Biology subjects

Kang, J.

Publications and source records attributed to Kang, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Serial femtosecond crystallography reveals the pH-driven allosteric mechanism of hexamer glargine

Insulin glargine is formulated at acidic pH but acts after transferring to near-neutral tissue, where its prolonged effect is commonly attributed to isoelectric depot formation. However, the structural pathway linking precipitation to delayed release has remained unresolved. Here we combine ambient-temperature serial femtosecond crystallography, solution biophysics, and multiscale network analyses to define the pH-dependent conformational landscape of hexameric glargine across pH 8.4, 7.3, 6.4, and 5.1. We resolve full hexameric glargine structures and identify a previously unreported, pH-coupled lattice transition from P1211 (near-neutral) to R3:H (acidic), accompanied by redistribution from compact phenolic Rf6-state assemblies to more plastic yet structurally coherent TRf/T3Rf3 states. This transition is accompanied by B-chain N-terminal unpeeling, phenol-pocket collapse, hydration loss, and electrostatic rewiring, and is mirrored in solution by oligomeric heterogeneity, Raman amide-I broadening, reduced thermal stability, and a blue-shifted intrinsic fluorescence maximum. Multiscale analyses further indicate that acidification does not create a new dynamical regime but reweighs pre-existing collective modes along a continuous free-energy landscape. These results support a revised mechanism in which isoelectric precipitation and delayed dissociation are mechanistically coupled through structurally organized molten-like intermediate states, linking glargine pharmacology to intrinsic allosteric redistribution within the hexamer. These findings establish a structural blueprint for benchmarking biosimilar glargine and for engineering next-generation basal insulins by tuning allosteric plasticity and intermediate-state stability.

biophysics↗

bioRxiv2026

Reciprocal-space mapping of diffuse scattering by serial femtosecond crystallography reveals analog-specific disorder in insulin analogs

Insulin detemir and insulin aspart are clinically complementary analogs engineered for distinct pharmacokinetic behavior, yet their comparative structural heterogeneity across temperature regimes remains insufficiently resolved. Here, we present a multi-scale crystallographic analysis integrating near-physiological serial femtosecond crystallography (SFX) with previously reported cryogenic and ambient multicrystal datasets for both analogs. Across conventional quality metrics, reciprocal-space intensity-field reconstructions, model-derived diffuse-scattering representations, Ramachandran stereochemical validation, solvent-accessibility coupling (SAArea-MSArea), and residue-level BDamage (a packing-normalized B-factor metric highlighting local mobility outliers) profiling, we identify a coherent ambient-versus-cryogenic contrast. Ambient datasets show broader reciprocal-space heterogeneity and more diffuse model-space distributions, consistent with increased conformational sampling outside cryogenic trapping. Despite this shared trend, disorder partitioning is analog-specific: detemir exhibits strong pseudo-translational signatures with moderate twinning, whereas aspart shows weak pseudo-translation but pronounced merohedral twinning approaching the theoretical twinned limit in ambient conditions. Importantly, backbone stereochemistry remains globally stable across all datasets, indicating that the observed differences reflect structured heterogeneity rather than model deterioration. Collectively, these findings support an ensemble-aware interpretation of insulin crystallography and provide transferable structural descriptors for analog comparison, stability assessment, and formulation-oriented design.

