Biology subjects

Teo, J.

Publications and source records attributed to Teo, J..

13 recordsLinked to original sources

bioRxiv2026

PROPEL: a high-throughput shear-stress platform reveals organotypic thresholds in endothelial mechano-adaptation

Endothelial cells exhibit organotypic specialization, yet the tools to decode whether hemodynamic shear shapes this diversity across vascular beds have remained limited. Here we present PROPEL, a tubing-free, magnetic stirrer-driven platform that delivers programmable laminar shear stress (2 to 60 dyn/cm{superscript 2}) to multiple cell types in parallel within the confines of a standard Petri dish, with the modular flexibility to easily introduce different substrate geometries including 3D vessel formats. Using this platform, we profiled six human endothelial subtypes across static, low, intermediate, and high shear. Phenotypic profiling revealed subtype-specific thresholds for alignment, elongation, and Golgi-nuclear polarization, including a dissociation between elongation and polarization in dermal microvascular and saphenous venous endothelial cells at low shear. Bulk RNA sequencing showed conserved transcriptional programs that shift progressively with shear magnitude, including induction of mechanotransduction pathways alongside suppression of proliferative programs. Phenotype-informed transcriptional comparisons further linked alignment transitions to engagement of cytoskeletal and metabolic signatures. In addition to conserved responses, organotypic-specific responses were also observed. Together, these findings establish PROPEL as a scalable platform for multi-endothelial, multi-shear transcriptomic and phenotypic profiling, and reveal that endothelial cells engage shear adaptation along two organotypic axes--a threshold axis governing when a subtype responds and a signature axis governing which the shear stress response--with implications for vascular bed-specific disease susceptibility.

cell biology↗

bioRxiv2026

Softer substrates mechanical primes sustained and metabolically fit CD8+ T cells for anti-tumor activity

Adoptive T cell therapy for solid tumors is limited by poor persistence of CD8+ T cells, a dysfunction that is often programmed during ex vivo expansion. Here, we show that, when biochemical inputs are held constant,substrate mechanics alone can direct durable anti-tumor function in primary human CD8+ T cells. Using polyacrylamide (PA) hydrogels of defined stiffness (soft [~]1 kPa; stiff [~]55 kPa) in both flat and bead formats, we first establish that contact geometry dominates early activation, whereas substrate stiffness governs the 14-day expansion trajectory. Across the rapid expansion protocol, flat PA substrates sustain proliferation, limit PD-1/LAG-3 acquisition, and preserve a balanced effector-regulatory cytokine profile. In contrast, Dynabeads-expanded cells exhibit net cell loss and a more pronounced decline in cytokine output over time. To define the underlying programs, RNA-seq identifies a 125-gene biomimetic core shared by both PA conditions but absent from Dynabeads, encompassing proliferation, OXPHOS, mechanobiology, and a stem-like precursor (Tpex) signature. Consistent with these transcriptional differences, metabolic profiling shows that flat soft PA best preserves dual glycolytic and mitochondrial capacity at day 14, indicating enhanced bioenergetic flexibility. Functionally, PA-primed CD8+ T cells display superior cytotoxicity against MDA-MB-231 and MCF-7 breast cancer cells in both 2D and collagen-based 3D co-cultures, with this advantage maintained under matrix constraints that mimic solid tumor microenvironments. Together, these findings establish substrate mechanics as a tunable and functionally decisive design parameter for engineering durable, solid-tumor-effective CD8+ T cell products in preclinical in vitro models of solid tumors.

immunology↗

bioRxiv2024

Mechano-mediated M2 macrophage polarization and immune suppression in stiffened tumor microenvironment

