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bioRxiv2025

Assessment of native mass spectrometry as a screening method to identify and characterize RNA-targeting small molecules

The intentional targeting of RNA with small molecules is recognized as a viable pathway to new therapeutics with potential to vastly expand the proportion of the human genome considered druggable. The practical considerations to deliberately target RNA are largely under development, including optimal screening methods to identify small molecules for binding to RNA. Native mass spectrometry (nMS) is established as a valuable biophysical method for identifying small molecule hits against diverse biomolecular targets, most frequently proteins and protein-protein interactions. Herein we assess nMS for studying the binding of small molecules with RNA aptamers as a model for nMS screening of RNA as a drug target. We first develop workflows for characterizing the binding of cognate RNA aptamer ligands and then establish a nMS method to screen a small molecule library against the RNA aptamers. nMS analysis permitted identification of binders, quantitation of binding strength and generation of structure-activity relationships with some dependence on the aptamer class. This work demonstrates the utility of nMS as a complementary and efficient target-based biophysical screening method that can characterize RNA-small molecule interactions and the potential of nMS becoming a powerful enabling tool in RNA-targeting drug discovery.

biophysics↗

bioRxiv2025

2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space

Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic environments involved in cellular functions. Proteins, nucleic acids, glycans and bio-compatible polymers are the machinery of cellular processes both in the cytosol and at the lipid membrane interface. Lipid species directly modulate membrane properties, and affect the interaction and function of other biomolecules. Natural molecular diffusion results in changes of local lipid distribution, affecting the membrane properties. Projecting biophysical and structural membrane and biopolymer properties to a two-dimensional plane can be beneficial to quantify molecular signatures in a reduced dimensional space to identify relevant interactions at the interface of interest, i.e. the membrane surface or biopolymer-surface interface. Here, we present a toolbox designed to project membrane and biopolymer properties to a two-dimensional plane to characterize patterns of interaction and spatial correlations between lipid-lipid and lipid-biopolymer interfaces. The toolbox contains two hubs implemented using MDAKits architecture, one for membranes and one for biopolymers, that can be used independently or together. Three case studies demonstrate the versatility of the toolbox with detailed tutorials in GitHub. The toolbox and tutorials will be periodically updated with other functionalities and resolutions to expand our understanding of the structure-function relationship of biomolecules in two-dimensions. SIGNIFICANCE2Danalysis is a significant contribution for the systematic analysis of membrane and biopolymers simulations at planar interfaces. Developed under the open-source MDAKit framework, it enables efficient analysis of trajectories and provides versatile tools for projecting biophysical properties onto a two-dimensional plane. These capabilities enhance the visualization of spatial and temporal changes in membrane characteristics, such as order parameters, and support the study of biopolymer-surface interactions by analyzing adsorption and confinement mechanisms at 2D interfaces. The users can customize the toolbox to study complex 2D phenomena from molecular simulation.

biophysics↗

bioRxiv2025

Deciphering the molecular mechanisms of FET fusion oncoprotein-DNA hollow co-condensates

Biomolecules such as nucleic acids and proteins can undergo liquid-liquid phase separation to form biomolecular condensates with diverse architectures. However, fundamental questions surrounding the biophysical principles that govern condensate architecture and their potential biotechnological applications remain unresolved. Here, we report that the FUS/EWS/TAF15 family fusion oncoprotein FUS-ERG forms hollow co-condensates with double-stranded DNA containing GGAA microsatellites. Through a combination of biochemical assays, super-resolution imaging, and mathematical modeling, we reveal that the interior surface of hollow co-condensates exhibits properties distinct from those of the external surface, a phenomenon we term nested asymmetric phase separation. Furthermore, we demonstrate that the self-organization and morphology control of FUS-ERG hollow co-condensates can be harnessed for DNA-based information manipulation, enabling targeted DNA deletion within dsDNA libraries and facilitating dynamic, hierarchical data selection. These findings provide critical insights into the biophysical mechanisms underlying multicomponent phase-separated cellular bodies and establish a foundation for leveraging condensate morphology in biotechnology.

biophysics↗

bioRxiv2025

A nutrient bottleneck limits antibiotic efficacy in structured bacterial populations

