Biology subjects

Zhou, D.

Publications and source records attributed to Zhou, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A compressed code for memory discrimination

The ability to discriminate similar visual stimuli has been used as an important index of memory function. This ability is widely thought to be supported by expanding the dimensionality of relevant neural codes, such that neural representations for the similar stimuli are maximally distinct, or "separated." An alternative hypothesis is that discrimination is supported by lossy compression of visual inputs, efficiently coding sensory information by discarding seemingly irrelevant details. A benefit of compression, relative to expansion, is that it allows the individual to efficiently retain fewer essential dimensions underlying stimulus variation--a process linked to higher-order visual processing--without hindering discrimination. Under the compression hypothesis, pattern separation is facilitated when more information from similar stimuli can be discarded, rather than preserving more information about distinct stimulus dimensions. We test the compression versus expansion hypotheses by predicting performance on the canonical mnemonic similarity task. First, we train neural networks to compress perceptual and semantic factors of stimuli, and measure lossiness of those representations using the mathematical framework underlying compression. Consistent with the compression hypothesis, and not the expansion hypothesis, we find that greater lossiness predicts the ease and performance of lure discrimination, particularly in later layers of convolutional neural networks shown to predict brain activity in the higher-order visual stream. We then empirically confirm these predictions across two sets of images, four behavioral datasets, and alternative metrics of lossiness. Finally, using task fMRI data, we identify signatures of lossy compression--neural dimensionality reduction and information loss--in the higher-order visual stream regions V4 and IT as well as hippocampal subregions dentate gyrus/CA3 and CA1 associated with lure discrimination performance. These results suggest lossy compression may support mnemonic discrimination behavior by discarding redundant and overlapping information.

neuroscience↗

bioRxiv2025

Atg16l1 promotes lung transplant tolerance by regulating glycolysis in macrophages

Lung transplant survival is limited by the development of chronic lung allograft dysfunction (CLAD), a type of graft rejection that lacks effective treatments. Autophagy plays a crucial role in maintaining cellular homeostasis. In a single-nucleotide polymorphism screen, we found that lung recipients with two copies of a common hypofunctional genetic variant of autophagy-related 16-like 1 rs2241880 (ATG16L1T300A/T300A), known to deplete this protein from macrophages, were more likely to develop early CLAD. To understand this, we used a mouse orthotopic lung transplant model. Recipients encoding myeloid cell-specific deletion of Atg16l1 (Atg16l1{Delta}/{Delta}) or who harbor an engineered orthologous mutation (Atg16l1T316A/T316A) showed similar susceptibility to CLAD. Transcript profiling and mitochondrial tracking studies indicated that increased mitochondrial damage and decreased autophagic removal of mitochondria in Atg16l1-deficient macrophages were associated with heightened activation of the hypoxia-inducible factor 1 (Hif1) pathway and accumulation of glycolytic transcripts. Metabolic analysis revealed reduced oxidative phosphorylation, increased glycolytic activity, and higher IL-1{beta} expression in Atg16l1-deficient macrophages. Notably, the development of CLAD in Atg16l1{Delta}/{Delta} lung recipients could be significantly prevented by additionally deleting Hif1 in myeloid cells or by treating with the glycolysis inhibitor 2-deoxyglucose. Our results show how a common autophagy-related genetic variant disrupts macrophage metabolism and impairs lung transplant tolerance, pointing toward potential therapeutic strategies to combat CLAD.

