Biology subjects

Tran, H.

Publications and source records attributed to Tran, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

Influenza A virus H5N1 and other H5 subtypes (H5Nx) have broad host ranges and pose a pandemic risk. Since early 2022, H5 clade 2.3.4.4b has predominated globally, causing unprecedented mortality in wild birds, poultry, and mammals, with spillovers to humans. Accurate viral classification is essential for tracking H5Nx variant emergence and spread, but reassortment among genome segments with distinct evolutionary histories complicates genotyping. H5Nx genotype assignment tools, GenoFlu in North America and Genin2 in Europe, assign segments to clusters by genetic similarity to reference sequences and define genotypes as constellations of segment clusters. However, genetic similarity does not necessarily imply recent shared ancestry because mutations may occur multiple times across the tree and branches may exhibit variable evolutionary rates. Furthermore, similarity is defined relative to references that may inadequately represent diversity. We evaluated the congruence of genetic similarity-based H5Nx clusters and genotypes with phylogenies of global sequences across eight segments. Publicly available H5Nx nucleotide sequences from 41,366 samples were assigned genotypes using GenoFlu and Genin2, and maximum likelihood phylogenies were inferred for each segment. Phylogenetic clusters were identified using TreeCluster for a range of patristic distance thresholds and CD-HIT clusters were identified for a range of genetic similarity thresholds. Clustering methods were evaluated based on phylogenetic purity, monophyly, and diversity. Reassortment within predominant GenoFlu and Genin2 genotypes was evaluated based on their phylogenetic cluster spans. Expectedly, GenoFlu was largely unable to assign genomes from outside of North America, South America, and Antarctica from 2022 to 2025, whereas Genin2 assignments struggled outside of Europe, Africa, and Western Asia. Only 14.2% of GenoFlu clusters were monophyletic, while Genin2 clusters were more variable across segments (overall 49.3% monophyletic). Despite CD-HIT yielding genetic distance clusters of similar size to TreeCluster, they were less monophyletic (44%) and encompassed greater phylogenetic diversity. We identified several genotypes, such as GenoFlu B3.13, D1.1, and D1.3, with internal segments that had diversified into contiguous clusters. Similarly, the wide phylogenetic span of GenoFlu genotypes B3.5 and A3, and Genin2 genotypes EA-2020-C, EA-2021-AB, and EA-2022-CH suggest they may erroneously combine multiple reassortants. Genetic similarity-based H5Nx genotyping tools are rapid, stable, and sufficient for broad categorization, but may group viruses with distinct evolutionary histories and fail to assign divergent viruses, risking biased surveillance, modeling, and risk assessment.

bioinformatics↗

bioRxiv2026

A Chemigenetic Fluorescence Lifetime Biosensor for Dopamine Sensing

Measuring the precise dynamics of specific neuromodulators in neurons is key to understanding how information is transmitted and processed in the brain. Despite the growing use of intensity-based neural activity sensors such as dLight in recent years, it remains challenging to monitor the dynamics of multiple neurochemicals simultaneously in live neurons. Unlike intensiometric sensors that are susceptible to artifacts caused by fluctuations in excitation power and rapid photobleaching, fluorescence lifetime-based sensors are less affected by these factors and can provide more stable measurements. Here we introduce dHaloLife635, a novel genetically encoded fluorescence-lifetime-based dopamine (DA) sensor that exhibits a fluorescence lifetime change up to -0.20 ns upon dopamine binding. dHaloLife635 consists of a G protein-coupled dopamine receptor (DRD1), a circularly permuted HaloTag (cpHaloTag), and a cell-permeable dye JF635 functionalized with a HaloTag ligand, a reactive chloroalkane linker (JF635-HTL). When dopamine binds to the dHaloLife635 sensor, it induces a conformational change in the cpHaloTag that alters the local environment of the conjugated dye, thereby changing its fluorescence lifetime. In live HEK293T cells and primary neurons, dHaloLife635 responds selectively to dopamine but not to serotonin, L-DOPA, or GABA, demonstrating excellent specificity. This dHaloLife635 sensor represents an initial step toward the establishment of a broader family of chemigenetic lifetime sensors that exhibit distinct fluorescence lifetime signatures upon binding their respective targets, thereby enabling highly specific and sensitive, real-time monitoring of multiple neurochemical dynamics in vivo.