biophysics↗

bioRxiv2026

MitoAtlas: a Domain-Resolved Spatial Map of the HumanMitochondrial Proteome

Mitochondrial function depends on the precise sub-organellar localization and topological orientation of its proteome. However, mapping this architecture with domain-level precision across the double-membrane system has remained challenging. Here, we present MitoAtlas, a spatial systems biology resource built on SR-PL (super-resolution proximity labeling) that resolves the sub-mitochondrial architecture of 861 proteins at domain-level resolution. By deploying 42 spatially restricted APEX2 and BioID/BioID2 baits across mitochondrial compartments and cytosol in HEK293T-REx cells, we mapped 13,440 unique proximity-labeled sites. Integrating high-density spatial data with a machine-learning classification pipeline and AlphaFold structural modeling, we resolved membrane topologies for 196 transmembrane proteins and assigned sub-mitochondrial localizations to 160 previously unannotated mitochondrial proteins absent from MitoCarta3.0, including MINPP1 as an intermembrane space resident. Coupling bait-specific proximity labeling signatures with AlphaFold structure prediction and metabolite docking identified 47 protein-protein interactions, including the LETM1-Citrate Synthase complex, and 155 protein-metabolite interactions. MitoAtlas is available at mitoatlas.org as a domain-resolution spatial map of mitochondrial architecture and metabolism.

cell biology↗

bioRxiv2026

Hippocampal Development in a Rat Model of Perigestational Opioid Exposure

Nearly one third of women of reproductive age in the United States are prescribed opioids annually; 14% of women fill an opioid prescription during pregnancy, and one in five report misuse. Opioid use during pregnancy has given rise to an increasing population of infants born with gestational opioid exposure. Although substantial clinical work has focused on treating these infants as they experience opioid withdrawal symptoms at the time of birth, notably few studies have examined the effects of gestational opioid exposure on brain development and long-term cognitive function. During typical brain development, endogenous opioids and their receptors are highly expressed by neural progenitor cells, neurons, and glia where they modulate cell proliferation, differentiation, and maturation. Thus, any disruption to the endogenous opioid system during the critical period of brain development may have lasting consequences on brain cell populations and the behaviors they influence. Indeed, opioid-exposed infants have smaller brains than age-matched peers and show significant neurodevelopmental impairment; they also have higher rates of learning disability at school age. To investigate how exposure to exogenous opioids during brain development affects neural maturation in the hippocampus, a brain region critical for learning and memory, our lab has developed a clinically relevant perigestational morphine exposure rat model. The current study reports that perigestational exposure to morphine delays postnatal hippocampal neuronal maturation, alters astrocyte and oligodendrocyte proliferation, and alters expression of brain-derived neurotrophic factor (BDNF), a protein crucial for healthy brain growth. Furthermore, we show that environmental enrichment rescues BDNF deficits, offering evidence for the effectiveness of non-invasive, non-pharmacological intervention for developmental consequences of perigestational opioid exposure.

neuroscience↗

bioRxiv2026

Cbfb2 gene dosage programs the differential lymphoid lineage developmental potential of fetal and adult hematopoietic progenitors

Innate-like lymphocyte subsets are generated predominantly during early-life windows, yet the mechanisms that restrict their development in adulthood remain unclear. Here we identify Cbfb2 gene dosage as a quantitative regulator of stage-specific lymphoid potential. We show that reduction of CBF{beta}2 levels unlocks fetal-like competence in adult hematopoietic progenitors, enabling robust generation of IL-17-producing {gamma}{delta} T (T{gamma}{delta}17) cells. Although Cbfb2 haploinsufficiency minimally alters steady-state transcription, chromatin profiling of H3K4me3 revealed promoter-level changes in adult lymphoid-primed multipotent progenitors consistent with altered developmental priming. In adult bone marrow chimeras, Cbfb+/2m progenitors efficiently generated functional V{gamma}2+ T{gamma}{delta}17 cells in lymph nodes and skin, and restoring Cbfb2 expression suppressed this capacity, establishing a dosage-dependent mechanism. Using an optimized in utero transplantation system, we further demonstrate that fetal niches amplify this latent competence and selectively favor IL-17-committed {gamma}{delta} T cell differentiation over conventional {beta} T cell output. Notch1 haploinsufficiency enhanced T{gamma}{delta}17 generation and phenocopied the effect of CBF{beta}2 dosage reduction, linking quantitative NOTCH1 signaling to innate-like lymphocyte developmental programming. Together, these findings reveal that fetal versus adult lymphopoiesis is governed by quantitative tuning of RUNX:CBF{beta} activity and uncover unexpected plasticity in adult hematopoiesis controlled by transcription factor dosage.

