Category Archives: 研究發表

蕭育源教授及朱智瑋研究團隊發表研究成果於Nucleic Acids Res.

連結網址：https://pubmed.ncbi.nlm.nih.gov/41533589/

Abstract

In nucleic acid-binding proteins, short linear motifs (SLiMs)-an important subclass of intrinsically disordered regions (IDRs)-offer diverse opportunities for therapeutic intervention, yet their structural and functional roles remain largely elusive. Away from the active site of cancer immunotherapy target exonuclease TREX1, a novel modulation site formed by the intrinsically disordered α7-α8 loop is discovered by X-ray crystallography with newly identified inhibitors. Despite that the structure of α7-α8 loop upon binding-coupled disordered-to-ordered transition is inhibitor specific, a pattern of multivertex clamping is consistently observed. Mechanistically, the fuzzy TREX1-inhibitor interactions elucidated by structural analysis and molecular dynamics simulations reveal an ensemble of chemical-scale amphiphilic units for inhibitor moieties to anchor to. Functional assays confirm that our newly identified inhibitors disrupt the DNA binding and immunosuppressive activity of TREX1, establishing α7-α8 loop as a druggable SLiM. This work provides a first collection of atomic details for small-molecule inhibition involving a DNA-binding SLiM, and the mechanistic principles uncovered here may be generalized to targeting IDRs in cancer immunotherapy.

趙瑞益教授研究團隊發表研究成果於J Adv Res.

連結網址：https://pubmed.ncbi.nlm.nih.gov/41730411/

Abstract

Introduction: Biomolecular condensates are membraneless organelles functionally involved in diverse processes, including cancer progression. Sequestosome-1 (SQSTM1)/p62 regulates liquid-liquid phase separation to drive biomolecular condensates, while programmed death-ligand 1 (PD-L1) promotes cancer cell growth. Although SQSTM1 has been shown to form condensates with several complexes, its full range of partners remains incompletely characterized.

Objectives: This study aimed to investigate the role of SQSTM1 in mediating PD-L1 condensate formation and its contribution to lung tumorigenesis.

Methods: The SQSTM1-PD-L1 interaction and condensate colocalization were examined by immunoprecipitation and immunofluorescence. Truncated SQSTM1 constructs validate the interacting domain with PD-L1, which is supported by computational AlphaFold3 analysis. We applied 1,6-hexanediol, FDA-approved PD-L1 antibody Atezolizumab, and CRISPR/Cas9-based SQSTM1 knockout to disrupt SQSTM1/PD-L1 biomolecular condensates, along with in vitro and in vivo experiments. The Survivin levels were analyzed using real-time quantitative PCR and immunoblotting. Clinical correlations of SQSTM1 and PD-L1 expression with prognosis were assessed using public datasets.

Results: Our research demonstrate that SQSTM1, by its Phox1 and Bem1 (PB1) domain, directly interacts with PD-L1 to facilitate the SQSTM1/PD-L1 biomolecular condensate formation. The formation of SQSTM1/PD-L1 condensates prevents PD-L1 from ubiquitin-proteasome-mediated degradation and stabilizes PD-L1 levels. Deletion of the PB1 domain in SQSTM1 inhibits the formation of PD-L1 biomolecular condensates and induces PD-L1 K48 ubiquitination for protein degradation. Disruption of SQSTM1/PD-L1 condensates with 1,6-hexanediol induces PD-L1 proteolysis and reduces cell viability. Knockout of SQSTM1 disrupts PD-L1 condensate formation, downregulates PD-L1 protein levels, and attenuates tumor growth. Treatment with PD-L1 antibody drug Atezolizumab inhibits SQSTM1/PD-L1 condensates and suppresses tumor formation. Clinically, high SQSTM1 and PD-L1 expression correlated with poor prognosis in lung cancer patients.

Conclusion: Together, the SQSTM1 directly interacts with non-membrane-associated PD-L1 to drive the formation of SQSTM1/PD-L1 biomolecular condensates, which prevent PD-L1 degradation, promote lung tumorigenesis, and serve as a potential therapeutic target in lung cancers.

