Biology subjects

Velazquez, S.

Publications and source records attributed to Velazquez, S..

5 recordsLinked to original sources

bioRxiv2026

High-Sensitivity Magnetic Levitation Reveals Intrinsic Protein Corona Heterogeneity on Identical Nanoparticles

The protein corona (PC), a layer of biomolecules that adsorbs onto nanoparticles (NPs) surfaces upon exposure to biological fluids, plays a key role in defining the biological identity and performance of nanomaterials. However, most current analytical approaches rely on pooled measurements of PC-coated NPs and therefore lack the resolution needed to detect subtle heterogeneity in PC composition, potentially masking important differences in NPs biological identity. Here, we used a high-sensitivity magnetic levitation (MagLev) platform capable of resolving extremely small density differences among nominally identical PC-coated NPs, enabling fractionation of particles based on subtle variations in PC composition. Compared with conventional standard MagLev systems (density resolution [~]10-3 g/cm3), the high-sensitivity MagLev improves density sensitivity by up to three orders of magnitude, allowing discrimination of density differences as small as 10-5 g/cm3. Using this approach, PC-coated NPs were separated along the MagLev column into multiple fractions corresponding to distinct density populations. Subsequent proteomic analysis across the extracted fractions identified more than 500 proteins and revealed a structured but continuous redistribution of protein composition across the column, including fraction-dependent differences in protein abundance, overlap, and biological identity. In particular, the fraction series captured hidden heterogeneity among nominally identical PC-coated NPs, with upper fractions retaining relatively stronger extracellular/plasma-associated signatures and lower fractions showing increasing representation of structural, membrane-associated, cytoskeletal, and metabolic proteins. These findings demonstrate that PC formation is intrinsically heterogeneous even on identical NPs and this heterogeneity is largely missed by conventional pooled analysis. High-sensitivity MagLev provides a simple, label-free framework for resolving PC heterogeneity and offers a new analytical approach for studying NP-biomolecule interactions, with important implications for nanomedicine design, biomarker discovery, and the clinical translation of NP-based systems. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/727410v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@155ad62org.highwire.dtl.DTLVardef@1ea3e3dorg.highwire.dtl.DTLVardef@19c40ceorg.highwire.dtl.DTLVardef@162ca8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Body Mass Index-Specific Nanoparticle Protein Corona Signatures in Late Pregnancy

The protein corona (PC) formed on the surface of nanoparticles (NPs) upon exposure to human biofluids is a dynamic interface that reflects the physiological and pathological status of the host. In this study, we investigated how maternal body mass index (BMI) influences the composition of the NPs PC during late pregnancy. Polystyrene NPs were incubated with plasma samples collected from third-trimester pregnant individuals across normal weight, overweight, and obese BMI categories. Comprehensive characterization using dynamic light scattering (DLS), zeta potential measurements, and transmission electron microscopy (TEM) confirmed BMI-dependent differences in PC thickness and colloidal stability. SDS-PAGE and label-free quantitative proteomics revealed distinct molecular compositions: PCs from obese individuals were enriched in inflammatory and lipid metabolism-associated proteins (e.g., APOE, CRP), while normal weight-derived PCs showed higher levels of complement regulators and extracellular matrix proteins. Principal component analysis (PCA) demonstrated clear clustering of proteomic profiles by BMI group, suggesting BMI-specific PC fingerprints. These findings indicate that maternal metabolic phenotype shapes nano-bio interactions at the proteomic level and highlight the potential of PC profiling as a non-invasive approach for assessing maternal health and metabolic status. This work lays the foundation for integrating NP-based proteomics into precision nanomedicine for maternal-fetal health monitoring.

biophysics↗

bioRxiv2026

Magnetic Levitation Derived Metabolomic Fingerprinting Enables Exploratory Discrimination of Breast Cancer Subtypes

Breast cancer (BC) consists of heterogeneous molecular subtypes with distinct biological behavior and therapeutic response, including triple negative breast cancer (TNBC), human epidermal growth factor receptor 2 positive (HER2+), and Luminal A tumors. Current subtype classification primarily relies on tissue biopsy and molecular pathology, highlighting the need for complementary non invasive analytical approaches capable of capturing systemic biochemical differences among BC subtypes. In this exploratory study, we investigate whether magnetic levitation (MagLev) derived plasma patterning combined with untargeted metabolomics analysis can distinguish BC subtypes based on subtype specific metabolomic fingerprints. Representative plasma samples from TNBC, HER2+, and Luminal A patients were levitated in a standard MagLev system containing superparamagnetic iron oxide nanoparticles (SPIONs), generating visibly distinct levitation patterns throughout the levitation process. Individual levitated plasma layers were subsequently extracted and subjected to untargeted metabolomics analysis. Multivariate analysis demonstrated clear subtype dependent metabolic separation among the three BC subtypes. Heatmap clustering, PLS DA analysis, and variable importance profiling identified distinct metabolic signatures involving glycolysis, pentose phosphate pathway metabolism, TCA cycle activity, amino acid metabolism, and lipid remodeling. Elevated levels of phosphoglycerate, pyruvate, ribose 5 phosphate, glutamate, and 2 oxoglutarate suggested enhanced proliferative and biosynthetic metabolism, while enrichment of long chain fatty acids in Luminal A samples indicated subtype specific lipid metabolic remodeling. These findings demonstrate the feasibility of combining MagLev derived plasma organization with metabolomics analysis to generate disease specific metabolomic fingerprints and establish a foundation for future large scale validation studies.