The tumor microenvironment (TME), which is composed of various cell types and the extracellular matrix (ECM), plays crucial roles in cancer progression and treatment outcomes. However, the impact of the mechanical properties of the ECM, specifically collagen fibril alignment and crosslinking, on macrophage behavior and polarization is less understood. To investigate this, we reconstituted 3D collagen matrices to mimic the physical characteristics of the TME. Our results demonstrated that stiffening the matrix through the alignment or crosslinking of collagen fibrils promotes macrophage polarization toward the anti-inflammatory M2 phenotype. This phenotype is characterized by increased expression of CD105 and CD206 and a distinct cytokine secretion profile. The increased stiffness and aligned fibrils activate mechanotransduction pathways, notably integrin {beta}1 and PI3K signaling, leading to increased IL-4 secretion, which acts in an autocrine manner to further promote M2 polarization. Interestingly, these stiffened microenvironments also suppressed the proinflammatory response. In coculture experiments with breast cancer cell lines (MDA-MB-231 and MCF-7), macrophages within stiffened or aligned matrices significantly increased cancer cell proliferation and invasion. These findings suggest that the mechanical properties of the ECM, specifically its alignment and crosslinking, create a more favorable environment for tumor progression by modulating macrophage activity. Overall, our study underscores the critical role of ECM mechanics in shaping immune cell behavior within the TME, highlighting the potential for therapies that target ECM properties and macrophage polarization to inhibit cancer progression and enhance treatment efficacy.

bioengineering↗

bioRxiv2024

Comparison of Cd concentration in rice grain between OsNramp5 knock-out mutants and OsHAM3-overexpressing line

Cadmium (Cd) is highly toxic and a carcinogen to humans. Rice is prone to absorbing Cd and accumulating it in the grain, which raises health concerns for rice consumers. OsNramp5 is a major transporter for Cd and manganese (Mn) uptake in rice, whereas OsHMA3 is a tonoplast-localized transporter for Cd detoxification. In this study, we compared the efficiency of OsNramp5 knockout mutation and OsHAM3 overexpression in reducing Cd content in the rice grain. The grain Cd content of the OsNramp5 knockout mutants was significantly lower than that of the wild-type rice T5105. However, the OsNramp5 knockout mutants still had much higher grain Cd content than the similar OsNramp5 mutants reported previously or the OsHAM3 overexpression line developed in our previous study. Pyramiding the OsNramp5 mutant allele and the OsHAM3 transgene in a double homozygous line could not further reduce grain Cd content. The OsNramp5 gene in T5105 has a haplotype II promoter, and its knockout mutation partially impairs Mn uptake in rice. Our results demonstrate that OsHMA3 overexpression works more efficiently in generating low-Cd rice grain than OsNramp5 knockout mutation without affecting Mn uptake in rice.

bioengineering↗

bioRxiv2024

Matrix fibril alignment and density modulate YAP-mediated T-cell immune suppression

T-cells navigate through various mechanical environments within the body, adapting their behavior in response to these cues. An altered extracellular matrix (ECM) characterized by increased density and enhanced fibril alignment, as observed in cancer tissues, can significantly impact essential T-cell functions critical for immune responses. In this study, we used 3D collagen matrices with controlled density and fibril alignment to investigate T-cell migration, activation, and proliferation. Our results revealed that dense and aligned collagen matrices suppress T-cell activation through enhanced YAP signaling. By inhibiting YAP signaling, we demonstrated that T-cell activation within these challenging microenvironments improved, suggesting potential strategies to enhance the efficacy of immunotherapy by modulating T-cell responses in dense and aligned ECMs. Overall, our study deepens our understanding of T-cell mechanobiology within 3D relevant cellular microenvironments and provides insights into countering ECM-induced T-cell immunosuppression in diseases such as cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/585707v1_ufig1.gif" ALT="Figure 1"> View larger version (101K): org.highwire.dtl.DTLVardef@ccb840org.highwire.dtl.DTLVardef@5490eforg.highwire.dtl.DTLVardef@1f74d8borg.highwire.dtl.DTLVardef@103f739_HPS_FORMAT_FIGEXP M_FIG Dense and aligned extracellular matrices suppress T-cell activation via YAP signaling, affecting immunotherapy efficacy in diseases such as cancer. C_FIG

bioengineering↗

bioRxiv2023

Tissue-bound hyaluronan molecular weight as a regulator of dendritic cell immune potency

