Biology subjects

Ng, T.

Publications and source records attributed to Ng, T..

At least 19 recordsLinked to original sources

bioRxiv2026

TOPII-targeting and MUS81 deficiency sensitise HER2-low tumour models to T-DXd

In this study, we identify Topoisomerase II (TopII ) targeting and MUS81 deficiency as sensitisers to trastuzumab deruxtecan (T-DXd), a HER2-targeting antibody-drug conjugate with a potent topoisomerase I poison payload that is of clinical importance in the treatment of HER2 expressing solid tumours in a range of cancer types. Using preclinical tumour spheroid models of breast and colorectal cancer, we show that TopII targeting with doxorubicin sensitises HER2-low tumour cells to T-DXd, elevating cell cytotoxicity, DNA damage, and checkpoint pathway activation. T-DXd treatment, both as a single agent and in combination with doxorubicin, increases TopII expression, highlighting this nuclear endonuclease as a potential candidate biomarker for T-DXd response in both the HER2-high and HER2-low setting. Using isogenic CRISPR models, we show that genetic loss of the MUS81 structure-specific endonuclease, a key processor of branched DNA structures and under-replicated DNA, sensitises HER2-low colorectal cancer cells to T-DXd. Given that reduced expression of MUS81 is closely related to metastasis and poor prognosis in colorectal carcinoma, our findings highlight the potential utility of these treatment combinations in a subset of colorectal cancer patients that present with HER2-positve/MUS81-low disease.

cancer biology↗

bioRxiv2026

Sleep renormalizes learning-perturbed cortical population dynamics to stabilize memory

The brain must preserve learning-induced circuit changes without destabilizing the network dynamics required for future learning. We show that sleep addresses this tension through perturbation-dependent renormalization of cortical dynamics. Using high-density electroencephalography in humans following declarative learning and a matched non-learning control, we found that learning displaced cortical population dynamics during wakefulness, followed by an opposing reorganization during non-rapid eye movement (NREM) sleep. The preceding waking perturbation constrained this sleep response across time, cortical space, and individuals: NREM activity evolved along the wake-defined state-space direction, regions with larger waking perturbations showed stronger opposing responses, and larger perturbations predicted stronger restorative trajectories. This cross-state geometry generalized to held-out participants and predicted sleep-specific memory benefit beyond either state alone or their simple difference. Neural stability is therefore achieved by regulating trajectories rather than returning to a fixed baseline, with plasticity-induced perturbations specifying how cortical state space is reorganized to preserve learned structure while enabling further change.

neuroscience↗

bioRxiv2026

Objective Quality Assessment for Precision Functional MRI Data

Precision functional mapping (PFM) enables individual-level characterization of brain network organization but requires substantially more and higher-quality fMRI data than is standard. Despite its growing use, objective criteria for data sufficiency and quality needed to ensure interpretable and replicable individual-level results remain unclear. Here, we introduce the Network Similarity Index (NSI), an objective measure of the extent to which functional connectivity (FC) patterns in an individual dataset express the large-scale network structure required for PFM. NSI captures the integrity of low-spatial-frequency, coherent network organization and denoising fidelity, and aligns closely with blinded expert assessments of PFM usability. NSI also accounts for variability in the rate at which FC becomes reliable across individuals. Here, we provide an open-source framework for NSI-based data quality evaluation and models for linking NSI values with expert-judged PFM suitability. This framework can also inform expected returns from additional data collection, enabling principled decisions about data sufficiency and replication in precision fMRI research.

neuroscience↗

bioRxiv2025

Nano-Sieve Enabled On Chip Concentration and Multiplexed Detection of Raman-Dye Labeled Nanocubes

To address persistent challenges in molecular detection--particularly signal variability, low analyte abundance, and poor spectral reproducibility--a portable bead-stacked nano-sieve platform was engineered to enable robust on-chip Raman signal amplification using silver nanocubes (AgNCs) functionalized with Raman-active thiolated ligands. The microdevice integrates deformable elastomeric channels with magnetic bead stacking to immobilize and concentrate AgNCs within confined nanoscopic junctions, thereby generating densely packed plasmonic hot-spot architectures that markedly enhance Surface-Enhanced Raman Scattering (SERS) efficiency. Time-resolved measurements revealed substantial increases in Raman intensity for both 4-mercaptobenzoic acid (4-MBA) and 4-aminothiophenol (4-ATP), outperforming corresponding off-chip assays and maintaining stable enhancement factors over a four-hour operational window. Furthermore, the platform successfully demonstrated multiplexed sensing capability: mixed-analyte experiments containing 4-MBA, 4-ATP, and cysteamine produced clearly distinguishable spectral fingerprints, even under serial dilution and dynamically pulsed sample delivery. Collectively, these results establish the bead-stacked nano-sieve as a versatile, label-free, and scalable diagnostic architecture capable of achieving high sensitivity and spectral fidelity under continuous-flow conditions. Our technology holds significant promise for real-time, non-invasive molecular surveillance, point-of-care diagnostics, and early disease monitoring in resource-limited or field-deployable settings.

