Biology subjects

Zhang, K.

Publications and source records attributed to Zhang, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Tumor-tropic E. coli engineered as living T and NK cell engagers

Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

bioengineering↗

bioRxiv2026

Swimming motility in the gut microbiota is diverse and increased in inflammation.

Swimming motility has long been studied as a virulence mechanism of enteric pathogens, while the resident microbiota's motility has only been inferred from proxies or explored through a few model species. This study presents a direct, functional analysis of gut bacterial motility in health and inflammation. Using phase-contrast microscopy and high-throughput 3D tracking, we quantified motile bacteria and characterized their swimming behaviours directly in diluted fresh gut content. In healthy mice, fewer than 3% of bacteria were motile along the digestive tract, and their swimming patterns were dominated not by the run-tumble behavior of model gut species but by diverse behaviours rich in reverses. In five mouse models with intestinal inflammation (spanning chemical, genetic, dietary and infectious etiologies) the motile fraction rose by at least 4-fold, correlating with elevated Lipocalin-2 where measured. Reverse-rich patterns remained prevalent in these inflamed conditions, with the notable exception of Salmonella infection. Paired metagenomics and metatranscriptomics showed enrichment of flagellar genes, while communities transferred into cecal water from inflamed mice raised their motile fraction within an hour, indicating that the rise reflects both enrichment of motile taxa and rapid modulation within existing populations. In vitro assays with human-derived isolates confirmed motility across several phyla, with variability down to strain level, and identified oxygen and viscosity as key modulators. These findings support increased motility as a hallmark of the inflamed gut and challenge established assumptions about gut bacterial motility.

microbiology↗

bioRxiv2026

SpatialMOC: Accurate reconstruction of spatial multi-omics landscapes through cross-modality prediction

Spatial multi-omics technologies provide unprecedented opportunities to characterize tissue organization by measuring complementary molecular layers within their native spatial context. However, simultaneous profiling of multiple molecular modalities remains technically challenging, limiting the widespread application of spatial multi-omics and leaving most studies reliant on single-modality measurements. Here, we present Spatial Multi-Omics Cross-prediction (Spatial-MOC), a computational framework that reconstructs missing spatial molecular modalities by integrating spatial context with cross-modality representation learning. Across multiple tissues, molecular modalities, developmental stages, sequencing platforms, and degraded datasets, SpatialMOC consistently outper-formed existing computational approaches in bidirectional molecular prediction. Beyond accurate prediction, SpatialMOC faithfully reconstructed tissue architecture, preserved dynamic molecular and regulatory heterogeneity, and recovered biologically meaningful spatial landscapes from technically compromised measurements. Together, these results establish SpatialMOC as a general framework for spatial multi-omics reconstruction, extending the analytical value of existing spatial omics datasets and facilitating comprehensive investigations of tissue organization, development, and disease.

bioinformatics↗

bioRxiv2026

The Capillary endothelial cell-governed niche sustains angiogenesis in proliferating infantile hemangioma via multilayer stromal support

Infantile hemangioma (IH), the most common benign vascular tumor in infants, is characterized by the aberrant proliferation of hemangioma endothelial cells (HemECs) and excessive angiogenesis. However, it is unclear how the tumor microenvironment sustains these active angiogenic signals. We performed single-cell RNA sequencing and spatial transcriptomic to profile 30 samples from proliferating IH, involuting IH, and normal skin. The results indicated that HemECs comprised distinct subpopulations. Among them, capillary endothelial cells (Cap.ECs) had an immature phenotype and functioned as the core drivers of IH. The endothelial-to-mesenchymal transition endothelial cells (endoMT-ECs) secreted collagen and engaged in CD44-mediated crosstalk with Cap.ECs to construct the angiogenesis-active niche in the tumor microenvironment (TME) of proliferating IH. Blockade of CD44-mediated intercellular communication effectively suppresses the angiogenesis of HemECs and promotes tumor regression. Beyond the endothelial layer, pericytes tightly enveloped Cap.ECs, with SERPINE2+ subtypes sustaining their angiogenic activity via ANGPT signaling. Pseudotime trajectory analysis revealed that the mesenchymal stem cells (MSCs)-enriched niche serves as a progenitor pool for Cap.ECs in proliferating IH. Our findings thus revealed that IH progression relies on CD44-mediated endoMT-EC-Cap.EC crosstalk and on both pericyte and MSC niches to sustain angiogenesis. HIGHLIGHTSO_LICapillary endothelial cells drive infantile hemangioma progression, with pericytes tightly ensheathing them. C_LIO_LICD44-mediated capillary and endoMT-derived endothelial cells crosstalk construct the angiogenic-active niche in the tumor microenvironment of proliferating infantile hemangioma. C_LIO_LIThe MSC-enriched niche provides a progenitor pool for the capillary endothelial cells in proliferating infantile hemangioma. C_LI

