Biology subjects

Yao, C.

Publications and source records attributed to Yao, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Auditory tracking magnitude, temporal alignment, and anatomical distribution during wakefulness and propofol-based anesthesia in human sEEG

General anesthesia attenuates auditory responses, but response magnitude alone does not describe how residual activity aligns with sound over time or varies across the brain. We jointly characterized these aspects of auditory tracking using stereoelectroencephalography (sEEG) in 13 patients with drug-resistant epilepsy during wakefulness and clinically defined unresponsiveness under propofol-based anesthesia. The same rhythmic humming sequences were presented at approximately 1.61 Hz in both sessions. During anesthesia, stimulus-rate power showed widespread reductions and phase alignment with the stimulus rhythm was less consistent, although responses remained detectable at some recording channels. During wakefulness, response strength decreased with cortical surface distance from posteromedial Heschl's gyrus; this distance-response relationship was weaker during anesthesia. In a contrastive learning analysis (CEBRA), low-dimensional embeddings derived from anesthesia recordings yielded lower acoustic-envelope decoding accuracy on held-out data and lower consistency across model fits. Together, these findings characterize how attenuated auditory tracking is expressed jointly in response magnitude, temporal alignment, and anatomical distribution.

neuroscience↗

bioRxiv2026

Regulatory-scale stripe analysis from single-cell Hi-C with scStripe

Chromatin stripes are a directional architectural feature of three-dimensional genome organization, but their analysis in single-cell Hi-C (scHi-C) at regulatory resolution is hindered by extreme sparsity. We developed scStripe, an imputation-free two-stage statistical framework that detects stripes from sparse cell-type--aggregated scHi-C maps and directly quantifies the resulting aggregate-defined stripes in raw individual-cell contact maps using per-cell stripe scores. Across three complementary benchmark settings, scStripe achieved the highest F1 scores and showed strong aggregate stripe enrichment, while the detected stripes recapitulated characteristic structural and regulatory features reported in bulk data. Per-cell stripe scores resolved recurrent configurations of the EBF1-anchored stripe, captured genome-wide variation associated with cell type, cell-cycle phase, and developmental stage, and identified positively associated gene--stripe pairs with pronounced cell-type specificity using matched scRNA-seq. Together, scStripe provides a practical, scalable framework for regulatory-scale stripe analysis across single cells without requiring single-cell enhancement or 3D reconstruction.

genetics↗

bioRxiv2026

Dissociating the intensity and phase origins of sleepiness through a threshold-distance model of sleep-wake dynamics

Sleepiness is a leading proximate cause of drowsy-driving fatalities, medical errors and industrial accidents, yet it has resisted mechanistic prediction; although it arises from well-characterized sleep-wake physiology, it is experienced as a subjective state and has lacked a quantitative link to the underlying dynamics. We previously showed that subjective sleepiness maps linearly, with a protocol-invariant form, onto the signed distance H - H+ between the homeostatic pressure H and the circadian-modulated sleep-onset threshold H+. This single quantity predicts sleepiness accurately but is mechanistically ambiguous: the same value can arise either because H sits far from the boundary or because the threshold H+(t) has shifted with circadian phase, and these two origins call for entirely different interpretations and interventions. Here we resolve this ambiguity by decomposing H - H+ into two mechanistically separable axes-intensity and phase. The intensity axis is the time-averaged margin [<] H - H+[>], set by how far, on average, H sits from the sleep boundary: slowed homeostatic accumulation accounts for the paradoxically blunted sleepiness of older adults, and pharmacological suppression of H accounts for the dose-dependent alerting effect of caffeine. The phase axis is set by the circadian modulation of H+(t): under a forced-desynchrony protocol, in which the pacemaker free-runs and the homeostatic and circadian processes are experimentally decoupled, sleepiness tracks the circadian profile of H+(t) across all phases while the intensity mapping itself remains unchanged-a clean dissociation of the two axes. By resolving felt sleepiness into these two physiological degrees of freedom, this framework renders previously isolated phenomena-aging, caffeine and circadian misalignment-commensurable within a single theory and provides a physiologically interpretable basis for prospective fatigue-risk prediction. Author summaryWhy people feel sleepy after sleep loss, or at particular times of day, remains difficult to predict from physiology alone. Sleep and wake are shaped by two interacting processes: a daily circadian rhythm and a homeostatic pressure that builds during wakefulness. In earlier work, we linked subjective sleepiness ratings to a simple geometric quantity-how close sleep pressure sits to a circadian sleep-onset boundary. That link is useful, but ambiguous: the same distance can arise either because pressure itself has changed, or because the boundary has moved with circadian phase. Here we use a computational model of the sleep-wake switch, extended to include the wake-stabilizing orexin system, to separate these contributions into an intensity axis and a phase axis. We find that aging and caffeine mainly alter how large the average distance to the boundary becomes, whereas forced desynchrony mainly alters how that distance varies across circadian phase. This dissociation offers a compact way to interpret several otherwise separate observations within one quantitative picture, and a step toward more physiologically grounded fatigue-risk assessment.

