Biology subjects

Kim, M.

Publications and source records attributed to Kim, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecule-resolved inference reveals the spatial organization of transcriptional programs

Transcriptional programs encode cellular identity and physiological activity, linking gene regulation to cellular phenotypes. Although spatial transcriptomics measures individual RNA molecules across intact tissues, most analyses aggregate them into cells or pixels, obscuring molecular level functional dynamics. We introduce FICTURE2, a statistical model that infers the transcriptional program from which each individual molecule is generated, using gene identity and spatial context alone without segmentation or binning. FICTURE2 learns programs with distinct spatial distributions, ranging from millimeter-scale continuous transition to micron-scale subcellular localization, the coexisting patterns of which then reveal both cellular identity and physiological activity with unified interpretations. FICTURE2 supports both unsupervised and reference-guided inference and is orders of magnitude more efficient than alternative approaches, enabling systematic analysis of large-scale spatial datasets as we demonstrate in data across diverse tissue types profiled by various spatial technologies.

genomics↗

bioRxiv2026

Firing rate adaptation in grid cells produces macroscopic hexadirectional modulation

Hexadirectional modulation (HexMod) of macroscopic neural activity by movement direction is widely used to measure grid cell activity in human neuroimaging, but its neuronal origin is unclear. Two mechanisms have been proposed: conjunctive gridxdirection cells whose preferred directions align with the grid axes, and firing rate adaptation, which reduces firing when grid fields are visited in quick succession during movement along grid axes. Analysing almost 4,000 grid cells from foraging rats, we found that conjunctive cells' directional tuning was broad and unaligned with grid axes, whereas firing was reduced shortly after grid field visits, consistent with firing rate adaptation. Simulations of realistic grid cell populations demonstrate HexMod with the typical trajectories of human experiments, and show how it depends on grid scale, adaptation time constant, movement speed, and controlling for variation with location. We show firing rate adaptation provides a plausible mechanism for HexMod and a framework for relating human neuroimaging to neuronal activity.

neuroscience↗

bioRxiv2026

Temporal Integration of Weak Acoustic Stress Leads to Delayed Cellular Responses

Sound is a pervasive physical stimulus with beneficial or adverse effects depending on exposure. While controlled sound-based interventions such as ultrasound have demonstrated clinical utility, epidemiological studies link chronic environmental noise to increased cardiovascular and metabolic risk. Despite these associations, how weak sound is sensed and integrated at the cellular level remains unclear. Here, we investigate cellular responsiveness to acoustic pulse-wave stimulation in human endothelial cells, using intracellular calcium changes as a readout of cellular activation. Cellular responses to acoustic stimulation were compared with over-threshold mechanical stimulation. Over-threshold mechanical stimulation induced immediate responses, whereas single sub-threshold acoustic exposures produced no detectable response. In contrast, sustained sub-threshold acoustic stimulation over minutes produced delayed activation, with onset times dependent on stimulus intensity. These results demonstrate that cells integrate weak physical inputs over time, revealing a delayed activation regime under sustained sub-threshold exposure.

biophysics↗

bioRxiv2026

Random mtDNA mutagenesis maps genotype-phenotype associations across metabolic contexts and lineages

Mitochondrial DNA (mtDNA) mutations cause inherited disease, accumulate with age, and recur in tumors, yet their effects remain unresolved because existing models interrogate one engineered allele at a time. We developed mtDIVE, a random C[->]T mutagenesis platform for pooled mitochondrial forward genetics in human epithelial cells and zebrafish embryos. mtDIVE generates genotypes ranging from single substitutions to >100 mutations per molecule, impairs respiration, and causes lineage-specific developmental delay. Coupling single-cell transcriptomics with mtDNA genotyping revealed that selection on mutant genomes and their transcriptional consequences depend on metabolic state and developmental lineage. Obligate OXPHOS eliminates highly mutated cells by apoptosis, whereas glycolytic conditions promote their competitive displacement. Individual loci exert modest but non-redundant effects that predict cell state beyond aggregate mutation burden, and cancer-recurrent variants are enriched among mutations linked to reduced mitochondrial transcription. Thus, mtDIVE links mtDNA genotypes to cellular phenotypes, separating the consequences of mutation identity from mutational load.

genomics↗

bioRxiv2026

Hybrid Mechanistic-Neural Modeling of Concentration-Time Dynamics Generalizes Human Pharmacokinetics Prediction Across Unseen Chemical Space