cancer biology↗

bioRxiv2026

Leishmanial GP63 acts as a protease for the small pore forming toxin aerolysin

The eukaryotic pathogen Leishmania major causes disfiguring cutaneous lesions, whose resolution can be complicated by secondary bacterial infections. Bacteria, including Aeromonas spp., also interact with L. major promastigotes in the sandfly midgut. The mechanisms by which L. major competes with bacteria and resists their toxins are poorly defined. Prior work proposed that L. major resists the Aeromonas-produced pore-forming toxin aerolysin using an altered GPI-anchor. However, we found that L. major is sensitive to aerolysin. Here, we determined the mechanism by which L. major promastigotes are sensitive to aerolysin, using flow cytometry and biochemical approaches to analyze promastigotes genetically deficient in enzymes that produce key membrane components. The virulence factor lipophosphoglycan protected L. major from aerolysin cytotoxicity. The metalloproteinase GP63 exerted the necessary furin-like protease activity to activate aerolysin. Leishmanial GPI-anchored proteins were necessary for aerolysin heptamerization and killing of L. major promastigotes. Finally, mutation of the GPI-anchor binding domain of aerolysin crippled its cytotoxicity, consistent with its reliance on the GPI-anchor binding site to engage GPI anchors on the surface of L. major promastigotes. Taken together, we propose the L. major virulence factor lipophosphoglycan defends against pore-forming toxins made by bacterial competitors, while the GP63 metalloproteinase activates pro-aerolysin like furin. Overall, this study highlights approaches microbes use to compete with each other. Graphical AbstractAerolysin cytotoxicity depends on gp63 and LPG in Leishmania major promastigotes. (A) Wild type Leishmania major promastigotes are sensitive to aerolysin, which forms lethal heptameric pore complexes in the plasma membrane (B) L. major lpg1-- promastigotes are highly sensitive to aerolysin challenge because they lack LPG. (C) L. major gp63-- promastigotes have wild type sensitivity to aerolysin challenge but resist pro-aerolysin. (D) L. major gpi8-- knockout promastigotes are resistant to aerolysin and show no heptameric pore complexes in the plasma membrane. Created in BioRender.

cell biology↗

bioRxiv2026

Maximizing the productivity of co-transcriptional in vitro transcription

mRNA therapeutics have demonstrated transformative potential in infectious disease, oncology and genetic disorders. Parallel to the rapid clinical advancement of mRNA therapies, research into in vitro transcription (IVT), the pivotal process of mRNA manufacturing, has intensified significantly. However, the majority of these studies omitted cap analog, an essential substrate for co-transcriptional capped IVT (co-IVT), likely to simplify experimental systems. Nevertheless, co-IVT remains the dominant industrial standard for the production of mRNA therapeutics. Here, we report an optimized co-IVT process that achieves a yield of more than 26 g/L while maintaining capping efficiency of over 99.5%, and achieving a 30-fold reduction in double-stranded RNA (dsRNA), the most critical process-related impurity. These performance gains substantially improve mRNA production efficiency and enhance mRNA quality, thereby accelerating the transition to commercial-scale manufacturing of mRNA therapeutics. Moreover, the performance was attained using either of two mechanistically distinct engineered T7 RNA polymerase (RNAP) mutants. Both mutants enabled robust mRNA synthesis under process conditions that have not been previously reported. These observations provide mechanistic insights into IVT and advance our fundamental understanding of this critical bio-manufacturing step.

bioengineering↗

bioRxiv2026

Maternal age at reproduction drives multigenerational variation in life-history traits