bioengineering↗

bioRxiv2026

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

Nuclear organization is a fundamental feature of cell identity and cell fate determination. Compared with differentiated cells, pluripotent stem cells exhibit markedly distinct nuclear architecture at multiple levels, including chromosome folding, lamina association, histone modification landscapes and nuclear body organization. Although individual aspects of this reorganization have been characterized, how and in what order these features are remodeled as cells commit to a lineage remains poorly understood. Here, we temporally map nuclear reorganization across five stages of an in vitro differentiation system of human embryonic stem cells through definitive endoderm and hepatoblast intermediates into hepatocyte-like cells. By integrating Hi-C, RNA-seq, ATAC-seq, ChIP-seq, and CUT&RUN data, we establish a genome-wide framework linking structural, epigenetic, and transcriptional changes across differentiation. Combined with immunofluorescence imaging, chromosome painting, and liquid chromatin Hi-C (LC-Hi-C) we show that nuclear reorganization proceeds in a stepwise and temporally ordered manner through three major transitions. In the first transition, chromosomes condense into defined territories concurrent with transient anchoring of centromere-proximal regions to the nuclear periphery. In a second transition, active and inactive chromatin segregate, leading to stronger compartmentalization. This coincides with deposition and peripheralization of H3K9me2-marked chromatin and morphological changes in nuclear speckles, while chromatin conformation at speckle-associated regions stabilizes. In a third transition, after lineage-specific genes are activated, chromatin interactions globally stabilize, establishing a more stable nuclear architecture on top of these earlier large-scale structural rearrangements. Together, our results define a stepwise framework for nuclear reorganization during human embryonic stem cell differentiation and reveal that the transition from pluripotency to a differentiated state proceeds through coordinated, temporally ordered structural events.

genomics↗

bioRxiv2026

Chromosomal mutational signatures of DNA damaging agents at single cell resolution

The chromosomal-scale mutational spectrum of small molecules that interact with DNA has been hard to study at scale, as mutational events are distributed in location and occur in parallel in different cells. Here, we present a framework that pairs phylogenetic ancestry reconstruction with mutational signature decomposition to characterise recent, cell-private copy number alteration (CNA) mutational patterns at single-cell resolution. We used this framework to characterise the cell-wise mutational spectrum of contemporaneous CNAs generated by double-strand-break-inducing chemotherapeutic drugs. We demonstrate that platinum salts, G-quadruplex stabilizers and topoisomerase II inhibitors, although mechanistically distinct, converge on a mutational signature dominated by telomere-bounded copy-number gains and losses. This signature is observed in different genetic backgrounds and in vivo in drug-treated patient-derived xenografts. We also observe a high rate of endogenous telomere-bounded mutational foreground in BRCA1 deficient cells. We show that the single cell genome derived signature exposures are drug dose-dependent, and use this to identify the decay of mutational load after drug withdrawal. We observe that both cisplatin and a G4 binder molecule (CX5461) exhibit foreground mutational signature persistence for at least 3 weeks after drug withdrawal, suggesting that residual effects of exposure may last longer than anticipated. Finally, extending the framework to serially drug-treated patient-derived xenograft (PDX) models, we show that telomere-bounded CNA signature exposure is associated with tumoural response to drug, consistent with loss of mutational activity on the genome after acquired resistance emerges. Together, our results show that our framework applied on scWGS identifies contemporaneous chromosomal mutation patterns induced by small molecules in human tissues.

cancer biology↗

bioRxiv2026

Flow alters fibrin molecular and network structure and decreases binding of fibrinolytic enzymes

