Yang-Chi-Dung Lin

Background/Objectives: ATPase family AAA domain-containing protein 2 (ATAD2) is an oncogenic chromatin regulator that amplifies E2F/MYC transcriptional programs, yet direct modulators remain scarce. Arecoline (ARE), the primary alkaloid of the areca nut, is a known carcinogen but paradoxically exhibits context-dependent anti-proliferative activities. In this study, we resolve this paradox by defining ARE’s anti-cancer mechanism. Methods: Breast cancer cell proliferation and colony formation assays were performed to evaluate the anti-proliferative effects of ARE. Cell-cycle distribution was analyzed to determine phase-specific effects. Transcriptomic profiling was conducted to identify affected gene networks. An unbiased Cellular Thermal Shift Assay–Mass Spectrometry (CETSA-MS) screening was used to identify direct protein targets, followed by CETSA–Western blotting for validation. Finally, in silico structure-based design was applied to generate novel derivatives with improved predicted properties. Results: ARE suppressed breast cancer cell proliferation and colony formation by inducing G1/S phase arrest. Transcriptomic analysis revealed that this phenotype was driven by profound suppression of the E2F/Cell Cycle gene network. CETSA-MS identified ATAD2 through multi-omics convergence, as the 67 direct targets were collectively most significantly enriched in the E2F pathway. CETSA–Western blotting confirmed that ARE binds and thermally stabilizes ATAD2. Mechanistically, ARE engagement of ATAD2 led to downregulation of key downstream proteins, including MYC and Cyclin D1, directly linking target modulation to G1/S arrest. Structure-based design further yielded novel derivatives with predicted enhanced ATAD2 binding and substantially reduced toxicity. Conclusions: Together, these findings uncover ATAD2 as a druggable target of ARE, establish proof-of-concept for repurposing this scaffold, and provide a rational framework for developing safer ATAD2-targeted therapies.

Reactive oxygen species (ROS) play a dual role in cellular homeostasis, but excessive levels of ROS lead to oxidative stress, accelerating skin aging. Environmental stressors like UV radiation induce ROS overproduction, overwhelming endogenous antioxidant defenses and causing cellular damage. While the skin possesses an intrinsic antioxidant network that provides moderate protection, excessive oxidative stress can trigger inflammatory responses, thereby necessitating exogenous antioxidant intervention. Microbe-derived antioxidants (MA), produced via probiotic fermentation of sea buckthorn and chestnut rose, have shown promise in mitigating ROS-induced damage. In this study, we evaluated two MA formulations, MA1 and MA2, for their ability to scavenge free radicals and alleviate hydrogen peroxide (H ₂ O ₂ )-induced oxidative stress in human dermal fibroblasts (HDF) and dermal papilla cells (HDP). Both formulations displayed dose-dependent DPPH radical scavenging activity and enhanced cell viability at low concentrations. Under H ₂ O ₂ -induced oxidative stress, MA1 and MA2 effectively restored intracellular ROS to baseline levels, demonstrating significant cytoprotective effects. UHPLC–MS/MS profiling identified 12 compounds shared by both formulations, and Gene Ontology Biological Process enrichment analysis revealed that their associated target genes were significantly enriched in antioxidant-related pathways. Five compounds—adenosine, citric acid, 5-hydroxymethylfurfural, myricetin, and phenylalanine—emerged as key contributors to the observed antioxidative effects. Together, these findings highlight the potential of fermented microbial antioxidants to re-establish redox homeostasis in human skin cells and support their further development as therapeutic or cosmetic interventions targeting oxidative stress and skin aging. Given the heightened oxidative sensitivity of aged fibroblasts, MA’s ability to alleviate ROS may offer novel therapeutic strategies against skin aging and related pathologies.

The photoprotective efficacy of natural skin-active complexes is well recognized, yet their ap-plication is often hindered by the challenge of deciphering their complex, multi-component, and multi-target mechanisms. To bridge the gap between established phenotypes and molecular mechanisms, we developed an AI-driven integrated platform that combines phytochemical profiling, network pharmacology, and deep learning-based target prediction with rigorous biophysical validation. We applied this platform to investigate RRBE, a bioactive complex refined from red rice bran extract. In vivo clinical studies confirmed that RRBE significantly accelerates the resolution of UV-induced erythema, while cellular and 3D tissue models demonstrated robust suppression of oxidative stress and DNA damage responses. To decode its material basis, the platform deconstructed RRBE into 10 distinct chemical modules. Leveraging our SCOPE-DTI deep learning model for global target prediction, we identified flavonoids (Module 1) and phenolic acids (Module 10) as the primary bioactive drivers relevant to photoprotection. These computational predictions were structurally supported by molecular docking and definitively validated in a physiological environment via Cellular Thermal Shift Assay-Mass Spectrometry (CETSA-MS). Mechanistically, RRBE functions through a synergistic polypharmacology: (1) Module 1 components, represented by procyanidin B2, target NDUFA7 to stabilize mitochondrial function and mitigate ROS; (2) Module 10 components, exemplified by caffeic acid, ferulic acid, and p-coumaric acid, engage FKBP11 and HSP90AA1 to regulate protein homeostasis and stress responses. This work not only deciphers the polypharmacological basis of RRBE’s photoprotective action but also validates a scalable “AI-guided, cell-validated” discovery pipeline, offering a rational paradigm for uncovering the protective benefits of complex natural extracts.