neuroscience↗

bioRxiv2026

Circadian-Modulated Thresholds for Sleep Patterns in Aging and Narcolepsy

In the two-process model of sleep-wake regulation, circadian-modulated thresholds time every sleep onset and awakening, yet they remain free parameters rather than quantities derived from neuronal dynamics. This limitation leaves the framework unable to predict how sleep patterns change when neuromodulatory drive is altered, as in aging and narcolepsy. Here we close that gap by deriving closed-form, circadian-modulated threshold expressions from the Phillips-Robinson model with explicit orexinergic excitation of the wake-promoting population. Within this single threshold geometry, aging and narcolepsy appear as opposite deformations along the orexinergic axis: age-related hyperexcitability of orexin neurons elevates the sleep-onset boundary and creates a fragility regime in which minor nocturnal disturbances trigger premature awakenings, whereas orexin loss depresses the same boundary toward the wake-onset threshold and produces the rapid state fragmentation of narcolepsy. Concurrently, reduced circadian amplitude compresses the inter-threshold corridor, advancing sleep onset and shortening sleep duration. These results convert the classical two-process thresholds from descriptive conveniences into mechanistic organizers of sleep-wake dynamics across healthy aging and orexin deficiency. Author summaryThe classical two-process model of sleep relies on a pair of switching thresholds that have been imposed by hand rather than derived from the neurons that actually stabilize sleep and wakefulness. Here we remove this limitation: starting from a biophysical mean-field model of the sleep- and wake-promoting populations, and adding the orexin system that stabilizes arousal, we derive the sleep-onset and awakening thresholds analytically from the bifurcation geometry of the underlying dynamical system. These closed-form thresholds depend explicitly on circadian phase, homeostatic state, and orexinergic tone, revealing that aging and narcolepsy are opposite deformations of a single threshold corridor along one orexinergic axis. In aging, orexin hyperexcitability raises the sleep-onset barrier past a sharp "arousal fragility boundary," beyond which a minor disturbance triggers irreversible awakening; in narcolepsy, orexin loss collapses the same barrier and fragments sleep while paradoxically preserving total sleep time. We further find, contrary to common assumption, that orexin sustains wakefulness chiefly by raising the barrier to falling asleep rather than by resisting awakening. This work turns phenomenological sleep thresholds into physics-derived organizers of behavior, providing a mechanistic bridge from neuronal circuitry to whole-organism sleep dynamics.

neuroscience↗

bioRxiv2026

Large-scale functional coupling and computational modelling reveal frontotemporal hotspots in distributed network connectivity during working memory recognition, encoding, and retrieval

Working memory depends on coordinated activity across distributed brain networks, but how these interactions support recognition, encoding, and retrieval remains unclear. Here, we analyzed intracranial local field potentials from 1,652 sites in 36 epilepsy patients performing a naturalistic card-matching task. Phase-amplitude and phase-phase coupling revealed widespread condition-dependent interactions, with frontal and temporal regions emerging as recurrent network hubs. Event-related analyses showed reproducible within-trial coupling dynamics across participants. Directed phase transfer entropy further identified frequency-specific information flow, including frontal regions acting as a theta-band source and an alpha-band sink. Finally, a time-delay-embedded hidden Markov model identified task-locked latent states with condition-dependent occupancy trajectories and distinct coherence profiles. Together, these results suggest that working memory is implemented through dynamic, directionally organized large-scale networks, in which frontotemporal hubs coordinate flexible transitions among distributed neural states rather than operating in isolation.