Thrombolysis with tissue Plasminogen Activator (tPA), approved for treating acute ischemic stroke (AIS) within 3-4.5 h of symptom onset, converts Plasminogen (Plg) to Plasmin to degrade fibrin, while fibrin also enhances Plg activation by binding to both tPA and Plg. Therefore, in this study, we investigated whether arterial-like flow, characteristic of AIS, alters fibrin structure and susceptibility to fibrinolysis. Using a newly developed platform for quantitative imaging and spectroscopy, we found that flow generates denser fibrin networks with reduced molecular transport despite reduced protofibril packing within fibrin fibers. Raman spectroscopy revealed an -helix-to-{beta}-sheet transition, accompanied by reduced Plg and tPA binding, although the reduction in tPA binding emerged only after prolonged flow exposure. Consistently, multi-scale molecular dynamics simulations showed that the Plg binding site destabilized at lower forces than the primary tPA binding site. Together, these multi-scale findings help explain the limited efficacy and narrow therapeutic window of thrombolysis.

biophysics↗

bioRxiv2026

Distinct sensorimotor encoding in tuft dendrites and somata associated with action, correction, and learning

Frontal cortex plays critical roles in action control and motor skill learning. Within the layer 1 apical tuft dendrites of layer 5 (L5) neurons in frontal cortex, precise input patterns and back-propagating action potentials can trigger powerful regenerative events that may be essential for flexible computation and learning. However, it remains unclear whether tuft activity in frontal cortical L5 circuits encodes sensorimotor information that differs from the information conveyed by their outputs to downstream targets. Using longitudinal two-photon calcium imaging, we investigated sensorimotor encoding in the apical tuft dendrites and somata of L5 extratelencephalic (ET) neurons in the frontal cortex of mice during learning of a discrete change to a cued dexterous action. During learning, movement errors either triggered corrective action or did not, allowing us to dissociate error signals from signals selective for corrective action. Somatic activity tracked both instructional cues and action, whereas tuft activity predominantly tracked instructional cues. Movement errors during learning revealed additional distinct tuft activity that was selectively associated with corrective actions. Furthermore, learning induced divergent changes in the response gain and net selectivity of tuft dendrites compared to somata. Our measurements uncover systematic differences between the tuft dendrites and somata in sensorimotor selectivity, sensitivity to corrective action, and functional plasticity, providing a foundation for investigating the contributions of dendritic computation to motor skill learning.

neuroscience↗

bioRxiv2026

SUMO mediates the coordinate regulation of meiotic chromosome length and crossover rate

Meiotic prophase-I chromosomes are organized into linear arrays of chromatin loops anchored to proteinaceous axes that define the interaction interfaces for the pairing and synapsis of homologous chromosomes. Chromatin loop size and axial chromosome length are inversely correlated and vary widely both between and within species, including between the sexes. The molecular basis of this variation remains unclear. Here, we provide evidence that the small ubiquitin-like modifier, SUMO, regulates loop-axis organization in mouse meiosis. Our analysis shows that the longer axes of oocyte chromosomes contain more SUMO per unit length than the shorter axes of spermatocyte chromosomes. In mouse models, the loss of SUMO1 results in shorter axes and longer chromatin loops. Conversely, increased SUMO1 conjugation, caused by mutation of the SENP1 isopeptidase, produces longer axes with shorter loops. Axis length positively correlates with meiotic recombination. Accordingly, Sumo1 and Senp1 mutations respectively decrease and increase crossover frequency. These findings identify SUMO as a key regulator of meiotic chromosome architecture and suggest a molecular basis for the physiological variation in chromosome length and recombination rates seen among species, sexes, individuals, and individual meiocytes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/710713v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@145c465org.highwire.dtl.DTLVardef@160c8aborg.highwire.dtl.DTLVardef@1165b76org.highwire.dtl.DTLVardef@ced5e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Modeling the effects of Huntington disease on age-related genes reveals CXXC4 as an epigenetic target to restore health and excitability of Drd1-expressing striatal neurons