The pharmacokinetics concentration-time profile encodes ADME dynamics. Its optimization in drug discovery curbs late-stage attrition, yet forecasting human pharmacokinetics from chemical structure remains difficult. Machine learning models ignore continuous ADME dynamics, whereas physiologically based pharmacokinetics (PBPK) models demand unavailable parameters and impose rigid, misspecified compartmental structures. We present PK-MUSE (PharmacoKinetic hybrid Mechanistic Universal System Equation), augmenting a two-compartment model with bounded, state- and time-dependent neural corrections to elimination and intercompartmental distribution. Molecular structure parameterizes compound-specific behavior, while learned corrections refine dynamic equations. Across scaffold and temporal out-of-distribution evaluations, PK-MUSE achieved the lowest mean exposure-endpoint MdFE, reducing MdFE by 7.2%, 45.2%, and 26.2% versus state-of-the-art machine learning (HML- RF), deep learning compartmental (DeepCt), and PBPK (PK-Sim) models. Interrogating the corrections localized misspecification to distribution rather than elimination. By extending mechanistic simulators with data-driven constrained neural dynamics that preserve interpretability and generalize to unseen chemotypes, PK-MUSE advances digital twins for drug discovery.

pharmacology and toxicology↗

bioRxiv2026

KRAS-driven metabolic reprogramming of enhanced MFSD2A-mediated lysophosphatidylcholine scavenging promotes survival and progression of pancreatic ductal adenocarcinoma

Oncogenic KRAS drives lipid reprogramming in pancreatic ductal adenocarcinoma (PDAC) to promote disease progression, and these changes are manifest in circulation. Using mass spectrometry, we performed lipidomic analyses on plasmas from a cohort of 93 newly-diagnosed resectable PDAC cases, 43 patients with chronic pancreatitis, and 93 age- and sex-matched healthy controls, the results of which revealed pronounced reductions in circulating lysophosphatidylcholines (LysoPC) as a prominent feature associated with PDAC. Using stable-isotope resolved lipidomics, we further found that PDAC cells exhibit a lipid scavenging phenotype characterized by preferential uptake of extracellular unsaturated LysoPCs to sustain pro-growth signals. Restricting bioavailability of extracellular unsaturated LysoPCs shifted the metabolic phenotype of PDAC cells towards enhanced de novo lipogenesis and autophagy, which was accompanied by suppression of AKT signaling activities and increased susceptibility to apoptosis. Using bulk, single-cell, and spatial transcriptomic datasets together with functional experiments, we identified oncogenic KRAS-mediated upregulation of major facilitator superfamily domain-containing protein 2a (MFSD2A) as a key mediator that facilitates extracellular uptake of LysoPCs in PDAC cells. Loss of MFSD2A expression mimicked LysoPC restriction and resulted in inhibition of AKT signaling and increased propensity of PDAC cells to undergo apoptosis in vitro and suppressed tumor growth in vivo. Therapeutic targeting of the KRAS-MFSD2A-LysoPC axis via repurposing of the synthetic alkyl-lysophospholipid edelfosine promoted potent anti-cancer effects in vitro that were mechanistically attributed to reduced extracellular uptake of LysoPCs, and attenuation of AKT signaling. Collectively, our findings describe a previously unrecognized onco-metabolic program of enhanced LysoPC scavenging mediated by MFSD2A that promotes PDAC progression and that is therapeutically targetable via repurposing edelfosine.

cancer biology↗

bioRxiv2026

QuImputer: an LD-informed QUBO/Ising formulation of genotype imputation with quantum-hardware execution

Genotype imputation offers a biological application for optimization methods that may eventually run on larger quantum computers. We developed QuImputer to encode allele-frequency priors and signed linkage disequilibrium (LD) in a reduced Ising/QUBO objective, with only missing genotypes represented as optimization variables. The same objective can be passed to exhaustive classical search, quantum approximate optimization algorithm simulation, or quantum hardware. We evaluated the formulation on 100 rice accessions across 12 chromosomes, estimating LD and allele frequency from the same post-masking observed matrix supplied to Beagle 5.4. Evaluation was restricted to known truth at sites with exact dosage coding and an alternate allele that was not the major allele, with MAF below 0.50, yielding 1.88 billion scored genotypes. Beagle achieved higher rare-ALT sensitivity (2.52% versus 0.54%), F1 (0.047 versus 0.011), Matthews correlation coefficient (0.088 versus 0.044), and pooled hard-call dosage R-squared (0.231 versus 0.014). QuImputer produced fewer false ALT calls, with Type I error of 0.038% versus 0.223%. Analyses of a chromosome-1 subset showed limited local LD support for many masked rare-ALT carriers. In five small IBM Fez validation problems, the selected minimum-energy outputs matched unique all-reference exact optima; the pooled frequency of those optima was 1.21-2.63%. Further IBM Fez executions covered eleven sparse instances with 12-97 variables and a separate 120-variable instance, retaining all measurements. Selected outputs recovered the exact optima in eight instances through 49 variables. Larger instances remained below the all-reference baseline; noiseless comparisons distinguished finite-shot sampling from deviations in hardware output. QuImputer provides an LD-informed formulation and a route to quantum-hardware execution, together with an empirical assessment of the limitations of the evaluated configuration. These results establish a basis for studying richer information models and alternative classical or quantum solvers.