Keywords: Biomolecular condensate; PB1 domain; PD-L1; SQSTM1; Tumorigenesis.

陳亭妏副教授研究團隊發表研究成果於J Hepatol.

連結網址：https://pubmed.ncbi.nlm.nih.gov/39763896/

Abstract

Most malignant hepatocellular tumors in children are classified as either hepatoblastoma (HB) or hepatocellular carcinoma (HCC), but some tumors demonstrate features of both HB and HCC^1-3. These tumors have been recognized under a provisional diagnostic category by the World Health Organization and are distinguished from HB and HCC by a combination of histological, immunohistochemical, and molecular features^4-6. Their outcomes and cellular composition remain an open question^7-9. The heterogeneous histological and molecular profiles of hepatoblastomas with carcinoma features (HBCs)⁴ may result from cells with combined HB and HCC characteristics (HBC cells) or from mixtures of cells displaying either HB or HCC signatures. We used multiomics profiling to show that HBCs are mixtures of HB, HBC, and HCC cell types. HBC cells are more chemoresistant than HB cells, and their chemoresistance-a driver of poor outcomes^10-12-is determined by their cell types, genetic alterations, and embryonic differentiation stages. We showed that the prognosis of HBCs is significantly worse than that of HBs. We also showed that HBC cells are derived from HB cells at early hepatoblast differentiation stages, that aberrant activation of WNT-signaling initiates HBC transformation, and that WNT inhibition promotes differentiation and increases sensitivity to chemotherapy. Furthermore, our analysis revealed that each HBC is the product of multiple HB-to-HBC and HBC-to-HCC transitions. Thus, multiomics profiling of HBCs provided key insights into their biology and resolved major questions regarding the etiology of these childhood liver tumors.

張晉源副教授研究團隊發表研究成果於J Am Chem Soc.

連結網址：https://pubmed.ncbi.nlm.nih.gov/41779877/

Abstract

The biosynthesis of α-cyclopiazonic acid (α-CPA) is notable for generating a complex pentacyclic scaffold using a minimal three-enzyme pathway. The final step, catalyzed by CpaO, converts linear β-CPA into α-CPA through an enigmatic oxidative cyclization. Here, we report the structural and mechanistic characterization of CpaO. X-ray crystallography reveals a three-domain architecture belonging to the flavin-dependent amine oxidase (FAO) superfamily, while CpaO represents a previously undescribed subfamily distinguished by an essential, covalently linked FAD (8α-N¹-histidyl) and divergent substrate-binding domains. High-resolution structures of the CpaO/β-CPA complex, validated by mutagenesis, identify key active-site residues (His165, Trp317, Asp412, Tyr283) that anchor the substrate. Combined structural, mutational, and molecular dynamics analyses further suggest distinct yet cooperative roles for Tyr283 and Ser167 in modulating substrate access and subsequent binding. Derived from these data, we propose a stereospecific mechanism initiated by FAD-mediated hydride abstraction, which triggers a bicyclization cascade to form the final C and D rings. This study resolves a long-standing biosynthetic mystery and expands the catalytic repertoire of flavoenzymes, offering a template for the chemoenzymatic synthesis of complex indole alkaloids.

高雅婷副教授研究團隊發表研究成果於Phys Chem Chem Phys.

