Biology subjects

Lu, Y.-W.

Publications and source records attributed to Lu, Y.-W..

6 recordsLinked to original sources

bioRxiv2026

L-Lactate reprograms tumor-associated macrophages to drive pancreatic cancer progression via BCL3 lactylation

Metabolic reprogramming fuels pancreatic ductal adenocarcinoma (PDAC) malignancy, creating a nutrient-deprived and waste-rich microenvironment. How this extreme metabolic pressure dictates the phenotypic remodeling of infiltrating immune cells remains largely unclear. Metabolomic profiling of PDAC reveals that robust tumor glycolysis proceeds without a commensurate accumulation of extracellular lactate. Integrated single-cell profiling and tissue multiplex immunofluorescence demonstrate that tumor-associated macrophages (TAMs) act as the primary consumers of tumor-secreted lactate. The uptake of L-lactate directs macrophages toward a pro-tumorigenic state through site-specific L-lactylation of the transcriptional co-regulator BCL3 at lysine 21 (K21). Functioning as a molecular switch, K21 lactylation triggers BCL3 nuclear translocation and enhances its interaction with the NF-{kappa}B p50 subunit. The ensuing BCL3-p50 complex competitively displaces the pro-inflammatory p65 subunit, rewiring the transcriptional output to suppress inflammation and enforce tumor-supporting networks. In vivo, macrophage-specific expression of a lactylation-deficient BCL3 mutant (K21R) abolishes lactate-driven phenotypic shifts and restricts tumor growth. Clinically, a BCL3-lactylated macrophage signature spatially correlates with CD8+ T cell exclusion and predicts poor patient survival, providing a strong rationale for targeting the BCL3-lactylation axis to reverse TAM-driven PDAC progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/710237v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@173159eorg.highwire.dtl.DTLVardef@9065f3org.highwire.dtl.DTLVardef@153e0aorg.highwire.dtl.DTLVardef@9c2678_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Tissue-guided multi-omics profiling identifies extracellular vesicle biomarkers indicative of lung pathology in acute respiratory distress syndrome

BackgroundAcute respiratory distress syndrome (ARDS) remains a lethal inflammatory lung condition lacking reliable biomarkers that reflect lung-specific pathology. Extracellular vesicles (EVs) circulate systemically and may carry molecular signals from injured organs, but the correspondence between EV cargo and lung tissue alterations remains unclear. MethodsWe established aspiration-, lipopolysaccharide (LPS)-, and COVID-19-induced murine ARDS models and applied a tissue-guided multiomics framework integrating proteomic and metabolomic analyses of lung tissue and plasma-derived EVs to identify lung-originating circulating biomarkers. ResultsFour proteins--haptoglobin (HP), inter-alpha-trypsin inhibitor heavy chains 3 and 4 (ITIH3, ITIH4), and clusterin (CLU)--were consistently upregulated in both lung tissue and plasma EVs across all ARDS etiologies. Metabolomic integration revealed dysregulation of arachidonic acid metabolism as a unifying inflammatory axis. Multiomics network analysis further distinguished etiology-specific molecular programs, including glycolytic activation in aspiration-induced, platelet aggregation in LPS-induced, and vascular smooth muscle dysregulation in COVID-19-induced ARDS. ConclusionsThis study establishes a tissue-informed EV profiling framework that links local lung pathology to systemic molecular signatures, revealing HP, ITIH3, ITIH4, CLU, and arachidonic-acid-related metabolites as potential diagnostic markers for ARDS. These findings provide a foundation for developing clinically translatable, EV-based biomarker assays for early detection and molecular subtyping of lung injury.

biochemistry↗

bioRxiv2020

The mitochondrial carrier SFXN1 is critical for Complex III integrity and cellular metabolism

Mitochondrial carriers (MC) mediate the passage of small molecules across the inner mitochondrial membrane (IMM) enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterized SFXN1, a member of the non-canonical, sideroflexin MC family. We find that SFXN1, an integral membrane protein in the IMM with an uneven number of transmembrane domains, is a novel TIM22 substrate. SFXN1 deficiency specifically impairs Complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. This CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and central carbon metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.