In response to environmental changes, bacteria have evolved sophisticated regulatory networks that incorporate small RNAs (sRNAs) and transcription factors (TFs) to fine-tune cellular physiology. Both sRNAs and TFs modulate gene expression, but the former function via post-transcriptional mechanisms, while the latter act at the transcriptional level. However, it remains unclear why both regulatory layers are conserved through evolution, rather than one being sufficient. Here, we experimentally identified that CRP, a global regulator, regulates 25 small RNAs (sRNAs) in Escherichia coli. Interestingly, CRP also controls 80% of the target genes of these sRNAs. This architecture led us to identify 34 novel sRNA-mediated feed-forward loops (sFFLs) circuits where CRP regulates both an sRNA and its target within the CRP regulon. Quantitative PCR analysis of 16 such sFFLs revealed that each type possesses a distinct cAMP dose-response profile, suggesting that different sFFL structures embody unique regulatory logic. Specifically, coherent and incoherent type 3 and 4 sFFLs exhibit broader dynamic ranges in their dose-response compared to open-loop controls. Coherent and incoherent type 1 and 2 sFFLs appear more energy-efficient. Altogether, we propose that sRNAs cooperate with TFs through sFFLs to optimize both the energy efficiency and the diversity of signal response profiles. Therefore, sRNAs serve as critical components integrating transcriptional and post-transcriptional networks across diverse cellular pathways.

MicroRNA-483 regulates multiple human disease categories, spanning oncology, cardiopulmonary, metabolic, immune, neurological, and musculoskeletal pathologies. We integrate experimentally validated interactions from 146 studies to construct a comprehensive regulatory network, encompassing transcription factors, long non-coding RNAs, circular RNAs, and messenger RNA targets. Our analysis reveals that miR-483 promotes tumorigenesis by suppressing tumor-suppressive checkpoints, yet it protects cardiopulmonary, metabolic, and neurological tissues from pathological injury. This functional duality arises from tissue-specific modulation of shared signaling pathways, particularly TGF-β and MAPK cascades, which function as the core hubs driving its context-dependent activity across six disease categories. By mapping miR-483 regulatory circuits across multiple diseases, we define the molecular determinants of its context-dependent activity. These findings establish miR-483 as both a diagnostic biomarker and a therapeutic target whose function is dictated by cellular context.

Recent studies have highlighted the importance of structure-function relationships in genetic regulatory networks, particularly in feed-forward loops (FFLs), where input-output behavior depends on both input signals and transcriptional interactions. This study elucidates the function of a CRP-LacI- lacZYA coherent type-4 FFL (Co-4 FFL) in Escherichia coli . We demonstrate that cyclic AMP receptor protein (CRP) directly represses the transcription of lacI , which encodes the Lac repressor. This finding was confirmed through multiple approaches: 1) the mRNA level of lacI decreased to one-fifth of the original level upon cAMP addition; 2) lacI expression increased 15-fold in a crp mutant; 3) DNase I footprinting identified a CRP binding site within the lacI promoter region, and a lacZ fusion assay and site-directed mutagenesis validated its functional role. Collectively, these results establish CRP as a direct repressor of lacI , thereby forming a Co-4 FFL with the lacZYA operon. Physiological studies on Co-4 FFLs in E. coli are scarce. Our model suggests that under glucose-lactose diauxic growth conditions, this circuit allows E. coli to enhance the efficiency of lactose metabolism for energy synthesis upon glucose exhaustion by repressing lacI via CRP. This work reveals how metabolic cues shape the behavior of genetic regulatory networks.