immunology↗

bioRxiv2026

O-GlcNAcylation and low glycolysis underpin Th2 polarization by dendritic cells

Activation of dendritic cells (DCs) is dependent on rewiring of their cellular metabolism. However, the metabolic requirements for DCs to prime T helper 2 (Th2) responses are still poorly understood. Using unbiased transcriptomics and non-targeted metabolomics we find that helminth antigen-conditioned human DCs suppress glycolysis while increasing hexosamine biosynthesis to fuel protein O-GlcNAcylation. Functionally, glycolytic inhibition of DCs selectively enhanced, while blocking O-GlcNAcylation impaired, Th2-priming capacity. In helminth infection and allergic challenge, Th2 responses were also attenuated in vivo in mice with specific deletion of O-GlcNAc Transferase (OGT) in CD11c-expressing cells. Mechanistically, through proteomic analysis and functional validation, we identified O-GlcNAcylation as a critical negative regulator of immune synapse formation by controlling cytoskeletal organization via Fascin-1 and Zyxin, thereby dampening TCR signalling to promote Th2 polarization. Altogether we reveal a novel metabolic program in DCs that governs Th2 polarization, that could potentially be harnessed to treat type 2 mediated inflammatory diseases.

immunology↗

bioRxiv2025

Optical Limits in Skin Reflectance Measurement: Quantifying Melanin-Dependent Constraints on Erythema Detection

As skin color measurement shifts from subjective classification to quantitative assessment, the assumption that objective measures are unbiased requires scrutiny. We provide a physics-informed framework for interpreting visible-range skin measurements, clarifying terminology, describing light-chromophore interactions, and surveying tools and output metrics. The physics of light-tissue interaction constrains what any visible-range observation can reveal: melanin and hemoglobin absorb across overlapping wavelengths, and as melanin increases, hemoglobins signature is masked. By analyzing over 15,000 spectra from the International Skin Spectra Archive, we demonstrate that this attenuation is systematic and most severe in the darkest skin, where data are scarcest. These limits arise from the physical properties of skins biological constituents and consequently apply to any sensor operating in the visible range. We conclude with guidance on analytical methods, sampling strategies, and extended wavelengths to improve measurement validity across the full range of human skin pigmentation. Graphical AbstractObjective skin measurements are not inherently unbiased: melanins broadband absorption progressively masks hemoglobins spectral signature, reducing the sensitivity of visible-range erythema detection in darker skin. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/696093v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@23ef00org.highwire.dtl.DTLVardef@11ff875org.highwire.dtl.DTLVardef@1f0eed4org.highwire.dtl.DTLVardef@cfca53_HPS_FORMAT_FIGEXP M_FIG C_FIG Summary PointsO_LIVisible-range skin reflectance measurements capture real optical information but do not directly measure chromophore concentrations; interpreting these signals requires understanding light-tissue interactions. C_LIO_LIMelanin and hemoglobin absorb at overlapping wavelengths, creating optical entanglement that limits the separability of pigmentation and erythema signals from reflectance data. C_LIO_LIHemoglobin spectral signatures are systematically attenuated as melanin increases, reducing the sensitivity of erythema detection in darker skin. This represents objective bias arising from physics, not subjective bias in assessment. C_LIO_LIDerivative analysis of full reflectance spectra can reveal hemoglobin-related structure that persists in darker skin even when standard indices show no signal. C_LIO_LIMelanin index distributions should be reported to assess sample representativeness, as demographic diversity does not guarantee adequate coverage of the pigmentation range relevant to optical measurement. C_LI LimitationsO_LISpectral overlap between melanin and hemoglobin is a physical property of these chromophores; no visible-range instrument or algorithm can fully overcome this constraint. C_LIO_LIThese optical limits apply to any visible-range sensor, including spectrophotometers, clinical photography, and AI systems trained on photographic data. C_LIO_LIExisting datasets remain sparse at the high end of the melanin index distribution, limiting validation of measurement approaches in the darkest skin. C_LI