Neurons adapt gene expression to counter aging, yet the mechanisms by which they harness age- related genes to resist neurodegenerative disease remain elusive. We found that transcriptionalaging inversion (TAGI) in the Drd1-expressing striatal neurons (Drd1 SNs) of Huntingtons disease (HD) knock-in (Hdh) mice exhibits discrete patterns against a TAG-like (TAGL) signature. Strikingly, TAGI dynamics may explain disease progression more accurately than TAGL. Moreover, in Drd1 SNs, genes affected by 3UTR accumulation during aging are predisposed to downregulation in aging and deregulation in Hdh mice. By integrating age-related 3UTR data and Hdh-mice data, we identified a CAG-repeat-dependent network of upregulated genes with compensatory potential. This network features (i) Atad-5, a P CNA unloader that modifies CAG expansion in human HD plasma samples, and (ii) CXXC4 (IDAX), an epigenetic regulator whose early-stage upregulation is lost as behavioral symptoms worsen in Hdh mice. Functionally, CXXC4 reduces the senescence marker p16INK4a and restores glutamate excitability in human HD iPS cell-derived SNs. Collectively, these findings suggest that Drd1 SN resilience capacity against HD relies on discrete age-related patterns and responses transiently activated in early disease stages. The reactivation of specific age-related genes such as CXXC4 may notably restore cortico-striatal function in HD.

neuroscience↗

bioRxiv2025

Viscoelasticity driven deformation dynamics of the substrate affect mechanically induced Ca2+ signals

The viscoelastic properties of the substrate are known to affect many aspects of cellular behavior from migration to differentiation. Cells are also known to sense deformations in the extracellular matrix (ECM). However, these mechanotransduction events have mostly been studied separately, and the emphasis has been on purely elastic materials although most tissues in the body are viscoelastic. We wanted to understand how the viscosity and elasticity of the substrate affect cells mechanosensation, i.e., how cells integrate passive (substrate viscoelasticity) and active cues (dynamic substrate deformation) into calcium transients. We used a light-controllable Disperse Red 1-glass (DR1-glass) coating together with a thin polyacrylamide (PAA) hydrogel with controllable viscoelasticity. This allowed us to generate local deformations in the cell-substrate interface on substrates with different viscoelastic properties. Inspecting the resulting calcium transients in a Madin Darby canine kidney type II (MDCK II) monolayer with the genetically encoded calcium indicator jRCaMP1b revealed that cells responded to deformation differently depending on the viscoelasticity of the substrate. On stiff elastic gels cells exhibited all in all the largest calcium responses as well as increased sensitivity to the magnitude of deformation, with larger deformations leading to stronger calcium signals, whereas on soft elastic and soft viscoelastic gels the magnitudes of deformation had less effect on the degree of calcium signals. Indeed, immunostainings showed that cells formed the strongest focal adhesions (FA) on stiff gels, albeit differences were surprisingly small. Instead, computational modeling revealed that forces generated at FAs were strongly dependent on the viscoelasticity of the substrate, with increased elasticity and decreased viscosity leading to larger forces. Moreover, viscoelasticity affected the dynamics of the force generation. On stiff elastic gels force increased in fast steps, whereas on soft gels the buildup was gradual and was further slowed down by increased viscosity. Surprisingly, experiments with PIEZO1 KO cells showed that the calcium responses to the substrate deformation did not require PIEZO1 channels. Instead, depleting the ER with thapsigargin (TG), depolymerizing the actin cytoskeleton with cytochalasin D (cyto D) and latrunculin A (Lat A), and inhibiting actomyosin II with y-27632, showed that the calcium was mainly released from the ER in an actin, but not actomyosin, dependent mechanism. The data therefore suggests that the forces subjected to FAs could be directly transmitted to the ER via an actin mediated tension that results in the opening of ER residing calcium release channels. Our results illustrate that the viscoelasticity of the cell niche controls cell behavior in two ways. Firstly, it affects how cells build adhesions to the ECM and thus the accumulation of mechanosensitive proteins. Secondly, it affects the dynamics of the deformations and forces that are sensed by FAs. In line with our previous findings, we show that the mechanically induced calcium responses are dependent on dynamics, with fast mechanical cues resulting in larger calcium responses. Moreover, our research suggests that cells may possess distinct response mechanisms that are selectively activated depending on the mechanical properties of their niche, and the type and dynamics of the mechanical stimulation.