neuroscience↗

bioRxiv2026

A human intracranial map of consciousness returning from anesthesia

How consciousness arises from the brain remains a central yet unsolved question. Although substantial effort has been devoted to characterizing the neural correlates of conscious perception during wakefulness, how consciousness re-emerges from unconscious states remains poorly understood. Here, we took advantage of the rare opportunity to record human intracranial local field potentials from propofol-induced general anesthesia through the transition to behavioral engagement and subsequent full wakefulness, capturing both the stable states of unconsciousness and consciousness and the reconstituting neural dynamics that bridge them. Anesthesia cannot be defined by any single electrophysiological signature; rather, it is an organized low-frequency regime characterized by a constellation of coordinated neural phenomena, including aperiodic slow waves, alpha/beta periodicity, global alpha synchronization, and slow-wave-alpha/beta phase-amplitude coupling. Following anesthetic cessation, this regime progressively dissolved as neural excitability and dynamical complexity climbed. The appearance of conscious behavior coincided with a fast and dramatic transformation in high-gamma activity, from stochastic and unpredictable bursts to structured responses that were distributed, task-selective, and event-locked. These findings suggest that the recovery of consciousness is a multiscale reorganization in which distinct neural underpinnings rise and fall. Together, this work charts an electrophysiological map of how conscious cognition is extinguished, reconfigured, and restored in the human brain.

neuroscience↗

bioRxiv2026

A microbial-sensory axis drives Pseudomonas aeruginosa-induced mechanical itch

Cutaneous bacterial infections frequently elicit severe pruritus, prominently featuring alloknesis, a pathological state where innocuous touch provokes intense itch. However, the peripheral mechanisms translating microbial cues into touch-evoked pruritus remain unresolved. Here, we establish an epicutaneous Pseudomonas aeruginosa infection model that robustly isolates mechanical alloknesis from spontaneous scratching. We identify bacterial flagellin as the critical virulence factor driving this specific sensory modality via Toll-like receptor 5 (TLR5) activation exclusively within Calb1+ A{beta} rapidly adapting low-threshold mechanoreceptors (RA-LTMRs). Mechanistically, pathogen-driven TLR5 signaling depletes intracellular PIP2, which suppresses KCNQ4-mediated M-currents and dismantles the biophysical brake on LTMR excitability. Our findings define a distinct microbial-neuronal axis that directly converts tactile stimuli into itch at the peripheral entry point, providing an infection-based framework for dissecting pathogen-sensory neuron interactions and uncovering precise therapeutic targets for chronic, touch-evoked pruritus. TEASER A bacterial flagellin-sensing touch neuron pathway converts innocuous touch into itch during skin infection.

neuroscience↗

bioRxiv2026

Syndecan-1 Promotes Alveolar Type 2 Epithelial Cell Senescence during Lung Fibrosis.

Idiopathic pulmonary fibrosis (IPF) is an age-related, progressive, and fatal interstitial lung disease for which effective therapies remain limited. Alveolar type 2 (AT2) epithelial cells serve as facultative stem cells essential for alveolar repair; however, AT2 cell senescence disrupts epithelial regeneration and contributes to fibrotic remodeling in IPF. Syndecan-1 is a transmembrane heparan sulfate proteoglycan predominantly expressed by lung epithelial cells, but its role in AT2 dysfunction during fibrosis is poorly defined. Here, we demonstrate that syndecan-1 is robustly upregulated in AT2 cells in IPF and other fibrotic lung diseases, as well as in murine bleomycin-induced lung fibrosis. Syndecan-1 expression was further enhanced with aging and associated with increased fibrotic burden in aged mice. Using integrated human transcriptomic analyses, mouse genetic models, and epithelial cell-based systems, we show that excess syndecan-1 promotes cell-autonomous epithelial senescence and impairs AT2 progenitor function. Elevated syndecan-1 reduced AT2 renewal capacity, disrupted differentiation, and diminished surfactant protein C level, whereas genetic loss of syndecan-1 attenuated senescence and preserved epithelial function following injury. Together, these findings identify syndecan-1 as a critical epithelial regulator of AT2 senescence and maladaptive repair in pulmonary fibrosis and support targeting syndecan-1-driven epithelial dysfunction as a potential therapeutic strategy.

cell biology↗

bioRxiv2026

The not-so-great speciator: Systematics and species limits in a rapid radiation, the Asiatic white-eye complex (Zosterops spp.)

