Biology subjects

Perez, M. A.

Publications and source records attributed to Perez, M. A..

8 recordsLinked to original sources

bioRxiv2025

Regression-guided computational design of auxetic scaffolds for soft tissue applications

The mechanical performance of tissue-engineered scaffolds plays a critical role in their effectiveness for regenerative medicine applications. Auxetic metamaterials, characterized by a negative Poissons ratio, offer enhanced conformability and tunable mechanical behavior, making them promising candidates for scaffold design. This study presents a computational framework combining finite element method (FEM) simulations with regression-based predictive modeling to optimize auxetic scaffold architectures. A design of experiments (DOE) strategy enabled the training of FEM-accurate regression models capable of predicting mechanical responses from scaffold microstructural parameters. Sensitivity analysis guided the development of robust optimization strategies for identifying optimal geometries. Validation of the predictive framework was performed using experimentally derived, skin-representative mechanical properties from published literature, demonstrating strong agreement with FEM results. To facilitate broader use, we developed a software tool integrating this pipeline. It includes a manual mode for direct input of design and geometry parameters, and a predictive mode that returns optimized scaffold designs based on target properties. This integrated methodology supports robust, customizable scaffold design, advancing patient-specific approaches in soft tissue engineering.

bioengineering↗

bioRxiv2025

Rational Design and Modeling of Auxetic Fiber Scaffolds for Soft Tissue Engineering via Melt Electrowriting

BackgroundThe development of regenerative biomaterial scaffolds with mechanical properties tailored to native soft tissues remains a challenge in tissue engineering. Mechanical metamaterials with auxetic architectures have taken enormous flight over the past years, as they offer improved control over mechanical function and performance through spatially defined material architecture. However, despite their potential, auxetic scaffold designs are often developed empirically, and the relationship between scaffold microarchitecture, mechanical function, and manufacturability remains poorly defined, limiting their applicability in tissue engineering. In this study, we present a computational framework for the rational design of auxetic fiber scaffolds manufactured using Melt Electro-writing (MEW) for soft tissue engineering. To address the challenge of tailoring scaffold mechanical properties to native tissue, we integrated finite element method (FEM) modeling with experimental validation to predict the mechanical behavior of the scaffolds. MethodThe micro-fibrous scaffolds with customizable auxetic re-entrant structures were designed using Python scripts for generating G-code used in fabrication and for model definition in FEM modeling, respectively. Four distinct auxetic structures - HCELL, SREG, SINV, and STRI - were selected for this study to cover the wide range of mechanical properties of soft tissue, and their geometry parameters were adjusted to reduce the pore size while considering printing resolution. FEM modeling was employed to predict the mechanical behavior of the scaffolds. To validate the predictions, the scaffolds were manufactured via MEW and characterized mechanically under biaxial tensile loading. Results and conclusionMEW manufacturing enabled the production of auxetic fiber scaffolds with sub-millimeter pore resolution, while rational design allowed to correct fabrication discrepancies and improve printed design fidelity. Experimental biaxial characterization of the scaffolds revealed design-dependent, biphasic, non-linear mechanical response, and the developed FEM model was capable of not only accurately simulating the observed mechanical response but also accounting for variations introduced by MEW during fabrication. Additionally, auxetic scaffolds supported fibroblast viability over 7 days, confirming biocompatibility as a first step toward soft tissue engineering. The good alignment between numerical predictions and experimental results highlights the value of FEM modeling as a powerful computational tool for guiding the design and optimization of auxetic scaffolds with tailored mechanical performance for specific soft tissue requirements. The presented methodology offers a significant advancement in the development of functional biomaterials for biomedical applications.

bioengineering↗

bioRxiv2024

Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs

T cells targeting epitopes in infectious diseases or cancer play a central role in spontaneous and therapy-induced immune responses. T-cell epitope recognition is mediated by the binding of the T-Cell Receptor (TCR) and TCRs recognizing clinically relevant epitopes are promising for T-cell based therapies. Starting from one of the few known TCRs targeting the cancer-testis antigen NY-ESO-1157-165 epitope, we built large phage display libraries of TCRs with randomized Complementary Determining Region 3 of the {beta} chain. The TCR libraries were panned against the NY-ESO-1 epitope, which enabled us to collect thousands of epitope-specific TCR sequences. We then trained a machine learning TCR-epitope interaction predictor with this data and could identify several epitope-specific TCRs directly from TCR repertoires. Cellular binding and functional assays revealed that the predicted TCRs displayed activity towards the NY-ESO-1 epitope and no detectable cross-reactivity with self-peptides. Overall, our work demonstrates how display technologies combined with machine learning models of TCR-epitope recognition can effectively leverage large TCR repertoires for TCR discovery.

