Biology subjects

Figueroa, A.

Publications and source records attributed to Figueroa, A..

12 recordsLinked to original sources

bioRxiv2026

Mitochondrial dysfunction plays a key role in premature musculoskeletal aging in hypochondroplasia mouse model

Hypochondroplasia (HCH) is a mild form of chondrodysplasia, caused by variants in fibroblast growth factor receptor 3 (FGFR3). Today, the biological mechanism underlying musculoskeletal aging in HCH remains largely unknown. In this study, we show that Hch mice exhibit phenotypic traits of bone fragility and accelerated age-dependent articular cartilage and subchondral bone changes. Hch mice also presented decreased muscle strength and reduction in muscle fibers size. Furthermore, proteomics analyses of the cortical bone revealed that Hch mice follow a different aging trajectory than control. FGFR3 mutation leads to a premature boost of the mitochondrial processes forcing the mutant to reach a physiological state much earlier than the control. Together, these findings demonstrate that aging in Hch mice is accompanied by bone fragility and osteoarthritis-like changes. Proteomics analyses highlighted the key role for mitochondria in the cortical bone of Hch mice, providing insight into the mechanisms underlying premature aging in HCH.

genetics↗

bioRxiv2026

Targeting Nitric Oxide Synthase 2 Reverses Learning Deficits in an Oligodendrocyte-Focused Model of Costello Syndrome

Oligodendrocyte (OL) functions greatly improve information processing in the brain; consequently, compromised OL biology negatively impacts brain function in various diseases. Young-adult Costello Syndrome (CS) patients present with learning disabilities and regression of psychomotor skills in correlation with abnormal brain white matter, delayed myelination, and dysmyelination. This suggests the involvement of OLs and myelin in abnormal brain physiology during and beyond development; however, the neuropathophysiology of CS remains poorly understood. Replacing the endogenous HRas gene with the CS-causing HRasG12V mutant gene in adult OLs (pHRasG/+ mice) induces structural myelin abnormalities; nonetheless, any functional impact is unknown. Here we show robust learning - but not memory - deficits in pHRasG/+ males and modest, delayed learning issues in females. Learning phenotypes are transient, likely involving compensatory responses from the OL lineage and microglia. Diffusion-weighted magnetic resonance imaging revealed regional time- and sex-dependent compromised myelin microstructure, coinciding with the peak of learning issues. Remarkably, transcripts associated with inflammation/immune function are upregulated and pharmacological control of nitric oxide synthase 2 restores learning in male pHRasG+/- mice. Our study supports the notion that abnormal nitric oxide signaling in mature OLs affects learning, suggests a chronic impact of glia-myelin mechanisms in CS neuropathology, and proposes molecular targets with therapeutic potential.

neuroscience↗

bioRxiv2026

Vascular Deformation Mapping Calibration with Physics-based Synthetic Data on Multi-axial Aortic Motion

Aortic stiffness is both heterogenous and anisotropic. Current non-invasive methods to estimate aortic stiffness are limited to characterizing the aortic tissue as isotropic due to the lack the techniques required to extract multi-axial strain from 3D dynamic images. Vascular deformation mapping (VDM) is a nonrigid image registration technique which has thus far been applied to map aortic growth using longitudinal imaging. In this study, we propose to use VDM to assess 3D aortic deformation by mapping diastolic and systolic images. During image registration process, penalty parameters are employed to fine-tune image alignment and penalize non-physiological deformations. These penalty parameters must be calibrated to ensure that VDM successfully reproduces multi-axial aortic motion patterns in health and disease. In this paper, we developed a calibration pipeline for these parameters using synthetic data. A rotation-free shell model was used to generate physics-based synthetic data on aortic motion incorporating patient-specific geometries, root motion, and blood pressure from a cohort of 14 subjects (healthy, Marfans syndrome and thoracic aortic aneurysm). An error metric was defined to quantify the quality of the VDM results. Furthermore, a k-means clustering technique was used to categorize the subjects into three clusters based on ascending aortic motion. Optimal penalty parameters were identified for each of the three clusters. The results indicated that patient clusters with smaller aortic root motion required larger rigidity penalty values. The calibrated parameters successively reduced errors in 3D displacement and multi-axial stretch compared to un-optimized VDM predictions, enhancing the accuracy of capturing aortic deformation from dynamic images. Among the different aortic regions, the ascending thoracic aorta exhibits the largest error reduction.

bioengineering↗

bioRxiv2026

A direct forcing immersed boundary method for biofluid simulations using a non-linear rotation free shell model on unstructured grids