bioengineering↗

bioRxiv2025

Advancing Knock-In Approaches for Robust Genome Editing in Zebrafish

Precise genome editing remains a major challenge in functional genomics, particularly for generating knock-in (KI) alleles in model organisms. Here, we introduce the mini-golden system, a versatile Golden Gate-based subcloning platform that enables rapid assembly of donor constructs containing homology arms and a gene of interest. This system offers a library of middle entry vectors including diverse genes, enhancing the preparation of donor minicircles for KI applications. Using the mini-golden system, we efficiently generated a foxd3CreER KI zebrafish line, allowing conditional recombination in neural crest cells. To further improve genome editing precision, we developed a synthetic exon-based donor template strategy combined with fluorescence screening. Using this approach, we successfully engineered a targeted isoleucine-to-valine substitution (Ile-to-Val) in hbaa1.2, one of the two adult hemoglobin alpha genes in zebrafish. Importantly, despite the high sequence similarity between hbaa1.2 and its paralog hbaa1.1, our strategy specifically edited hbaa1.2, demonstrating the effectiveness of the synthetic exon approach. This method minimized undesired recombination and significantly improved the identification of lines carrying the edited genome. Together, we provide a robust toolkit for efficient and precise genome engineering in zebrafish, with broad applicability to other model systems.

developmental biology↗

bioRxiv2025

Primary Cilia Dysfunction in Brown Fat Results in Fatal Thermogenesis Failure in Neonatal Mice

Primary cilium, microtubule-based sensory organelle that has emerged as a central player in coordinating numerous signaling pathways. Although primary cilia are known to regulate cellular signaling and energy metabolism, the relationship between these roles in the context of ciliopathies and brown adipose tissue (BAT) dysfunction remains poorly understood. To elucidate the role of primary cilia in BAT, we generated Ucp1-Cre;Ift88flox/flox mice with BAT-specific ciliary loss. There were no significant differences in body size, weight, or BAT weight relative to body weight between P0 Ucp1-Cre;Ift88flox/flox and P0 Ucp1-Cre;Ift88+/+ pups. Embryos examined at E14.5 and E18.5 also showed no discernible differences in size, morphology, or histology. However, P0 Ucp1-Cre;Ift88flox/flox pups exhibited neonatal lethality caused by defective thermogenesis, despite preserved Ucp1 expression. These mice displayed markedly reduced ketone body levels in both BAT and serum, accompanied by downregulation of Hmgcs2, a key enzyme in ketogenesis. Loss of primary cilia in BAT suppressed ketogenesis and increased ROS production through HMGCS2 downregulation, ultimately impairing non-shivering thermogenesis. Remarkably, neonatal lethality of Ucp1-Cre;Ift88flox/flox pups was completely rescued by thermoneutral housing or {beta}-hydroxybutyrate supplementation. Our findings identified a previously unrecognized mechanism by which primary cilia regulate non-shivering, UCP1-independent thermogenesis via ketogenesis.

cell biology↗

bioRxiv2025

Discovery of a potent anti-Zika virus benzamide series targeting the viral protein NS4B