Background/Objectives: Glioblastoma (GBM), the most aggressive primary malignant brain tumor, has a dismal prognosis and limited treatment options. The dried rhizome of Ligusticum chuanxiong Hort. (Chuanxiong, CX) is a traditional Chinese medicinal herb frequently prescribed in formulas intended to invigorate blood circulation. CX also exhibits anti-glioma activity, but its molecular mechanisms remain incompletely understood. Methods: In this study, we combined transcriptomics and Raman spectroscopy to investigate the effects of reconstituted CX-dispensing granules (hereafter referred to as CXG solution) on U87MG cells, suggesting their dual role in promoting cell death and modulating collagen deposition and lipid metabolism. Results: Mechanistically, we demonstrated that the CXG solution downregulates hsa-miR-10a-5p, which directly targets BCL2L11, known to induce pro-apoptotic effects, as validated by qPCR and dual-luciferase reporter assays. Furthermore, the CXG solution and hsa-miR-10a-5p suppress lipid metabolism through a coherent feed-forward loop via targeting transcription factors SREBF1 and E2F1. An electrophoretic mobility shift assay (EMSA) confirmed E2F1 binds to the hsa-miR-29a promoter, leading to the synergistic repression of hsa-miR-29a-3p by SREBF1 and E2F1. Network pharmacology analysis combined with molecular docking suggested that the ferulic acid and adenosine in CX potentially modulate EGFR-the E2F1-hsa-miR-10a-5p axis. Conclusions: These findings elucidate CX’s multi-target anti-GBM mechanisms and propose a novel therapeutic strategy combining metabolic intervention with miRNA-targeted therapy, providing novel insights into feed-forward loop regulation in miRNA networks.

Background/Objectives: The rising global prevalence of metabolic diseases (e.g., obesity, type 2 diabetes mellitus) underscores the need for effective interventions. Omega-3 polyunsaturated fatty acids (PUFAs) exhibit therapeutic potential, yet their molecular mechanisms remain unclear. This systematic review synthesizes a decade (2014–2024) of omics research to elucidate Omega-3 PUFA mechanisms in metabolic diseases and identify future directions. Methods: A PRISMA-guided search of the Web of Science identified studies on Omega-3 PUFAs, metabolic diseases, and omics. After excluding reviews, non-English articles, and irrelevant studies, 72 articles were analyzed (16 multi-omics, 17 lipidomics, 10 transcriptomics/metabolomics/microbiomics each, and 6 proteomics). Results: Omics studies demonstrated that Omega-3 PUFAs, particularly EPA and DHA, improve metabolic health through interconnected mechanisms. They regulate epigenetic processes, including DNA methylation and miRNA expression, influencing genes linked to inflammation and insulin sensitivity. Omega-3 PUFAs reduce oxidative stress by mitigating protein carbonylation and enhancing antioxidant defenses. Gut microbiota modulation is evident through increased beneficial taxa (e.g., Bacteroidetes, Akkermansia) and reduced pro-inflammatory species, correlating with improved metabolic parameters. Mitochondrial function is enhanced via upregulated fatty acid oxidation and TCA cycle activity, while anti-inflammatory effects arise from NF-κB pathway suppression and macrophage polarization toward an M2 phenotype. Challenges include interindividual variability in responses and a limited understanding of dynamic metabolic interactions. Conclusions: Omega-3 PUFAs target multiple pathways to improve metabolic health. Future research should prioritize chemoproteomics for direct target identification, multi-omics integration, and personalized strategies combining Omega-3 with therapies like calorie restriction.

As an agri-food by-product, the rice bran of pigmented rice, encompassing varieties such as red, black, and purple rice, has garnered increasing attention due to its richness in terms of bioactive compounds. Being mainly composed of the pericarp, aleuron, seed coat, and germ, the brown outer layer of the rice kernel offers potential health benefits and has applications in skincare. Human skin serves as the primary barrier against external threats, including pathogens, pollutants, and ultraviolet (UV) radiation. Notably, UV radiation accelerates the aging process and contributes to various skin issues. Recent trends suggest a heightened interest in incorporating pigmented rice into skincare regimens, motivated by its potential to mitigate oxidative stress, inflammation, and pigmentation, which are pivotal factors in skin aging and photodamage. With increasing consumer demand for natural and sustainable ingredients, pigmented rice has emerged as a promising candidate within the skincare and personal care sectors, effectively bridging the gap between nutrition and dermatological health. This review examines the applications of pigmented rice in skincare, with a particular focus on its bioactive components and potential mechanisms of action that contribute to skin health. The unique chemical composition of pigmented rice, which includes compounds such as anthocyanins, flavonoids, phenolic acids, and vitamin E, underlies its antioxidant, anti-inflammatory, and skin-protective properties. Despite the increasing recognition of its benefits, a comprehensive understanding of the underlying mechanisms remains limited, underscoring the necessity for further research to exploit the potential of pigmented rice in skincare applications fully.