連結網址：https://pubmed.ncbi.nlm.nih.gov/41431324/

Abstract

Fatty acid photodecarboxylases (FAPs) utilize blue light to convert fatty acids into Cn-1 hydrocarbons and CO2, providing a sustainable route to photobiocatalytic fuel production. Despite increasing interest, substrate-dependent phenomena-such as binding affinity, initial electron-transfer (ET) dynamics, and the influence of residues near the FAD cofactor-remain insufficiently characterized. Here, we systematically analyzed substrate binding, substrate-to-product conversion, and initial ET dynamics for three fatty acids of varying chain lengths using two cosolvent buffer systems. Ethanol improved substrate solubility but increased enzyme flexibility, leading to an extended FAD-substrate distance (DFAD-substrate) and diminished fluorescence quenching. Fluorescence titrations revealed chain-length-dependent binding, with palmitic acid (C16) and arachidic acid (C20) exhibiting stronger binding than lauric acid (C12). A fluorometric assay enabled quantification of product formation and catalytic half-lives, revealing that the fastest turnover arises from binding competition between substrate and product. Time-resolved fluorescence measurements further demonstrate that ET rates increase with substrate chain length. Longer fatty acids position their carboxylate groups closer to the FAD cofactor, reducing DFAD-substrate and accelerating the initial ET step. Finally, targeted mutagenesis at residue N170-located adjacent to the isoalloxazine ring-shows that local active-site interactions strongly modulate the partitioning of the excited 1FAD* pathways, thereby tuning photocatalytic efficiency and photostability.

何信瑩教授研究團隊發表研究成果於Scientific Reports

連結網址：https://sciety.org/articles/activity/10.21203/rs.3.rs-7424363/v1?utm_source=sciety_labs_article_page

Abstract

Early diagnosis and treatment of postoperative infection (POI) are crucial for optimizing clinical outcomes. However, current POI prediction models remain unsatisfactory due to their limited interpretability and lack of personalized risk insights, restricting precise antibiotic use and personalized postoperative care strategies. This study aims to develop an interpretable model for predicting the individual POI risk within 30 days after liver resection. This retrospective study included 785 liver resection patients with 125 preoperative and early postoperative clinical factors. The dataset was divided into training (n = 551) and test (n = 234) sets in a 7:3 ratio. An interpretable evolutionary learning-driven method, EL-PIRLR, was proposed to develop a POI risk prediction model after liver resection. EL-PIRLR performs optimal feature selection in conjunction with an XGBoost classifier. EL-PIRLR identified 27 risk factors for modeling and achieved an accuracy of 87.50% and an AUC of 0.889 on the test set. Postoperative fever patterns, surgical difficulty, and the Charlson Comorbidity index emerged as crucial predictors of the POI risk. Using an uncertainty plot analysis, defining risk scores between 0.1 and 0.9 as the uncertainty region, EL-PIRLR achieved 92.05% accuracy for confidently predicted cases, covering 84.62% of the dataset. This demonstrates high reliability with a 98.70% negative predictive value in identifying non-infection patients. EL-PIRLR outperformed several state-of-the-art feature selection techniques and classification models. Precise POI prediction significantly impacts infection management and postoperative care. EL-PIRLR enhances the precision of hepatectomy POI risk prediction, facilitating personalized risk evaluations and aiding clinical decision-making.

李明家副教授研究團隊發表研究成果於JACS Au

連結網址：https://pubs.acs.org/doi/full/10.1021/jacsau.5c01533

Abstract

In this study, we introduce a system that is both nonconjugated and nonaromatic, specifically engineered to generate luminescence via cluster-triggered emission in its aggregated state. By integrating a chiral moiety, N-(tert-butoxycarbonyl)-cysteine methyl ester (cys) as a side group into a linear poly(methyl vinylsiloxane) (PMVS) backbone, we successfully achieved pronounced circularly polarized luminescence (CPL). The formation of the helical conformation was evaluated by vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy. Furthermore, the 2D NMR analyses indicated that intramolecular hydrogen bonding significantly contributes to the stabilization of this structure, because of the intrinsic flexibility of the PMVS backbone, the resultant material demonstrates mechanically tunable CPL properties, underscoring its potential as a versatile chiroptical platform for material applications.

廖光文教授研究團隊發表研究成果於Molecular Medicine

連結網址：https://www.mdpi.com/2073-4468/14/4/106

Abstract

Background: PD-L1 immunotherapy plays a crucial role in cancer treatment, but PD-L1 peptide vaccines have low immunogenicity. A potent peptide derived from the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a significant adjuvant effect, which may increase the immunogenicity of the PD-L1 peptide. This study evaluates whether the PD-L1-SARS peptide enhances PD-L1 immunotherapy and analyzes its potential synergistic effects with anti-PD-L1 antibodies.