Offspring phenotypes are often influenced by maternal age at reproduction. However, the persistence of such effects across multiple generations remains poorly understood, especially in rare cases where offspring of older mothers exhibit enhanced performance. Using the predatory mite Amblyseius herbicolus, we experimentally tested whether maternal age at reproduction influences offspring life history across two generations under contrasting dietary conditions. We found that grandmaternal (F0) and maternal (F1) age affected offspring (F2) developmental time and body size, but not hatching success, survival, or oviposition. The effect of maternal age on body size depended on grandmaternal age, suggesting that grandmaternal age mediates how mothers adjust offspring provisioning. Diet strongly influenced offspring traits but showed limited interaction with age effects. To our knowledge, this is the first study to demonstrate the persistence of an inverse Lansing effect across generations, whereby enhanced immature development is maintained without detectable trade-offs in reproduction or adult survival. These results identify maternal age as a key driver of transgenerational phenotypic variation, with important implications for population dynamics and responses to environmental change at the population level.

zoology↗

bioRxiv2026

Decoding the Oral-Cardiac Axis: FCN1 and LYN as Key Players in the Molecular Dialogue between Acute Myocardial Infarction and Periodontitis

BackgroundAcute myocardial infarction (AMI) and periodontitis (PD) have been epidemiologically linked, but the molecular mechanisms underlying this association remain elusive. We aimed to elucidate shared pathogenic signatures between AMI and PD using a comprehensive bioinformatics approach. MethodsWe integrated transcriptomic data from multiple Gene Expression Omnibus datasets, including an AMI cohort profiled from enriched circulating endothelial cells (GSE66360) with whole-blood validation (GSE48060), and PD gingival tissue cohorts (GSE16134 and GSE10334). Weighted gene co-expression network analysis, protein-protein interaction network analysis, and LASSO-based feature selection were applied. Functional enrichment, immune deconvolution, transcription factor-gene regulatory network analysis, and single-cell RNA sequencing analysis were performed to characterize shared molecular features. ResultsWe identified 95 shared differentially expressed genes (DEGs) between AMI and PD. By intersecting the shared upregulated DEGs with disease-associated WGCNA modules, we obtained 46 candidate shared genes. LASSO-based feature selection further highlighted FCN1 and LYN as overlapping candidates, which showed good discriminative performance in both training and external validation cohorts in ROC analyses. Enrichment analyses suggested that the shared signature was mainly related to myeloid cell migration, phagocytosis, and neutrophil-related inflammatory pathways (e.g., neutrophil extracellular trap formation). Immune deconvolution in PD gingival tissues suggested increased plasma cells and neutrophils and decreased resting memory CD4+ T cells; immune deconvolution results in the AMI cohort were interpreted cautiously due to the CEC-enriched sample source. Single-cell analysis revealed that FCN1 and LYN were predominantly expressed in macrophage/monocyte-derived populations. ConclusionsOur study suggests a shared inflammatory and immune-mediated transcriptomic program linking AMI and PD, and identifies FCN1 and LYN as candidate shared immune markers. These findings provide a molecular rationale for the oral-cardiovascular association and are hypothesis-generating, warranting future experimental and prospective validation.

bioinformatics↗

bioRxiv2026

Higher-order assembly of a type IX retron enables exploitation for designer antimicrobials

Bacterial defense systems provide a rich reservoir for biotechnological innovation. Retrons are tripartite abortive infection systems that detect phage invasion using reverse-transcribed DNA (msDNA), but how they structurally couple threat detection to effector activation remains poorly understood. Here, we determine the cryo-EM structure and activation mechanism of retron-Kva2, a type IX retron from the human pathogen Klebsiella variicola. We reveal that retron-Kva2 assembles into an asymmetric, higher-order ribonucleoprotein complex that sequesters a toxic dimeric HEPN RNase at its core. We identify a natural phage trigger as the phage T5 protein D5, which activates the retron through structural mimicry. Mirroring the retron-Kva2 winged-helix protein, the helix-turn-helix fold of D5 binds the msDNA sensor, driving conformational remodeling that unleashes HEPN-mediated tRNA cleavage and growth arrest. Because retron-Kva2 surveils a structural fold via msDNA binding, rather than a primary sequence, this recognition mechanism provides a broadly exploitable pathway for programmable activation. Harnessing this structure-based logic, we computationally designed de novo synthetic triggers that activate retron-Kva2-mediated bacterial growth arrest in vivo. Our findings reveal the architectural basis of type IX retron immunity and establish a structure-guided paradigm for repurposing bacterial defense systems into precision-honed antimicrobial therapeutics.

microbiology↗

bioRxiv2026

An engineered IdeS variant with enhanced activity and performance for IgG degradation

