Biology subjects

Li, Z.

Publications and source records attributed to Li, Z..

At least 289 records · Page 16Linked to original sources

bioRxiv2026

Mucosally sourced complement factor B modulates the host response to colitis

Distinct host factors maintain intestinal homeostasis but are incompletely understood. The complement system is primarily liver-derived and serum-operative. However, there is growing recognition for complement-mediated host defense at mucosal surfaces. The alternative pathway, which is constitutively active at low levels and amplifies complement activation independent of antibodies, requires Complement Factor B (CFB). Despite its evolutionary conservation, the spatial, cellular, and functional roles of CFB in the intestine are poorly understood. Here, we show that CFB is produced in the human colon and is increased in patients with active inflammatory bowel disease. To isolate the role of local CFB in mucosal responses, we interrogated a mouse strain that has no circulating, liver-derived CFB but retains intact CFB expression in the gut. Global CFB-deficient mice succumb to colitis compared to these liver-specific knockout mice, suggesting that locally synthesized CFB mitigates colitis. Single-cell analyses identify enterocytes and fibroblasts as key CFB producers in the gut. Compartment-specific deletion of CFB from epithelial or stromal cells abrogates mucosal protection independent of circulating levels, which corroborates with pharmacological CFB inhibition. These findings redefine complement in the intestine as a locally regulated mucosal defense system and establish gut-derived CFB as a critical determinant of intestinal homeostasis. BRIEF SUMMARYThe role of local immune mediators in gut mucosal immune responses is still not entirely understood. In this study, we demonstrate a novel role for complement protein Factor B, a key component of the alternative pathway, which is locally sourced through epithelial and stromal cells. In vivo modeling of impaired local Factor B synthesis results in worse colitis, revealing a key role for mucosal sourced components of the alternative pathway.

immunology↗

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

Mitochondrial depolarization stabilizes the vitamin B12 chaperone MMADHC in the cytosol to increase MTR activity

Of the [~]1100 mitochondrial proteins, only a handful like PINK1 and ATFS-1 are known to stabilize and relocalize upon collapse of the proton motive force (PMF) to execute signaling roles. To systematically identify genes that increase exclusively at the protein level upon PMF collapse, we performed a joint proteomic and RNA-seq screen. The screen revealed 10 candidates (six mitochondrial), including the vitamin B12 chaperone MMADHC and cytosolic B12-dependent methionine synthase (MTR). MMADHC is short-lived across cell types and we show that its levels increase with PMF collapse. MMADHC stabilization precedes PINK1 activation in a time course of increasing mtDNA depletion, suggesting greater sensitivity to PMF collapse. MMADHC accumulates in mitochondria with LONP1 inhibition but in the cytosol upon PMF collapse, likely due to mitochondrial import failure. Cytosol-stabilized MMADHC increases MTR levels and activity. Altogether, the mitochondrial PMF regulates the cytosolic B12-dependent MTR, integral to one-carbon metabolism, by controlling the stability and compartmentalization of the B12 chaperone MMADHC. Significance StatementHumans have only two vitamin B12-dependent enzymes - mitochondrial MMUT and cytosolic MTR - and both require a common B12 chaperone MMADHC. We discover that MMADHC is a low abundant, short-lived protein that is continuously imported and degraded by energized mitochondria. Upon collapse of the mitochondrial proton motive force, MMADHC accumulates in the cytosol and increases the levels and activity of MTR, critical for one-carbon metabolism. This PMF-dependent regulation of MMADHC stability and localization is important for understanding cofactor rationing and spatiotemporal compartmentalization of B12 metabolism.