Antibiotic resistance is a growing global health threat. Therefore, it is critically important to optimize how existing antibiotics act against bacterial infections. Although antibiotic activity is well studied at the single cell level, many infections are caused by spatially structured multicellular populations. In such populations, cellular consumption of scarce nutrients establishes strong spatial variations in their abundance. These nutrient variations have long been hypothesized to help bacterial populations tolerate antibiotics, since single-cell studies show that antibiotic tolerance depends on metabolic activity, and thus, local nutrient availability. Here, we directly test this hypothesis by visualizing cell death in Escherichia coli populations with defined structures upon exposure to nutrient (glucose) and antibiotic (fosfomycin). We find that nutrient availability acts as a bottleneck to antibiotic killing, causing death to propagate through the population as a traveling front--a phenomenon predicted over 20 years ago, but never verified until now. By integrating our measurements with biophysical theory and simulations, we establish quantitative principles that explain how collective nutrient consumption can limit the progression of this "death front," protecting a population from a nominally deadly antibiotic dose. While increasing nutrient supply can overcome this bottleneck, our work reveals that in some cases, excess nutrient can unexpectedly promote the regrowth of resistant cells. Altogether, this work provides a key step toward predicting and controlling antibiotic treatment of spatially structured bacterial populations, yielding fundamental biophysical insights into collective behavior and helping to guide strategies for more effective antibiotic stewardship.

biophysics↗

bioRxiv2025

Differential interfacial tension between oncogenic and wild-type populations forms the mechanical basis of tissue-specific oncogenesis in epithelia

Why does the same oncogenic mutation drive tumor formation in some tissues but not in others? While cancer driver mutations are well-documented, their tissue-specific effects remain largely attributed to genetic factors, leaving the biophysical aspects underexplored. Here, we demonstrate that mechanical interactions, specifically interfacial tension between newly transformed and wildtype epithelial cells are critical in determining survival and growth of HRasV12 oncogenic mutants in human mammary and bronchial epithelia, leading to contrasting outcomes in the two tissues. In mammary epithelium, isolated oncogenic cells are extruded-a typical mechanism of defense against cancer in epithelia-while oncogenic groups become spatially confined in a kinetically arrested, jammed state, marked by an actomyosin belt at the interface. In contrast, bronchial epithelium permits persistent spreading of the same oncogenic cells, which form long protrusions regardless of colony size. Furthermore, oncogenic clusters in these two tissues exhibit distinct biophysical properties, including variations in cell shapes, intracellular pressure, cell-cell tension, and cellular motility. Using a cell shape-tension coupled bi-disperse vertex model, we reveal that differences in interfacial tension at mutant-wild-type boundaries dictate whether oncogenic cells are eliminated, restrained, or expanded and that modulating the heterotypic interfacial tension alters mutant cell fate within the epithelium. Together, our findings uncover a mechanical basis for tissue-specific oncogenesis by highlighting how differential cellular mechanics at the oncogenic-host cell interface regulate tumor initiation and progression.

biophysics↗

bioRxiv2025

Biofilm Vertical Growth Dynamics Are Captured by An Active Fluid Framework

Bacterial biofilms, surface-attached microbial communities, grow horizontally across surfaces and vertically above them. Although a simple heuristic model for vertical growth was experimentally shown to accurately describe the behavior of diverse microbial species, the biophysical implications and theoretical basis for this empirical model were unclear. Here, we demonstrate that this heuristic model emerges naturally from fundamental principles of active fluid dynamics. By analytically deriving exact solutions for an active fluid model of vertical biofilm growth, we show that the governing equations reduce to the same form as the empirical model in both early- and late-stage growth regimes. Our analysis reveals that cell death and decay rates likely play key roles in determining the characteristic parameters of vertical growth. The active fluid model produces a single, simple equation governing growth at heights above and below the diffusion limit; surprisingly, this "full" expression is simpler than the heuristic. With this theoretical basis, we explain why the vertical growth rate reaches a maximum at a height greater than the previously identified characteristic length scale. These results provide a theoretical foundation for a simple mathematical model of vertical growth, enabling deeper understanding of how biological and biophysical factors interact during biofilm development.