1.Zika virus (ZIKV), a member of the Flaviviridae family, causes significant public health concerns through congenital Zika syndrome and Guillain-Barre syndrome, yet no effective anti-ZIKV drugs or vaccines are available. To address this critical need, we conducted phenotypic, cytopathic effect-based, high-throughput screening followed by medicinal chemistry optimization and discovered novel benzamide anti-ZIKV leads. Current best compounds demonstrated superior potency (EC50 values 40-400 nM, CC50 > 50 {micro}M) compared to NITD-008, the most potent known anti-ZIKV agent. Time-of-addition assays, resistant virus selection studies, and biophysical binding experiments confirmed that NS4B interference constitutes the primary antiviral mechanism. Notably, resistance mutations mapped to the C-terminus of NS4B, distinct from other flavivirus NS4B inhibitors targeting dengue or yellow fever viruses, revealing novel insights into a critical function of the region. These findings establish NS4B as an Achilles heel for flaviviruses and support the development of pan-flavivirus therapeutics targeting this essential viral protein. 2. AUTHOR SUMMARYSince its pandemic spread in 2015-2016, Zika virus infection remains a significant public health threat worldwide. The virus can cause severe brain damage in developing babies and serious neurological complications like Guillain-Barre syndrome in adults. Despite these devastating consequences, we currently lack effective medicines or vaccines to prevent the virus from spreading through communities or from mothers to their unborn children. To address this critical gap, we conducted a large-scale screening of chemical compounds and discovered a promising new class of molecules that can effectively stop Zika virus from replication. Using medicinal chemistry techniques, we were able to make these compounds even more potent against the virus. In follow-up studies, we found that our compounds work by interfering with a specific viral protein called NS4B, which the virus needs to replicate its genome within the cell. Remarkably, other research teams studying related other flaviviruses (e.g., dengue and yellow fever virus) have independently discovered that this same protein is a vulnerable target. Our findings suggest that NS4B represents a universal weakness across the entire flavivirus family, making it an attractive target for developing broad-spectrum antiviral treatments.

microbiology↗

bioRxiv2025

Compact Tape-Driven Sample Delivery System for Serial Femtosecond Crystallography

We developed a compact tape-drive with on-demand sample delivery (CoT) for time-resolved serial femtosecond crystallography (SFX) experiments that can deliver sample droplets and/or initiate reactions with a drop-on-drop strategy. Two disposable piezoelectric injectors are positioned in tandem along the tape to produce a queue of nanoliter-scale droplets. X-ray free-electron laser (XFEL) pulses arrive perpendicular to and pass through the broad face of the tape where the pulse is synchronized and aligned to the droplets and thereby enables very highly efficient SFX data collection. The tape transport speed and the delivery distance can be varied to control the mixing time from approximately 130 ms to tens of seconds. We conducted time-resolved SFX experiments utilizing a basic enzymatic reaction model of hen egg white lysozyme (HEWL) and N-acetyl-D-glucosamine (GlcNAc) to demonstrate the drop-on-drop capabilities of CoT, and the full binding process of GlcNAc to HEWL was observed at 1.3-9.7 s. SynopsisTape-driven liquid sample droplet delivery system for serial femtosecond crystallography

biophysics↗

bioRxiv2025

Merits and challenges of plasma proteomics on association replicability

Developments in proteomic platforms have enabled the generation of large-scale high-throughput plasma proteomics data [1-3]. With recent breakthroughs in AI modelling, these data have significantly enhanced our understanding of molecular mechanisms underlying human behaviors and diseases [4-6]. However, the replicability of associations between plasma proteomics and phenotypes remains underexplored. Here, we systematically assessed the replicability of associations with recent plasma proteomics data in the UK biobank. Over 75% of cognitive function and mental health traits demonstrated high overall (proteomics-wide) replicability when brain-related traits were considered as phenotypes. Although mean cortical thickness (CT) as phenotype exhibited clearly reduced replicability, total cortical surface area (CSA) and cortical volume (CV) showed high overall replicability across hemispheres and over twenty brain regions. In comparative multi-omics analyses based on the same cohort of participants, proteomics outperformed genomics across all brain-related traits, and exceeded metabolomics for over half of traits where metabolomics also exhibited high overall replicability. Furthermore, we developed a predictive framework to estimate the replicability for potential future proteomics panels based on the crucial influential factors including dilution level, proportion of samples below the limit of detection (LOD), and sample size. Moreover, we constructed an individual replicability index for proteins and identified eleven proteins with highly replicable associations across cognitive function and mental health traits, which was in line with the recent identifications of pleiotropic proteins in large-scale population studies. Collectively, our results revealed the challenges in the association replicability of plasma proteomics under reduced data quality (from "Explore" to "Expansion" assay panels), and we further explored how to sustain high replicability in potential future panels. Fundamentally, our findings affirm the merits of plasma proteomics: this molecular omics platform enables highly replicable associations for mapping biomedical signatures.