bioengineering↗

bioRxiv2025

End-to-end automation of repeat-target cryo-EM structure determination in CryoSPARC

Single particle cryo-EM is a valuable and growing technique for life science and drug discovery. Currently, obtaining state-of-the-art results from cryo-EM data analysis requires a human in the loop to analyze intermediate results and make image processing decisions. This bottleneck limits the achievable throughput of structure determination, especially in high-throughput settings such as structure-based drug design. In this work, we develop an end-to-end automation strategy for repeat-target structure determination using new tools in CryoSPARC. We demonstrate completely hands-off processing of 21 challenging G protein-coupled receptor (GPCR) datasets. In 17 of 21 cases, automated processing meets or exceeds published resolution and map quality and, in several cases, provides significant improvement in receptor and ligand density that allows improved model building. Our results on both active and inactive state GPCRs show that our automation strategy generalizes easily to new target classes, and that complete automation of data processing is straightforward to achieve in CryoSPARC. We provide downloadable CryoSPARC Workflow files so that users can import, replicate, adapt and extend our automated workflow for their own targets, enabling cryo-EM to be applied at larger scales and to answer larger biological questions.

biophysics↗

bioRxiv2025

A new heme enzyme family forms hydrazine groups in diverse biosynthetic pathways

Nitrogen-nitrogen (N-N) bond formation is an inherently challenging chemical process that plays a key role in the global nitrogen cycle. An array of microbial metalloenzyme complexes has evolved to shuttle nitrogen between biologically accessible reduced or oxidized states and its inert form as dinitrogen (N2) gas. More recently, N-N bond formation has been observed in a more specialized context, natural product biosynthesis. Here, we report the discovery of a unique metalloenzyme complex that forms hydrazine functional groups in the biosynthetic pathways of structurally diverse natural products. This heterodimeric system consists of a heme enzyme from a previously unidentified family and a partner ferredoxin. Together, these enzymes effect the unprecedented four-electron reduction of nitrite (NO2-) to form a hydrazine functional group on a substrate amino acid in an oxygen-independent reaction that resembles primary microbial nitrogen metabolism. These enzymes are unexpectedly widespread among bacteria and are present in diverse genomic contexts, including cryptic biosynthetic gene clusters, highlighting the importance of this previously uncharacterized protein family. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/656397v1_ufig1.gif" ALT="Figure 1000"> View larger version (30K): org.highwire.dtl.DTLVardef@232c7forg.highwire.dtl.DTLVardef@13e46f1org.highwire.dtl.DTLVardef@1a3a2e9org.highwire.dtl.DTLVardef@1c7e32_HPS_FORMAT_FIGEXP M_FIG TOC C_FIG

biochemistry↗

bioRxiv2025

WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response

The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibitors (WEE1i) are largely unknown. A genome-wide insertional mutagenesis screen revealed that mutation of EIF2A, a translation regulator, sensitized to WEE1i. Mechanistically, WEE1i treatment triggers a translational shut-down, which is lethal in combination with the reduced translation of EIF2AKO cells. A genome-wide CRISPR-Cas9 screen revealed that inactivation of integrated stress response (ISR) kinases GCN1/2 rescued WEE1i-mediated cytotoxicity. WEE1i induced GCN2 activation, ATF4 upregulation, and altered ribosome dynamics. Loss of the collided ribosome sensor ZNF598 conversely increased sensitivity to WEE1i. Notably, the ISR was not required for WEE1i to induce DNA damage, premature mitotic entry or sensitization to DNA-damaging chemotherapeutics. ISR activation was independent of CDK1/2 activation. Importantly, WEE1i-mediated ISR activation was independent of WEE1 presence, pointing at off-target effects, which are shared by multiple chemically distinct WEE1i. This response was also observed in peripheral blood mononuclear cells. Importantly, low-dose WEE1 inhibition did not induce ISR activation, while it still synergized with PKMYT1 inhibition. Taken together, WEE1i triggers toxic ISR activation and translational shutdown, which can be prevented by low-dose or combination treatments, while retaining the cell cycle checkpoint-perturbing effects.