biophysics↗

bioRxiv2025

Putting a lid on it: The N-terminal helix of Arf1 inhibits switching via stabilization of the overall native state

The Arf (and Arf-like) GTPases, unlike all other Ras family GTPase members, exhibit a repressed conformation in the inactive, GDP-bound form. The N-terminal helix of Arf GTPases, which is missing in the other Ras family members, caps the switch region, confining it to this repressed state. Nucleotide exchange and activation involve a massive conformational change made possible by the dissociation of the N-terminal helix from the core of the protein. Spontaneous switching in Arfs is enhanced upon deletion of this helix. While the structural and functional role of the N-terminal helix in Arf proteins is well-known, the energetic basis for its effects have not been established. Here we mapped the local stability of the Arf1{Delta}17 variant, deleted for the N-terminal helix, using high pressure biophysical approaches and compared it to that of full-length Arf1. Deletion of the N-terminal helix decreased Arf1 stability across the entire structure. Thus, rather than imposing a specific structural pathway for repression, the N-terminal helix exercises global control of Arf1 stability to repress switching. Statement of SignificanceEnergetic mapping of the N-terminal deletion mutant of Arf1 using high pressure biophysical approaches reveals that this helix maintains the protein in the repressed state unique to Arf and Arf-like GTPases via overall stabilization of the native state rather than unique allosteric communication with the switch region.

biophysics↗

bioRxiv2025

Intrinsically Dominant Conformational Diversity in PDZ1 within the Tandem PDZ1-PDZ2 of Human Syntenin-1 Underlined by Crystal Structures.

The intrinsic dynamic asymmetry between homologous PDZ domains in multidomain scaffold proteins offers critical insights into evolutionary mechanisms enabling multivalent partner recognition. Through systematic X-ray crystallographic analysis of human syntenin-1s PDZ1-PDZ2 tandem, we resolve nine high-resolution structures that uncover fundamental differences in conformational plasticity between these sequentially similar domains. Pairwise root-mean-squared deviation (RMSD) analysis of 20 PDZ1 structures across multiple crystal forms reveals substantial structural variability concentrated in the Lys119-Ile125 and Ala181-Glu184 loops - key regions governing ligand specificity within PDZ1s binding cleft. In stark contrast, PDZ2 maintains remarkable structural conservation across all crystallographic environments, indicating divergent evolutionary constraints on these tandem domains. Crucially, comparative analysis of isotropic B-factors demonstrates their inadequacy in capturing the full scope of conformational heterogeneity, emphasizing the necessity of multi-structure comparisons for mapping dynamic landscapes. Molecular dynamics (MD) simulations implemented through GROMACS corroborate these crystallographic observations, showing elevated residue-specific fluctuation (RMSF) values in PDZ1s ligand-binding interface compared to analogous PDZ2 regions. This consistency across experimental and computational approaches confirms that PDZ1s conformational diversity represents an inherent biophysical property rather than crystallographic artifact. The observed dynamic asymmetry suggests a functional division of labor: PDZ1s structural plasticity enables broad ligand recognition via conformational selection mechanisms, while PDZ2s rigid architecture likely stabilizes the tandem domain arrangement. These findings provide an atomic-level rationale for syntenin-1s pleiotropic roles in cellular signaling and establish a structural blueprint for developing domain-selective therapeutics. Given syntenin-1s clinical relevance in cancer metastasis, viral pathogenesis, and neurodevelopmental disorders, our work advances strategies for selectively modulating PDZ1-mediated interactions while preserving PDZ2s scaffolding functions through structure-guided inhibitor design. Highlights{lozenge} Crystal structures of human Syntenin-1s PDZ1-PDZ2 tandem reveal intrinsic conformational plasticity in PDZ1, particularly in ligand-binding loops, contrasting with PDZ2s rigid architecture {lozenge}Pairwise RMSD analysis of 20 PDZ1 structures demonstrates substantial structural variability in the Lys119-Ile125 and Ala181-Glu184 loops, key regions governing ligand specificity {lozenge}Molecular dynamics simulations confirm that PDZ1s conformational diversity is an inherent biophysical property, not a crystallographic artifact {lozenge}The asymmetric dynamics between PDZ1 and PDZ2 suggest a functional division: PDZ1s plasticity enables broad ligand recognition while PDZ2 stabilizes the tandem arrangement {lozenge}These findings provide a structural basis for developing domain-selective Syntenin-1 inhibitors with potential applications in cancer metastasis, viral pathogenesis, and neurodevelopmental disorders

biophysics↗

bioRxiv2025

Structural Acrobatics of IAA7: Exercising Fuzzy Regions to Aid Auxin-Mediated Catalysis