cell biology↗

bioRxiv2025

Somatic copy number mutations contribute to fitness in transplantation models of spontaneous human breast cancer metastasis

The contribution of somatic gene dosage mutations (CNA) to breast cancer metastasis remains poorly defined. Using 9 transplantable human neoadjuvant-naive triple-negative breast cancer xenografts, we studied the fitness of copy number clones in spontaneous metastasis from orthotopic transplant sites. Metastatic site preference was strongly patient-dependent, and the emergence of metastases exhibited a general trend toward slower growth at the orthotopic site. In our models, single-cell whole-genome sequencing of primary and metastatic sites showed that distant metastases were most often the result of minor prevalence clones at the orthotopic site, suggesting that some metastatic phenotypes may be weakly negatively fit at the primary site. We validated the existence of a fitness hierarchy of copy number clones using a previously established paradigm of remixing and retransplanting clones. Single-cell clone analysis of competitive repopulation and re-emergence of metastases showed that CNAs arising in cancer evolution can mediate metastatic fitness. Moreover, some clones displaying strong metastatic tendency exhibited weaker survival at the primary site, consistent with the notion that metastatic phenotypes could have a fitness cost at the primary site. Finally, we conducted RNA-seq analysis combined with DriverNet analysis to dissect the contribution of CNA-mediated versus genome-independent transcriptional states. CNA mutations appeared to contribute strongly to transcriptional differences between clones. Among clones of high metastatic potential, we observed CNA-mediated and CNA-independent convergence on pathways such as epithelial-mesenchymal transition (EMT), established as mediators of metastatic cell survival at distant sites. Taken together, our data point to a contribution of CNA-mediated cancer evolution to metastatic states and identify distant-site context as a key determinant of CNA-mediated fitness.

cancer biology↗

bioRxiv2025

Transcranial Alternating Current Stimulation can disrupt or reestablish neural entrainment in a primate model of Parkinson's disease

Transcranial alternating current stimulation (tACS) is a non-invasive brain stimulation method which can affect brain oscillations by inducing neuronal entrainment through modulation of spike timings. tACS has high potential for clinical applications in many neurological disorders in which the stimulation can be delivered to modulate oscillatory activity and disrupt pathological brain oscillations. For instance, in Parkinsons Disease (PD), electrophysiological activity in the motor network often exhibits excessive and hyper-synchronized beta oscillations. However, the development of tACS as a therapeutic intervention for pathological oscillations requires the prior establishment of physiologically effective stimulation parameters. We recorded neuronal activity in the motor cortical area of three parkinsonian non-human primates and examined the influence of tACS-induced electric fields on neural firing patterns. We found that weak extracellular electric fields first disrupt beta-band spike timing patterns by changing the preferred spiking phase of neurons but eventually reestablish neural entrainment with altered phase preferences when electric fields are high. Additionally, we show that frequency-matched stimulation, when stimulation frequency corresponds to endogenous oscillatory activity, significantly enhances neural entrainment. Thus, tACS exhibits significant potential for controlling and modulating pathological oscillatory patterns in many neurological disorders such as PD.

neuroscience↗

bioRxiv2025

Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development

The spatial organization of chromosomes in the nucleus is fundamental to cellular processes. Contact frequency maps from Hi-C and related chromosome conformation capture assays are increasingly available for a wide variety of biosamples and conditions, creating opportunities for comprehensive studies of genome compartmentalization and long-range interactions. However, the conventional dimensionality reduction approach to study long-range contact frequency profiles projects individual datasets into different and incomparable linear subspaces, making the resulting embeddings unsuitable for large-scale integrative analysis. To address this shortcoming and overcome the computational constraints involved in doing so, we introduce an analytic framework and Python toolkit that leverages incremental principal component analysis to project interchromosomal contact frequency profiles across arbitrarily many Hi-C datasets onto a common set of components or basis vectors. Our approach produces robust and directly comparable first and higher-order principal component (PC) scores that collectively capture biologically meaningful information beyond traditional A/B compartments. By applying our framework to a collection of 89 human Hi-C samples, we uncover distinct patterns of nuclear architecture reflecting cell state categories, associated with different heterochromatin state compositions. We also demonstrate that jointly-derived higher-order PCs improve the prediction of gene expression and regulatory element activity during differentiation. Together, our joint decomposition approach provides a powerful and scalable foundation for systematically investigating genome organization, providing critical insights into its role in development and disease.