bioinformatics↗

bioRxiv2023

Biomimetic actin cortices shape cell-sized lipid vesicles

Animal cells are shaped by a thin layer of actin filaments underneath the plasma membrane known as the actin cortex. This cortex stiffens the cell surface and thus opposes cellular deformation, yet also actively generates membrane protrusions by exerting polymerization forces. It is unclear how the interplay between these two opposing mechanical functions plays out to shape the cell surface. To answer this question, we reconstitute biomimetic actin cortices nucleated by the Arp2/3 complex inside cell-sized lipid vesicles. We show that thin Arp2/3-nucleated actin cortices strongly deform and rigidify the shapes of giant unilamellar vesicles and impart a shape memory on time scales that exceeds the time of actin turnover. In addition, actin cortices can produce finger-like membrane protrusions, showing that Arp2/3-mediated actin polymerization forces alone are sufficient to initiate protrusions in the absence of actin bundling or membrane curving proteins. Combining mathematical modeling and our experimental results reveals that the concentration of actin nucleating proteins, rather than actin polymerization speed, is crucial for protrusion formation. This is because locally concentrated actin polymerization forces can drive a positive feedback loop between recruitment of actin and its nucleators to drive membrane deformation. Our work paints a picture where the actin cortex can either drive or inhibit deformations depending on the local distribution of nucleators. Significance StatementThe cells in our body must actively change shape in order to migrate, grow and divide, but they also need to maintain their shape to withstand external forces during tissue development. Cellular shape control results from an interplay between the plasma membrane and its underlying cortex, a shell composed of crosslinked actin filaments. Using cell-free reconstitution and mathematical modelling, we show that minimal biomimetic actin cortices can mechanically rigidify lipid vesicles while at the same time driving membrane protrusion formation. Our observations suggest that the spatial distribution of actin nucleation determines whether the actin cortex drives or inhibits membrane deformations.

biophysics↗

bioRxiv2022

Dynamics of asymmetric membranes and interleaflet coupling as intermediates in membrane fusion

Membrane fusion is a tool to increase the complexity of model membrane systems. Here, we use silica nanoparticles to fuse liquid-disordered DOPC giant GUVs and liquid-ordered DPPC:Cholesterol (7:3) GUVs. After fusion, GUVs display large membrane domains as confirmed by fluorescence confocal microscopy. Laurdan spectral imaging of the membrane phases in the fused GUVs shows differences compared to the initial vesicles indicating some lipid redistribution between phase domains as dictated by the tie lines of the phase diagram. Remarkably, using real-time confocal microscopy we were able to record the dynamics of formation of asymmetric membrane domains in hemifused GUVs and detected interleaflet coupling phenomena by which the DOPC-rich liquid-disordered domains in outer monolayer modulates the phase state of the DPPC:Cholesterol inner membrane leaflet which transitions from liquid-ordered to liquid-disordered phase.. We find that internal membrane stresses generated by membrane asymmetry enhance the efficiency of full fusion compared to our previous studies on symmetric vesicle fusion. Furthermore, under these conditions, the liquid disordered monolayer dictates the bilayer phase state of asymmetric membrane domains in >90% of observed cases. By comparison to the findings of previous literature, we suggest that which monolayer phase dominates the bilayer properties could be a mechanoresponsive signalling mechanism sensitive to the local membrane environment. Statement of SignificanceNatural biomembranes are highly asymmetric in lipid composition between the two leaflets of its bilayer structure. While the majority of membrane biophysics studies are conducted on symmetric lipid bilayers, it has become increasingly apparent that these asymmetric lipid compositions have a strong impact on the overall properties and behaviours of the membrane. However, achieving controlled membrane asymmetry in artificial model membranes is non-trivial, making the study of related biophysical mechanisms challenging. Here, we present an experimental framework to image the dynamics of asymmetric membrane domains formed as intermediates during membrane fusion of giant unilamellar vesicles (GUVs) triggered by silica nanoparticles. We directly observe interleaflet coupling of the phases in asymmetric membranes, where the liquid disordered domains most commonly dominate. By comparison with other literature on asymmetric membranes, this may indicate that the phase state of asymmetric membranes can be mechanoresponsive to its local environment. Furthermore, enhanced efficiency of full fusion of these GUV membranes indicates that stresses generated by membrane asymmetry can promote the formation of the full fusion pore during vesicle fusion processes.

