Biology subjects

Kim, J.

Publications and source records attributed to Kim, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro

Spatial transcriptomics enables the study of how cells coordinate their molecular states within tissue, providing insight into both normal function and disease processes. A key challenge is to identify gene expression programs that vary continuously across space and are coordinated between cell types. We present CoPro, a computational framework for detecting the spatially coordinated progression of cellular states. CoPro can operate in both supervised and unsupervised modes to identify gene programs that co-vary within or between cell types, and to disentangle multiple overlapping spatial patterns. CoPro can be applied to single-cell-level spatial transcriptomics datasets, including MERFISH, SeqFISH+, Xenium, and histology-imputed transcriptomic data. We demonstrate the utility of CoPro with data collected from colon, brain, liver, and kidney tissues. In the colon, CoPro separates epithelial differentiation along the crypt axis from spatially localized inflammatory signals. In the aging liver, it identifies multiple aging-associated cellular programs superimposed on anatomical zonation. In the brain, the flexible kernel design enables the decoupling of the gene expression gradient along the dorsal-ventral and medial-lateral axes. In the kidney, CoPro identifies tubule-vasculature coordination that is essential in nephron function. These results demonstrate CoPros utility for analyzing spatial coordination of gene expression in complex tissues and disentangling overlapping biological processes, such as anatomical organization and disease-associated variation.

bioinformatics↗

bioRxiv2026

A microbiota-derived bile acid overcomes antibiotic-induced hyporesponsiveness to immune checkpoint therapy by enhancing CD8+ T cell antitumor immunity

Gut microbiota are critical determinants of effective immune checkpoint therapy (ICT), yet the microbial mediators and host mechanisms that enhance antitumor immunity remain poorly understood. Here, we identify the microbiota-derived bile acid taurodeoxycholic acid (TDCA) as a metabolite associated with immune checkpoint therapy (ICT) response. TDCA administration alone is sufficient to overcome antibiotic-induced ICT hyporesponsiveness across multiple murine tumor models. Mechanistically, TDCA directly enhances CD8 T cell-mediated antitumor immunity, increasing cytotoxicity. These effects required signaling through the bile acid receptor TGR5. Together, these findings reveal TDCA as a gut microbial metabolite that restores ICT efficacy after antibiotic disruption by directly augmenting CD8 T cell anti-tumor activity. This work supports metabolite replacement as a therapeutic strategy to mitigate antibiotic-associated loss of cancer immunotherapy response. SignificanceTDCA is a microbiota-derived metabolite that restores immune checkpoint therapy efficacy after antibiotic disruption by directly enhancing CD8 T-cell-mediated anti-tumor immunity through bile acid receptor TGR5 signaling. Our findings suggest that supplementation with defined microbial metabolites can mitigate antibiotic-associated loss of immunotherapy response without requiring broader microbiome reconstitution.

cancer biology↗

bioRxiv2026

Agent-Guided De Novo Design of Nanobody Binders Against a Novel Cancer Target

Therapeutic antibody discovery remains slow and resource-intensive, with traditional methods providing limited control over epitope selection. We present a workflow for de novo nanobody design applied to a novel Desmoplastic Small Round Cell Tumor target encompassing four stages: (1) epitope identification guided by our hotspot recommendation agent using physical chemistry-based structure and sequence analysis tools with two curated databases (IEDB, PFAM), (2) de novo nanobody generation using three independent methods (RFantibody, IgGM, mBER) across multiple predicted antigen structures and nanobody frameworks, (3) multi-metric scoring including structural metrics from folding models, and in silico binding affinity from our sequence-based predictor, (4) high-throughput yeast surface display (YSD) screening followed by surface plasmon resonance (SPR) characterization of the specific binders. We generated 288,000 nanobody designs spanning eight target epitope regions and three variable domains of heavy chain-only antibody (VHH) frameworks. Multi-objective Pareto filtering with our candidate selection agent yielded 100,000 candidates for YSD screening with fluorescence-activated cell sorting (FACS). Of 116 enriched candidates advanced to SPR characterization, 46/116 (39.7%) produced reliable kinetic fits with Rmax [≥] 30 RU, yielding KD values from 0.66 nM to 305 nM (median 31.7 nM). These results show that an agent-guided computational workflow can design nanomolar to sub-nanomolar nanobody binders against a novel target without experimental structure or prior antibody information.