Abstract/SummaryHere we untangle the systematics of the Asiatic white-eye complex (Zosterops spp.) to better understand the early stages of a recent island radiation. We adopt an integrative approach involving allelic data, genome-scale single nucleotide polymorphisms (SNPs), and museum-based morphometrics coupled with a comprehensive sampling to provide the most holistic understanding of the group to date. The island lineages of Asiatic white-eyes across Indonesia, the Philippines, East Asia, the adjacent oceanic islands of the Western Pacific underwent a deep split separating Zosterops everetti and Z. nigrorum in the Phillippines from a very rapid radiation including Z. japonicus, Z. meyeni, and Z. montanus in the Philippines, Japan, and Indonesia. Z. nigrorum catarmanensis on Camiguin South in the Philippines was found to be nested within Z. montanus and a species limit between Z. nigrorum populations on Panay and Luzon was strongly supported. Phylogenetic splits and population structure were detected within the clade containing Z. japonicus, Z. meyeni, and Z. montanus. A well-supported split separates a northern group including Northern Philippines Z. montanus subspecies, Z. meyeni, and Z. japonicus from the southerly Z. montanus taxa. This creates a paraphyletic Z. montanus. However, based on speciation rates within the broader Asiatic white-eye clade this break likely does not yet represent evolutionarily independent species lineages. Morphological evolution is taking place within the Asiatic white-eyes especially within the robust, large-billed subspecies of Z. japonicus on the oceanic islands of Japan and in the newly identified yellow-morph of Z. montanus on Camiguin South.

evolutionary biology↗

bioRxiv2026

Circadian-Modulated Thresholds as a Mechanistic Basis for Sleep-Wake Transitions, Recovery, and Sleepiness

Human sleep-wake cycles arise from the interplay between homeostatic sleep pressure and circadian rhythms, yet the underlying mechanistic basis by which these drives jointly govern state transitions, recovery from sleep loss, and subjective sleepiness remains unclear. Here, we use the extended Phillips-Robinson model incorporating circadian excitation of orexin and locus coeruleus populations, yielding analytically tractable, circadian-modulated thresholds for sleep onset and awakening, and delineating the roles of circadian and homeostatic drives. We show that homeostatic feedback alone generates intrinsic sleep-wake oscillations via a saddle-node on invariant circle bifurcation, while circadian drive reshapes the stability landscape to account for immediate sleep onset and partial first-night recovery after prolonged deprivation, and enables analytic predictions of sleep timing and duration. We further define sleepiness as the distance between the homeostatic state and the active circadian sleep threshold, which robustly predicts subjective sleepiness across various deprivation, restriction, extension, and recovery protocols. Together, these results establish circadian-modulated thresholds as a unifying dynamical principle linking sleep-wake transitions, recovery dynamics, and sleepiness, with implications for circadian misalignment, shift work, and individualized sleep interventions. Author summarySleep and wakefulness arise from the interaction between circadian timing and the gradual accumulation and dissipation of sleep pressure. Although existing computational models have advanced understanding of these processes, most rely on fixed or heuristic rules for switching between sleep and wake states, limiting their ability to explain behavior under sleep deprivation, extension, or restriction. Here, we present a mechanistic description of state switching in which circadian and homeostatic influences act as separable but interacting control dimensions, providing a framework for how circadian modulation shapes state stability, recovery sleep, and subjective sleepiness, without invoking separate mechanisms for normal and perturbed conditions. By recasting sleep regulation in terms of state-dependent dynamical boundaries, our results offer a unified perspective on sleep timing, duration, recovery, and vulnerability to fatigue. This work provides a more physiologically grounded foundation for sleep-wake modeling and a principled basis for understanding circadian misalignment, shift work, jet lag, and other real-world challenges to sleep health.

neuroscience↗

bioRxiv2026

Reversible RNA Acylating Reagents with Nitro Reduction Strategy

We developed a series of nitro reduction-reversible acylating reagents. Following optimization of the acylation conditions, these reagents were tested for deacylation with sodium dithionite in vitro. We applied this reversible acylation to modulate RNAzyme-mediated pre-tRNA maturation, demonstrating its ability to regulate RNA-RNA interactions. Furthermore, the in vitro reversible acylation of EGFP mRNA indicated effective control of its translational activity. To explore cellular applications, we validated NQO1-mediated deacylation in vitro and then induced hypoxia in HepG2 cells using cobalt chloride, thereby reactivating the function of acylated EGFP mRNA via endogenous NQO1. Overall, this study highlights the potential for developing nitro reduction-reversible acylation as a new strategy for RNA functional control and RNA-based drug modification.