bioinformatics↗

bioRxiv2026

RELAX does not reproduce its own estimates at default settings, and its output does not show it

Selection-intensity estimates from RELAX are reported as a point value of K with a likelihood-ratio P. We report that, at default settings and on data of ordinary size, the program does not reproduce its own fits. Of 27 enzyme entries refitted under two optimiser configurations, none reproduced its log-likelihood to within 0.01 units; the median change was 103 units, the largest over 3,400, and four verdicts reversed. Eighty null orthologues reproduced none. A byte-identical command returned a distinct likelihood on every repetition, single-threaded, across three releases, and on alignments simulated under the fitted model, where 3.3 per cent of replicates reproduced. The documented random-number seed never reaches the generator when assigned on the command line, yet reads back as the value supplied. PAML localises the cause: its two-ratio model, without site classes, reproduced its log-likelihood for all 288 genes; its site-class models agreed for 27 to 67 per cent. The instability follows the mixture over sites, not the program. The output does not show it: 46 of 410 fits ended with a negative likelihood-ratio statistic, impossible under convergence, and 123 of 410 report a K re-estimated under a domain restriction rather than the unconstrained maximum. Of 234 published studies using RELAX, none reported a seed. Seeding while holding the thread count at one reproduced sixty of sixty runs on twenty genes under two releases; the seed alone reproduced none of five, and no documentation states the second condition. We recommend that fits be repeated and their dispersion published.

evolutionary biology↗

bioRxiv2026

Single-Cell and Spatial Analysis Reveals Retention of FCRL4⁺ Memory B Cells in Pediatric Tonsillar Hypertrophy

Pediatric tonsillar hypertrophy is a leading cause of sleep disordered breathing in children, yet the immune mechanisms sustaining tonsillar enlargement remain unclear. Using integrated single cell and spatial profiling of pediatric tonsils in a discovery cohort (n = 45) and independent validation cohort (n = 32), we identify a selective expansion and follicular retention of FCRL4+ memory B cells within the mantle zone of hypertrophic tonsils. These cells exhibit a quiescent, tissue-adapted phenotype characterized by NFATC1 repression and reciprocal RUNX1/RUNX2 regulation. Their accumulation is orchestrated by follicular type 1 regulatory T (Tr1) cells, which engage CTLA-4/CD86 checkpoint interactions to suppress plasma cell differentiation and reinforce a local immune tolerance program. Together, these interactions establish a persistent follicular niche enriched in regulatory FCRL4+ memory B cells. Our findings delineate a mechanistic Tr1/FCRL4+ B cell axis underlying follicular hypertrophy and highlight potential immunomodulatory targets for nonsurgical management of pediatric sleep-disordered breathing.

immunology↗

bioRxiv2026

Proton FLASH radiotherapy enhances control of triple-negative breast cancer through STING-IRF3 and CD8+ T-cell immunity

FLASH radiotherapy delivers radiation at ultra-high dose rates and has been demonstrated to spare normal tissue compared to standard radiotherapy, but it is not known if dose rate also modifies tumor response. Here we compare a single 13.5 Gy fraction of proton irradiation delivered at FLASH (F-PRT) or Standard (S-PRT) dose rate in immunocompetent C57BL/6 mice bearing EO771 or AT3 triple-negative mammary tumors. At this identical physical dose, F-PRT delays tumor growth more than S-PRT at both heterotopic and orthotopic sites. The effect is largest in EO771, where F-PRT also prolongs tumor-volume endpoint-free survival and reduces the emergence of lung metastases relative to S-PRT. F-PRT induces earlier intratumoral STING expression and IRF3 nuclear translocation, higher type I interferon levels and greater CD8+ T-cell infiltration. CD8+ T-cell depletion or systemic STING inhibition abolishes the F-PRT advantage. Combined with anti-PD-1 and agonistic anti-CD40, both modalities produce durable complete responses that reject contralateral rechallenge, but F-PRT limits tumor progression before response and accelerates regression. FLASH proton radiotherapy not only improves normal-tissue tolerance, but also antitumor immunity, suggesting that ultra-high dose rate could widen the therapeutic window from both sides.