immunology↗

bioRxiv2025

Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics

In humans, the bone marrow becomes the primary site for B lymphopoiesis during the second trimester of pregnancy and continues throughout life. Prenatal and adult B cell progenitors play distinct roles in the aetiology and pathology of paediatric and adult hematopoietic malignancies, though the molecular drivers of these differences remain unclear. Here, we created a comprehensive multiomics atlas of over 500k cells covering immune and stromal compartment from prenatal and adult bone marrow, enabling high-resolution analysis of the cell-intrinsic and cell-extrinsic processes that modulate prenatal and adult B lymphopoiesis. Even though B cells follow broadly similar developmental trajectories, we identify a novel postnatal lateCLP subset equivalent to prenatal preProB cells, and uncover prenatal cells carry several signatures characteristic of leukemias, including enhanced proliferation, higher RAG1/RAG2 activity, extrinsic B cell signals such as IL7, and lower retention signals in the bone marrow. We also developed and characterised, at both cellular and molecular levels, a new experimental framework for generating B cell precursors from human induced pluripotent stem cells (hiPSCs), and show that it faithfully recapitulates key stages of B cell differentiation. Together, our single-cell multiomics atlas of B lymphopoiesis in vivo and in vitro offers detailed insights into the unique molecular features of prenatal and adult B cell lymphopoiesis, and serves as a powerful resource for investigating the early events that contribute to haematological disorders.

immunology↗

bioRxiv2025

NAT10 Suppresses RNA Sensing Induced IFN-β Transactivation to Promote Viral Infection via Interfering with IRF3 Activities

Cells can sense invading viruses and trigger type I interferons (IFN-/{beta}) to evoke antiviral innate immune response. Induction of IFNs needs to be fine-tuned to achieve the antiviral consequence while avoiding severe disruption of host cell homeostasis. Here, we reported that NAT10, the acetyltransferase of histone and N4-acetylcytidine (ac4C) RNA modification, promotes infection of RNA viruses via regulation of type I IFN signaling. Depletion of NAT10 increased the expression of IFN-{beta} and interferon-stimulated genes (ISGs) upon stimulation of type I IFN antiviral signaling, while it impaired viral replication. NAT10 dynamically associated with the IFN-{beta} promotor and negatively regulated IRF3 through modulation of long non-coding RNAs (lncRNAs) that inhibit IRFs. Consistently, the small molecule inhibitor of NAT10, Remodelin, increased IFN-{beta} expression while inhibiting viral infections. Overall, our findings indicated that NAT10 is a negative regulator of type I IFN signaling, suggesting its potential as a target of antiviral treatment.

microbiology↗

bioRxiv2025

Quiescent OXPHOS-high triple-negative breast cancer cells that persist after chemotherapy depend on BCL-XL for survival

The persistent residual tumor cells that survive after chemotherapy are a major cause of treatment failure, but their survival mechanisms remain largely elusive. These cancer cells are typically characterized by a quiescent state with suppressed activity of MYC and MTOR. We observed that the MYC-suppressed persistent triple-negative breast cancer (TNBC) cells are metabolically flexible and can upregulate mitochondrial oxidative phosphorylation (OXPHOS) genes and respiratory function ("OXPHOS-high" cell state) in response to DNA-damaging anthracyclines such as doxorubicin, but not to taxanes. The elevated biomass and respiratory function of mitochondria in OXPHOS-high persistent cancer cells were associated with mitochondrial elongation and remodeling suggestive of increased mitochondrial fusion. A genome-wide CRISPR editing screen in doxorubicin-persistent OXPHOS-high TNBC cells revealed BCL-XL gene as the top survival dependency in these quiescent tumor cells, but not in their untreated proliferating counterparts. Quiescent OXPHOS-high TNBC cells were highly sensitive to BCL-XL inhibitors, but not to inhibitors of BCL2 and MCL1. Interestingly, inhibition of BCL-XL in doxorubicin-persistent OXPHOS-high TNBC cells rapidly abrogated mitochondrial elongation and respiratory function, followed by caspase 3/7 activation and cell death. The platelet-sparing proteolysis targeted chimera (PROTAC) BCL-XL degrader DT2216 enhanced the efficacy of doxorubicin against TNBC xenografts in vivo without induction of thrombocytopenia that is often observed with the first-generation BCL-XL inhibitors, supporting the development of this combinatorial treatment strategy for eliminating dormant tumor cells that persist after treatment with anthracycline-based chemotherapy.

cancer biology↗

bioRxiv2025

Single-Assay Characterization of Ternary Complex Assembly and Activity in Targeted Protein Degradation

