Biology subjects

Cho, E. J.

Publications and source records attributed to Cho, E. J..

4 recordsLinked to original sources

bioRxiv2026

Structural proteomics reveals a coagulation-complement accessibility signature of macrovascular invasion in hepatocellular carcinoma

Macrovascular invasion (MVI) and extrahepatic spread (EHS) define the most aggressive, treatment-refractory hepatocellular carcinoma (HCC), yet blood-based markers that report the underlying protein-network biology are lacking. Conventional proteomics measures protein abundance but not the conformational and protein-protein-interaction (PPI) states that govern function. We applied covalent proteome painting (CPP)--a dimethylation-based accessibility assay that reads out binding-site openness--to matched tumor and serum, reasoning that intravascular tumor dissemination remodels plasma protein complexes in a manner detectable as changes in accessibility. Eight treatment-native HCC patients were profiled by CPP using matched FFPE tumor and top-14- depleted serum on a Q Exactive Orbitrap HF. The 85 tumor-serum common proteins defined an 81-protein targeted panel, validated by multiple-reaction-monitoring (MRM) mass spectrometry with heavy stable-isotope-standard peptides (296 peptides; 3,717 light/heavy transition pairs) in 22 FFPE tumors and 22 matched sera. Accessibility was the light/heavy ratio (high, open; low, closed). We assessed differential accessibility, serum-tissue translatability, pathway enrichment, and biomarker/survival performance. Aggressive disease showed broadly decreased protein accessibility. MVI-associated changes were directionally concordant between tumor and serum (Spearman {rho}=0.21; 59% concordant), driven by coagulation and complement proteins (FGG, CTSD, LBP, C4BPA); the EHS axis did not translate. Decreased-accessibility proteins were enriched for complement-coagulation cascades and IGF/IGFBP transport. A six-protein serum accessibility signature discriminated MVI (leave-one-out cross-validated AUC 0.80; best single markers ceruloplasmin 0.83 and haemoglobin- 0.77), and MVI status trended with shorter overall survival (log-rank p=0.06). Accessibility-based serum proteomics captures MVI-associated protein-complex remodeling that abundance assays miss, nominating a coagulation/complement-anchored serum signature for vascular-invasive HCC that warrants prospective validation.

systems biology↗

bioRxiv2025

Proteomic Signatures of Hepatitis B Virus Mutations Reveal Genotype-Specific Host Responses and Biomarker Candidates

Hepatitis B virus (HBV) remains a global health challenge, with viral genetic heterogeneity and mutation-driven resistance complicating treatment outcomes. While previous genomic and transcriptomic studies have characterized HBV mutations, the proteomic consequences of these variants remain underexplored. In this study, we applied liquid chromatography- mass spectrometry (LC-MS)-based proteomics and systems biology approaches to serum samples from 60 HBV-infected patients, stratified by mutation-defined genotype signatures. Four genotype groups were generated, including those harboring mutation related to liver disease progression (rt269/s184) and basal core promoter/precore mutations (A1762T/G1896A). Comparative analyses of 406 high-abundance plasma proteins revealed distinct proteomic signatures, particularly in the ##AG group lacking mutation related to liver disease progression motifs. This group exhibited elevated CRISPLD2 and HSPD1 expression, implicating a dual axis of anti-inflammatory buffering and chaperone-mediated viral processes. Network and co-expression analyses identified modules enriched in focal adhesion, extracellular matrix remodeling, angiogenesis, and PI3K/Akt signaling--pathways tightly linked to hepatocarcinogenesis. Protein-protein interaction enrichment further highlighted disruption of chaperone networks, cytoskeletal regulation, and unfolded protein response. These findings provide molecular evidence for genotype-specific host-virus interactions, nominate CRISPLD2 and HSPD1 as biomarker candidates, and suggest therapeutic strategies targeting PI3K/Akt and microenvironmental pathways. Our results underscore the value of proteomics in refining genotype-informed risk stratification and personalized management in chronic HBV.