cancer biology↗

bioRxiv2026

Unicellular and Multicellular Modes of Selection Impose Distinct Constraints on Cellular Phenotype Evolution

Single-cell sequencing data have revealed that cellular phenotypes, such as gene expression states, are often low-dimensional, suggesting that cellular variation may arise from combinations of a smaller set of gene expression programs. A genome therefore defines a repertoire of cellular phenotypes that can be configured through different combinations of programs. However, organisms vary in how much of this repertoire is exposed to selection. In unicellular organisms, different phenotypes are often expressed across environments or life-cycle stages, so selection in a given context acts primarily through the phenotype expressed there. In multicellular organisms, multiple phenotypes can coexist within an individual and contribute jointly to fitness. Here, we use a geometric model to ask how selection acting through cellular phenotypes separately or jointly constrains the ability of a shared genome to evolve and maintain differentiated phenotypes across multiple functional demands. We vary the number of functional demands and how many corresponding phenotypes contribute jointly to fitness. We find similar evolutionary outcomes when demands are weakly divergent. Under strongly divergent demands, however, selection on one phenotype at a time leads to reduced differentiation as demands accumulate, even when sufficient programs are available. As more phenotypes contribute jointly to fitness, differentiation and performance improve. When all phenotypes contribute jointly, differentiation is maintained until demands outnumber programs. Our results suggest that how cellular phenotypes are organized in time and space can impose distinct constraints on the evolution of differentiation from a shared genome.

evolutionary biology↗

bioRxiv2026

Skin-Related Effects of Corynebacterium amycolatum SB-1 Ferment Filtrate and Functional Characterization of Ellagic Acid

Previous research has established a link between the genus Corynebacterium in the skin microbiota and skin health; however, studies investigating the specific effects of Corynebacterium-derived substances on skin cells remain limited. In this study, we isolated eight strains of Corynebacterium from the facial skin of female participant. To investigate the potential skin improvement effects of these isolates, three cultured skin cell lines (Hs68, HaCaT, and B16-F10) were treated with the supernatants of each strain. We then evaluated and compared the gene expression levels (ELN, COL1A1, IL-1{beta}, and HAS3) alongside their inhibitory effects on melanin biosynthesis. Corynebacterium amycolatum SB-1 was selected as the final candidate for subsequent analysis, primarily based on its rapid growth rate and high cell yield. Using LC-TOF/MS, we screened the postbiotic candidates from the SB-1 strain and identified ellagic acid as a known polyphenolic antioxidant with potent anti-melanogenic effects beneficial for skin improvement. To validate the effects of ellagic acid on skin cells, we assessed FLG gene expression and its inhibition of melanin biosynthesis. Additionally, RNA sequencing was performed to elucidate the underlying molecular mechanisms, revealing that ellagic acid is significantly involved in inhibiting melanogenesis and promoting collagen synthesis. Taken together, our results highlight ellagic acid derived from strain SB-1 as a highly effective bioactive compound for improving skin health, specifically targeting hyperpigmentation and skin aging.

genomics↗

bioRxiv2026

Bacteriostatic lethality emerges from turgor-induced physiological stress

With new antibiotic discovery slowing, maximizing the efficacy of existing drugs is crucial. Bacteriostatic antibiotics are regarded as inferior to bactericidal drugs because they are thought to merely arrest growth without inflicting cellular damage and cell death. Contrary to conventional views, we show that bacteriostasis is a physiologically stressed state, which can be exploited to unmask its lethality. Through quantitative measurements and live-cell imaging, we found that translation inhibition by bacteriostatic antibiotics induces intracellular turgor pressure buildup by perturbing physiological balance in E. coli. This pressure manifests as osmotic swelling, leading to lysis in a subset of cells, while surviving cells depend on PBP1-mediated cell-wall repair, which alleviates mechanical strain. This protective mechanism led us to predict, and we experimentally confirmed, that inactivating PBP1 with a {beta}-lactam amplifies the lethality of bacteriostatic drugs, challenging the general assumption of antagonism between bacteriostatic and bactericidal antibiotics. These findings show bacteriostasis as a physiologically unstable state and provide a systems-level framework for its lethality, enabling the rational design of optimized therapies.