Hyaluronic acid (HA) is a major glycosaminoglycan found in the extracellular matrix (ECM) and exhibits immunoregulatory properties depending on its molecular weight (MW). However, the impact of tissue bound HA on dendritic cell (DC) functions is not well understood due to the varying distribution of HA MW under different physiological and pathological conditions. To investigate DCs in defined biosystems, we used three-dimensional (3D) collagen matrices modified with HA of specific MW, while maintaining similar microstructure and HA levels. Using these matrices, we examined the influence of HA on cytokine binding and observed distinct properties depending on the presence and MW of HA, suggesting modulation of cytokine availability by the different MW of HA. Our studies on DC immune potency revealed that low molecular weight HA (LMW-HA; 8-15 kDa) enhances immature DC (iDC) differentiation and antigen uptake, while medium (MMW-HA; 500-750 kDa) and high molecular weight HA (HMW-HA; 1250-1500 kDa) increase cytokine secretion in matured DCs (mDCs). Interestingly, the modulation of DCs surface marker expression and cytokine secretion by different MW of HA appeared to be independent of CD44. However, we found that cytokine secretion of DCs was dependent on the CD44 receptor regardless of the presence or absence of HA in the matrix. Additionally, we observed reduced migratory capacity of iDCs and mDCs when cultured on MMW- and HMW-HA matrices, and this effect was dependent on CD44. In summary, our findings provide new insights into the MW-dependent effects of tissue-bound HA on DCs, opening avenues for the design of DC-modulating materials to enhance DC-based therapy.

bioengineering↗

bioRxiv2022

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n=46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole genome sequencing data from CPE isolates (n=159) helped identify sub-strain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.

genomics↗

bioRxiv2022

Environmental and genetic disease modifiers of haploinsuffciency of A20

Monogenic diseases can often manifest diverse clinical phenotypes and cause diagnostic dilemmas. While monoallelic loss-of-function variants in TNFAIP3 (Haploinsufficiency of A20; HA20) cause a highly penetrant autoinflammatory disease, the variable expressivity suggest a role for additional genetic and environmental disease modifiers. Here, we identify critically ill children who inherited a family-specific TNFAIP3 deletion from one of their otherwise healthy parents. Each of the probands also inherited in trans a subtle loss-of-function I207L TNFAIP3 variant that is common in Oceania, originally introgressed from Denisovans. Modelling this compound heterozgous state in mice under specific pathogen free conditions demonstrated a reduced threshold to break immune tolerance. Exaggerated immune responses were precipitated by inheriting the two genetic hits on the TNFAIP3 checkpoint coupled with increasing the microbial challenge to immune tolerance, either by co-housing with pet store mice carrying a wild microbial burden or by transient dietary exposure to a chemical that diminishes the intestinal mucin barrier separating gut microbes from immune sensing systems. These data illuminate second-hit genetic and environmental modifiers contributing to complex inflammatory and autoimmune disease. Increased mechanistic understanding of the presence and contribution of disease modifiers will aid diagnostic and prognostic patient stratification and potentially reveal novel therapeutic opportunities.

immunology↗

bioRxiv2020

bioPROTACs establish RAS as a degradable target and provide novel RAS biology insights

ABSTRACTMutations to RAS proteins (H-, N-, and K-RAS) are amongst the most common oncogenic drivers and tumors harboring these lesions are some of the most difficult to treat. Although the recently discovered covalent small molecules against the KRASG12C mutant have shown promising efficacy against lung cancers, traditional barriers remain for drugging the more prevalent KRASG12D and KRASG12V mutants. Targeted degradation has emerged as an attractive alternative approach but for KRAS, identification of the required high-affinity ligands continues to be a challenge. Another significant hurdle is the discovery of a hybrid molecule that appends an E3 ligase-recruiting moiety in a manner that satisfies the precise geometries required for productive polyubiquitin transfer while maintaining favorable drug-like properties. As a tool to gain insights into the advantages and feasibility of KRAS targeted-degradation, we applied the bioPROTAC approach. This workflow centers on the intracellular expression of a chimeric protein consisting of a high-affinity target-binding domain fused to an engineered E3 ligase adapter. We generated a series of anti-RAS bioPROTACs that span different RAS isoform/nucleotide-state specificities and leverage different E3 ligases. Overall, our results provide definitive evidence for the degradability of RAS proteins. We further elucidate the functional consequences of RAS degradation, the susceptibility and degradation kinetics of various mutant KRAS, and the prevalence of different nucleotide-states in WT and mutant KRAS. Finally, if delivery challenges can be addressed, anti-RAS bioPROTACs will be exciting candidates for clinical development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cancer biology↗