genomics↗

bioRxiv2025

Sp Transcription Factors Establish the Signaling Environment in the Neuromesodermal Progenitor Niche During Axial Elongation

Neuromesodermal competent progenitors (NMCs) are located in the caudal epiblast near the node and primitive streak and give rise to spinal cord and somitic mesoderm during trunk and tail elongation. Their self-renewal depends on an autoregulatory loop involving Wnt3a and Fgf signaling, and the Tbxt and Cdx transcription factors, but the mechanisms underlying loop formation and the establishment of the niche are poorly understood. Here, we identify the zinc-finger transcription factors Sp5 and Sp8 (Sp5/8) as essential regulators of NMC maintenance. Sp5/8 expression is controlled by Wnt, Fgf and retinoic acid signaling, and they cooperate with Tbxt, Tcf7 and Cdx2 to sustain a robust autoregulatory network that promotes high Wnt/Fgf and low retinoic acid activity in the niche. These factors bind a novel enhancer essential for Wnt3a expression and feedback-loop integrity. Mechanistically, Sp5/8 regulate the dynamic exchange of activating and repressive Tcf complexes at Wnt-responsive enhancers. Our findings define a transcriptional module centered on Sp5/8 that stabilizes niche signaling and transcriptional circuitry essential for NMC fate decisions and trunk development.

developmental biology↗

bioRxiv2025

Immune-parenchymal multicellular niches are shared across distinct thyroid autoimmune diseases

Thyroid hormone, produced in the thyroid gland, regulates metabolism, development, and cardiac function. The thyroid is susceptible to autoimmune attack by both cellular and humoral immunity exemplified by Hashimotos thyroiditis (HT) and Graves Disease (GD), respectively. In HT, immune-mediated destruction impairs thyroid hormone production, while in GD, stimulating autoantibodies promote over-production. Here, we generated a multi-modal atlas of 604,076 human thyroid and blood cells from HT, GD, and control patients. We found that, despite markedly different clinical presentations and distinct antigenic triggers, HT and GD exhibit convergent cellular dynamics resulting in a shared continuum of immune infiltration. Along this continuum, a key feature is a thyrocyte niche containing CD8+ T cells that may segregate pathogenic T cells from regions with preserved thyroid hormone production. These findings of a shared disease continuum characterized by spatially defined immune niches provide a new framework for understanding tissue homeostasis in human autoimmune disease.

immunology↗

bioRxiv2025

Antennal RNAseq reveals odorant receptors with sex-biased expression in the common eastern firefly, Photinus pyralis

BackgroundWith their charismatic nighttime flashes, fireflies are a classic organismal system for studying visual mating signal evolution. However, across their diversity, fireflies employ a variety of mating strategies that include both chemical and visual signals. While phylogenetic evidence points to a common ancestor that relied on long-range pheromones, behavioral evidence suggests that light-dependent flashing fireflies do not use smell for mating. We tested this hypothesis by investigating the olfactory genetics of the nocturnal, light-using common eastern firefly, Photinus pyralis. In insects, odors are primarily detected by odorant receptor (OR) proteins embedded in the dendritic membranes of olfactory receptor neurons. If pheromones are part of mate signaling in light-using fireflies, then one or more OR genes should be upregulated in the antennae of the searching sex (males). We therefore annotated the complete suite of ORs from the genome of P. pyralis and measured expression of OR genes between the sexes. ResultsWe identified 102 ORs in the Photinus pyralis genome, including the conserved single-copy Orco. Our phylogenetic analysis showed lineage-specific OR diversification in P. pyralis relative to other beetle species. Differential expression analysis of male and female antennae and hind legs revealed that a subset of ORs are upregulated in antennae as compared to legs, suggesting a role in adult olfaction. Notably, PpyrOR6 was one of two genes, and the only OR, that was significantly upregulated between male and female antennae, suggesting a role in mating. ConclusionsThese findings increase known diversity of insect ORs in an understudied beetle family and suggest that bioluminescent fireflies use multimodal signals during mating.