biophysics↗

bioRxiv2026

MXene Protein Corona Interfaces for Molecular Profiling of Alzheimers Disease

The protein corona (PC) that forms on the surface of nanomaterials upon contact with biological fluids provides a molecular snapshot of the hosts physiological and pathological state. Here, we investigate two-dimensional (2D) titanium carbide (Ti3C2Tx) MXene nanosheets as nanobiointerfaces for capturing Alzheimers disease (AD)-associated plasma protein signatures. Ti3C2Tx MXene flakes were incubated with plasma from clinically diagnosed AD patients and age-matched healthy controls (HC), leading to the formation of Ti3C2Tx MXene-PC complexes. Physicochemical characterization using dynamic light scattering, zeta potential analysis, and transmission electron microscopy revealed disease-dependent changes in hydrodynamic size, surface charge, and PC profile. Proteomic analysis of the isolated PC layers quantified 1,611 proteins without prior fractionation, demonstrating effective enrichment of low-abundance plasma components. Principal component analysis (PCA) revealed consistent separation between AD- and HC-derived Ti3C2Tx MXene-PC proteomes despite inter-individual heterogeneity. Differential abundance analysis identified selective enrichment of heterogeneous nuclear ribonucleoproteins (hnRNPs), annexins, and inflammatory mediators in AD-derived PC, implicating dysregulated RNA metabolism, membrane stress responses, and immune activation, hallmark processes in AD pathology. Our findings demonstrate that Ti3C2Tx MXene-PC interfaces act as selective molecular filters that reshape the detectable plasma proteome, enabling disease-associated molecular phenotyping and establishing a versatile nanointerface-driven framework for uncovering AD-related plasma signatures, providing a foundation for future translational diagnostic development.

biophysics↗

bioRxiv2026

A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

The basal ganglia (BG) underlie motor control, reward processing, and many neurological and psychiatric disorders, but a comprehensive epigenomic and 3D-genome atlas of the human BG is lacking. Here we present a multimodal single-cell atlas profiling DNA methylation and 3D chromatin conformation in 261,331 nuclei (snm3C-seq) across eight subregions, resolving 12 classes, 31 subclasses, and 59 groups. Harmonized under the HMBA basal-ganglia consensus taxonomy, this atlas integrates with matched RNA, ATAC-seq, and histone-modification data across five regulatory layers. We identify millions of cell-type- and region-specific differentially methylated regions enriched for distinct transcription factor motifs and link them to disease-associated heritability. Neuron-specific loops dominate cell-type-specific 3D contact remodeling, while most non-neuron-specific loops are constitutive. Among spiny projection neurons (SPNs), chromatin loops, rather than TAD boundaries, distinguish D1, D2, and eccentric SPN subclasses, with eccentric SPNs showing the most loop-level reorganization among the three. We characterize STR D2 SMYD2-HTR7 SPN, a newly recognized POU6F2 D2-SPN subtype, and reveal region-specific methylation and contact gradients of disease-associated genes, including CADM1 and PDE8B. Integrative gene-regulatory networks reconstruct cell-type-resolved enhancer-promoter links to interpret Parkinsons disease risk variants at SNCA. Finally, MERFISH spatial profiling combined with cross-species Patch-seq identifies non-SPN neuronal subtypes, including a MOXD1 striosomal STR FS PTHLH-PVALB GABA subtype with distinct electrophysiology, partitioning across the striatal matrix-striosome boundary. HighlightsO_LIA multimodal single-cell atlas maps DNA methylation and 3D genome architecture across human basal ganglia cell types and subregions. C_LIO_LINeuron-specific loops dominate cell-type-specific 3D contact remodeling in the human BG, whereas most non-neuron-specific loops are constitutive. C_LIO_LISpiny Projection Neuron (SPN) subtypes exhibit regionally organized epigenomic and 3D genome signatures that align with dorsal-ventral identities. C_LIO_LIChromatin loops are the primary distinguishing feature among D1, D2, and eccentric SPN subclasses, with eccentric SPNs being the most 3D-reorganized. C_LIO_LIIntegrated regulatory maps link cell-type-specific enhancers to disease-associated genetic risk in the human basal ganglia. C_LIO_LINon-SPN interneurons differ in distribution and in transcriptional and epigenetic identity across the matrix-striosome boundary. C_LI

neuroscience↗