biophysics↗

bioRxiv2021

Long-term Pannexin 1 ablation promotes structural and functional modifications in hippocampal neurons through the regulation of actin cytoskeleton and Rho GTPases activity.

Enhanced activity and overexpression of Pannexin 1 (PANX1) channels contribute to neuronal pathologies, such as epilepsy and Alzheimers disease (AD). In the hippocampus, the PANX1 channels ablation alters glutamatergic neurotransmission, synaptic plasticity, and memory flexibility. Nevertheless, PANX1-knockout (KO) mice still preserve the ability to learn, suggesting that compensatory mechanisms work to stabilize neuronal activity. Here, we show that the absence of PANX1 in the adult brain promotes a series of structural and functional modifications in KO hippocampal synapses, preserving spontaneous activity. Adult CA1 neurons of KO mice exhibit enhanced excitability, complex dendritic branching, spine maturation, and multiple synaptic contacts compared to the WT condition. These modifications seem to rely on the actin-cytoskeleton dynamics as an increase in actin polymerization and an imbalance between Rac1 and RhoA GTPase activity is observed in the absence of PANX1. Our findings highlight a novel interaction between PANX1, actin, and small Rho GTPases that appear to be relevant for synapse maintenance as a long-term compensatory mechanism for PANX1 deficiency.

neuroscience↗

bioRxiv2020

miRNome profiling of clonal stem cells in Ph+ CML

Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of CML LSC, normal hematopoietic stem cells (HSC) obtained from the same CML patients, and stem and progenitor cells obtained from healthy donors (HD) by next-generation sequencing. We detected a global decrease of microRNA levels in LSC and HSC from CML patients, and decreased levels of microRNAs and snoRNAs from a genomic cluster in chromosome 14, suggesting a mechanism of silencing of multiple non-coding RNAs. Surprisingly, HSC from CML patients, despite the absence of BCR-ABL1 expression, showed an altered miRNome. In silico analysis revealed an association between validated microRNAs and multiple metabolic pathways, suggesting that these molecules may be mediators of the previously reported dysregulation of LSC metabolism. This is the first report of the LSC miRNome that distinguishes between BCR-ABL1+ LSC and their BCR-ABL1- counterparts, providing valuable data for future studies.

cancer biology↗

bioRxiv2019

Dietary Induction and Modulation of Ferroptosis in Caenorhabditis elegans

Ferroptosis is an iron-dependent form of regulated cell death associated with oxidized polyunsaturated phospholipids. Understanding the role of this process in vivo has been slowed by the lack of readily accessible model systems. Exposing the nematode Caenorhabditis elegans to the polyunsaturated fatty acid dihomogamma-linolenic acid (DGLA; 20:3n-6) causes germ cell death and sterility that is largely independent of the canonical apoptosis pathway. Here we demonstrate that DGLA-induced germ cell death is modulated by small molecule ferroptosis inhibitors, genetic manipulation of ferritin, NADPH oxidase, and glutathione peroxidases, and by dietary co-supplementation with oleic acid. Thus, DGLA-induced germ cell death in C. elegans is highly analogous to ferroptosis in mammalian cells. DGLA can also induce ferroptosis in human cells, further highlighting this omega-6 PUFA as a metabolic instigator of ferroptosis. Together, these results establish C. elegans as a powerful animal model to study the induction and modulation of ferroptosis by dietary fats.\n\nHighlights- Dietary dihomogamma-linolenic acid (DGLA)-induced germ cell death in C. elegans is alleviated by small molecule antioxidants and iron chelators\n- Dietary and endogenous oleic acid protects from DGLA-induced ferroptosis\n- Ether-lipid deficiency increases sensitivity to DGLA-induced ferroptosis\n- DGLA specifically induces ferroptosis in human cancer cells

cell biology↗