Targeted protein degradation (TPD) is a rapidly advancing therapeutic strategy that selectively eliminates disease-associated proteins by co-opting the cells protein degradation machinery. Covalent modification of proteins with ubiquitin is a critical event in TPD, yet the analytical tools for quantifying the ubiquitination kinetics have been limited. Here, we present a real-time, high-throughput fluorescent assay utilizing purified, FRET-active E2-Ub conjugates to monitor ubiquitin transfer. This assay is highly versatile, requiring no engineering of the target protein or ligase, thereby accelerating assay development and minimizing the risk of artifacts. The single-step, single-turnover nature of the monitored reaction enables rigorous and quantitative analysis of ubiquitination kinetics. We show that this assay can be used to measure key degrader characteristics such as degrader affinity for the target protein, degrader affinity for the ligase, affinity of ternary complex assembly, and catalytic efficiency of the ternary complex. The high sensitivity and accuracy of this comprehensive, single-assay approach to ternary complex characterization will empower the discovery and optimization of heterobifunctional degraders and molecular glues.

biochemistry↗

bioRxiv2025

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-matched reference panel to model protein expression using genetic variants as features and determine the proteins impact on phenotype. However, reference panels from underrepresented populations remain relatively limited. In this study, we developed an analytic framework that borrows information from potentially multiple ancestries to boost the protein abundance prediction accuracy in an underrepresented population. We illustrate the frameworks utility and reproducibility through application to PWAS in East Asians: BioBank Japan (BBJ), Korean Genome and Epidemiology Study (KoGES), and Taiwan Biobank (TWB). An ensemble of information-sharing approaches was integrated to build the Multi-Ancestry-based Best-performing Model (MABM). MABM substantially improved the prediction performance with higher performance observed in both cross-validation and an external validation dataset (Tongji-Huaxi-Shuangliu Birth Cohort). Leveraging the BBJ, we identified three times as many significant PWAS associations with MABM as with the baseline Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced gene/protein prioritization for downstream functional validation by (1) confirming a greater number of well-established gene/protein-trait associations and (2) identifying previously uncharacterized trait-associated genes. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research, develop a new reference resource of genetic models of protein abundance, and facilitate trait-relevant protein discovery in underrepresented populations.

genomics↗

bioRxiv2025

GPCR Antagonism via Antibody-Mediated Rewiring of Receptor Trafficking and Degradation

G-protein coupled receptors (GPCRs) represent one of the most important yet incompletely targeted classes of therapeutic proteins. Here, we report a novel strategy for functional GPCR antagonism through antibody-mediated endocytosis and lysosomal degradation. Our engineered bispecific antibodies, termed GPCR-TfR1 Targeting Chimeras (GTACs), achieve potent and selective downregulation of various GPCRs, including RXFP1 and CCR6, critical cancer and immune drug targets that are difficult to antagonize with conventional approaches. GTACs led to complete inhibition of receptor activity with over 100-fold greater potency than conventional antibody antagonists. Using four-color imaging, we elucidated the trafficking mechanism of both the target protein and TfR1 in living cells. The GTAC platform enables robust antagonism of signaling across diverse GPCR families and establishes induced endocytosis and lysosomal trafficking as a fundamentally new paradigm for therapeutic GPCR modulation.

bioengineering↗

bioRxiv2025

Functional contributions of quantal and non-quantal hair cell synaptic transmission in the vestibular periphery