bioinformatics↗

bioRxiv2025

Polycomb Repressive-Deubiquitinase Complex Safeguards Oocyte Epigenome and Female Fertility by Restraining Polycomb Activity

Mouse oocytes exhibit a unique chromatin landscape characterized by broad H3K27ac and H3K27me3 domains, demarcating euchromatin and facultative heterochromatin, respectively. However, the mechanisms underlying this non-canonical landscape remain elusive. Here we report BAP1, a core component of the Polycomb Repressive-Deubiquitinase (PR-DUB) complex, as a key negative regulator of Polycomb activity during oogenesis. BAP1 restricts pervasive H2AK119ub1 accumulation in oocytes and protects oocyte-specific broad H3K27ac, particularly within gene-poor regions, from ectopic H3K27me3 deposition. While PR-DUB has been linked to gene repression, in oocytes BAP1 primarily promotes transcription and contributes minimally to Polycomb-mediated silencing. BAP1-dependent transcriptional activation is essential for oocyte developmental competence and female fertility. BAP1 loss disrupts the maternal-to-zygotic transition and impairs embryonic enhancer activation, ultimately compromising preimplantation development. Notably, while H3K27ac patterns are reset after fertilization, the aberrant H3K27me3 landscape established in BAP1-deficient oocytes persists in early embryos. Together, these findings reveal a critical role for PR-DUB in safeguarding the oocyte epigenome by protecting euchromatin from ectopic Polycomb activity, rather than enforcing transcriptional repression.

developmental biology↗

bioRxiv2025

Deciphering the altered conformational states of bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

The thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle represents one of the most efficient mechanisms for CO2 fixation discovered to date. Within this cycle, the enzyme encoded by Nmar_1308 from Nitrosopumilus maritimus SCM1 plays a crucial role due to its dual functionality as both a crotonyl-CoA hydratase (CCAH) and a 3-hydroxypropionyl-CoA dehydratase (3HPD). Although the importance of a bifunctional enzyme for lowering the cost of biosynthesis, the details of structural dynamics are still missing. Here, in addition to our cryogenic temperature structures, we determined the first ambient temperature structures of the Nmar_1308 protein by Serial Femtosecond X-ray Crystallography (SFX). The determined structures capture previously unobserved conformational dynamics of the Nmar_1308 protein, providing invaluable information for future synthetic biology applications.

biochemistry↗

bioRxiv2025

A hierarchical abscission program regulates reproductive allocation in Prunus yedoensis and Prunus sargentii

O_LIorgan abscission is essential for optimal reproduction, yet its regulation in perennial woody plant species is poorly understood. To investigate how abscission is spatially and temporally regulated during reproduction, we analyzed five sequential abscission events in the cherry species Prunus yedoensis and Prunus sargentii: abscission of the petals, calyces, flower pedicels, fruit pedicels, and peduncles. C_LIO_LIThe abscission zone (AZ) of the calyx formed de novo upon activation, whereas other AZs were pre-formed but developmentally arrested. Localized ethylene responsiveness reactivated these zones, promoting cell division, differentiation of residuum and secession cells on either side of the AZ, and lignin deposition in some cases. This progression was accompanied by reactive oxygen species accumulation and pH shifts. C_LIO_LIWe observed species-specific differences during early floral abscission: P. yedoensis shed petals rapidly in a pollination-independent manner, whereas P. sargentii retained petals on unpollinated flowers, which later abscised with the pedicel, potentially extending the fertilization window. C_LIO_LIBoth species employed a post-fertilization checkpoint via fruit pedicel abscission to selectively eliminate small, slow-growing fruits. These findings reveal that Prunus species coordinate a hierarchical abscission program functioning as a multilayered reproductive filter, progressively refining investment decisions to determine the final fruit set. C_LI

plant biology↗

bioRxiv2025

Spatio-temporal mass spectrometry in living cells reveals regulators of cuproptosis