biochemistry↗

bioRxiv2020

Adenine Nucleotide Translocase regulates the airway epithelium, mitochondrial metabolism and ciliary function

Airway hydration and ciliary function are critical to airway homeostasis and dysregulated in chronic obstructive lung disease (COPD). COPD is the 4th leading cause of death in the US and is impacted by cigarette smoking with no therapeutic options. We utilized a genetic selection approach in the amoeba Dictyostelium discoideum as a comparative discovery tool in lung biology to identify genetic protectors from cigarette smoke (CS). Adenine nucleotide translocase (ANT), a mitochondrial ADP/ATP transporter, was protective against CS in Dictyostelium and human bronchial epithelial cells. ANT2 gene expression is reduced in lung tissue from COPD patients and in a mouse smoking model. ANT1 and ANT2 overexpression resulted in enhanced oxidative respiration and ATP flux. In addition to ANTs presence in the mitochondria, ANT1 and ANT2 reside at the plasma membrane in airway epithelial cells and this localization plays a role in how ANTs regulate airway homeostasis. ANT2 overexpression stimulates airway surface liquid hydration by ATP and maintains ciliary beating after CS exposure, which are key functions of the airway. Our study highlights the potential of ANT modulation in protecting from dysfunctional mitochondrial metabolism, airway hydration, and ciliary motility in COPD.

cell biology↗

bioRxiv2020

A transferrable and interpretable multiple instance learning model for microsatellite instability prediction based on histopathology images

BackgroundMicrosatellite instability (MSI) is a negative prognostic factor for colorectal cancer (CRC) and can be used as a predictor of success for immunotherapy in pan-cancer. However, current MSI identification methods are not available for all patients. We propose an ensemble multiple instance learning (MIL)-based deep learning model to predict MSI status directly from histopathology images. DesignTwo cohorts of patients were collected, including 429 from The Cancer Genome Atlas (TCGA-COAD) and 785 from a self-collected Asian data set (Asian-CRC). The initial model was developed and validated in TCGA-COAD, and then generalized in Asian-CRC through transfer learning. The pathological signatures extracted from the model are associated with genotypes for model interpretation. ResultsA model called Ensembled Patch Likelihood Aggregation (EPLA) was developed in the TCGA-COAD training set based on two consecutive stages: patch-level prediction and WSI-level prediction. The EPLA model achieved an area-under-the -curve (AUC) of 0.8848 in the TCGA-COAD test set, which outperformed the state-of-the-art approach, and an AUC of 0.8504 in the Asian-CRC after transfer learning. Furthermore, the five pathological imaging signatures identified using the model are associated with genomic and transcriptomic profiles, which makes the MIL model interpretable. Results show that our model recognizes pathological signatures related to mutation burden, DNA repair pathways, and immunity. ConclusionOur MIL-based deep learning model can effectively predict MSI from histopathology images and are transferable to a new patient cohort. The interpretability of our model by association with genomic and transcriptomic biomarkers lays the foundation for prospective clinical research.

bioengineering↗

bioRxiv2019

Diverse flanking sequence types of blaNDM in IncX3 and IncB/O/K/Z plasmids in Escherichia coli isolated from poultry

We identified 33 blaNDM-harboring Escherichia coli in 470 poultry samples from Shandong and Guangdong provinces during 2016 to 2017 and included the subtypes blaNDM-1, blaNDM-5 and blaNDM-9. The blaNDM gene possessed by all strains was plasmid-borne and ranged in size from 46 to 265 kb. The plasmids included the replicon types IncX3, IncY, IncB/O/K/Z and IncHI2 and most were transferable and stable in recipient host bacteria. Sequences flanking blaNDM in IncX3 and IncB/O/K/Z plasmids were diverse and the mobile element IS26 played an important role in the evolution of the IncB/O/K/Z blaNDM plasmids.

microbiology↗