biochemistry↗

bioRxiv2025

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

Genetics studies have identified a core set of regulators essential for pancreatic {beta} cell development, many of which are mutated in monogenic diabetes. However, how these mutations alter developmental trajectories to produce pathological cell states remains elusive. Here we introduce a knockout village framework that enables longitudinal scRNA-seq profiling of 79 human pluripotent stem cell mutant lines targeting 30 developmental regulators, including 15 diabetes genes, across five islet differentiation stages. We show that loss of lineage regulators impairs {beta} cell formation in a stage-specific manner and rewires developmental trajectories towards competing lineages. Notably, several monogenic diabetes gene mutations drive a shift from {beta} cells to enterochromaffin (EC)-like cells, a recently recognized non-canonical islet cell fate. These EC-like cells exhibit incomplete activation of hormone regulation programs, along with elevated neuron signatures. Leveraging the diversity of cell fate outcomes across mutants, we predicted and experimentally validated ISL1 as a key downstream effector of PDX1 and PAX6 that safeguards {beta} cell identity against an EC-like fate. Together, our findings reveal cell fate rewiring as a widespread, previously underappreciated pathological mechanism in monogenic diabetes and establish a scalable platform for uncovering developmental vulnerabilities in human genetic disorders.

developmental biology↗

bioRxiv2025

The natural flavonoid dihydromyricetin targets senescent cells via PRDX2 and alleviates age-related diseases

Aging is a preeminent risk factor for chronic diseases, with cellular senescence as one of the major hallmarks and an effective target to delay, prevent or alleviate age-related disorders. Here we report in vitro screening outputs from a natural medicinal agent (NMA) library, wherein dihydromyricetin (DMY), a natural flavonoid, showed senotherapeutic potential. DMY protected senescent fibroblasts from further DNA damage and attenuated the senescence-associated secretory phenotype (SASP), acting as a senomorphic agent. Proteomics suggested that DMY promotes nuclear translocation of peroxiredoxin 2 (PRDX2), a reactive oxygen species (ROS) scavenger, facilitating DNA repair in senescent cells. In prematurely aged mice, DMY administration mitigated tissue aging changes and age-related physiological decline. In anticancer regimens, DMY improved outcomes of chemotherapy. However, DMY demonstrated senolytic activity against senescent microglial cells, wherein basal PRDX2 expression remains low, by impairing mitochondrial function to promote ROS-mediated apoptosis. In mice developing an Alzheimers disease (AD)-like state, DMY eliminated senescent microglial cells from amyloid {beta}-protein (A{beta}) plaques, alleviating A{beta}-associated pathological phenotypes. Together, our study proposes DMY to be a natural senotherapeutic agent representing a therapeutic solution for mitigating age-related morbidities including but not limited to cancers and AD.

cell biology↗

bioRxiv2025

mMap: a comprehensive and continuously updated species distribution database facilitating the understanding of mosquito diversity and distribution patterns

Mosquitoes, as vectors of deadly diseases like malaria and dengue, exhibit complex and dynamic global distribution patterns influenced by climate change and human activity. However, gaps in species-level data and biases in existing databases hinder accurate risk assessments. Here, we present mMap (v1.01), a comprehensive and curated mosquito distribution database integrating multi-source records from literature (36,242 entries across 1,809 studies), museum collections, and field reports in 6 languages. Systematic data harmonization and validation workflows address taxonomic and spatial uncertainties, enabling family-level analyses previously constrained by fragmented data. Our results reveal significant range expansions for 28 invasive species (e.g., Aedes albopictus in Europe) and corrections to historical distributions (e.g., Ae. vexans in 22 new countries). The interactive mMap platform (accessible at https://mos-map.vercel.app/) provides open-access tools for visualizing spatial-temporal trends, automated SDM forecasting, and expert-curated species profiles. By unifying dispersed data into a scalable framework, mMap advances research on mosquito biodiversity, invasion ecology, and disease risk mapping, offering a critical resource for global health strategies in an era of rapid environmental change.