Auxin is the paragon of small molecules driving recognition of proteins for their ubiquitylation and degradation, enabling rapid decoding of external signals into transcriptional responses. Auxin functions as a molecular glue, enhancing interactions between the TRANSPORT INHIBITOR RESPONSE 1 (TIR1) and other TIR1-like proteins with various AUXIN INDUCIBLE/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors. A Cullin RING E3 ubiquitin ligase, SCFTIR1/AFBs, mediates the ubiquitylation and degradation of AUX/IAA proteins by positioning them for ubiquitin transfer, leading to their rapid degradation by the 26S proteasome. AUX/IAAs contain a Phox Bem 1 (PB1) domain, a degron, and intrinsically disordered regions (IDRs) that influence auxin sensing and their polyubiquitylation by interacting with TIR1. However, the precise role of IDRs in AUX/IAA positioning for ubiquitylation, and the mechanism of multisite ubiquitylation within AUX/IAAs remain unclear. We used biophysical techniques and coarse-grained simulations (CGS) to study the structural behavior of IDRs in IAA7, a model AUX/IAA protein from Arabidopsis thaliana. Our findings show that IAA7 expands by approximately 2.6 nm upon binding to TIR1 in the presence of auxin, likely increasing the proximity between a lysine acceptor in IAA7 and the active site of the SCFTIR1 E3 ligase for ubiquitylation. Our data also suggest that IAA7 remains conformationally heterogeneous when bound to TIR1, forming numerous transient contacts along its IDRs and C-terminal PB1 with TIR1. We propose that these transient interactions outside the IAA7 degron interface enhance the TIR1{middle dot}IAA7 association, resulting in highly dynamic and heterogeneous complexes that facilitate IAA7 multisite ubiquitylation, targeting it for rapid proteasomal degradation. Significance StatementIn this study, we use biophysical techniques to elucidate the implications of AUX/IAA intrinsic disorder on their conformational ensemble and processing by the E3 ubiquitin ligase, SCFTIR1. Our findings demonstrate that IAA7 undergoes a structural expansion upon binding to TIR1 and remains highly dynamic, facilitating multisite ubiquitylation. These insights enhance our understanding of how ubiquitylation targets engage with their E3 receptor modules and underscore the structural advantages of intrinsic disorder in protein ubiquitylation targets.

biophysics↗

bioRxiv2025

Calicivirus assembly and stability are mediated by the N-terminal domain of the capsid protein with the involvement of the viral genome