bioinformatics↗

bioRxiv2026

Light-sheet excitation-encoded volumetric spectroscopy for fast multiplexed imaging and quantitative physicochemical mapping in cells

Understanding how cellular organization relates to function requires imaging approaches that resolve structural and physicochemical information throughout three-dimensional volumes. Here we introduce light-sheet excitation spectroscopic microscopy (LS-ExSM), a method that captures full excitation spectra with [~]10 nm spectral resolution at each voxel for multiplexed imaging and quantitative spectroscopic readout. Excitation-wavelength encoding makes this spectroscopic readout compatible with single-objective wide-field light-sheet imaging while maintaining high spectral fidelity. Combined with sparse volumetric sampling and deep-learning-based reconstruction, LS-ExSM achieves high-speed volumetric imaging while preserving structural and spectral information. We demonstrate six-color volumetric imaging of live cells at near-second temporal resolution with minimal crosstalk, enabling visualization and quantitative analysis of dynamic organelle interactions in three dimensions. We further apply LS-ExSM to three-dimensional mapping of lipid-droplet polarity at near-diffraction-limited resolution. Together, these results establish excitation-encoded volumetric spectroscopy as a route to whole-cell imaging of subcellular organization and physicochemical state.

cell biology↗

bioRxiv2026

A circuit-to-muscle signaling axis controls locomotor gait transitions in C. elegans

Animals switch between locomotor gaits to adapt to changing environments, yet how defined neural circuits and genes coordinate gait transitions remains poorly understood. Here, we show that the head motor neuron SMB acts as a critical gating node that enables the transition from crawling to swimming in Caenorhabditis elegans. SMB ablation disrupts head-body synchronization, prolongs muscle activation, and impairs curvature switching during swimming, indicating that the SMB neurons function to constrain motor output to stabilize swimming-specific oscillations. Through an unbiased forward genetic screen, we identify the NALCN channel complex component UNC-79 and the muscle nicotinic acetylcholine receptor subunit UNC-29 as key molecular determinants of gait transition. UNC-79 functions across multiple head interneuron modules to stabilize circuit-wide excitability required for sustained swimming, whereas UNC-29 acts cell-autonomously in body wall muscles to refine calcium amplitude and propagation dynamics. Genetic epistasis analyses position the SMB neurons upstream of UNC-29-mediated muscle activation, establishing a circuit-to-muscle signaling axis that links defined head motor neurons to downstream molecular effectors. Together, our findings show that gait transition emerges from coordinated modulation of neuronal excitability and muscle calcium dynamics, providing a mechanistic framework for how neural circuits reconfigure motor states to adapt locomotor behavior. HIGHLIGHTSO_LIThe SMB head motor neurons govern the crawl-to-swim transition C_LIO_LIUNC-79/NALCN stabilizes circuit excitability for sustained swimming C_LIO_LIMuscle nAChR subunit UNC-29 tunes calcium gain during gait transition C_LIO_LIA circuit-to-muscle pathway coordinates locomotor state transition C_LI IN BRIEFGait transitions require coordinated changes in neural circuit activity and muscle output. Moon et al. show that the SMB head motor neurons regulate the switch from crawling to swimming in C. elegans by coupling distributed circuit excitability to muscle calcium gain control, defining a circuit-to-muscle pathway that stabilizes locomotor state transitions.

neuroscience↗

bioRxiv2026

Native architecture, allosteric modulation and gating mechanism of glycine-dependent NMDA receptors

N-methyl-D-aspartate receptors (NMDARs) mediate excitatory signaling essential for synaptic plasticity and memory. Unlike GluN2-containing NMDARs, GluN3-containing receptors are activated solely by glycine, exhibit profound desensitization and paradoxical potentiation by GluN1-selective antagonists, including CGP-78608 (CGP). Although GluN3 NMDARs regulate synapse pruning, excitotoxicity, and are associated with schizophrenia, autism and stroke, their native stoichiometry and gating mechanism poorly defined. Using single-molecule pulldown analysis, we show that native GluN3A receptors are diheteromeric assemblies. Cryo-EM analysis of GluN1/GluN3A receptors in antagonist-bound, pre-active, active, and desensitized states, augmented by electrophysiology and pharmacology experiments, show how glycine activates the receptor solely via GluN3A-dependent conformational changes, opening the gate with [~]2-fold symmetry, and induces a [~]4-fold symmetric desensitized state. CGP-bound GluN1 restricts GluN3A rotation, promoting glycine-induced activation by blocking desensitization. These findings illuminate how CGP potentiates GluN3A receptor activity, place the receptor gating mechanism on a solid structural foundation, and define the molecular basis for pharmacological modulation.