ecology↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

Multiomics Integration Reveals a Metabolic Myopathy in Cardiometabolic HFpEF

BackgroundSkeletal muscle dysfunction is a major peripheral determinant of exercise intolerance and physical disability in heart failure with preserved ejection fraction (HFpEF). Metabolic and mitochondrial dysfunction are considered to be key components of skeletal muscle dysfunction, but comprehensive profiling of metabolic pathways has not been conducted. Elucidation of dysregulated metabolic pathways is essential to determine viable targets for the treatment of exercise intolerance in HFpEF. MethodsMale ZSF1 Obese rats (HFpEF) and Wistar Kyoto (WKY) lean normotensive controls were studied at 26 weeks of age. Gastrocnemius was subjected to bulk RNA-seq, proteomics, metabolomics, and lipidomics analysis. The R package limma was used to determine differential expression in all omics layers (absolute fold-change>1.5, FDR0.05, unless otherwise indicated). Additional targeted plasma and skeletal muscle (soleus and EDL) metabolomics and lipidomics were performed on HFpEF and control rats. ResultsPathway level analysis for RNA seq and proteomics revealed significant downregulation of oxidative phosphorylation (NES -2.1, p<0.005), electron transport chain (NES -2.0, p<0.005), and TCA cycle (-1.8, p<0.05). The most upregulated pathways were PPAR signaling (NES 2.2, p<0.0001), tryptophan metabolism (NES 1.8, P<0.005), and amino acid oxidation (NES 1.8, p<0.005) pathways. Metabolomics revealed an accumulation of TCA cycle intermediate, isocitrate, and phosphate reduction. Branched-chain amino acids were significantly increased, whereas amino acids related to tryptophan metabolism were reduced and shifted towards increased serotonin accumulation. Phospholipid species were differentially regulated with increased palmitoylated phosphatidylcholines but reduced arachidonoyl-PC species. Phosphatidylethanolamines (PE) species (16:0/16:1-18:0/18:2) were increased. ConclusionOur multiomics analysis of skeletal muscle in HFpEF revealed severe mitochondrial dysfunction that was characterized by reduced complex I and II activity. Mitochondrial and peroxisomal lipid overload results in a shift in membrane phospholipid accumulation and composition. Reduced BCAA oxidation and dysregulation of tryptophan metabolism are key features of amino acid metabolism that reduce anaplerosis and promote the accumulation of toxic metabolites. Comparative analysis of other skeletal muscle disorders suggests that an acquired metabolic myopathy exists in cardiometabolic HFpEF.

physiology↗

bioRxiv2025

Structural basis for the inhibition of Trypanosoma brucei enolase by a camelid single-domain antibody

Trypanosoma brucei is an extracellular protozoan that causes neglected tropical diseases in both humans and livestock. The parasite has a bipartite life cycle involving an insect vector and a mammalian host. Within the latter, it mainly thrives as a blood-borne parasite that relies on glycolysis to support its energy metabolism. It is for this reason that trypanosomal glycolytic enzymes have been investigated as potential targets for the development of trypanosome-killing drugs. Recent work from our lab has shown that they are also interesting biomarkers for the detection of active trypanosome infections. T. brucei enolase (TbrENO) is a trypanosomal glycolytic enzyme that has gathered interest in both drug and diagnostics development. In this paper, we report the discovery of a camelid single domain antibody (sdAb aka nanobody) that specifically recognises and inhibits TbrENO. The sdAbs inhibitory mechanism is unraveled through a combination of protein biochemistry, biophysics, and structural biology. Author summaryTrypanosoma brucei is a unicellular parasite that lives in the bloodstream of humans and animals, where it causes serious but often overlooked diseases. Because it depends heavily on breaking down glucose to produce energy, the parasites glucose-processing proteins (called glycolytic enzymes) have become important targets for both new treatments and improved diagnostic tools. One of these proteins, called T. brucei enolase (TbrENO), has recently drawn attention for its potential in drug development and disease detection. In this study, we discovered a special type of antibody, known as a camelid single-domain antibody (sdAb aka nanobody), that can specifically recognize and block the activity of TbrENO. We employed a combination of various laboratory techniques to understand exactly how the sdAb binds to and inhibits the enzyme. Our findings provide new insight into how TbrENO can be inhibited in a way that does not require active site binding and highlight the value of sdAbs as precise tools for targeting key parasite proteins.

