Biology subjects

Tay, A.

Publications and source records attributed to Tay, A..

9 recordsLinked to original sources

bioRxiv2026

Cutibacterium acnes-derived short-chain fatty acids drive lipogenesis and induce holocrine secretion in human sebocytes

Sebum lipids are one of the key ecological determinants of skin microbiome composition, where sebaceous sites are enriched with sebum utilising microbes such as Cutibacterium acnes. While sebaceous gland (SG) activation and sebogenesis are classically viewed as host-regulated processes, the association of C. acnes expansion with sebum production in the skin suggests a possible bidirectional host-microbe regulation. Using bacterial supernatants, we combined image-based lipid quantification, GC-FID metabolite profiling, lipid secretion quantification, and transcriptomic analysis to determine the metabolic drivers of the interaction between C. acnes and sebocytes. We found that C. acnes secretome significantly increased lipid droplet accumulation in sebocytes and propionate as the primary driver of this lipogenic response. Mechanistically, propionate reprogrammed the central carbon metabolism, redirecting carbon flux toward energy production and generation of precursors for lipid biosynthesis. Propionate also promoted lipid assembly pathways and modulated the composition of the secreted lipids from the treated sebocytes. We further show that propionate promotes expression of late sebocyte differentiation markers associated with holocrine secretion. Together, these findings redefine the relationship between microbiome and sebaceous glands, and identify C. canes as an active regulator promoting both sebogenesis and holocrine secretion for the release of lipids in the pilosebaceous unit.

molecular biology↗

bioRxiv2026

Multi-omics and functional analysis of a bioengineered vascularized pancreatic cancer model reveal an immunosuppressive and therapy-resistant niche

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease characterized by therapy resistance and an immunosuppressive tumor microenvironment. To comprehensively characterize the complex stromal-immune cell interactions that drive PDAC aggressiveness, we applied an integrated multi-modal approach combining single-cell RNA sequencing, spatial transcriptomics, proteomics, immunofluorescence, and microfluidic-based functional assays to bioengineered spheroid models with increasing cellular complexity (up to four cell types) integrating human pancreatic cancer cells, pancreatic stellate cells, endothelial cells, and monocyte-derived macrophages. By incorporating vascularization within the OrganiX microfluidic platform, we enable studies of immune cell trafficking in vascularized tumors. Multi-omics phenotyping revealed coordinated molecular programs in our four-cell organotypic spheroid models, including enhanced hypoxic and glycolytic pathways, NF-{kappa}B activation, and ECM remodeling. Stromal and immune cells acquired tumor-associated phenotypes mirroring patient heterogeneity, including IL-1{beta}+ macrophages, inflammatory cancer-associated fibroblasts (iCAFs), and antigen-presenting CAFs (apCAFs). The four-cell model exhibited superior clinical relevance, with gene expression signatures that correlated more closely with poor-prognosis patient cohorts and cancer hallmarks that were functionally validated through microfluidic-based assays demonstrating enhanced tumor invasion, angiogenesis, and therapeutic resistance. Finally, live imaging combined with transcriptomic readouts captures dynamic interactions between neutrophils and cancer cells in the vascularized microtumor, enabling direct observation of intravascular events relevant to metastatic dissemination. This integrated analysis demonstrated the recreation of a human-relevant aggressive PDAC niche, establishing a framework that bridges in vitro cellular crosstalk studies with patient-relevant therapeutic responses, offering a powerful translational tool for therapy development in PDAC.

cancer biology↗

bioRxiv2026

NR4A1 limits CD8⁺ T Cell effector responses and protection in tuberculosis

During Mycobacterium tuberculosis (Mtb) infection, CD8+ T cells exhibit dysfunction with impaired cytotoxicity and limited localization to granuloma cores. Using knockout mice, adoptive-transfer models and validation in macaque and human datasets, we identified the nuclear receptor NR4A1 as a key restrainer of CD8+ T cell immunity in tuberculosis (TB). Mtb-infected Nr4a1-/- mice displayed reduced bacterial burden, attenuated pathology, higher lung CD8+/CD4+ T cell ratios, and enhanced CD8+ T cell effector functions. Bulk and single-cell RNA sequencing revealed suppression of gene expression program linked with exhaustion, and expansion of Nkg7+ and Granzyme+ cytotoxic CD8+ T cell subsets in Nr4a1-/- mice. Spatial analyses demonstrated increased infiltration of Nkg7+ activated CD8+ T cells in Nr4a1-/- lesions. ChIP-qPCR showed NR4A1 binding to Nkg7 promoter, and Nkg7 knockdown abrogated the enhanced cytotoxicity of Nr4a1-/- CD8+ T cells. Pharmacologic inhibition of NR4A1 reduced Mtb burden and pathology, and restored Nkg7 expression and CD8+ T cell infiltration in the lung. Together, these findings identify NR4A1 as a negative regulator of CD8+ T cell-mediated immunity in TB and suggest the NR4A1-NKG7 axis as a novel host-directed therapeutic target. A one-sentence summary of your paperNR4A1 suppresses CD8+ T cell infiltration and cytotoxicity in TB lesions, and its inhibition enhances host resistance to Mtb infection.