neuroscience↗

bioRxiv2026

Targeting Noncanonical TEAD Axis to Overcome DNA Repair-Driven Chemoresistance

How transcription factors contribute to DNA damage repair (DDR) independent of canonical gene regulation remains poorly understood. Here, we show that DNA double-strand break (DSB) triggers a functional state transition in TEAD, disengaging it from YAP-dependent transcription and translocating it to DNA lesions as a chromatin-associated DDR factor. Upon genotoxic stress, TEAD is rapidly recruited to damaged chromatin through a biphasic mechanism involving early poly(ADP-ribose)-dependent recruitment followed by ATM-driven {gamma}H2AX-mediated retention. At DNA lesions, TEAD constrains chromatin over-relaxation, suppresses excessive end resection, and promotes non-homologous end joining (NHEJ) independent of its canonical function. Conserved residues within the TEA domain mediate this noncanonical chromatin engagement of TEAD and define a druggable N-terminal interface. Pharmacological targeting of this interface impaired TEAD-dependent DSB repair and sensitized tumors to chemotherapy. Together, these findings establish noncanonical TEAD as a critical DNA repair factor and a clinically actionable driver of chemoresistance, while providing a conceptual framework for understanding how broader families of transcription factors may be repurposed as targetable DNA damage regulators in cancer.

cancer biology↗

bioRxiv2026

Connective tissue growth in a mouse model of Kosaki overgrowth syndrome is limited by STAT1

Mutations in platelet-derived growth factor receptor beta (PDGFR{beta}) cause Kosaki overgrowth syndrome (KOGS). Patients exhibit increased linear growth, craniosynostosis, and thin skin with increased elasticity and scarring. Of the KOGS patients identified to date, three unrelated individuals carried a P584R mutation in the juxtamembrane domain of PDGFR{beta}, resulting in constitutive receptor activation. Due to the limited number of patients, extensive phenotyping and exploration of the molecular basis of disease, including modifier genes, has not been completed. We generated conditional knock-in mice to express mouse PDGFR{beta} with a P583R mutation, corresponding to human P584R, under control of the endogenous Pdgfrb gene. Mutant mice were born at the expected ratio and appeared normal at birth. At 3 weeks of age, mutants began to exhibit connective tissue changes: increased body weight and bone length, craniosynostosis, ectopic bone in the tail and tendons, thin lipodystrophic skin, and high incidence of penile and rectal prolapse. To identify signaling changes caused by mutant PDGFR{beta} signaling, we performed western blotting and phosphoproteomics on dermal fibroblasts. This uncovered increased phosphorylation of PDGFR{beta}, PLC{gamma}, Akt1, Shp2, STAT1, STAT2, STAT3, and STAT5. Analysis of 6,621 proteins and 5,386 phosphopeptides identified upregulation of interferon signaling genes linked to STAT1. In many cell types, STAT1 has tumor-suppressor functions and acts to inhibit cell cycle. We generated Stat1-/- Pdgfrb+/P583R mice to test the contribution of STAT1 to KOGS phenotypes. Stat1-deletion exacerbated overgrowth and calvaria dysmorphogensis, and caused keloid-like skin fibrosis. No phenotypes present in the original Pdgfrb+/P583R mice were reverted to normal after Stat1 deletion. Therefore, the P583R mouse model mirrored KOGS phenotypes and increased activation of multiple PDGFR{beta} signaling mediators; in this context, STAT1 activity opposes PDGFR{beta}-driven overgrowth and fibrosis.

developmental biology↗

bioRxiv2026

Dysregulation of Hippo Signaling Pathway as a Convergent Mechanism Underlying Choroid Plexus Defects in Bipolar Disorder