bioRxiv2019

Development and evaluation of a rapid on-site water pathogen detection system for water quality monitoring

Timely response to outbreak of water-borne diseases caused by bacteria requires efficient monitoring and rapid detection strategies. Herein, we report a rapid DNA-based on-site detection system for specific detection of Pseudomonas aeruginosa. To evaluate the test performance of our method against spiked water samples, parallel tests based on real-time PCR and standard culture methods were concurrently performed. Test sensitivities of between 96.7% and 92.3% were obtained, based on the calculation obtained from qPCR and culture test, respectively, with a corresponding level of specificity of 92.9% and 83.3%. Time-to-result is around 45 min, with a detection limit of 1 CFU/100 mL. Here, a fully-deployable detection method where bacteria of-interest can be detected rapidly with high accuracy was described. This test method can be modified to detect other bacteria of-interest and can also be used in different applications. The test results can be obtained on-site and can therefore be particularly useful in public facilities health surveillance, where regulators can quickly determine if a site is safe or if other emergency response measures are required.\n\nIMPORTANCEPseudomonas aeruginosa is a well-established water quality biomarker, known to be associated to humans health risks. To ascertain the presence of this pathogen, relevant stakeholders currently rely on standard quantitative ISO methods (APHA 9213E) which require 6 days from sampling to results. This window could potentially lead to waterborne outbreaks if the contaminated water features are not shut down for proper and urgent mitigation. This manuscript describes a method to detect this disease-causing microorganism in its viable forms under 1 hour, with a sensitivity of 1 CFU/100mL. Besides providing valuable information of the quality of water system, this direct monitoring of pathogens can reduce substantial time needed from sampling to reporting. This method can be established as a platform technology for other pathogenic microorganisms. On-going work to develop economic point-of-care prototypes could facilitate quick screening of targeted waterborne pathogens and results in better assessment of public health risk and quick in devising emergency response measures and other management strategies.

microbiology↗

bioRxiv2019

bioPROTACs as versatile modulators of intracellular therapeutic targets: Application to proliferating cell nuclear antigen (PCNA)

Targeted degradation approaches have recently generated much excitement as a paradigm shift to address human disease in unprecedented ways. Amongst these, small molecule based approaches such as Proteolysis targeting chimeras (PROTACs) have attracted the lions share of attention due to their potential to tackle historically intractable targets and achieve greater potency, efficacy, and specificity over traditional small molecule inhibitors. Despite their promise, the identification of high-affinity ligands that can serve as starting points for PROTAC strategies remains challenging. As a complementary approach, we describe herein a class of intracellular biologics termed bioPROTACs. The substrate binding component of these fusion proteins consists of a peptide or an antibody-mimetic which allows for an unprecedented diversity of protein targets that can be addressed. The high-affinity binder is linked directly to an E3 ubiquitin ligase to harness the power of targeted degradation. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. Indeed, 9 out of 16 binder-E3 combinations tested resulted in greater than 70% target clearance. Through a systematic approach, we then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA), a sliding DNA clamp with critical roles in DNA replication and repair. The bioPROTAC, termed Con1-SPOP, elicited rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Compared to RNAi-based approaches which typically take days to manifest, PCNA knockdown using Con1-SPOP was evident within 4 h. The advantage of degradation versus stoichiometric inhibition was also clearly demonstrated with bioPROTAC strategies. Combining superior pharmacological inhibition and relative ease of development, bioPROTACs are powerful tools for interrogating the degradability of a substrate, for guiding the identification of the fittest E3 ligase, for studying the functional consequences associated with target protein down-regulation, and potentially for making therapeutic impacts.