IgG-degrading enzymes have emerged as innovative therapeutic agents for treating conditions driven by pathogenic antibodies. Here, we used structure-guided rational design to engineer IdeSM33, a double mutant (K167R/D226E) of the IgG-specific bacterial protease IdeS from Streptococcus pyogenes, with improved catalytic efficiency. Biolayer interferometry revealed a fourfold increase in binding affinity relative to wild-type IdeS (IdeSWT). This enhancement is likely attributable to mutations that strengthen hydrogen bonding at the enzyme-IgG Fc interface. In vitro, IdeSM33 has higher performance than IdeSWT in cleaving serum IgG. In vivo studies in rabbits demonstrated that IdeSM33 effectively depleted circulating IgG and showed better performance at a dose of 0.005 mg/kg than the IdeSWT. Although doses greater than 0.2 mg/kg demonstrated higher plasma concentrations of IdeS and a larger AUClast, they did not show a significant enhancement in the pharmacodynamics of IgG degradation. Importantly, a single dose of IdeSM33 (0.2 mg/kg) potently degraded binding and neutralizing antibodies against AAV9 within 1-2 days and restored hepatic AAV9 transduction in pre-immunized animals. Together, these findings highlight IdeSM33 as a potent and safe engineered enzyme with therapeutic potential for autoimmune disorders, transplant rejection, and overcoming pre-existing humoral immunity in gene therapy.

bioengineering↗

bioRxiv2026

Slc25a34-Mediated Mitochondrial-to-Cytoplasmic AMP Transport Activates Brown Adipose Tissue Thermogenesis

Metabolites are emerging as signaling molecules that mediate cellular function, extending beyond their well-established roles in metabolic pathways. Members of the solute carrier (SLC) family mediate metabolite transport across cellular compartments, raising the possibility that these proteins may sense environmental stimuli and regulate cellular biological processes by triggering signaling cascades linked to metabolite transport. This study investigated the response of the SLC25A family, a unique set of inner mitochondrial membrane-localized transporters, to cold as an environmental stimulus in mediating metabolic reprogramming; and whether this reprogramming, driven by the metabolites transported by SLC25A proteins, subsequently promotes the activation of thermogenesis in brown adipocytes. After screening members of the SLC25A family for their responsiveness to cold stimuli and brown adipose tissue (BAT) activation, we found that Slc25a34 was robustly induced under these conditions. We further demonstrated that Slc25a34 mediates the transport of adenosine monophosphate (AMP), derived from de novo glucose synthesis, from mitochondria to the cytosol. This transport potentiates AMP-activated protein kinase (AMPK) signaling and glycolytic flux in brown adipocytes, both of which facilitate BAT thermogenesis during cold exposure. Intriguingly, cold exposure directly promoted the activation of peroxisome proliferator-activated receptor gamma (PPAR{gamma}), which transcriptionally upregulated Slc25a34 expression. More importantly, genetic ablation of Slc25a34 impaired BAT thermogenesis. Thus, our study reveals a novel cold-induced metabolite-sensing pathway, where Slc25a34-mediated AMP transport between mitochondria and the cytosol serves as a critical signal for activating BAT thermogenesis. These findings provide compelling evidence that metabolite transport across cellular compartments acts as a key driver of cellular physiology, thereby offering novel insights into metabolite-based therapeutic strategies for metabolic diseases. HighlightsO_LISlc25a34 is cold-responsive and transcriptionally regulated by PPAR{gamma}. C_LIO_LISlc25a34 functions specifically to mediate the mitochondrial-to-cytosolic transport of AMP in brown adipocytes. C_LIO_LIMitochondrially sequestered de novo synthesized AMP acts as a signaling reservoir, and its Slc25a34-mediated efflux to the cytosol activates AMPK and glycolysis, supporting BAT thermogenesis. C_LI

cell biology↗

bioRxiv2026

A Selective Multivalent NET-Associated Chromatin Neutralizer Resolves Infection-Associated Inflammation in Severe Sepsis