Bipolar disorder (BD) is a prevalent and highly heritable psychiatric condition. Developmental mechanisms are implicated but the specific molecular origins remain unclear. The choroid plexus (ChP), which regulates cerebrospinal fluid (CSF) and brain homeostasis, has been implicated in BD, but its role is poorly understood. Here, we identify aberrant expansion of ChP in human cortical (hCOs) and ChP organoids (hChPOs) derived from, and in vivo structural magnetic resonance imaging (sMRI) scans of, individuals with BD compared to healthy comparison individuals. Single-cell transcriptomics revealed a lineage bias toward ChP fate in BD hCOs, accompanied by structural enlargement observed in both BD hChPOs and ChP in sMRI scans from individuals with BD. Comprehensive transcriptomic profiling implicates early hyperactivation of the Hippo signaling pathway in neural progenitor cells as a convergent mechanism driving ChP overgrowth. Whole-genome and genome-wide association study analyses highlight recurrent genetic variants in Hippo regulators, including STK4 and YAP1, suggesting genetic priming. BD hChPOs exhibit disrupted epithelial junctions and altered in vitro CSF secretion. These findings position the ChP as a genetically and developmentally predisposed to pathology in BD and highlight organoids as a platform for translational discovery in diagnostics and therapeutics.

developmental biology↗

bioRxiv2026

The Central Coupler of the AAA+ ATPase ClpXP Controls Intersubunit Communication and Couples the Conversion of Chemical Energy into the Generation of Force

ClpX is a clockwise hexameric helical arrangement that hydrolyzes ATP to unfold proteins and translocate them into the proteolytic chamber. We investigate the central coupler, a three -helix module conserved among AAA+ ATPases, which is proposed to enable intersubunit communication and mechanochemical coupling. Although fundamental in AAA+ ATPases, the molecular mechanism underlying these processes remains elusive in ClpX. By combining single-molecule optical tweezers, biochemical assays and single particle cryo-EM we demonstrate that the central coupler, of the second-highest subunit of the ClpX clockwise helical arrangement, positions its Arginine-finger, sensor-I and sensor-II to contact the ATP of the anticlockwise neighbor subunit to trigger its hydrolysis. Then, the central coupler of the highest subunit rapidly couples the ATP hydrolysis with the downward motion of its substrate-translocating loop, enabling fast force generation to swiftly unfold protein substrates while maximizing the thermodynamic efficiency of the motor.

biophysics↗

bioRxiv2026

Partial EMT Drives Persistent Collective Migration via Collision Guidance in Heterogeneous Populations

The epithelial-mesenchymal transition (EMT) alters cell-cell interactions to facilitate collective or individual migration during embryonic development, wound repair, or tumor invasion. Epithelial cells are typically cohesive and stationary while mesenchymal cells are individually dispersed and motile. Additional "partial" EMT states are thought to occur with distinct adhesive and migratory behaviors, but these functional phenotypes are poorly understood. Here, we show that cells treated with moderate TGF-{beta} concentration exhibit collective migration that is fast and directionally persistent despite heterogeneity in epithelial, partial, and mesenchymal states. We find cells coordinate their motility by reorienting in similar directions after transient contacts, a distinct "collision guidance" mechanism that differs from epithelial arrest or mesenchymal repulsion. Moreover, partial EMT cells sustain collision guidance when interacting with epithelial or mesenchymal cells, which otherwise have increased tendency to repel. We corroborate these experimental observations with a computational model using self-propelled interacting particles that align their motion or repel upon contact. Finally, we show that partial EMT enables tissue monolayer fronts to overwhelm and displace monolayers of other cell types after collision. Overall, these results reveal that partial EMT promotes coherent and emergent behaviors that bridge from cell to tissue length scales, with potential implications for shaping epithelial tissue formation, regeneration, or disorganization.

biophysics↗

bioRxiv2026

Genetic interaction between Adgrg6 and Sox9 reveals a feedforward mechanism for postnatal spinal stability

Adolescent idiopathic scoliosis (AIS) is the most common spinal disorder in children and is best understood as a complex polygenic condition. Genome-wide association studies (GWAS) have identified several AIS risk loci, including regions near ADGRG6 and SOX9, yet the functional mechanisms underlying AIS heritability remain poorly defined. Here, we use spatial transcriptomics to characterize altered gene expression in the spine of a conditional Adgrg6 mutant mouse model of AIS (Adgrg6-cKO), revealing reduced expression of Sox9 and several components of extracellular matrix organization in the intervertebral disc. We further show that SOX9 occupies regions of open chromatin within the Adgrg6 locus in cells isolated from the mouse intervertebral disc. Finally, we demonstrate a strong genetic interaction between Adgrg6-cKO and a hypomorphic Sox9 allele that increases both the penetrance and severity of AIS-like pathology in mice. Collectively, these findings support a self-reinforcing feedforward regulatory circuit, where Adgrg6 and Sox9 are co-regulated to maintain extracellular matrix gene expression in the annulus fibrosus and paraspinal tissues. These findings provide mechanistic insight into the functional significance of AIS-associated GWAS loci near ADGRG6 and SOX9 and establish combined Adgrg6-Sox9 insufficiency as a tractable model of polygenic scoliosis susceptibility. O_LIAdgrg6 maintains Sox9 and extracellular matrix gene expression in the intervertebral disc C_LIO_LISOX9 directly occupies open chromatin at the Adgrg6 locus in SOX9 skeletal cells C_LIO_LIAdgrg6 and Sox9 genetically interact to increase scoliosis incidence and severity C_LIO_LICombined loss of Adgrg6 and Sox9 drives ectopic cartilage formation and reduced vertebral bone mineral density in the thoracic spine C_LI