cancer biology↗

bioRxiv2025

A cardiac microphysiological system for screening lipid nanoparticle/mRNA complexes predicts in vivo efficacy for heart transfection

Lipid nanoparticle (LNP)/mRNA complexes have tremendous potential for treating cardiac diseases but lack the transfection efficiency required for successful heart therapeutics. A challenge preventing the development of cardiac LNPs is the lack of in vitro screening platforms that maximize transfection and predict efficacy. Here, we demonstrate that a phenotypic cardiac microphysiological system (MPS), constructed from a human induced pluripotent stem cell cardiomyocytes (hiPSC-CM) Cre-reporter line, can identify LNP/mRNA complexes that diffuse efficiently within 3D cardiac micromuscles and transfect cardiomyocytes with high efficiency. Successful LNP formulations contained an acid-degradable PEG (ADP)-lipid, where ADP-LNPs containing 10% PEG had enhanced diffusion and gene editing efficiency in the cardiac MPS. The in vivo delivery of LNP/mRNA complexes, including luciferase and CRE mRNA, into Ai6 mice confirmed the cardiac MPS screening outcomes. It revealed that ADP-LNPs achieved notably superior transfection in the heart with reduced off-target liver uptake compared to a standard LNP formulation. The cardiac MPS showed strong LNP transfection in vitro and pinpointed a promising formulation for in vivo mRNA delivery to the heart.

bioengineering↗

bioRxiv2025

Pillar arrays as tunable interfacial barriers for microphysiological systems

We report on the design and fabrication of a novel circular pillar array as an interfacial barrier for microfluidic microphysiological systems (MPS). Traditional barrier interfaces, such as porous membranes and microchannel arrays, present limitations due to inconsistent pore size, complex fabrication and device assembly, and lack of tunability using a scalable design. Our pillar array overcomes these limitations by providing precise control over pore size, porosity, and hydraulic resistance through simple modifications of pillar dimensions. Serving as an interface between microfluidic compartments, it facilitates cell aggregation for tissue formation and acts as a tunable diffusion barrier that mimics diffusion in vivo. We demonstrate the utility of barrier design to engineer physiologically relevant cardiac microtissues and a heterotypic model with vasculature within the device. Its tunable properties offer significant potential for drug screening/testing and disease modeling, enabling comparisons of drug permeability and cell migration in MPS tissue with or without vasculature.

bioengineering↗

bioRxiv2024

Does slow oscillation-spindle coupling contribute to sleep-dependent memory consolidation? A Bayesian meta-analysis

The active system consolidation theory suggests that information transfer between the hippocampus and cortex during sleep underlies memory consolidation. Neural oscillations during sleep, including the temporal coupling between slow oscillations (SO) and sleep spindles (SP), may play a mechanistic role in memory consolidation. However, differences in analytical approaches and the presence of physiological and behavioral moderators have led to inconsistent conclusions. This meta-analysis, comprising 23 studies and 297 effect sizes, focused on four standard phase-amplitude coupling measures including coupling phase, strength, percentage, and SP amplitude, and their relationship with memory retention. We developed a standardized approach to incorporate non-normal circular-linear correlations. We found strong evidence supporting that precise and strong SO-fast SP coupling in the frontal lobe predicts memory consolidation. The strength of this association is modulated by memory type, aging, and dynamic spatio-temporal features, including SP frequency and cortical topography. In conclusion, SO-fast SP coupling should be considered as a general physiological mechanism for memory consolidation.