systems biology↗

bioRxiv2025

Ser500 phosphorylation acts as a conformational switch to prime eEF-2K for activation

Eukaryotic elongation factor-2 kinase (eEF-2K), a member of the -kinase family of atypical kinases, phosphorylates eukaryotic elongation factor 2 (eEF-2), thereby inhibiting ribosomal translocation and downregulating translational elongation in response to diverse cellular cues. eEF-2K is activated by Ca{superscript 2}/calmodulin (CaM) and integrates upstream inputs from diverse signaling pathways, including PKA and mTOR, which target regulatory sites on a disordered regulatory loop. Among these, serine 500 (S500) has been identified as a key phosphorylation site targeted by both eEF-2K and PKA. However, the influence of this post-translational modification on the properties of eEF-2K has remained unclear. Prior studies have shown that S500 phosphorylation accelerates autophosphorylation of eEF-2K at its primary activating site, threonine 348 (T348). Here, we demonstrate that S500 phosphorylation, mimicked by a S500D mutation, works in conjunction with T348 phosphorylation to enhance the intrinsic (CaM-independent) activity of eEF-2K. Hydrogen-deuterium exchange mass spectrometry reveals that CaM binding, and consequent enhancement in eEF-2K activity, is accompanied by conformational changes proximal to S500. Deletion of S500 and surrounding residues mimics the effects of S500D, promoting robust CaM-independent activity. These data suggest that CaM binding or S500 phosphorylation have similar effects, likely relieving an inhibitory constraint to enhance activity. Further, S500 phosphorylation enhances binding to both apo-CaM and Ca2+/CaM, suggesting a mechanism for maintaining basal activity and priming the kinase for rapid reactivation in response to Ca2+ transients. These findings support a model in which phosphorylation on T348 and S500 synergize to stabilize the active conformation of eEF-2K.

biochemistry↗

bioRxiv2023

Unexpected inhibition of the lipid kinase PIKfyve reveals an epistatic role for p38 MAPKs in endolysosomal fission and volume control

p38 mitogen-activated protein kinases (MAPKs) regulate early endocytic trafficking, but their effects on late endocytic trafficking remain unclear. Herein, we report that the pyridinyl imidazole p38 MAPK inhibitors, SB203580 and SB202190, induce a rapid but reversible Rab7-dependent accumulation of large cytoplasmic vacuoles. While SB203580 did not induce canonical autophagy, phosphatidylinositol 3-phosphate [PI(3)P] accumulated on vacuole membranes, and inhibition of the class III PI3-kinase (PIK3C3/VPS34) suppressed vacuolation. Ultimately, vacuolation resulted from the fusion of ER/Golgi-derived membrane vesicles with late endosomes and lysosomes (LELs), combined with an osmotic imbalance in LELs that led to severe swelling and a decrease in LEL fission. Since PIKfyve inhibitors induce a similar phenotype by preventing the conversion of PI(3)P to PI(3,5)P2, we performed in vitro kinase assays and found that PIKfyve activity was unexpectedly inhibited by SB203580 and SB202190, corresponding to losses in endogenous PI(3,5)P2 levels in treated cells. However, vacuolation was not entirely due to off-target inhibition of PIKfyve by SB203580, as a drug-resistant p38 mutant suppressed vacuolation. Moreover, genetic deletion of both p38 and p38{beta} rendered cells dramatically more sensitive to PIKfyve inhibitors, including YM201636 and apilimod. In subsequent washout experiments, the rate of vacuole dissolution upon the removal of apilimod was also significantly reduced in cells treated with BIRB-796, a structurally unrelated p38 MAPK inhibitor. Thus, p38 MAPKs act epistatically to PIKfyve to promote LEL fission; and pyridinyl imidazole p38 MAPK inhibitors induce cytoplasmic vacuolation through the combined inhibition of both PIKfyve and p38 MAPKs.

cell biology↗