Cuproptosis is a unique form of regulated cell death triggered by excessive copper accumulation in mitochondria. To decipher the mechanisms of cuproptosis, we develop Spatio-Temporal Mass Spectrometry (STMS) technique to characterize dynamic subcellular proteomic changes during its early stage. STMS analysis reveals distinct subcellular proteome alterations and unique trafficking patterns over time. Through a genetic functional screen, we discover that copper stress reduces OXA1L in mitochondria, disrupting MRPL20 import and impairing oxidative phosphorylation complex I synthesis. This mitochondrial dysfunction promotes MRPL20 nuclear translocation, triggering the mitochondrial unfolded protein response as an adaptive mechanism to restore mitochondrial proteostasis during early cuproptosis. Meanwhile, AMPK phosphorylates ISCU at serine 29, stabilizing ISCU protein, and increasing the abundance of Fe-S cluster-containing proteins, which, in turn, enhances cells susceptible to cuproptosis. Building on this mechanistic insight, we develop AMPK-SPARK, a phase separation-based EGFP reporter for real-time visualization of endogenous AMPK activity in living cells during cuproptosis. Additionally, we identify COMMD4 as a cuproptosis sensor and establish a GFP-tagged COMMD4 cell model for high-content drug screening. Using this platform, we identify three FDA-approved drugs including Plerixafor, Dithranol, and Bleomycin as potential cuproptosis inhibitors. Overall, our work advances the understanding of cuproptosis regulation and provides valuable molecular tools and data resource for future research in this area.

cell biology↗

bioRxiv2025

Tumor Cells Enriched for Interferon and Inflammatory Programs Pre-Exist in High Grade Serous Ovarian Cancer and are Proportionately Significantly Increased Post Chemotherapy

Drug-tolerant, high-grade serous ovarian cancer (HGSOC) cells that persist after first-line chemotherapy and subsequently relapse often retain sensitivity to secondary treatment, suggesting a therapeutic window before stable chemoresistance emerges. We performed single-cell RNA sequencing (scRNA-seq) on seven matched pairs of tumors, collected pre- and post-chemotherapy, to define vulnerabilities in these reversibly-resistant cells. Treatment induced a marked enrichment of tumor and stromal cell populations expressing correlated interferon (IFN) and inflammatory (IFM) gene signatures, with a concurrent depletion of proliferation-related and MYC-associated states in the tumor cells. Cross-cohort single cell sequencing analysis of >130 treatment-naive tumors revealed heterogeneity in the abundance of IFN/IFM-expressing cells. Multiplex immunofluorescence imaging of IFN-stimulated gene (ISG) products confirmed the presence of spatially clustered ISG-positive tumor cells in all cases, as well as in serous tubal intraepithelial carcinomas (STIC lesions), the presumptive HGSOC precursors. ISG expression correlated strongly with ORF1P, a protein encoded by the endogenous retrotransposon LINE1. These data suggest that early oncogenic events drive LINE1 derepression and innate immune activation, establishing an IFN-rich transcriptional state that persists in tumor subpopulations and is strongly enhanced by chemotherapy.

cancer biology↗

bioRxiv2025

Pupil-linked arousal does not differ between white, pink and brown noises

Coloured noises, such as white, pink, and brown noise, have gained attention in popular media as potential tools for enhancing memory consolidation, sleep quality, attentional focus, and more. These terms refer to distinct spectral slopes, which give rise to perceptually different noise stimuli. Although empirical research on their effects remains limited, a prevailing hypothesis suggests that their influence may be mediated by differential effects on arousal. In this study, we investigated this hypothesis using pupillometry, a physiological marker closely linked to arousal. Participants (N = 31) listened to three types of noise (white, pink, and brown), each presented for 10 sec, while their pupil diameter was recorded. The results showed no significant modulation of pupil size across noise conditions. These findings suggest that, despite widespread claims about the distinct arousing or calming properties of coloured noises, they do not differentially affect sustained pupil-linked arousal.

physiology↗