microbiology↗

bioRxiv2026

DNA Sequence-Programmed Protein Coronas Determine Intracellular Fate and Proteostatic Stress of Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) show promise for optical biosensing, imaging, and drug delivery, but turning them into safe, precision nanomedicine tools requires understanding how nanotube surface chemistry dictates recognition and processing by cells. Like other nanomaterials, carbon nanotubes acquire a biomolecular corona on contact with biological fluids, and corona identity is increasingly recognized as central to sensor performance and drug delivery efficacy. However, whether corona identity also governs the intracellular fate of carbon nanotubes remains largely unknown. Here, we show that the single-stranded DNA wrapping of (6,5)-enriched single-walled carbon nanotubes reprograms their protein corona, intracellular trafficking, and macrophage response. By profiling (AT)15, (GT)15, and (CT)15 wrapped SWCNTs, we show that the wrapping sequence programs both the protein corona and the resulting proteostatic stress on macrophages. Photoluminescence imaging and confocal Raman measurements reported that (AT)15 is internalized the most yet leaves the proteome and nanotube structure largely undisturbed, whereas (CT)15, taken up the least, undergoes the most aggressive intracellular degradation and drives the highest oxidative and proteostatic stress. Corona proteomics indicated that all three tested nanotubes form coronas with distinct functional identities that are responsible for divergent intracellular routes. Time-resolved intracellular proteomics combined with functional assays resolved how the host cell reorganizes its biomolecular complexity over time, including oxidative outputs, aside from a sequence-independent core response involving particle engagement, phagosomal sorting, and lysosomal processing. These findings provide mechanistic insight into nanomaterial-cell interactions and the wrapping sequence as a tunable, nucleotide-level design handle for controlling the intracellular fate of carbon nanomaterials, with potential implications for safe and effective nanomedicine platforms.

bioengineering↗

bioRxiv2026

Spatial Mapping of the Lung Cancer Ecosystem Reveals Distinct Patterns of Intratumoral and Internodular Heterogeneity

The spatial organization of malignant and non-malignant cells within the tumor microenvironment (TME) critically influences tumor evolution and therapeutic response. However, the architecture of micro-niches remains incompletely understood. Leveraging Xenium-based spatial transcriptomics, we comprehensively mapped the spatial ecosystem of an orthotopic murine lung cancer model, identifying distinct spatial domains that form unique, organized cellular neighborhoods. These domains cluster into three major communities: (1) non-tumoral regions that recapitulate canonical normal lung structures; (2) a heterogeneous peri-tumoral region composed of spatial domains characterized by mesenchymal remodeling, active immune checkpoint signaling, and immunosuppressive myeloid populations; and (3) intra-tumoral regions that reveal marked tumor nodule heterogeneity, with unique tumor-specific domains exhibiting hallmark cancer pathways. Furthermore, our analytic approach was applicable to human lung cancer tissue. Notably, spatial domain analysis allowed us to resolve tumor nodules into multiple biologically distinct subtypes, defined by domain composition, hallmark cancer programs, and intercellular communication patterns within the TME.

cancer biology↗

bioRxiv2026

Four-species Aspergillus pan-GWAS reveals rare genome expansion in pathogenicity and contraction in domestication