biochemistry↗

bioRxiv2025

Fast and slow architectures of cortical dynamics in human brain

The human brain operates across a vast temporal range, from fast perception and action to slow physiological regulation. The capacity has attributed to a unitary cortical gradient of intrinsic timescales, yet such a unidimensional model cannot explain how local circuits simulateously support both rapid external behavior and slow internal body-coupled dynamics. Using SPLIT (spectral piecewise-linear inference of timescales) on a large-scale intracranial stereo-electroencephalography (8,619 contacts, 185 individuals), we identified dissociable fast (~10-100 Hz) and slow (~1-10 Hz) temporal components. Only the fast-component timescales followed the canonical sensorimotor-to-association cortical hierarchy. Slow-component timescales showed no hierarchical gradient, but were instead covaried with heart rate and enriched at site with heart-related neural responses. This dual temporal architecture persisted across wakefulness, rest, sleep, and anesthesia, challenging the unitary view of brain timescales and revealing an intrinsic bipartite organization that is associated with cortical hierarchy or neurophysiology.

neuroscience↗

bioRxiv2025

Senescent host-derived extracellular vesicles potentiate antitumor immunity via bystander T cell activation

Extracellular vesicles (EVs) are key mediators of intercellular communication, and those from the plasma of aged individuals are typically viewed as drivers of aging or even cancer. Here, we uncover a latent, potent antitumor capacity inherent to EVs derived from aged hosts. Specifically, we demonstrate that extracellular vesicles from the plasma of aged mice (A-EVs) exhibit robust tumor-suppressive activity in young tumor-bearing recipients. Mechanistically, A-EVs engage a dual mode of action: they directly induce senescence in cancer cells, enhancing their immunogenicity. More importantly, they concurrently activate non-tumor-specific bystander CD8 T cells within the tumor microenvironment via cross-presentation of pathogen-derived antigens, thereby reshaping the immunosuppressive tumor microenvironment. This synergistic interplay potently reinvigorates antitumor immunity and sensitizes tumors to PD-L1 checkpoint blockade. Our findings establish A-EVs as a novel class of endogenous immunomodulators with broad therapeutic potential for cancer immunotherapy.

immunology↗

bioRxiv2025

Automatic binding of basic sensory features requires consciousness

Conscious awareness requires establishing coherent percepts. Yet, whether consciousness is necessary for initiating the integration of basic sensory features remains unclear. Competing theories implicate distinct functional regimes of consciousness in the process of feature binding and creating conscious percepts. We used a novel multi-feature oddball paradigm with intracranial stereo-electroencephalography (sEEG) recordings in awake and anesthetized states to investigate the functional boundary of consciousness. In the awake state, the auditory attributes of loudness and tone, as well as the binding of the two features, were automatically encoded without attention to the stimuli in a functionally localized sensory cortical network. In the anesthetized state, the cortical registration of single attributes was preserved, whereas the binding was abolished. Moreover, anesthesia mostly influenced later cortical processes after stimuli offset. These results reveal the borderline of exertion of consciousness between the encoding and manipulation of basic sensory features in local cortical circuits - the functional boundary of consciousness constrains the feedforward binding and recurrent process directly at local rather than global level computations.

neuroscience↗

bioRxiv2025

Phosphatidylcholine Metabolism Controls Alveolar Progenitor Renewal and Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease marked by alveolar type 2 (AT2) stem cell dysfunction and excessive matrix deposition, with no effective treatments. Recent advances have recognized that AT2 cells act as stem cells, in addition to their role in the production of pulmonary surfactants in the distal alveolar space. We and others have reported a failure of AT2 regeneration and a loss of AT2 cells in IPF. We recently further reported that there is a defect in lipid metabolism in IPF AT2 cells and we discovered a selective loss of lysophosphatidylcholine acyltransferase 1 (LPCAT1) in AT2 cells from IPF, as well as in AT2 cells from bleomycin-injured mice. Pharmacological and genetic experiments confirm that LPCAT1 is required for AT2 cell renewal in 3D organoid assays. AT2 cell-specific Lpcat1 deletion resulted in reduced AT2 renewal, spontaneous lung fibrosis, and heightened susceptibility to bleomycin-induced fibrosis in mice in vivo. Expression-based high-content drug screening with an LPCAT1 knock-in cell line identified several drug families that upregulated LPCAT1 expression. We further confirmed that anti-malarial artesunate and PLA2 inhibitor ONO-RS-082 increased LPCAT1 mRNA expression, promoted AT2 renewal, and attenuated bleomycin-induced lung fibrosis in mice in vivo. Our findings establish LPCAT1 as a critical regulator of AT2 renewal and lipid metabolism in IPF, suggesting that reactivation of LPCAT1 could offer a novel therapeutic strategy for restoring alveolar progenitor function and mitigating lung fibrosis.