neuroscience↗

bioRxiv2024

Localized in vivo prodrug activation using radionuclides

Radionuclides used for imaging and therapy can show high molecular specificity in the body with appropriate targeting ligands. We hypothesized that local energy delivered by molecularly targeted radionuclides could chemically activate prodrugs at disease sites while avoiding activation in off-target sites of toxicity. As proof-of-principle, we tested whether this strategy of "RAdionuclide induced Drug Engagement for Release" (RAiDER) could locally deliver combined radiation and chemotherapy to maximize tumor cytotoxicity while minimizing exposure to activated chemotherapy in off-target sites. MethodsWe screened the ability of radionuclides to chemically activate a model radiation-activated prodrug consisting of the microtubule destabilizing monomethyl auristatin E caged by a radiation-responsive phenyl azide ("caged-MMAE") and interpreted experimental results using the radiobiology computational simulation suite TOPAS-nBio. RAiDER was evaluated in syngeneic mouse models of cancer using fibroblast activation protein inhibitor (FAPI) agents 99mTc-FAPI-34 and 177Lu-FAPI-04, the prostate-specific membrane antigen (PSMA) agent 177Lu-PSMA-617, combined with caged-MMAE or caged-exatecan. Biodistribution in mice, combined with clinical dosimetry, estimated the relationship between radiopharmaceutical uptake in patients and anticipated concentrations of activated prodrug using RAiDER. ResultsRAiDER efficiency varied by 250-fold across radionuclides (99mTc>177Lu>64Cu>68Ga>223Ra>18F), yielding up to 1.22{micro}M prodrug activation per Gy of exposure from 99mTc. Computational simulations implicated low-energy electron-mediated free radical formation as driving prodrug activation. Clinically relevant radionuclide concentrations chemically activated caged-MMAE restored its ability to destabilize microtubules and increased its cytotoxicity by up to 600-fold compared to non-irradiated prodrug. Mice treated with 99mTc-FAPI-34 and caged-MMAE accumulated up to 3000x greater concentrations of activated MMAE in tumors compared to other tissues. RAiDER with 99mTc-FAPI-34 or 177Lu-FAPI-04 delayed tumor growth, while monotherapies did not (P<0.03). Clinically-guided dosimetry suggests sufficient radiation doses can be delivered to activate therapeutically meaningful levels of prodrug. ConclusionThis proof-of-concept study shows that RAiDER is compatible with multiple radionuclides commonly used in nuclear medicine and has the potential to improve the efficacy of radiopharmaceutical therapies to treat cancer safely. RAiDER thus shows promise as an effective strategy to treat disseminated malignancies and broadens the capability of radiopharmaceuticals to trigger diverse biological and therapeutic responses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/606075v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@18aef37org.highwire.dtl.DTLVardef@5f36eforg.highwire.dtl.DTLVardef@10fa0ccorg.highwire.dtl.DTLVardef@105c416_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Loss of TLR9 expression in breast cancer tumour cells and its role in the cell cycle.

Toll-like receptor 9 (TLR9), primarily expressed in human dendritic and B cells, recognizes double-stranded DNA motifs from pathogens, initiating an inflammatory response. Recent studies have revealed TLR9s involvement beyond its conventional role in immune response, notably during the tumorigenesis of various cancers such as head and neck, cervical, and ovarian cancers. Here we show by immunohistochemistry analysis demonstrated significantly lower TLR9 levels in breast cancer tumors compared to normal breast tissue epithelium. Similarly, TLR9 downregulation was also observed in several transformed breast cancer cell lines versus untransformed breast epithelial cell lines. Furthermore, overexpression of TLR9 led to reduced proliferation potential of breast cancer cell associated with activation of senescence as was evident by upregulation of proinflammatory cytokine IL-6, chemokines IL-8 and CXCL1; and growth factor GM-CSF. These findings support TLR9s regulatory role in mitigating breast cancer and highlight its critical connection between the inflammatory response and tumor immunity.

cell biology↗

bioRxiv2023

Boosting bactericidal immunity of a recombinant Mycobacterium smegmatis strain via zinc-dependent ribosomal proteins

Tuberculosis (TB) continues to be a major global health burden and kills over a million people annually. New immunization strategies are required for the development of an efficacious TB vaccine that can potentially induce sterilizing immunity. In this study, we first confirmed that various strains of the IKEPLUS vaccine confer a higher survival benefit than BCG in a murine model of intravenous Mycobacterium tuberculosis (Mtb) infection. We have shown that there was a significant increase in the expression of the Rv0282 when IKEPLUS was grown in low zinc and iron containing Sauton medium. We confirmed on biofilm assays that zinc plays a vital role in the growth and formation of Mycobacterium smegmatis (M. smegmatis) biofilms. IKEPLUS grown in low zinc media led to better protection of mice after intravenous challenge with very high dosage of Mtb. We also showed that various variants of IKEPLUS induced apoptotic cell-death of infected macrophages at a higher rate than wild type M. smegmatis. We next attempted to determine if zinc containing ribosomal proteins such as rpmb2 could contribute to protective efficacy against Mtb infection. Since BCG has an established role in anti-mycobacterial efficacy, we boosted BCG vaccinated mice with rmpb2 but this did not lead to an increment in the protection mediated by BCG.