Aspergillus species are ecologically diverse and deeply entangled with human health and industry. A. fumigatus and A. flavus are the two principal species of invasive aspergillosis. A. niger and A. oryzae, on the other hand, are responsible for global enzyme production, organic acid production, and koji-based fermentation industries. The question of whether these similar phenotypes share the same genomic mechanisms across the genus is not yet understood. To address this, we constructed per-species pangenomes for the four Aspergillus species (929 initial genomes filtered to 210 ANI-verified, high-quality assemblies for a total of 88 A. fumigatus, 70 A. flavus, 33 A. oryzae, and 19 A. niger assemblies) alongside a genus-level pangenome of 15,163 orthogroups, and conducted phenotype-labeled pan-genome-wide association studies (pan-GWAS) with kinship correction across all species. Pan-GWAS identified up to 117 significant orthogroup presence/absence associations per species-phenotype comparison. However, convergence analysis showed that among the 92 and 62 distinct gene families significant for human pathogenicity in A. fumigatus and A. flavus respectively, the two species seldom agreed on whether the pathogenicity was associated with the enrichment or the depletion of a specific gene family. Convergence analysis of the functional annotations also yielded zero significant results at FDR < 0.05. A literature-curated gene panel analysis also showed that a species labeled pathogenic and another labeled GRAS carried the same aflatoxin and virulence genes, suggesting that gene presence alone cannot readily explain their phenotypic differences. Instead, we propose that niche adaptation operates through the use of the pangenomic rare genome. Reclassifying rare genes by homology identified truly rare subsets (156 to 391 orthogroups per species) distinct from paralogs and gene fragments. Human-pathogenic strains showed significant rare genome expansion of 2.44-fold for both A. fumigatus and A. flavus (kinship corrected, p = 6.6 e-08). Conversely, industrial strains showed rare genome contraction where both A. niger and A. oryzae industrial strains carried 0.57-fold (kinship corrected, p = 0.015) fewer rare genes than their non-industrial counterparts. Hence, we claim that Aspergillus niche evolution proceeds through directional rare genome changes, where there is expansion under pathogenic selection, and contraction under industrial domestication. The rare genome, often discarded as noise, may represent the primary evolutionary source for clinical and biotechnological adaptation in this genus.

genomics↗

bioRxiv2026

Atypical MDM2 p53 Regulation and Chemosensitivity Induced by Proximal PAS Deletion

This study proposes a novel therapeutic strategy to suppress cancer growth by modulating the MDM2-p53 axis via Alternative Polyadenylation (APA). MDM2 normally promotes tumorigenesis by ubiquitinating and degrading the tumor suppressor p53. In cancer cells, preferential use of proximal polyadenylation signals (PAS) results in shortened 3'UTRs, allowing oncogenic transcripts like MDM2 to evade nuclear sequestration mediated by Inverted Alu (IRAlu) double-stranded RNA structures. We hypothesized that forcing distal PAS usage would elongate the MDM2 mRNA, promoting its nuclear retention and reducing protein translation, thereby restoring p53 activity. Using CRISPR-Cas9, we targeted and deleted the most frequent proximal PAS in the MDM2 3'UTR of A549 cells. Successful genome editing was confirmed via PCR. As expected, Western blot analysis showed a significant reduction in MDM2 expression in PAS-edited cells. However, experimental outcomes contradicted our initial hypothesis: edited cells exhibited higher viability under doxorubicin treatment compared to wild-type cells. Furthermore, despite decreased MDM2 levels, a concurrent reduction in phosphorylated p53 (p-p53) was observed. These unexpected results suggest that MDM2 3'UTR elongation may trigger a non-canonical regulatory mechanism that bypasses the traditional MDM2-p53 interaction. This study highlights the complexity of post-transcriptional regulation and suggests that APA-mediated gene modulation can induce unforeseen compensatory survival pathways in cancer cells, necessitating further investigation into the broader functional landscape of elongated 3'UTRs.

cancer biology↗

bioRxiv2026

Large oncosomes reprogram bone marrow mesenchymal stem cells to establish a pre-metastatic niche

Metastatic progression depends on the systemic remodeling of distant tissues before tumor cell arrival, yet the cancer-derived signals that orchestrate this process remain poorly understood. Large oncosomes (LOs) are atypically large (>1 um), tumor-derived extracellular vesicles shed by invasive cancer cells. Here, we demonstrate that LOs function as systemic mediators of pre-metastatic niche formation by activating innate immune sensing in bone marrow mesenchymal stem cells (BM-MSCs). Systemic administration of prostate- and breast cancer-derived LOs to immunocompetent tumor-bearing mice did not affect primary tumor growth but increased metastatic burden. LOs induced a robust, dose-dependent interferon-driven inflammatory program, characterized by interferon-stimulated genes and neutrophil chemokines. Mechanistically, this response was driven by LO-associated nucleic acids activating convergent cytosolic DNA- and RNA-sensing pathways in recipient stromal cells. LO-conditioned BM-MSCs promoted the accumulation and polarization of neutrophils toward an immunosuppressive, polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) phenotype. In vivo, genetic suppression of LO shedding in tumor cells reduced PMN-MDSC accumulation in the bone marrow, which was reverted by systemic LO administration. Together, these findings establish LOs as specialized carriers of immunomodulatory signals that reprogram the bone marrow microenvironment to support metastatic colonization, identifying a previously unrecognized mechanism linking tumor vesiculation to immune remodeling at distant sites.

cancer biology↗