developmental biology↗

bioRxiv2026

Somatic DNA methylation heterogeneity predicts extreme transgenerational epimutation hotspots in Arabidopsis

Spontaneous epimutations are stochastic and heritable changes in cytosine methylation that arise independently of DNA sequence alterations. In plants, they occur predominantly at CG sites, accumulate across generations at high and clock-like rates, and contribute substantially to constitutive epigenetic diversity. Although these features are well established, the developmental origin of spontaneous epimutations remains poorly understood. One model proposes that they arise during somatic growth in different cell layers of the shoot apical meristem, where lineage bottlenecks enable nascent epimutations to clonally propagate into developing organs. Such layer-specific dynamics are expected to generate spatial mosaics of methylation states within tissues that manifest as heterogeneity in bulk bisulfite sequencing data. Here, we quantified genome-wide CG methylation heterogeneity in single Arabidopsis leaves using read-level methylation discordance metrics adopted from cancer epigenomics. We identified thousands of highly heterogeneous loci and show that they overlap extreme transgenerational epimutation hotspots. Analysis of multiple leaves from the same individuals further revealed that methylation divergence at these loci scales with developmental distance and recapitulates the branching architecture of the shoot. Together, these results support a meristematic origin of spontaneous epimutations and highlight a shared susceptibility to methylation-maintenance errors in both developmental and transgenerational contexts.

genetics↗

bioRxiv2026

D-gluconate drives Salmonella growth during acute and chronic infection

Monosaccharides support Salmonella enterica serovar Typhimurium colonization of the gut, yet the role of their oxidized derivatives remains understudied. Sugar acids are largely diet-independent carbon sources generated by host-driven oxidative processes, but their contribution during infection - particularly that of less oxidized aldonic and uronic acids - has not been defined. Here, we systematically assess the role of sugar acids derived from D-glucose and D-galactose in S. Typhimurium SL1344 colonization. Among D-glucose-derived acids, D-gluconate accumulated to the highest levels and was the dominant substrate supporting luminal expansion in streptomycin-pretreated mice, exceeding the more oxidized acids D-glucuronate and D-glucarate. During chronic infection, D-glucose-derived sugar acids became increasingly important for pathogen persistence. Ecological niche invasion assays identified these compounds as a principal metabolic niche, whereas D-galactose-derived acids contributed minimally. Consistent with a transient, inflammation-linked nutrient niche, sugar acid utilization pathways were similarly prevalent in Escherichia coli from individuals with and without inflammatory bowel disease. Together, these findings identify D-gluconate as a key inflammation-dependent nutrient source that fuels Enterobacteriaceae expansion in the inflamed gut.

microbiology↗

bioRxiv2026

Sub-cellular Systems Drift Drives Mosaic Evolution of Mammalian Neurons.

Evolution of the mammalian brain has been described as mosaic evolution wherein natural selection for behavioral function promotes independent evolution of specific functional units despite developmental constraints that might govern overall change1,2. Evidence of mosaic evolution has been reported at the level of gene expression in individual structures3, cell type abundances4, as well as gene regulatory changes at the single cell level5-7. In particular, it has been hypothesized that brain evolution involves changes in circuit organization6,8. Circuit-level changes involve sub-cellular compartments that mediate synaptic activity, raising the question whether mosaic brain evolution might be found at the sub-cellular scale. Here, we examine the rate of evolutionary divergence between Mus musculus (C57BL/6) and Rattus norvegicus (Sprague-Dawley) for their dendritic transcriptome, which shapes the post-synaptic proteome through sub-cellular localization and local translation9. We address the problem of variable assessment of the dendritic transcriptome by micro-dissecting individual hippocampal pyramidal neurons to create matched single cell libraries of the soma and the dendrites from the same cell and apply a machine learning model to predict localization. Our results show that the dendritic transcriptome is significantly more divergent than the soma, but the core functional roles of the dendritically localized genes are conserved. Examining gene families for their localization suggests enrichment of family level conservation or localization. We propose that the observed divergence may arise from a combination of adaptive modulation and system drift under selection for core function. Our study suggests fine-grained mosaic evolutionary dynamics at the scale of synaptic function that mediates information processing and neural connectivity.