Information about head motion and gravity is conveyed to the brain by vestibular nerve afferents which are subdivided by their spontaneous firing properties into regular and irregular subtypes thought to be differentially responsible for vestibulo-ocular vs vestibulo-spinal reflexes. In the vestibular periphery, afferents make glutamatergic synapses with type II hair cells (HCs) in all vertebrates. During the evolutionary transition to land, however, amniotes (reptiles, birds, and mammals) additionally developed type I vestibular HCs in which unique calyceal afferent terminals cover the basolateral walls of one or more HCs, enabling a nonquantal (NQ) form of synaptic transmission. Most afferents receive inputs from both types of HCs, but the roles of type I vs type II HCs in generating vestibular afferent firing patterns and behaviors remains unclear. Using optogenetics in mice (both sexes), we confirm that stimulation of type II HCs drives conventional quantal glutamatergic transmission, whereas type I HC stimulation evokes nonquantal responses. In mice with disrupted glutamatergic quantal transmission, NQ transmission effectively drove afferent responses to a wide range of head movement frequencies, as assessed by both vestibular sensory evoked potentials and the vestibulo-ocular reflex. Although the distribution of afferent discharge regularity was unaffected, loss of glutamatergic transmission impaired detection of gravity as evidenced by abnormal contact righting reflex behavior. These results indicate that nonquantal glutamatergic transmission from type I HCs is sufficient to generate normal afferent firing patterns and dynamic vestibular behaviors and that glutamatergic release from type II HCs is required for the detection of gravity. Significance StatementThe vestibular system enables balance and spatial orientation by detecting head movements and gravity. During vertebrate evolution, amniotes developed a unique form of synaptic communication--non-quantal (NQ) transmission--between type I hair cells and calyceal afferent nerve fibers in vestibular sensors. This study reveals that NQ transmission can robustly drive vestibular responses across a wide stimulus range, even in the absence of conventional glutamate-based (quantal) signaling. Using electrophysiology, optogenetics and behavioral assays, we show that NQ and quantal transmission serve distinct but complementary roles: NQ supports rapid, broad-range signaling, while quantal transmission is critical for precise gravity detection. These findings highlight how evolutionary innovations in synaptic transmission enhance vestibular function, contributing to our understanding of balance disorders and sensory processing.

neuroscience↗

bioRxiv2025

Cytoplasmic Abundant Heat-Soluble Proteins from Tardigrades Protect Synthetic Cells Under Stress

Cytoplasmic abundant heat-soluble (CAHS) proteins, a stress-responsive intrinsically disordered protein from tardigrades, have been discovered to form gel-like networks providing structural support during dehydration, thus enabling anhydrobiosis. However, the mechanism by which CAHS proteins protect the dehydrating cellular membrane remains enigmatic. Using giant unilamellar vesicles (GUVs) as a model membrane system, we show that encapsulated CAHS12 undergoes a reversible structural transformation that reinforces membrane integrity and preserves encapsulated components, mimicking natural anhydrobiosis. CAHS12-containing GUVs demonstrated stability for weeks and mechanical robustness under dehydration, elevated temperature, and osmotic stresses. Molecular simulations suggest that CAHS12 forms a filamentous network within the vesicle lumen that mitigates membrane collapse and preserves compartmental architecture. Synthetic cells with cell-free transcription-translation capabilities withstand desiccation and recover biochemical activities, akin to the tun state of the tardigrade. This discovery opens up synthetic cell applications in bioengineering, cold-chain-independent biomanufacturing, and adaptive biointerfaces.

synthetic biology↗

bioRxiv2025

Neural dynamics underlying the persistence of perseverative thought in depression and anxiety

Depression and anxiety are characterized by transdiagnostic symptoms, including perseverative thought: a class of thoughts such as rumination and worry that are negative, repetitive, and difficult to control. These thoughts contribute to substantial distress, poor treatment response, and increased risk of relapse. What makes perseverative thoughts persevere? Using task-based fMRI, we compared how adults with no lifetime psychopathology and adults with major depressive disorder, generalized anxiety disorder, or both, engaged top-down control processes to switch from personally-relevant perseverative or neutral thought to a working memory task. For only adults with clinical depression or anxiety, stopping perseverative thought was associated with more probable frontoparietal deactivation and more frequent default-mode activation versus stopping neutral thought. Using network control theory, we identified key control points that lead to these activity dynamics. We found that clinical perseverative thought elicited less controlled activity in the anterior cingulate cortex relative to thoughts in adults with no lifetime psychopathology, and lower control energy correlated with greater depression severity. The occipital-temporal, lateral prefrontal, and insular cortices also used less control energy in clinical perseverative thought. Low energy is characteristic of attractor states in dynamical systems theory, deep channels wherein the flow of activity naturally settles, analogous to how a ball needs little energy to roll to the bottom of a bowl yet more energy to leave it. Entrenchment in attractors provides a computational perspective on why top-down control signals relate to the persistence of clinical perseverative thought. These insights advance our understanding of the dynamic processes of perseverative thought, paving the way for novel interventions for depression and anxiety.