immunology↗

bioRxiv2025

A Machine Learning Approach Reveals CRISPR-Cas I-F as a Genomic Marker of Antibiotic Susceptibility in Uropathogenic E. coli

BackgroundAntimicrobial resistance (AMR) in Escherichia coli is a critical global health challenge, particularly in urinary tract infections, where first-line treatments are increasingly compromised. While horizontal gene transfer (HGT) via mobile genetic elements is a major driver of AMR, the genomic factors that may constrain resistance gene acquisition remain underexplored. CRISPR-Cas systems, which provide adaptive immunity against foreign DNA, could influence AMR dynamics, but their role in E. coli remains incompletely understood. MethodsWe conducted a comprehensive whole-genome analysis of uropathogenic E. coli isolates, including a newly sequenced collection from Australian clinical samples and an independent, globally sourced validation cohort. Antimicrobial susceptibility profiles were integrated with CRISPR-Cas subtype classification, resistance gene burden, and mobile element content. Elastic net regression, adaptive lasso, and tree-based machine learning models were used to identify genomic predictors of resistance, with performance validated across both datasets. ResultsCRISPR-Cas subtype I-F was consistently associated with susceptibility to antibiotics commonly acquired through HGT, including trimethoprim and ampicillin, and linked to lower ARG and MGE burden. In contrast, Type I-E arrays, especially when co-occurring with orphan I-F arrays, were associated with increased resistance. These associations remained robust after adjusting for phylogroup, plasmid content, and genomic background, and were validated across datasets. ConclusionsSubtype-specific CRISPR-Cas systems shape antibiotic resistance profiles in E. coli, with Type I-F functioning as a potential genomic barrier to ARG acquisition. These findings highlight CRISPR array typing as a novel biomarker for AMR risk prediction and surveillance, and suggest new opportunities for leveraging CRISPR-based mechanisms to limit resistance propagation in clinical contexts.

genomics↗

bioRxiv2025

Bioengineered human tonsil organoids as an immuno-engineering platform for evaluating immune functions

Although animal models remain the preclinical gold standard, they are constrained by interspecies differences in adaptive immunity, including antibody class-switching, affinity maturation, and multicellular interactions. To address this gap, we established a more physiologically relevant platform, a bioengineered tonsil organoid (BTO) system that combines autologous tonsil-derived stromal cells with immune cells to generate highly uniform organoids, preserving multicellular complexity and sustained stromal-immune interactions. BTO cultures mounted robust, antigen-specific recall responses to influenza, tetanus, and COVID-19 antigens. Notably, stimulation with ovalbumin and SARS-CoV-1 spike protein expanded antigen-recognizing B cells, indicating capacity for naive responses. Digital spatial transcriptomics and proteomics analysis confirmed immune-stromal crosstalk underpinning both humoral and cellular responses of BTO after challenge. These data highlight stromal cells as active scaffolds that not only maintain 3D architecture but also facilitate immune activation, memory recall, and recognition of naive antigens. Together, BTO offers a human-relevant model for mechanistic immunology and for pre-clinical evaluation on immunotherapies and vaccines not achievable with 2D cultures or animal models.

bioengineering↗

bioRxiv2025

Efficient CRISPR-Cas9-mediated genome editing of the cane toad (Rhinella marina)

Invasive species inflict major ecological, economic, social, and cultural harm worldwide, highlighting the urgent need for innovative and effective control strategies. Genome editing offers exciting possibilities for creating highly targeted control methods for invasive species. Here, we demonstrate CRISPR-Cas9 genome editing in the cane toad (Rhinella marina), one of Australias most notorious invasive species, by targeting the tyrosinase gene to produce albino phenotypes that provide clear visual markers for assessing editing efficiency. Microinjection of Cas9 protein and guide RNAs into one-cell zygotes resulted in 87.6% of mosaic larvae displaying nearly complete albinism, with 2.3% exhibiting complete albinism. For completely albino individuals, genomic analysis confirmed predominantly frameshift mutations or large deletions at the target site, with no wild-type alleles detected. Germline transmission rates reflected the extent of albinism in the mosaic adult, where we achieved maternal germline transmission rates of almost 100%. This technology, representing the first application of CRISPR-Cas9 in the Bufonidae family, opens possibilities for exploring both basic research questions and strategies for population control.