bioengineering↗

bioRxiv2025

RPRM (Reprimo) triggers SCF(FBXW11)-mediated DNA-PKcs degradation to block non-homologous end joining and radiosensitize tumors

Targeting DNA damage repair pathways represents a promising strategy in cancer radiotherapy, however, the limited insight into the regulation of the non-homologous end joining (NHEJ) repair pathway in cancer cells severely restricts the development of precise radiosensitization approaches. Here, we identify Reprimo (RPRM), a p53-inducible tumor suppressor, is a potent inhibitor of NHEJ in which RPRM promotes proteasomal degradation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylated at the T2609 site. Upon irradiation, RPRM quickly translocates into the nucleus to enhance the transcription of FBXW11, a F-box protein gene that encodes the substrate recognition component of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex. In the nucleus, RPRM is also able to scaffold the assembly of the SCFFBXW11 E3 ligase complex by binding to both CUL1 and FBXW11. This complex can specifically ubiquitylate phosphorylated DNA-PKcs (T2609), leading to reduced levels of both phosphorylated DNA-PKcs (T2609) and total DNA-PKcs, thereby suppressing NHEJ-driven repair and enhancing tumor radiosensitivity. In consistence, inhibiting the SCFFBXW11 E3 ligase complex eliminates RPRM-mediated radiosensitization by protecting DNA-PKcs. Clinically, high RPRM expression in non-small cell lung cancer (NSCLC) predicts better patient prognosis. Moreover, RPRM expression correlates positively with FBXW11 and PRKDC (DNA-PKcs) in the tumor tissues of the NSCLC patient cohort. Significantly, high expression of RPRM protein is linked to enhanced radiosensitivity of patient-derived organoids (PDOs) from these NSCLC patients. These results establish RPRM as a key negative regulator in NHEJ repair pathway and the RPRM-SCFFBXW11-DNA-PKcs axis as a potential target to enhance cancer radiosensitivity.

cancer biology↗

bioRxiv2025

Identification of Vector Organisms and Their Carried Pathogens by Metagenomic Sequencing

Vector surveillance is vital for public health, yet traditional methods often face limitations. This study assessed the use of metagenomic sequencing for analyzing mosquitoes, cockroaches, flies, and rodents from Zhongshan, China. The results revealed a high concordance between metagenomic and Sanger sequencing for species identification (Kappa = 0.667, P = 0.011). Metagenomic analysis identified vector-specific dominant bacteria, including Wolbachia in mosquitoes, Blattabacterium sp. in cockroaches, Bartonella tribocorum and Leptospira interrogans in rodents, and Vagococcus teuberi in flies. It also detected numerous classical pathogens, such as Enterococcus faecalis, L. interrogans, and Klebsiella pneumoniae. Among the identified fungi and viruses, 19 were human pathogens, while seven posed a threat to agriculture, notably Pepper mild mottle virus and Tomato brown rugose fruit virus. These findings systematically characterize the microbial communities associated with various vectors, highlight the potential of metagenomics for broad pathogen screening, and underscore its utility in large-scale vector surveillance and public health protection. ImportanceVectors are major carriers of numerous diseases and present risks fot cross-border transmission. Existing detection methods for vectors and their pathogens remain inefficient, insensitive, and prone to difficulties in species identification. Despite extensive efforts in vector identification, the potential threats posed by their associated pathogens remain unclear, demonstrating the need for more effective diagnostic strategies. Metagenomic sequencing offers a promising solution to this challenge. In this study, we applied metagenomic sequencing to vectors collected from urban and port areas in Zhongshan, China, to evaluate its efficacy in pathogen detection. Overall, our work contributes to a better understanding of the public health risks posed by vector-borne pathogens.

microbiology↗

bioRxiv2025

Stereoselective Degradation of Diacylglycerol Kinases Potentiate T cell Activation and Tumor Cell Cytotoxicity

