome this bottleneck, we present a single-aliquot, enrichment-free, paired-run dual-omics pipeline that concurrently profiles the global plasma proteome and N-glycoproteome from unenriched plasma. Following depletion of top14 abundant plasma proteins, we implemented sequential 23-min narrow-window data-independent acquisition (DIA) and 42-min stepped-collision-energy data-dependent (SCE-DDA) runs from the same plasma digest, delivering a clinical throughput of [~]24 patients/day with deep proteome coverage of 3,756{+/-}413 protein groups (PGs) and 1,226{+/-}78 glycopeptides per sample, including 303 FDA-approved drug targets. Cross-platform benchmarking with a previous generation instrument demonstrated significantly faster (>10-20 fold) profiling speed to achieve 113 PGs/min and high protein abundance reproducibility (Pearson r > 0.9), confirming cross-instrument transferability. Application to a 300-participant lung cohort (cancer, LDCT-detected non-cancer nodules, and controls) revealed differential expression of S100 and annexin family proteins between cancer and nodules. Paired glycoproteomic analysis (n=30) identified site-specific N-glycosylation alterations in FN1, IGHG2, C3, and MET independent of total protein abundance, uncovering additional biomarker candidates for early lung cancer detection. Together, this dual-omics strategy enables deep, scalable, and reproducible plasma analysis, supporting longitudinal biomarker discovery and validation across instruments and laboratories.

biochemistry↗

bioRxiv2025

Phosphoglycerate kinase 1 cooperates with AP-2 complex to promote endocytosis

Adaptor proteins play a critical role in intracellular protein transport by binding to cargoes and facilitating their sorting into vesicles. The adaptor protein 2 (AP-2) complex specifically recognizes sorting motifs on cargo proteins such as epidermal growth factor receptor (EGFR) and transferrin receptor (TfR) for proper cargo sorting. However, the coordination of these adaptor proteins in cargo recognition remains unclear. Here, we uncover the non-canonical role of glycolytic enzyme phosphoglycerate kinase 1 (PGK1) in protein endocytosis, acting independently of its catalytic activity. PGK1 serves as a co-adaptor to directly engage cargoes and reinforce AP- 2 complex stability, orchestrating efficient cargo sorting to promote endocytosis. Furthermore, PGK1 also integrates into the AP-2-clathrin complex, enhancing cargo recognition and internalization. Collectively, our findings establish a previously unidentified coat protein complex containing PGK1, highlighting its dual role as a cargo adaptor and stabilization of the AP-2 complex.

cell biology↗

bioRxiv2025

Mapping Risk and Resilience Across Indo-Pacific Reefs with Shark Genomescapes

Overfishing has severely depleted marine populations worldwide, including within protected areas. Illegal and unreported fishing are major contributors to this decline. Large-bodied apex predators such as sharks are among the most affected, with overfishing causing dramatic species declines and ecosystem destabilization due to trophic downgrading. Key barriers to effective marine conservation and management include: Data deficiencies that hinder population benchmarks and impact assessments, limited surveillance, allowing illegal fisheries to disproportionately affect apex predators, and insufficient capacity in vulnerable nations to monitor and protect species within their waters. Our study addresses these challenges through a novel genomic framework that enables assessment of shark population diversity and health, while also improving fisheries traceability by detecting instances of illegal fishing across the Indian and Pacific Oceans. We present the Reefshark Genomescape, the first genome-wide reference database for Indo-Pacific reef sharks, an assessment of genetic diversity, structure, and connectivity of two key species across their Indo-Pacific range and geographic assignment of fished individuals using population-specific genetic signatures. We show that grey reef shark (Carcharhinus amblyrhynchos) populations exhibit high genetic diversity, strong population structure, and elevated Fst values, with previously unknown connectivity between the central and western Indian Ocean and clear isolation of populations in the Andaman Sea. In contrast, silvertip sharks (Carcharhinus albimarginatus) display high connectivity, but show genomic signals of declining population health, supporting a reassessment of their IUCN status. Using supervised machine learning with Monte Carlo cross-validation, we assigned geographic origins to fished grey reef sharks with 96% accuracy. These findings provide critical insights into population structure, connectivity, and health of two ecologically important reef shark species, while establishing a robust method for assigning geographic origin. We anticipate this framework will support regional conservation assessments and targeted management. Moreover, by enabling the identification of fishing hotspots and detection of IUU fishing, it lays the groundwork for a broader traceability system in marine ecosystems. Much like the landmark elephant ivory tracing study, our approach has the potential to transform marine conservation globally. Graphical AbstractWe developed the Reefshark Genomescape, a genomic framework for assessing shark population health and fisheries traceability across the Indo-Pacific. Genome-wide data from grey reef and silvertip sharks revealed contrasting patterns, unexpected connectivity, and genomic signals of decline. Geographic assignment of fished individuals reached 96% accuracy, enabling detection of illegal fishing and identification of hotspots. This framework strengthens regional management, supports IUCN reassessments, and lays the foundation for global marine traceability systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/676358v2_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@1eafd3aorg.highwire.dtl.DTLVardef@96ebd1org.highwire.dtl.DTLVardef@541d02org.highwire.dtl.DTLVardef@3c9ca2_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

The phosphorylation of Pak1 by Erk1/2 for cell migration requires Arl4D acting as a scaffolding protein