Caliciviruses are important human and animal pathogens that cause varying clinical signs including gastroenteritis, respiratory illness, and hepatitis. Despite the availability of numerous calicivirus structures, relatively little is known about the mechanisms of capsid assembly and stability, or about genome packaging. Here we present the atomic structure of the RHDV virion and several related non-infectious virus-like particles, determined using cryo-EM at 2.5-3.3 [A] resolution. The inherent molecular switch, responsible for the conformational flexibility of the capsid protein VP1, is located in its N-terminal arm (NTA). The NTA establishes an extensive network of interactions on the inner capsid surface that stabilizes the hexamers and pentamers. For this structural polymorphism, we show that the NTA must interact with the RNA viral genome, that is, the genomic RNA acts concomitantly with the NTA as a molecular switch. The NTA-RNA interaction leads to specific conformational states that result in two types of VP1 dimers (the basic building blocks) necessary for T=3 capsid assembly. In addition, we used atomic force microscopy (AFM) to assess whether differences in genomic RNA content influence viral properties such as capsid stiffness in physiological conditions. These analyses highlight the mechanical role of packed RNA genome in RHDV virions, as the virion capsid pentamers are strengthened by interactions of the NTA star-like structure promoted by the viral genome. These results indicate that the interactions between the NTA and the viral genome guide the conformational states of VP1 dimers, directing capsid assembly and modulating its mechanical properties. Through interference with intermediate assemblies, the NTA network promoted by the genome could be an attractive target in future antiviral strategies. Author SummaryRabbit hemorrhagic disease virus (RHDV) is a highly contagious, often fatal calicivirus that poses a significant threat to rabbit populations worldwide. Although considerable progress has been made in elucidating the structural organization of RHDV capsids at near-atomic resolution, information regarding the nucleic acid organization within these virions and its interactions with the viral capsid remains limited. Understanding these interactions is essential for identifying mechanisms of structural polymorphism of the capsid protein, as well as virion assembly and stability. We report the cryo-electron microscopy structure, at near-atomic resolution, of RHDV virions and distinct virus-like particles, together with characterization of their biophysical properties using atomic force microscopy. The N-terminal region of the capsid protein, essential for its structural polymorphism, requires its interaction with genomic RNA. The interaction between N-terminal arms and the viral genome governs the conformational states of capsid protein dimers, thereby orchestrating capsid assembly and influencing its biophysical properties. By interfering with intermediate assemblies, the NTA network promoted by the genome could constitute an attractive target in antiviral strategies for several major human calicivirus pathogens that cause acute gastroenteritis and respiratory illness, including norovirus and sapovirus.

biophysics↗

bioRxiv2025

Viral Nucleosome-Like Particles Exhibit Dynamic Flexibility and Reduced Thermodynamic Stability

DNA packaging imposes fundamental physical constraints on genomes across the tree of life. However, most of our mechanistic understanding of these processes comes from the eukaryotic nucleosome, where highly basic histones, along with their flexible tails, coordinate DNA compaction and gene accessibility. Large DNA viruses challenge this paradigm by assembling nucleosome-like particles with a divergent histone architecture. These viral assemblies lack canonical histone tails, contain covalently fused domains linked by structured connectors, and exhibit altered surface electrostatics, features that collectively impose unique biophysical properties on viral chromatin. Here, we use multi-microsecond all-atom molecular dynamics simulations to dissect how histone fusion, tail loss, and connector architecture reshape the structural and thermo-dynamic behavior of the Melbournevirus nucleosome, a model system for studying viral chromatin organization. We find that viral systems exhibit elevated DNA unwrapping, weaker and more transient histone-DNA contacts, and localized flexibility at connector regions. Conformational adaptation at histone junctions partially offsets these effects, with structural shifts tuned to local DNA geometry during wrapping transitions. By capturing how nucleosome dynamics shift across time and sequence, our study reveals how conserved biophysical principles of chromatin architecture are reconfigured across life to meet distinct evolutionary demands.

biophysics↗

bioRxiv2025

Influence of Substrate on Supported Lipid Bilayers: Membrane Pinning, Stretching, Pores, and Remodelling

Model membranes offer a simplified representation of biomembranes, allowing for controlled structural and functional studies without the inherent complexity of biological systems. Due to the confined space and strong interactions with the support, supported lipid bilayers (SLBs) exhibit markedly distinct properties compared to those of their free-standing counterparts. However, the nano and microscale origins of these differences, structural effects and the related biophysical consequences remain incompletely understood. Using a combination of spectroscopy and micromanipulation techniques, we reveal that SLBs are pinned to the support, creating barriers for lipid diffusion. Furthermore, they are intrinsically stretched and under tension, causing membrane rupture and the formation of stable [~]2 nm aqueous pores that allow the permeation of small hydrophilic molecules. Despite strong adhesion, SLBs can undergo localized shape changes associated with membrane fusion, and membrane nanotubes can be extruded under optical forces. The findings underscore the very distinct properties of model membranes, and we anticipate that they will have important consequences in the field of drug-delivery systems and membrane biophysics.

biophysics↗

bioRxiv2025

Reconstructing the Mitochondrial Proton Motive Force Using Physics-Informed Neural Networks and Surrogate Bioenergetic Signals