Stereoselective recognition is a powerful means to differentiate selective versus non-specific activity of small molecules in complex biological systems. Here, we disclose stereochemically defined, sulfonyl-triazole inhibitors of the lipid enzyme diacylglycerol kinase-alpha (DGK), a key metabolic checkpoint for T cell effector function. Acute treatment with the covalent DGK inhibitor AHL-7160 recruited endogenous DGK to the plasma membrane in a stereoselective and isozyme-specific manner. The membrane translocation activity of AHL-7160 correlated with blockade of cellular phosphatidic acid production and potentiation of primary T cell-mediated killing of a glioblastoma cell line. Quantitative chemoproteomics revealed Y669 and K411 as sites of AHL-7160 modification on endogenous DGK in cells. Extended treatments resulted in proteasome-dependent and proteome-wide selective degradation of DGK in T cells. Collectively, these findings establish covalent DGK ligands as potent molecular glues with translational potential in immunotherapy.

biochemistry↗

bioRxiv2025

Bacteroidetes promote hepatocellular carcinoma progression and resistance to immunotherapy

Background and AimsGrowing evidence highlight the critical role of the gut microbiome in tumorigenesis and response to immunotherapies. However, the impact of gut microbes on hepatocellular carcinoma (HCC) progression and response to immune-checkpoint blockade (ICB) remains unclear due to the lack of combined preclinical and clinical studies. Approach & ResultsWe performed 16S rRNA of cross-cohort stool samples from 10 HCC responders (R) and 40 non-responders (NR) to ICB at baseline and on-treatment time-points. We identified an enrichment of Bacteroidetes in NR. To study the role of the microbiome in the cancer immune response, we generated an immunogenic mouse model of HCC via hydrodynamic tail-vein injection (HDTVI) of DNA plasmids mimicking common HCC alterations and immunogenicity by expressing model antigens (MYC-lucOS;CTNNB1 tumors). We found that antibiotic (ABX)-induced dysbiosis promoted a pro-tumorigenic effect in the MYC-lucOS;CTNNB1 HCC model by the expansion of a specific Bacteroidetes, Parabacteroides distasonis. Colonization of mice carrying MYC-lucOS;CTNNB1 HCCs with Parabacteroides distasonis confirmed its pro-tumorigenic effect in vivo. Furthermore, we explored the effects of colonizing with microbiotas from patients and showed that microbiota from a NR donor enriched in Bacteroidetes promoted faster tumorigenesis than microbiota from a R donor with reduced Bacteroidetes. We isolated 6 Bacteroidetes species from the NR donor, cultured them, and used them as a cocktail to colonize mice; similarly, mice transplanted with this cocktail showed increased tumorigenesis and reduced survival. ConclusionsThis study identified Bacteroidetes enrichment as a potential biomarker of ICB resistance in HCC and, by using immunogenic mouse models, established that Bacteroidetes abundance influences tumor development.

cancer biology↗

bioRxiv2025

Lysosomal swelling triggers LRRK2 activity

LRRK2 is implicated in lysosomal functions, but the physiological upstream cues that engage endogenous LRRK2 activity are incompletely defined. Here we show that lysosomal swelling serves as a selective and reversible trigger for LRRK2-mediated Rab phosphorylation, without requiring membrane damage. Acute inhibition of PIKfyve, but not the general disruption of phosphoinositide signaling, induces the robust accumulation of phosphorylated Rabs across endolysosomal membranes. Rescue of swelling through pharmacological restoration of lysosomal ionic imbalances from PIKfyve inhibition suppresses LRRK2 activation without restoring lysosomal function. Mechanical lysosomal swelling from indigestible osmolyte uptake causes a dose-dependent increase in LRRK2-mediated Rab phosphorylation on both swollen and non-swollen lysosomes. Together, these findings identify LRRK2 as a sensor of lysosomal volume and mechanical stress, not specifically membrane damage or PIKfyve inhibition. As lysosomal swelling is a shared pathological feature across LRRK2-linked diseases, these results reframe LRRK2 as part of an endolysosomal surveillance system responsive to lysosomal distension.