microbiology↗

bioRxiv2023

Expansion of a frontostriatal salience network in individuals with depression

Hundreds of neuroimaging studies spanning two decades have revealed differences in brain structure and functional connectivity in depression, but with modest effect sizes, complicating efforts to derive mechanistic pathophysiologic insights or develop biomarkers.1 Furthermore, although depression is a fundamentally episodic condition, few neuroimaging studies have taken a longitudinal approach, which is critical for understanding cause and effect and delineating mechanisms that drive mood state transitions over time. The emerging field of precision functional mapping using densely-sampled longitudinal neuroimaging data has revealed unexpected, functionally meaningful individual differences in brain network topology in healthy individuals,2-5 but these approaches have never been applied to individuals with depression. Here, using precision functional mapping techniques and 11 datasets comprising n=187 repeatedly sampled individuals and >21,000 minutes of fMRI data, we show that the frontostriatal salience network is expanded two-fold in most individuals with depression. This effect was replicable in multiple samples, including large-scale, group-average data (N=1,231 subjects), and caused primarily by network border shifts affecting specific functional systems, with three distinct modes of encroachment occurring in different individuals. Salience network expansion was unexpectedly stable over time, unaffected by changes in mood state, and detectable in children before the subsequent onset of depressive symptoms in adolescence. Longitudinal analyses of individuals scanned up to 62 times over 1.5 years identified connectivity changes in specific frontostriatal circuits that tracked fluctuations in specific symptom domains and predicted future anhedonia symptoms before they emerged. Together, these findings identify a stable trait-like brain network topology that may confer risk for depression and mood-state dependent connectivity changes in frontostriatal circuits that predict the emergence and remission of depressive symptoms over time.

neuroscience↗

bioRxiv2023

Chemotherapeutic regulation of the ROS/MondoA-dependent TXNIP/GDF15 axis; and derivation of a new organoid metric as a predictive biomarker

Chemotherapy, the standard of care treatment for cancer patients with advanced disease, has been increasingly recognised to activate host immune responses to produce durable outcomes. Here, in colorectal adenocarcinoma (CRC) we identify chemotherapy-induced Thioredoxin Interacting Protein (TXNIP), a MondoA-dependent tumor suppressor gene, as a negative regulator of Growth/Differentiation Factor 15 (GDF15). GDF15 is a negative prognostic factor in CRC and promotes the differentiation of regulatory T cells (Tregs), through CD48 ligation. Intriguingly, multiple models including patient-derived tumor organoids demonstrate that loss of TXNIP/GDF15 axis functionality is associated with advanced disease or chemotherapeutic resistance, with transcriptomic or proteomic GDF15/TXNIP ratios showing potential as a prognostic biomarker. These findings illustrate a potentially common pathway where chemotherapy-induced epithelial stress drives local immune remodelling for patient benefit, with disruption of this pathway seen in refractory or advanced cases.

cancer biology↗

bioRxiv2023

CytoPb: Segmentation-free and threshold-free analysis of highly multiplexed images of biological tissue

We present a novel method and code, CytoPb, for the analysis of multiplexed images that is segmentation-free and threshold-free and produces results that correlate well with existing methods but is faster to run, needs minimal training and removes subjectivity associated with the validation of single-cell segmentation and thresholding. In three data sets cell abundance measures correlate with previous methods (Pearsons coef. >0.75). Neighbourhood analysis and cell-cell proximity are possible.

immunology↗

bioRxiv2022

Perivascular macrophages collaborate to facilitate chemotherapy resistance in cancer

A subset of tumor associated macrophages (TAMs) identified by their expression of the lymphatic vessel endothelial hyaluronan receptor-1 (Lyve-1) reside proximal to blood vasculature and contribute to disease progression. Using a spontaneous murine model of mammary adenocarcinoma (MMTV-PyMT), we show that Lyve-1+ TAMs, which co-express heme oxygenase-1, form coordinated multi-cellular nest structures in the perivascular niche. We show that TAM nest formation is dependent on IL-6 and a communication axis involving CCR5 and its cognate ligands CCL3/4. We demonstrate that Lyve-1+ TAM nests are associated with CD8+ T-cell exclusion from the tumor and the resistance to immune-stimulating chemotherapeutics. This study highlights an unappreciated collaboration between TAMs and uncovers a spatially driven therapeutic resistance mechanism of these cells in cancer which can be therapeutically targeted.

cancer biology↗

bioRxiv2021

RUNIMC: An R-based package for imaging mass cytometry data analysis and pipeline validation

We propose a novel pipeline for the analysis of imaging mass cytometry data, comparing an unbiased approach, representing the actual gold standard, with a novel biased method. We made use of both synthetic/ controlled datasets as well as two datasets obtained from FFPE sections of follicular lymphoma, and head and neck patients, stained with a 14 and 29-markers panels respectively. The novel pipeline, denominated RUNIMC, has been completely developed in R and contained in a single package. The novelty resides in the ease with which multi-class random forest classifier can be used to classify image features, making the pathologists and expert classification pivotal, and the use of a random forest regression approach that permits a better detection of cell boundaries, and alleviates the necessity of relying on a perfect nuclear staining.

cancer biology↗