The mitochondrial proton motive force (PMF) underlies ATP synthesis, metabolite transport, and energy coupling. Yet, direct measurement of PMF remains technically challenging due to probe invasiveness, calibration drift, and compartmental averaging. Here, we introduce a physics-informed neural network (PINN) framework that reconstructs PMF from surrogate signals including NADH, oxygen, electron flux, proton leak, and reactive oxygen species (ROS). Using a synthetic curriculum dataset derived from biophysical ranges reported in the literature, our model achieved high predictive accuracy (R2 {approx} 0.99, RMSE < 1 mV) under normoxia and hypoxia. SHAP-based interpretability revealed distinct feature contributions: flux and NADH dominated under normoxia, while oxygen and ROS became more influential under hypoxia. Extended analyses demonstrated that PINNs generalize robustly across cross-validation folds, preserve biophysical constraints, and can be adapted to time-series dynamics, capturing PMF decline and recovery during simulated hypoxia-reoxygenation. To our knowledge, this is the first application of PINNs to mitochondrial bioenergetics, bridging machine learning with the chemiosmotic theory. This proof-of-concept establishes a foundation for non-invasive PMF estimation and opens avenues for studying mitochondrial adaptation in physiology and disease.

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bioRxiv2025

Cells dynamically adapt their nuclear volumes and proliferation rates during single to multicellular transitions

Tumour development and progression are associated with biophysical alterations that manifest across multiple spatial scales, from the subcellular to multicellular tissue scale. While cells dynamically regulate their biophysical properties like volumes and mechanics in dependence of cell state and function, it is unclear how these properties are controlled in the dense multicellular environment of a developing tumour. Here, we quantified cell and nuclear volumes of single cancer cells, while they grew into multicellular tumour spheroids within well-defined, tuneable biohybrid polymer hydrogels. We quantitatively showed that the formation of multicellular structures is associated with marked reductions of cellular and nuclear volumes, cell cycle delays as well as cell mechanical alterations, and that these changes are coupled. Single-to-multicellular transitions coincided with a drastic decrease in median nuclear volumes by up to 60%, as well as overall cell volume decrease. Nuclear volume decrease could not be explained by compression due to confining microenvironments. Instead, cell cycle adaptions were one significant contributor, with smaller-sized G1 cells accumulating in growing clusters, an effect that was reversed by CDK1 inhibition. Another contributor was nuclear volume decrease in cells within clusters that was associated with higher mass density and stiffness and could be abrogated upon cell release from clusters. In turn, multicellular-to-single cell transitions that happened in cells that invaded from a tumour spheroid into the surrounding matrix, were accompanied by nuclear volume increases and cell softening. Taken together, our study provides insights into how cells dynamically adapt their cellular/nuclear volumes, cell cycle progression and mechanics in dependence of the multicellular state.

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bioRxiv2025

Lipid acyl chain length and unsaturation modulate membrane surface charge and interactions with amphiphilic DNA nanoprobes

Biological membranes actively regulate their composition to fine-tune their packing, fluidity, phase and surface charge, key properties that influence biomolecular interactions driving essential cellular pathways. While membrane surface charge is often attributed to specific lipid headgroups, the role of acyl-chain chemistry in modulating the interplay between these biophysical membrane properties remains unexplored. Here, we systematically investigate how variations in acyl chain length and saturation modulate lipid packing, fluidity, and membrane surface charge in zwitterionic lipid membranes. Using amphiphilic DNA nanoprobes as model charged biomolecules, we describe the interplay between packing, fluidity, phase and charge, identifying a packing-dependent guiding principle for membrane interactions that persists in the presence of anionic lipids. We also demonstrate that the identity and hydrophobicity of membrane anchors in nanoprobes significantly influence their binding to membranes. By integrating acyl-chain chemistry with membrane biophysical properties into design criteria for biomolecular attachment, our findings provide a mechanistic framework to engineer membrane interactions with both DNA nanoprobes and DNA-based coacervates. Beyond direct application to biomimetic platforms and synthetic cell engineering, these insights are relevant to lipid-based vaccine nanotechnologies and fundamental understandings of membrane-biomolecule interactions in living cells.