neuroscience↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

Dynamic alterations of DNA methylation and transcriptome in adaptation to and recovery from the space environment

Space exploration presents tremendous health challenges. Here, we report time series of multi-omic and phenotypic profiles of seventeen astronauts from six China Manned Space missions with continuous spaceflight durations ranging from 13 to 180 days. We revealed a key role of DNA methylation regulation in reshaping gene expression patterns to adapt to the space environment. Long-duration spaceflight showed more alterations in epigenetic modifications correlated with alternative splicing and protein acetylation. During recovery, an "overrange rebound" phenomenon was observed, furthermore, a mathematical model was established to describe this implying important phenomenon. Moreover, we revealed the correlations between molecular alterations and phenotypic changes such as coagulation activation and bone intensity loss. Additionally, we performed ground-based simulation experiments to estimate the impacts of individual stressors in the space environment on DNA methylation. In summary, our study highlights the importance and complexity of epigenetic regulation in adaptation to and recovery from the space environment.

genomics↗

bioRxiv2025

Multiomic characterization, early detection, and therapeutic targeting of myeloid sarcoma

Myeloid sarcoma, an aggressive extramedullary subtype of acute myeloid leukemia (AML), occurs in [~]10% of patients, and has not yet been included in large-scale genomic studies. The critical biological changes that drive tumor evolution are unknown, its detection in asymptomatic patients remains a clinical challenge, and treatment options are limited as patients are often excluded from clinical trials, rendering it a neglected disease entity. Based on comprehensive multi-omic profiling, we demonstrate that myeloid sarcoma evolves from medullary AML with distinct sitespecific clonal evolution patterns. Additionally, we show that circulating tumor DNA sequencing can serve as a non-invasive method for molecular profiling of myeloid sarcoma, offering a novel avenue in molecular diagnostics. We characterize unique transcriptional profiles of myeloid sarcoma, reflecting immune evasion and adaptation to an extramedullary microenvironment. We provide evidence for a key role of RAS pathway activation and demonstrate in murine models of myeloid sarcoma that RAS inhibition effectively reduces tumor burden. Overall, our data highlight key differences between medullary AML and myeloid sarcoma including universal molecular evolution and RAS pathway activation as hallmarks of the disease and nominate RAS inhibition as a promising therapeutic strategy for patients with myeloid sarcoma.

cancer biology↗

bioRxiv2025

Mechanical cues of an interpenetrating polysaccharide matrix regulate self-assembly of collagen fibers

Collagen molecules self-assemble into supramolecular fibers within a molecularly crowded, polysaccharide-rich extracellular matrix (ECM). The ECM typically has fluid-like, viscoelastic properties that can be quantified rheologically. Here, we determine that the viscoelasticity of a polysaccharide alginate ECM regulates the assembly of type I collagen fibers. The viscoelasticity and shear moduli of the alginate network were tuned by the polymer weight percentage and degree of cooperative ionic and covalent norbornene-tetrazine crosslinking. Stepwise shear strain applied to covalently-crosslinked hydrogels generated higher stress than in ionic hydrogels. Hydrogels with reduced viscoelasticity also showed a reduction in water permeability. Second-harmonic generation confocal imaging revealed that decreasing viscoelasticity significantly suppressed collagen fiber self-assembly. Simulations demonstrated a mechanical coupling of the hydrogel network and the aggregate size of collagen molecules. Increased covalent crosslinking impaired the rate and magnitude of self-assembly in simulations and experimental results. These results suggest that ECM viscoelasticity plays a role in modulating the assembly and structural organization of collagen within the matrix. More broadly, they provide a framework for understanding how ECM mechanical properties can influence the assembly and organization of fibrillar macromolecules.

bioengineering↗