Activation of extracellular signal-regulated kinases 1 and 2 (Erk1/2) at the plasma membrane typically results in their translocation to other intracellular sites for substrate targeting. This targeting requires scaffolding proteins to bring Erk1/2 and their substrates together. In the case of platelet-derived growth factor (PDGF)-induced signaling that activates Erk1/2 to phosphorylate Pak1 for cell migration, Erk1/2 remain at the plasma membrane. Thus, it has been unclear in this case whether a scaffolding protein is needed for substrate targeting by Erk1/2. The small GTPase Arf-like protein (Arl) 4D also promotes cell migration by targeting Pak1 to the plasma membrane. However, as this recruitment also results in the phosphorylation of Pak1, it has been unclear how this phosphorylation is achieved. Furthermore, because both Erk1/2 and Arl4D promote the role of Pak1 in cell migration, the relationship between these two processes has also been unclear. Addressing these outstanding questions, we show that Arl4D acts as a scaffolding protein by recruiting Erk1/2 and Pak1 to the plasma membrane for their assembly into a protein complex. Our findings identify Arl4D as a novel regulator of Erk1/2, reveal a conserved role for scaffolding proteins in substrate targeting by Erk1/2, as well as uncovering a previously unknown interplay among Arl4D, Erk1/2, and Pak1. Moreover, as all these factors are known to be involved in cell migration, we have shed new mechanistic insights into how this fundamental cellular process occurs.

cell biology↗

bioRxiv2020

Epigenetic therapy remodels the immune synaptic cytoskeleton to potentiate cancer susceptibility to γδ T cells

{gamma}{delta} T cells are a distinct subgroup of T cells that bridge the innate and adaptive immune systems and can attack cancer or virus-infected cells in an MHC-unrestricted manner. Despite its antitumor ability in both autologous and allogeneic settings, earlier trials of adoptive {gamma}{delta} T cell transfer in solid tumors had limited success due to limitations in cell expansion and the lack of a strategy to modulate tumor lytic interactions between {gamma}{delta} T and cancer cells. Here, we show through quantitative surface proteomics and gene enrichment analyses that DNA methyltransferase inhibitors (DNMTis) upregulate multiple surface molecules related to {gamma}{delta} T cell activation in cancer cells. DNMTi treatment of human lung cancer potentiates tumor lysis by ex vivo-expanded {gamma}{delta} T cells using a clinical-grade expansion protocol developed by our team to enrich for the V{delta}1 subset while preserving their antitumor effector functions. Mechanistically, DNMTis enhance immune synapse formation and stabilize the synaptic cleft to facilitate {gamma}{delta} T-mediated tumor lysis. Through integrated analysis of RNA-seq, DNA methylation, and ATAC-seq, we demonstrate that depletion of DNMTs induces coordinated pattern alterations of immune synaptic-cytoskeletal networks at the cancer side of the immune synapse. In addition, single-cell mass cytometry reveals enrichment of polyfunctional {gamma}{delta} T subsets by DNMTis. Combined DNMTi and adoptive {gamma}{delta} T transfer in a mouse lung cancer model offers a significant survival benefit. Consistently, the DNMTi-associated cytoskeleton signature identifies a subset of lung cancer patients with improved survival. Our results demonstrate that epigenetic mechanisms are crucial for cytoskeletal remodeling in cancer to potentiate immune attack and support a combinatorial strategy of DNMTis and {gamma}{delta} T cell-based immunotherapy in lung cancer management. One Sentence SummaryDNA methyltransferase inhibitors potentiate the killing of lung cancer by {gamma}{delta} T cells through remodeling cytoskeletal-immune synaptic networks.

cancer biology↗

bioRxiv2019

Fucosyltransferase 4 shapes oncogenic glycoproteome to drive metastasis of lung adenocarcinoma

Aberrant fucosylation plays a critical role in lung cancer progression. Identification of the key fucosyltransferase as a therapeutic target may refine lung cancer management. Here, we identified a terminal 1,3-fucosyltransferase, FUT4, as the key prognostic predictor for lung adenocarcinoma through transcriptomic screens in lung cancer cohorts. Overexpression of FUT4 promotes lung cancer invasion, migration and cell adhesion in vitro and provokes distant metastases in mouse xenograft models. RNA-seq and glycoproteomics analyses revealed that FUT4 mediates aberrant fucosylation of intracellular transport and signal transduction proteins, which facilitates concurrent transcriptional activation of multiple cellular processes, including membrane trafficking, cell cycle, and major oncogenic signaling pathways. Notably, knockdown of FUT4 markedly curtailed lung colonization and distant metastases of lung cancer cells in mouse xenograft models. In addition, the metastatic phenotype provoked by FUT4-mediated fucosylproteomic networks can be diminished by targeted pathway inhibitors. Collectively, FUT4 represents a promising therapeutic target in lung cancer metastasis. Our data highlight the potentials for integration of glycomics into precision medicine-based therapeutics.

cancer biology↗

bioRxiv2018

Glucose intake hampers PKA-regulated HSP90 chaperone activity

Aging is an intricate phenomenon associated with the gradual loss of physiological functions, and both nutrient sensing and proteostasis control lifespan. Although multiple approaches have facilitated the identification of candidate genes that govern longevity, the molecular mechanisms that link aging pathways are still elusive. Here, we conducted a quantitative mass spectrometry screen and identified all phosphorylation/dephosphorylation sites on yeast proteins that significantly responded to calorie restriction, a well-established approach to extend lifespan. Functional screening of 135 potential regulators uncovered that Ids2 is activated by PP2C under CR and inactivated by PKA under glucose intake. ids2{Delta} or ids2 phosphomimetic cells displayed heat sensitivity and lifespan shortening. Ids2 serves as a co-chaperone to form a complex with Hsc82 or the redundant Hsp82, and phosphorylation of Ids2 impedes its association with chaperone HSP90. Thus, PP2C and PKA orchestrate glucose sensing and protein folding to enable cells to maintain protein quality for sustained longevity.

cell biology↗