Targeting the overwhelming inflammation driven by neutrophil extracellular traps (NETs) during infection provides an opportunity to manage severe sepsis. This potential needs to be realized by exploring selective NET-neutralization materials, which remains a challenge. Herein, we report a multivalent macromolecular strategy that targets NET-associated DNA-histone chromatin complexes while preserving antibacterial activity of aminoglycoside. We identify 8-arm PEG-conjugated netilmicin (8-arm Netil) as a lead NETs-neutralizer from a library of multivalent aminoglycoside-displayed materials. When compared with 2- and 4-arm counterparts, 8-arm Netil exhibits potent antibacterial activity and high-affinity binding to DNA-histone chromatin complexes through stable multivalent noncovalent interactions, thereby suppressing NET-induced TLR4/TLR9 activation and macrophage inflammatory responses. In severe septic mice, intravenously administered 8-arm Netil preferentially accumulates in inflamed tissues, leading to improved survival protection, owing to the reduction of bacterial dissemination, NET accumulation, systemic cytokine production, and multiple-organ injury. These findings establish NET-associated DNA-histone chromatin complexes as actionable extracellular targets and demonstrate multivalent chromatin targeting as a rational material design strategy for selective NET neutralization and inflammation control in severe sepsis.

bioengineering↗

bioRxiv2026

Myeloid Suclg2 deficiency attenuates aortic dissection by reshaping succinate-associated macrophage remodelling

BackgroundSuccinate has emerged as an immunometabolic mediator of cardiovascular diseases. However, the enzymatic mechanisms linking macrophage succinate metabolism to aortic dissection remain incompletely understood. This study investigated whether Suclg2, which encodes the GDP-forming {beta}-subunit of succinyl-CoA ligase, regulates succinate-associated macrophage remodelling and aortic dissection progression. MethodsSuclg2 expression was examined in BAPN-induced AD and human acute type A aortic dissection tissues by Western Blot and immunofluorescence. Myeloid- and smooth muscle cell-specific Suclg2 conditional knockout mice were subjected to BAPN treatment to evaluate survival, aortic outcomes, histological injury and aortic morphology. Aortic RNA-seq was used to discover transcriptional changes. Bone marrow-derived macrophages were analysed under basal, M1-like and M2-like conditions to assess macrophage-intrinsic transcriptional responses. Plasma succinate levels and untargeted metabolomic profiles were further examined. ResultsSuclg2 was increased in murine and human dissected aortas and partially localized to CD68 cells. Myeloid Suclg2 deletion markedly reduced BAPN-induced aortic rupture and dissection, whereas smooth muscle cell Suclg2 deletion did not confer comparable protection. Aortic transcriptomic analysis showed that myeloid Suclg2 deficiency attenuated inflammatory adhesion and matrix-destructive programmes. In macrophages, Suclg2 deletion did not induce a simple M1/M2 polarization shift; instead, it remodelled lipid-handling, phagolysosomal, adhesive and matrix-remodelling pathways across stimulation states. Metabolic profiling showed reduced circulating succinate and broader changes in central carbon, lipid-associated, nucleotide and redox-related metabolites after myeloid Suclg2 deletion. ConclusionsMyeloid Suclg2 is a succinate-associated immunometabolic regulator of aortic dissection. Its deficiency protects against aortic dissection by reshaping macrophage inflammatory-remodelling programmes and the systemic metabolic environment.

Cell Biology↗

bioRxiv2026

Engineering of CAR-less lentiviral vectors via ER retention-mediated CAR blockade

Chimeric antigen receptor (CAR)-T cell therapies have transformed the treatment of various tumor types by redirecting and activating T cells against tumor cells. However, CAR-T cell manufacturing approaches remain challenging and limit their widespread use in clinical settings. In vivo CAR-T therapy bypasses ex vivo cell manufacturing and patient preconditioning limitations; however, it faces a significant safety concern as CAR proteins on viral packaging cells are incorporated into budding virions, leading to off-target transduction of tumor cells. Here, we address this risk by developing the CAR-Less ER-Anchor Vector (CLEAN-V) system. By exploiting endoplasmic reticulum (ER) retention, CLEAN-V prevents the CAR protein from trafficking to the cell surface during viral packaging, thereby blocking its incorporation into the viral envelope. CLEAN-V particles exhibit near-complete loss of CAR-mediated tumor cell transduction. Furthermore, CLEAN-V integrates seamlessly into existing third-generation LVV workflows in four- or five-plasmid formats and generates CAR-T cells with preserved phenotypic and functional integrity. These results establish CLEAN-V as a robust platform for developing safe, targeted lentiviral vectors for in vivo CAR-T therapy.