evolutionary biology↗

bioRxiv2026

Copper Import via CTR1 Supports the β3-Adrenergic Thermogenic Program

Adaptive thermogenesis requires coordinated activation of mitochondrial oxidation and metabolic remodeling, yet the signals driving this coordination are incompletely understood. Here, we show that cold exposure and {beta}3-adrenergic receptor ({beta}3-AR) stimulation upregulate the high-affinity copper (Cu) importer CTR1 and promote Cu accumulation in thermogenic adipose tissues. Adipocyte-specific Ctr1 knockout (ACKO) mice exhibit markedly reduced energy expenditure and develop severe hypothermia during acute cold challenge. Proteomic analysis of brown adipose tissue (BAT) from ACKO mice reveals coordinated suppression of oxidative phosphorylation and thermogenic metabolic programs, accompanied by attenuation of lipolytic pathways. Cu deficiency also impairs cold- and {beta}3-AR-induced lipolytic activation, including reduced HSL phosphorylation and lipid clearance in both BAT and inguinal white adipose tissue (iWAT). Although BAT-specific Ctr1 deletion (BCKO) leaves acute {beta}3-adrenergic responses largely intact, these mice still exhibit cold intolerance, indicating that BAT Cu homeostasis is indispensable for sustaining thermogenic capacity during cold challenge. Treatment with the Cu ionophore elesclomol partially restores mitochondrial oxidative capacity and improves cold tolerance in ACKO mice. Together, these findings identify CTR1-dependent Cu import as a dynamically regulated component of the {beta}3-adrenergic thermogenic program and establish intracellular Cu availability as a key determinant of thermogenic capacity during adaptive thermogenesis.

molecular biology↗

bioRxiv2026

Chiral methionine oxidation reagents reveal stereospecific proteome modifications

Life is predicated on chirality, a molecular asymmetry akin to the left and right versions of human hands. Here we show that privileged protein residues are predisposed for chiral regulation. We developed enantiomeric oxaziridine reagents that systematically identify pro-(S) and pro-(R) methionine oxidation sites across proteomes that can be erased by stereospecific methionine sulfoxide reductase enzymes A and B, respectively. These probes reveal that chiral regulation of methionine oxidation-reduction processes can allosterically regulate protein function, as shown in cell and murine models of oxidative stress where selective (R)-methionine sulfoxide formation on M69 of biphenyl hydrolase-like protein leads to hydrolase inhibition and amplification of proteome N-homocysteinylation modifications. This work introduces a platform for characterizing sites of asymmetric methionine oxidation and the functional consequences concomitant with an individual chiral single-atom modification.

biochemistry↗

bioRxiv2026

Single-cell Transcriptomic Variance Analysis Reveals Intercellular Circadian Desynchrony in the Alzheimer's Affected Human Brain

Bulk tissue rhythms arise from the coordination of thousands of individual cellular oscillations. Bulk rhythm amplitude differences may reflect changes in the amplitude of the underlying cellular oscillators or changes in their temporal coherence. To resolve this fundamental ambiguity, we developed ORPHEUS (Oscillatory Rhythm Phase Heterogeneity Estimated Using Statistical-moments), an analytical method that quantifies cellular desynchrony by leveraging the unique 12hr rhythmic signature it imparts on intercellular expression variance. After validating ORPHEUS in silico and on data from the mouse suprachiasmatic nucleus (SCN), we applied it to data from the mouse liver and human brain to uncover disease- and pathway-related differences in intercellular synchrony. In both tissues, we found that circadian synchrony is higher in cells and samples with higher MTORC activity. Most critically, we observed a dramatic loss of cellular synchrony in excitatory neurons from subjects with Alzheimers Disease (AD) dementia. By decoupling the influence of cellular amplitude and synchrony, ORPHEUS introduces a new, interpretable tool for analyzing circadian coordination in time-course single-cell data.

bioinformatics↗