evolutionary biology↗

bioRxiv2025

Adaptive Plasticity Tumor Cells Modulate MAPK-Targeting Therapy Response in Colorectal Cancer

MAPK pathway inhibitors (MAPKi) are increasingly used in the treatment of advanced colorectal cancer, but often produce short-lived responses in patients. Although acquired resistance by de novo mutations in tumors have been found to reduce response in some patients, additional mechanisms underlying the limited response durability of MAPK targeting therapy remain unknown. Here, we denote new contributory tumor biology and provide insight on the impact of tumor plasticity on therapy response. Analysis of MAPKi treated patients revealed activation of stemness programs and increased ASCL2 expression, which are associated with poor outcomes. Greater ASCL2 with MAPKi treatment was also seen in patient-derived CRC models, independent of driver mutations. We find ASCL2 denotes a distinct cell population, arising from phenotypic plasticity, with a proliferative, stem-like phenotype, and decreased sensitivity to MAPKi therapy, which were named adaptive plasticity tumor (APT) cells. MAPK pathway suppression induces the APT phenotype in cells, resulting in APT cell enrichment in tumors and limiting therapy response in preclinical and clinical data. APT cell depletion improved MAPKi treatment efficacy and extended MAPKi response durability in mice. These findings uncover a cellular program that mitigates the impact of MAPKi therapies and highlights the importance of addressing tumor plasticity to improve clinical outcomes.

cancer biology↗

bioRxiv2024

Aging disrupts spatiotemporal coordination in the cycling ovary

Throughout the female reproductive lifespan, the ovary completes hundreds of cycles of follicle development, ovulation, and tissue regeneration1-3. These processes rely on the precisely coordinated intricate multicellular interactions across time and space4. How aging disrupts these interactions, leading to an overall decline in reproductive and endocrine functions, remains understudied. To understand the multicellular dynamics that underlie ovarian function and their changes with age, here we use Slide-seq, a near-cellular spatial transcriptomics method, to profile 22 mouse ovaries across the reproductive cycle and chronological age, representing 610,620 near-cellular spots across 69 spatial transcriptomic profiles5,6. We develop a segmentation analysis to identify spatial niches that capture different states of folliculogenesis from static snapshots in situ, allowing us to examine the multicellular dynamics of 358 oocytes, 668 follicles, and 236 corpora lutea. We find that aging disrupts both the spatial organization and temporal coordination of folliculogenesis before the cessation of cycling, which may contribute to the dysregulation of hormone production and signaling. These disruptions are marked by altered immune cell dynamics, inflammatory signaling, and global tissue disorganization that impair the cyclic remodeling required for ovarian function. Our findings reveal how multicellular niches orchestrate ovarian function and demonstrate how age-related breakdown of tissue organization across time and space precedes reproductive decline.

genomics↗

bioRxiv2024

The impact of sugar diet on humidity preference, survival, and host landing in mosquitoes

Mosquito-borne diseases have caused more than one million deaths each year. There is an urgent need to develop an effective way to reduce mosquito-host interaction to mitigate disease transmission. Sugar diets have long been linked to abnormal physiology in animals, making them potential candidates for mosquito control. Here, we show the impact of sugar diets on humidity preference and survival in Aedes aegypti and Culex pipiens. With two-choice assays between 100% and 75% relative humidity (RH), we demonstrate that the effect of sugar diets on humidity preference is species-specific where Ae. aegypti showed significant differences and the reduced effects were noted in Cx. pipiens. Among the sugar diets, arabinose significantly reduced the survival rate of mosquitoes even at low concentrations. Moreover, we found that host landing was not impacted by feeding on different sugar types. Our study suggests that specific sugar treatments could be applied to mosquito control by dampening their humidity preference and reducing their lifespan, thus reducing mosquito-borne disease transmission.

physiology↗