Methods: In vivo experiments compared prevention, therapy, and combination therapy using PD-L1 versus PD-L1-SARS peptides in mice. Cytokine multiplex arrays, ELISpot, and IHC were used to evaluate adjuvant effects. Molecular docking (hypothesis-generating), RNA-seq, and LC-MS/MS were used to explore putative mechanisms.

Results: The PD-L1-SARS peptide enhanced the Th1 immune response and increased CD8 and Th17 cell infiltration, effectively inhibiting tumor growth and liver metastasis. Additionally, it promoted M1 macrophage polarization and improved anti-PD-L1 antibody efficacy. Proteomics and bioinformatic analyses were consistent with IFN-γ-linked pathways, and an exploratory docking screen nominated candidate receptors/pathways potentially connecting the adjuvant motif to innate sensing.

Conclusions: Embedding a SARS-derived adjuvant-like motif within a PD-L1 peptide vaccine and delivering it in situ may re-condition the tumor microenvironment toward an immune-activating, Th1/Th17-biased state and complement PD-L1 blockade.

Keywords: Bioinformatics analysis; Melanoma; PD-L1; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

廖光文教授研究團隊發表研究成果於Antibodies

連結網址：https://www.mdpi.com/2073-4468/14/4/106

Abstract

Background: Short peptide epitopes are valuable for mechanistic studies, yet their intrinsic low immunogenicity and lack of commercial antibodies hinder rapid antibody generation. Methods: We developed a reproducible, sequence-level workflow combining cross-species/structural triage, independent MHC-I/II prioritization, and conservative heteroclitic-style substitutions to enhance predicted MHC affinity while preserving native epitope features. Using visfatin as a model, two optimized fragments were conjugated to KLH and tested in mice for antibody titers, isotype profiles, and binding kinetics. Results: Mutant peptides improved MHC-binding prediction, elicited stronger antibody titers, and promoted isotype maturation (increased IgG1). Importantly, antibodies maintained measurable binding to wild-type sequences, indicating preserved cross-recognition. Similar effects were reproduced with additional antigens. Conclusions: This proof-of-concept study, based on small exploratory mouse cohorts (n = 3 per group), demonstrates that strategic, minimal sequence edits can significantly enhance peptide immunogenicity while preserving native epitope recognition. This streamlined workflow provides a low-barrier route to generate epitope-directed antibodies when commercial reagents are unavailable.

Keywords: peptide immunogenicity; sequence-level antigen engineering; conservative (heteroclitic) mutagenesis; cross-reactive antibodies

曾慶平教授研究團隊發表研究成果於International Journal of Molecular Sciences Macromolecules

連結網址：https://pubmed.ncbi.nlm.nih.gov/41241351/

Abstract

The immunoregulatory effects of probiotics have been widely studied, particularly in maintaining immune balance. Conventional in vitro functional screening of probiotics relies on fresh donor-derived primary immune cells, which often exhibit significant inter-individual and temporal variability, limiting reproducibility and interpretation. As an alternative, human-induced pluripotent stem cell (iPSC)-derived dendritic cells were co-cultured with five probiotic strains in the current study to evaluate their immunomodulatory interactions. To assess whether cytokines produced by probiotic-stimulated dendritic cells can influence T cell differentiation, human CD4+ T cells were exposed to the conditioned medium derived from co-cultures. Enzyme-linked immunosorbent assay results demonstrated that iPSC-derived dendritic cells secreted cytokines at distinct concentrations in response to different probiotic strains, suggesting that these cells can distinguish between different microbial stimuli, and supporting their use in functional probiotic screening. Among the five strains tested, Lactiplantibacillus plantarum LPA-56, Limosilactobacillus reuteri RU-23, and Lactobacillus fermentum Fem-99 induced cytokine production levels that promoted the differentiation of the human CD4+ T cells into regulatory T cells. These findings demonstrate that iPSC-derived dendritic cells have immunomodulatory potential, are reliable for in vitro screening of probiotics, and offer a promising strategy for selecting potent immunoregulatory probiotic candidates.

Keywords: CD4+ T cell; co-culture; dendritic cell; induced pluripotent stem cell; probiotic.