cell biology↗

bioRxiv2025

BACH2 dosage establishes the hierarchy of stemness and finetunes antitumor immunity in CAR T cells

Self-renewing stem-like T cells promote the efficacy of cancer immunotherapy and are a heterogeneous population with sub-lineages demonstrating different degrees of stemness. At the apex of this hierarchy is long-term (LT) stem-like T cells with the highest capacity of persistence, repopulation and response to immune checkpoint inhibitors (ICI). However, the pathway that establishes the hierarchy of stemness in chimeric antigen receptor (CAR) T cells and its role in antitumor efficacy of CAR T cells are unclear. Here, we demonstrate that LT stem-like differentiation and antitumor immunity of CAR T cells are dose-dependently regulated by BACH2. Pre-infusion LT stem-like CAR T cells showed epigenetic activation of BACH2 and superior antitumor response in mice and humans. After clearing tumor in vivo, LT stem-like T cells emerged as a CAR subset that transcriptionally and epigenetically upregulated BACH2 and downregulated TOX. Loss-of-function experiments revealed an essential role of BACH2 in the antitumor response of CAR T cells and the transcriptional program of LT stem-like CAR T cells. In exhaustion-prone GD2 CAR T cells with high tonic signaling, we showed that quantitative control of BACH2 protein level by a small molecule drug finetuned the degree of stemness and exhaustion in CAR T cells. Chemically inducing temporal BACH2 activation during manufacture of GD2 CAR T cells imprinted greater antitumor immunity against solid tumor after infusion. Together, we show that BACH2 dosage establishes the hierarchy of stem-like CAR T cells and can be temporally and tunably controlled in CAR T cells to optimize differentiation and antitumor immunity.

cancer biology↗

bioRxiv2025

Single-cell clonal lineage tracing identifies the transcriptional program controlling the cell fate decisions by neoantigen-specific CD8+ T cells

Neoantigen-specific T cells specifically recognize tumor cells and are critical for cancer immunotherapies. However, the transcriptional program controlling the cell fate decisions by neoantigen-specific T cells is incompletely understood. Here, using joint single-cell transcriptome and TCR profiling, we mapped the clonal expansion and differentiation of neoantigen-specific CD8+ T cells in the tumor and draining lymph node in mouse prostate cancer. Compared to other antitumor CD8+ T cells and bystanders, neoantigen-specific CD8+ tumor-infiltrating lymphocytes (TILs) upregulated gene signatures of T cell activation and exhaustion. In the tumor draining lymph node, we identified TCF1+TOX- TSCM, TCF1+TOX+ TPEX, and TCF1-TOX+ effector-like TEX subsets among neoantigen-specific CD8+ T cells. Clonal tracing analysis of neoantigen-specific CD8+ T cells revealed greater clonal expansion in divergent clones and less expansion in clones biased towards TEX, TPEX, or TSCM. The TPEX subset had greater clonal diversity and likely represented the root of neoantigen-specific CD8+ T cell differentiation, whereas highly clonally expanded effector-like TEX cells were positioned at the branch point where neoantigen-specific clones exited the lymph node and differentiated into TEX TILs. Notably, TSCM differentiation of neoantigen-specific CD8+ clones in the lymph node negatively correlated with exhaustion and clonal expansion of the same clones in the tumor. In addition, the gene signature of neoantigen-specific clones biased toward tumor infiltration relative to lymph node residence predicted a poorer response to immune checkpoint inhibitor. Together, we identified the transcriptional program that controls the cell fate choices by neoantigen-specific CD8+ T cells and correlates with clinical outcomes in cancer patients.

cancer biology↗

bioRxiv2025

Multiplexed quantum sensing reveals coordinated thermomagnetic regulation of mitochondria

Mitochondria are multifunctional organelles that convert the potential energy stored in nutrients and intermediary metabolites into both heat and an electrochemical proton-motive force. However, how these outputs are synchronized in cells remains an enduring question. In this work, leveraging multiplexed nanodiamond quantum sensors to monitor both changes in temperature and magnetic field fluctuations in single primary cells obtained from diverse tissues in adult mice, we identified thermomagnetic correlation profiles uncovering a regulatory feedback loop in which the cell draws upon available intracellular iron to maintain the mitochondrial electrochemical gradient. These profiles reverse in cells derived from a mouse model of Leigh syndrome and raise the intriguing possibility that primary mitochondrial diseases can be understood as disorders of thermomagnetic homeostasis.

biophysics↗