bioengineering↗

bioRxiv2026

A Tripartite Map of the Ventromedial Prefrontal Cortex

The ventromedial prefrontal cortex (VMPFC) has been repeatedly implicated in affect, valuation, and social cognition, yet how these diverse functions are organized within a single cortical territory has remained unresolved. Here, we integrate large-scale meta-analysis, individual-level task fMRI, artificial neural-network encoding models, and multimodal connectivity analyses to reveal the internal functional architecture of the human VMPFC. Across four complementary studies, we identify a robust tripartite organization along the anterior-posterior axis, comprising posterior affective, middle valuation, and anterior social functional motifs. Connectivity fingerprinting demonstrates that each motif is preferentially embedded within distinct large-scale brain networks, providing a mechanistic account of VMPFC functional specialization. This organization is reproducible at the level of individual subjects, generalizes to naturalistic stimuli, extends across development, and shows cross-species correspondence with non-human primates and multiple neurobiological markers. Together, these findings resolve a long-standing organizational question and establish a biologically grounded framework for interpreting VMPFC function.

neuroscience↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

Spatial Organization of Lipids Drives GPCR Conformational Equilibria

Despite the widespread use of lipid nanodiscs for structure-function studies of membrane proteins, little is known about how lipids are spatially organized within nanodiscs and how this organization influences embedded proteins. The activity and conformational equilibria of the human A2A adenosine receptor, a class A G protein-coupled receptor, are highly sensitive to anionic lipids that directly interact with the receptor. We leverage this lipid-dependent sensitivity to probe the accessibility of anionic lipids across nanodiscs of varying sizes. We identify a threshold concentration of anionic lipids required to fully populate active receptor conformations that is higher for POPS than for POPG. Computational simulations reveal that POPS and POPG each form lipid clusters reducing the effective availability of anionic lipids to interact with the receptor. This effect is stronger for POPS and scales with increasing nanodisc size, correlating with experimental biophysical and biochemical measurements. Simulations further identify positively charged residues within the membrane scaffold protein that coordinate anionic lipid headgroups. Targeted protein engineering reduces the threshold concentration of anionic lipids required for receptor activation, supporting strategies to control lipid accessibility within nanodiscs. Because membrane scaffold proteins are derived from apolipoprotein A-I, similar lipid-protein interactions may also influence lipid organization within biological systems such as HDL particles.

biophysics↗

bioRxiv2026

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

Nucleosome spacing influences higher-order chromatin fiber organization in vitro but how this relates to cellular chromosome structure remains contentious. To address this, we developed Ligation Analysis of Single-molecule Sequence Interactions (LASSI), a single-molecule epigenomic method that combines proximity ligation with near-nucleotide resolution, long-read adenine methyltransferase footprinting. LASSI measures nucleosome spacing patterns on interacting segments of chromatin genome-wide in cells, quantifying coupled chromosome organization in 1D and 3D. Applying LASSI to mouse embryonic stem cells (mESCs), we discover a genome-wide structural pattern we term fiber homotypy, where chromatin fibers with similar nucleosome spacing patterns interact more frequently in 3D. This pattern persists over long intrachromosomal distances in cis and interchromosomally in trans. Fiber homotypy negatively scales with genomic distance, though differently than contact probability, implying distinct mechanisms. It is further promoted by topologically associated domains (TADs), A/B compartments, and shared histone modification domains, suggesting instructive roles for each of these processes. Coarse-grain molecular dynamics simulations of chromatin fibers informed by LASSI reveal that the intrinsically heterogeneous spacing of nucleosomes along chromatin fibers in cells is a key regulator of homotypy. This variability tunes the free energy landscape of chromatin fiber interactions, promoting the compartmentalization of similar 1D chromatin structures via specific types of fiber-fiber interaction. Further linking compartmentalization and fiber homotypy, we demonstrate that loop extrusion antagonizes this phenomenon. Depletion of the cohesin subunit RAD21 in mESCs increases fiber homotypy genome-wide, while depletion of the cohesin unloader WAPL decreases fiber homotypy, consistent with effects seen on A/B compartmentalization. Our results demonstrate that fiber-fiber interactions driven by shared nucleosome spacing patterns instruct higher-order chromosome organization. Moreover, we show clear structural interdependence across cellular chromatin length-scales, likely tuned by processes ranging from nucleosome positioning to loop extrusion.

genomics↗