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bioRxiv2025

Single-particle multi-parametric microscopy reveals structural, size, and payload heterogeneity in mRNA-loaded lipid nanoparticles

Deciphering the heterogeneity of mRNA-containing lipid nanoparticles (LNPs) is essential for understanding the relationship between their microscopic properties and therapeutic function. Here, by combining alternating laser excitation (ALEX) with Convex Lens-induced Confinement (CLiC) microscopy, we simultaneously measure size, multi-color fluorescence, mRNA payload, and Forster resonance energy transfer (FRET) of individual suspended LNPs containing labeled lipid and mRNA molecules. By varying formulation parameters, including ionizable lipids, formulation buffers, and molecular ratios, we investigated and correlated key microscopic properties for relevant vaccine formulations. While the per-particle lipid fluorescence was lower for empty versus mRNA-loaded particles for all formulations, the relative size of empty versus mRNA-loaded particles depended upon the formulation and intraparticle structure. When comparing CLiC-ALEX to cryogenic transmission electron microscopy measurements (Cryo-TEM), for the LNP formulations that display blebs, the fraction of bleb LNPs is in close agreement with the fraction of mRNA-containing LNPs. CLiC-ALEX also enabled quantification of the per-particle mRNA fluorescence and FRET signals, and thus the heterogeneity in the mRNA copy number and mRNA-LNP structural arrangements, where the results were compared with biophysical estimates based on the LNP formulations. These rigorous biophysical insights are critical to inform our understanding of structure-activity relationships and inform rational design of nanomedicines.

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bioRxiv2025

Quantitative phase deformability cytometry (QP-DC) for precise and clinically relevant multiparametric immune cell profiling

Imaging flow cytometry enables the detailed analysis of cell morphology and internal structures through high-throughput cell imaging, and quantitative phase imaging (QPI)-based microfluidic approaches have extended this by providing label-free measures such as dry mass and refractive index (RI). Building on these developments, we present quantitative phase deformability cytometry (QP-DC), which integrates QPI with deformability cytometry to simultaneously measure morphology, mechanics, and intrinsic biophysical parameters such as mass density and dry mass. Numerical refocusing ensures in-focus images independent of axial position, improving precision in contour detection and feature extraction. Using microspheres and whole blood, we validated QP-DC and then applied it to neutrophils under lipopolysaccharide (LPS) stimulation and from patients with systemic lupus erythematosus (SLE). QP-DC revealed LPS-induced reductions in neutrophil mass density and identified heterogeneous subpopulations in SLE. These results demonstrate the capability of QP-DC for precise biophysical and mechanical characterization, offering significant potential for research and clinical diagnostics.

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bioRxiv2025

Cytokines control the physical state of immune tissue

Unlike most solid-like tissues, immune tissue is protean and reconfigurable--its component cells can patrol vast territories, find rare cellular partners, and dynamically self-organize into functional structures like germinal centers or tertiary lymphoid structures. The ability of immune cells to collectively behave as an active material that switches physical state is essential for adaptive immunity. Yet the principles governing the control of the physical properties of immune tissues, and how chemical and mechanical forms of control interplay remain obscure. Inspired by minimal immune cell components that recapitulate germinal center (GC) dynamics, we developed an agent-based model that predicted that a tissues ability to program its own physical properties governs the efficiency of antibody evolution. This motivated our search for biomolecular forms of control capable of tuning this material property. Using a tractable in vitro model, we found that CD40L-stimulated human B cells self-organize into active, liquid-like condensates that round, fuse, and internally mix. GC cytokines IL-4 and IL-21 tuned this effective temperature, driving phase transitions from cohesive, liquid-like states to dispersed, gas-like morphologies. These findings demonstrate that cytokines control tissue fluidity, suggesting a previously unrecognized biophysical form of immune regulation. Significance StatementThe bodys immune system is uniquely flexible, allowing cells to organize into temporary structures, like germinal centers or tertiary lymphoid structures, to fight intruders. How this physical flexibility is controlled is a major question. We discovered that the physical state of immune tissue is chemically programmable. We show that self-organized multicellular B cell structures behave like liquid droplets, and we used this framework to demonstrate that signals (cytokines) can modulate their physical properties. This finding identifies a new biophysical axis of immune control, suggesting the body actively tunes its tissue fluidity to optimize the immune response.

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