synthetic biology↗

bioRxiv2021

Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh

Yogurt quality mainly depends on nutritional properties, microbial diversity and purity of starter culture. This study aimed to assess the nutritional composition and microbiome diversity in yogurt. Microbial diversity was analyzed by 16S and 18S rRNA based high-throughput sequencing. Significantly (P<0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt whereas sour varieties had significantly higher ash and minerals. Metagenomic investigation showed that 44.86% and 55.14% reads were assigned to bacterial and fungal taxa, respectively, with significantly higher taxonomic richness in sour yogurt. A significant difference in bacterial (Ppermanova=0.001) and fungal (Ppermanova=0.013) diversity between sweet and sour yogurt was recorded. We detected 76 bacterial and 70 fungal genera across these samples which were mostly represented by Firmicutes (>92%) and Ascomycota (98%) phyla, respectively. Among the detected genera, 36.84% bacterial and 22.86% fungal genera were found in both yogurt types. Our results suggest that Streptococcus (50.82%), Lactobacillus (39.92%), Enterobacter (4.85%), Lactococcus (2.84%) and Aeromonas (0.65%) are the most abundant bacterial genera, while Kluyveromyces (65.75%), Trichosporon (8.21%), Clavispora (7.19%), Candida (6.71%), Iodophanus (2.22%), Apiotrichum (1.94%), and Issatchenkia (1.35%) are the most abundant fungal genera in yogurt metagenomes. This is the first study on nutritional properties and microbiome diversity of Bangladeshi yogurt that would be a benchmark for safe production of quality yogurt by commercial manufacturers.

microbiology↗

bioRxiv2021

The Dual Mechanisms of Cognitive Control dataset: A theoretically-guided within-subject task fMRI battery

Cognitive control is a critical higher mental function, which is subject to considerable individual variation, and is impaired in a range of mental health disorders. We describe here the initial release of Dual Mechanisms of Cognitive Control (DMCC) project data, the DMCC55B dataset, with 55 healthy unrelated young adult participants. Each participant performed four well-established cognitive control tasks (AX-CPT, Cued Task-Switching, Sternberg Working Memory, and Stroop) while undergoing functional MRI scanning. The dataset includes a range of state and trait self-report questionnaires, as well as behavioural tasks assessing individual differences in cognitive ability. The DMCC project is on-going and features additional components (e.g., related participants, manipulations of cognitive control mode, resting state fMRI, longitudinal testing) that will be publicly released following study completion. This DMCC55B subset is released early with the aim of encouraging wider use and greater benefit to the scientific community. The DMCC55B dataset is suitable for benchmarking and methods exploration, as well as analyses of task performance and individual differences.

neuroscience↗

bioRxiv2020

Single cell RNA-seq reveals immunosuppressive gastric stem-like cancer cells as a poor prognostic factor

ObjectiveGastric cancer (GC) tumors are highly heterogenous with different subpopulations of epithelial cells. We employed single cell RNA sequencing (scRNA-seq) to dissect the heterogeneity and identified subpopulations of cancer cells with stem-like properties. We further investigated their resistance to oxaliplatin chemotherapy and their contribution to gastric cancer outcome. DesignWe performed scRNA-seq on FACS sorted epithelial and immune cells from paired samples of GC tumors and normal adjacent tissues. We identified two epithelial subpopulations (STMN1+IQGAP3+ and STMN1+IQGAP3-) with stem-like properties. We characterized and compared them to known healthy gastric stem cell populations. We also cultivated GC derived organoids to study the chemoresistance of similarly marked populations. Lastly, we employed immunohistochemistry (IHC) staining to ascertain the predicted immunosuppressive interactions. ResultsThe STMN1+IQGAP3+ subpopulation showed a higher tumor mutation burden, upregulated proliferative pathways and transcriptomically resembled proliferative healthy gastric isthmus stem cells. The STMN1+IQGAP3- subpopulation were comparatively quiescent and transcriptomically resembled enteroendocrine cells. Both transcriptomic signatures were associated with worse mortality than other epithelial subpopulations with the quiescent being associated with the poorest patient survival. GC tissue derived organoids were dominated by STMN1+IQGAP3+ cells but the STMN1+IQGAP3- compartment was more resistant to chemotherapy. We also verified the likely suppression of CD8 T cell cytotoxicity by STMN1+IQGAP3+ cells through the NECTIN2/TIGIT interaction. ConclusionsCancer cells with stem-like characteristics are associated with poor survival through chemoresistance and immunosuppression. Reactivating the immune system through checkpoint blockade is an opportunity to eliminate these cells. What is already known on this topicMultiple gastric stem cell populations have been identified and linked to tumor initiation in rodent-based studies. However, none of them have been conclusively proven in human tumors. Isolating and characterizing tumor cells with stem-like properties will help shed light on their possible origin and possible mitigation strategies. What this study addsHere we identified two sets of stem-like gastric cancer cells that are associated with poorer patient prognosis. One set is highly proliferative and exhibits oxaliplatin susceptibility. It also engages in immunosuppressive interactions such as NECTIN2/TIGIT. The other set is quiescent and highly resistant to oxaliplatin. How this study might affect research, practice or policyThe transcriptome signatures of the identified stem-like cells can aid in patient prognosis and identify patients who can benefit from checkpoint blockade therapy to reactivate their immune response towards gastric cancer cells.

immunology↗