neuroscience↗

bioRxiv2025

Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences. Notably, cFOOT-seq, combined with FootTrack analysis, predicts TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.

molecular biology↗

bioRxiv2025

Stiffness sensing fuels matrix-driven metabolic reboot for kidney repair and regeneration

Kidney repair after acute kidney injury (AKI) relies on a finely tuned extracellular matrix (ECM) that provides structural integrity and mechanical cues. As primary ECM architects, fibroblasts and pericytes rapidly mobilize to the injury site post-AKI, yet the ECM-driven repair mechanisms remain incompletely defined. Here, leveraging tissue engineering, genetic and pharmacological models, and multi-omics, we profiled the proteome landscape of decellularized kidney matrix scaffold post-AKI and highlighted microfibrillar-associated protein 2 (Mfap2) as a key core matrisome component primarily sourced from fibroblasts and pericytes. Mfap2 loss disrupted kidney architecture and metabolism, aggravating AKI. Global proteomics revealed that Mfap2 deficiency suppressed tubular 3-hydroxy-3-methylglutaryl-CoA synthase 2 (Hmgcs2) expression via estrogen receptor 2 (Esr2)-mediated transcriptional repression and increased protein succinylation. Phosphoproteomics and spatial transcriptomics further demonstrated a shift in mechanical signaling, with Mfap2 loss hyperactivating mitogen-activated protein kinases and upregulating large tumor suppressor kinase 1 (Lats1) in tubular cells without altering integrin receptor activities. In turn, Lats1 suppressed Esr2 transcription independent of its canonical Yap/Taz effectors, without affecting ubiquitin-mediated Esr2 degradation. Therapeutically, Esr2 agonists restored kidney function in Mfap2-deficient models. These findings position Mfap2 as a key regulator of ECM dynamics and mechanosignaling, linking tissue stiffness to metabolic reprogramming required for kidney repair.

cell biology↗

bioRxiv2025

Paclitaxel-induced mitotic arrest results in a convergence of apoptotic dependencies that can be safely exploited by BCL-XL degradation to overcome cancer chemoresistance

Paclitaxel and other microtubule-targeting agents are cornerstone therapies for diverse cancers, including lung, breast, cervical, pancreatic, and ovarian malignancies. Paclitaxel induces tumor cell apoptosis during mitosis by disrupting microtubule dynamics required for chromosome segregation. However, despite initial responsiveness, many tumors develop resistance, limiting therapeutic durability. Here, we used high-grade serous ovarian carcinoma (HGSOC), the most common and lethal subtype of ovarian cancer, as a model to dissect the mechanisms underlying this resistance. We find that paclitaxel-induced mitotic arrest triggers degradation of the pro-survival protein MCL-1 and upregulation of BCL-XL, followed by inactivating phosphorylation of BCL-XL at Ser62 to promote apoptosis. In resistant cells, this MCL-1 downregulation is insufficient to commit cells to apoptosis but instead results in a transient convergence of apoptotic dependencies by forcing BCL-XL to sequester the pro-apoptotic proteins BIM, BAX, and BAK. During this state, BCL-XL inhibition induces synergistic apoptosis, even in chemoresistant cells. Surprisingly, we also discover that loss of substrate attachment recapitulates this apoptotic convergence both in vitro and in vivo, with HGSOC cells growing in metastasis-promoting malignant ascites displaying heightened apoptotic priming and dependence on BCL-XL relative to solid tumors. In HGSOC xenografts, targeted degradation of BCL-XL using the platelet-sparing proteolysis-targeting chimera (PROTAC) DT2216 matches the efficacy of paclitaxel monotherapy while avoiding the chronic thrombocytopenia induced by BCL-XL inhibitors such as navitoclax (ABT-263). Strikingly, combination therapy leveraging the synergy between paclitaxel and DT2216 leads to complete eradication of HGSOC cell line and patient-derived xenografts. Moreover, DT2216 treatment blunts the rapid apoptotic adaptation caused by other BCL-XL inhibitors, indicating that targeted degradation of pro-survival proteins may yield more durable responses than inhibition alone. These findings uncover a mechanistic framework for safely exploiting the apoptotic dependency convergence caused by mitotic arrest and substrate detachment and support the clinical development of BCL-XL-targeting PROTACs to overcome chemoresistance in ovarian cancer and other solid tumors.