cell biology↗

bioRxiv2017

The Acquisition of Resistance to Carbapenem and Macrolide-mediated Quorum Sensing Inhibition by Pseudomonas aeruginosa via a Novel Integrative and Conjugative Element ICETn43716385

Pseudomonas aeruginosa can cause persistant and life-threatening infections in immunocompromised patients. Carbapenems are the first-line agents to treat P. aeruginosa infections; therefore, the emergence of carbapenem-resistant P. aeruginosa strains has greatly challenged effective antibiotic therapy. In this study, we characterised the full-length genomes of two carbapenem resistant P. aeruginosa clinical isolates that produce the carbapebemase New Delhi metallo-{beta}-lactamase-1 (NDM-1). We found that the blaNDM-1 gene is encoded by a novel intergrative and conjugative element (ICE) ICETn43716385, which also carries the macrolide resistance gene msr(E) and the florfenicol resistance gene floR. The msr(E) gene has rarely been described in P. aeruginosa genomes. To investigate the functional roles of msr(E) in P. aeruginosa, we exogeneously expressed this gene in P. aeruginosa laboratory strains and found that the acquisition of msr(E) could abolish the azithromycin-mediated quorum sensing inhibition in vitro and the anti-Pseudomonas effect of azithromycin in vivo. In addition, the expression of msr(E) almost completely restored the azithromycin-affected P. aeruginosa transcriptome, as shown by our RNA sequencing analysis. We present the first evidence of blaNDM-1 to be carried by intergrative and conjugative elements, and the first evidence of co-transfer of carbapenem resistance and the resistance to macrolide-mediated quorum sensing inhibition into P. aeruginosa genomes.\n\nImportanceCarbapenem resistant P. aeruginosa has recently been listed as the top three most dangerous superbugs by World Health Organisation. The transmission of blaNDM-1 gene into P. aeruginosa can cause extreme resistance to carbapenems and fourth generation cephalosporins, which greatly compromises the effectiveness of these antibiotics against Pseudomonas infections. However, the lack of complete genome sequence of NDM-1-producing P. aeruginosa has limited our understanding of the transmisibility of blaNDM-1 in this organism. Here we showed the co-transfer of blaNDM-1 and msr(E) into P. aeruginosa genome by a novel integrative and conjugative element (ICE). The acquisition of these two genes confers P. aeruginosa with resistance to carbapenem and macrolide-mediated quorum sensing inhibition, both of which are important treatment stretagies for P. aeruginosa infections. Our findings highlight the potential of ICEs in transmitting carbapenem resistance, and that the anti-virulence treatment of P. aeruginosa infections by macrolides can be challenged by horizontal gene transfer.

genomics↗

bioRxiv2017

Network analysis of patient flow in two UK acute care hospitals identifies key sub-networks for A&E performance

The topology of the patient flow network in a hospital is complex, comprising hundreds of overlapping patient journeys, and is a determinant of operational efficiency. To understand the network architecture of patient flow, we performed a data-driven network analysis of patient flow through two acute hospital sites of Kings College Hospital NHS Foundation Trust. Administration databases were queried for all intra-hospital patient transfers in an 18-month period and modelled as a dynamic weighted directed graph. A core subnetwork containing only 13-17% of all edges channelled 83-90% of the patient flow, while an ephemeral network constituted the remainder. Unsupervised cluster analysis and differential network analysis identified sub-networks where traffic is most associated with A&E performance the following day. Increased flow to clinical decision units was associated with the best A&E performance in both sites. The component analysis also detected a weekend effect on patient transfers which was not associated with performance. We have performed the first data-driven hypothesis-free analysis of patient flow which can enhance understanding of whole healthcare systems. Such analysis can drive transformation in healthcare as it has in industries such as manufacturing.

bioinformatics↗