cancer biology↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Stochastic gates for covariate selection in population pharmacokinetics modelling

Covariate selection in population pharmacokinetics modelling is essential for understanding interindividual variability in drug response and optimizing dosing. Traditional stepwise covariate modelling is often time-consuming, compared to the new machine learning alternatives. This study investigates the use of Neural Networks with Stochastic Gates for automated covariate selection, aiming to efficiently identify relevant covariates while penalizing excessive covariate inclusion. On various synthetic datasets the approach demonstrated robustness in detecting important covariates, overcoming challenges such as high correlations, low covariate frequencies, high interindividual variability and complex covariate dependencies. In real clinical data from a monalizumab study, the method successfully identified covariates that matched those found by experts. However, for tixagevimab/cilgavimab, it identified a superset of covariates, indicating a potential need for further pruning. This machine learning-based method enhances the covariate pre-selection process in population pharmacokinetics model development, offering significant time savings and improving efficiency even under challenging scenarios. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/656586v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1f5180borg.highwire.dtl.DTLVardef@1fd97e7org.highwire.dtl.DTLVardef@1ffc3d0org.highwire.dtl.DTLVardef@90c207_HPS_FORMAT_FIGEXP M_FIG C_FIG Study HighlightsO_ST_ABSWHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC?C_ST_ABSCovariate selection in population pharmacokinetics modelling is a crucial step in drug development and dosing determination. Traditionally, this process is conducted in a stepwise manner, which can be very time-consuming. Recently, fast machine learning (ML)-based methods for covariate selection have emerged in the literature, offering more efficient alternatives. WHAT QUESTION DID THIS STUDY ADDRESS?Can we use Neural Networks with Stochastic Gates, incorporating explicit penalization on the number of covariates, to select superior set of covariates compared to prior ML-based methods? WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE?Neural Networks with Stochastic Gates provide a reliable approach in accurately detecting covariates because they can effectively eliminate irrelevant covariates even in cases with high inter-covariates correlation. HOW MIGHT THIS CHANGE DRUG DISCOVERY, DEVELOPMENT, AND/OR THERAPEUTICS?This approach accelerates pharmacokinetic model development by significantly reducing the time required for covariate evaluation. Additionally, it allows for the screening of a wider set of covariates, potentially leading to fewer falsely missed covariates and better-quality models, a task that would be infeasible with traditional stepwise covariate modelling.

pharmacology and toxicology↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2025

Unraveling Tyrosine-Kinase Inhibitor Resistance in NSCLC Cells via Same-cell Measurement of RNA, Protein, and Morphological Responses

Non-small cell lung cancer (NSCLC) frequently develops resistance to tyrosine kinase inhibitors (TKIs), limiting the long-term success of targeted therapies. A deeper understanding of resistance mechanisms at the molecular and cellular levels may enable the development of more effective treatment strategies. Here, we applied the Teton detection assay on the AVITI24 platform to measure concurrently RNA, protein, and cellular morphology in NSCLC cell lines treated with the TKIs gefitinib and osimertinib. This single-cell, multiomic analysis revealed distinct expression and morphological profiles between drug-sensitive and resistant cells, including differences in MAPK-related pathway activity. Stratifying responses at the single-cell level uncovered subtle responses not detectable in bulk measurements. We identified CDK4/6 activity as a route of cell survival under TKI treatment and demonstrated that co-treatment with the CDK4/6 inhibitor palbociclib enhanced TKI efficacy. The ability to measure multiomics and cellular morphology in the same cells opens new avenues for future studies aimed at improving personalized treatment strategies in NSCLC and overcoming the obstacles posed by drug resistance.

genomics↗