Thin structures such as heart valves and aortic dissection flaps interact dynamically with blood flow in human vessels. Their flexibility and capacity for large deformations generate complex, highly transient hemodynamic patterns over the cardiac cycle. Accurately resolving these interactions remains challenging for conventional boundary-fitted fluid-structure interaction approaches. We present an immersed boundary method for simulating thin structures in incompressible flow on unstructured grids. The method couples a stabilized finite element fluid solver with a nonlinear, rotation-free shell formulation through a direct forcing immersed boundary approach. The framework supports both weak (explicit) and strong (implicit) time-coupling strategies, enabling stable simulations over a wide range of solid-to-fluid density ratios. Hydrodynamic forces acting on thin structures are computed from fluid solutions sampled on both sides of the structure, allowing accurate force reconstruction for zero-thickness shells. To our knowledge, this is the first immersed boundary formulation that couples an unstructured finite element fluid solver with a two-dimensional, rotation-free shell model to simulate interactions between thin structures and incompressible flow. Fluid-structure coupling is achieved using predefined finite element shape functions, which provide consistent projection between Eulerian and Lagrangian fields without additional interpolation procedures. The framework is validated using three-dimensional benchmark problems involving thin structures. Then, valve-like model is used to compare strong and weak coupling strategies. Finally, the method is applied to an idealized type-B aortic dissection model. The proposed approach is implemented within the open-source software CRIMSON, a finite element platform for cardiovascular simulation.

bioengineering↗

bioRxiv2025

Hakai links m6A RNA methylation to immune regulation in colorectal cancer

BackgroundThe mA modification is the most abundant RNA epigenetic mark in colorectal cancer (CRC). In this study, we focused on Hakai, a methyltransferase writer-associated protein whose molecular function within the complex and link to CRC immune regulation remain poorly characterized. MethodsWe performed RNA-seq to assess transcriptomic changes after Hakai silencing in CRC models and MeRIP-seq to profile methylation alterations. Validation was carried out by Western blot, flow cytometry, ELISA, and RT-qPCR. Protein interactions within the writer complex were analysed by co-immunoprecipitation, and changes in protein localization by cell fractionation assays. Peripheral blood from healthy donors and lamina propria mononuclear cells from CRC patients were incubated with supernatants from Hakai-silenced CRC cells to evaluate effects on immune responses. ResultsHakai silencing induced phenotypic changes in both monolayer and 3D CRC cultures, while its impact on the global transcriptome was limited. However, significant alterations in the methylation of immune response-related genes and reduced total mA levels were observed. Hakai interacted with the writer-associated protein VIRMA, and its silencing altered the subcellular localization of METTL3. Moreover, conditioned media from Hakai-silenced CRC cells modulated the expression of immune response markers in patient-derived gut immune cells. ConclusionsHakai acts as a component of the mA writer complex in CRC cells, influencing RNA methylation and the expression of immune-related genes. These findings suggest that Hakai silencing may enhance antitumour immune activity and represent a potential strategy to boost cancer immunity in colorectal cancer.

cancer biology↗

bioRxiv2025

E3 ubiquitin-ligase Hakai induces LRP4 degradation and regulates Wnt/beta-catenin signalling in colorectal cancer cells

The epithelial-mesenchymal transition (EMT) is closely linked to the acquisition of cancer stem cell (CSC) properties, which contribute to treatment resistance and metastasis. This study investigates the role of the E3 ubiquitin-ligase Hakai, the first identified post-translational regulator of E-cadherin stability, in promoting CSC traits in colorectal cancer (CRC). To examine Hakais involvement in CSC regulation, we used an inducible shRNA in a HT29 cells. Under conditions that promote CSC characteristics, we silenced Hakai and evaluated tumoursphere formation and CSC marker expression. Proteomic and bioinformatic analyses were performed to identify Hakai-regulated proteins in tumoursphere cultures. Additionally, Western blot, RT-qPCR, co-immunoprecipitation, immunofluorescence and TOPFlash assays were employed to study CSC-related protein regulation in response to Hakai expression. Furthermore, we assessed the impact of Hakin-1, the pharmacological inhibitor specifically targeting Hakais HYB domain responsible for its E3 ubiquitin-ligase activity, on tumoursphere properties. Hakai silencing significantly reduced tumoursphere size and number accompanied by decreased expression of CSC markers and Wnt target genes. CSC-related proteins regulated by Hakai were identified, including LRP4, a negative regulator of Wnt/{beta}-catenin pathway. Hakai interacts with LRP4, promoting its ubiquitination and degradation. Moreover, Hakai overexpression induces hyperactivation of Wnt/{beta}-catenin sand disrupts LRP4s inhibitory effect. Treatment with Hakin-1 effectively inhibited self-renewal and promoted differentiation within tumourspheres. These findings suggest that Hakai promotes CSCs properties by hyperactivation of the Wnt/{beta}-catenin pathway via LRP4-mediated modulation. Additionally, Hakin-1 emerges as a promising therapeutic agent targeting CSCs by enhancing differentiation and attenuating Wnt/{beta}-catenin activity, highlighting Hakai as a potential target for improving CSC treatment.

cancer biology↗

bioRxiv2025

Precision Neuromodulation with Real-Time Brain Decoding for Working Memory Enhancement

Transcranial magnetic stimulation (TMS) has transformed non-invasive brain therapies but faces challenges due to variability in outcomes, likely stemming from inter-individual differences in brain function. This study aimed to address this challenge by integrating personalized functional networks (PFNs) derived from functional magnetic resonance imaging (fMRI) with a neural network-based decoder to optimize stimulation in real time during a working memory (WM) task. After identification of individualized stimulation targets, participants completed a TMS/fMRI session, performing a WM task while receiving rTMS at randomized frequencies. Decoder outputs and behavioral data during this session guided selection of optimal and suboptimal stimulation frequencies. Participants then underwent six stimulation sessions (three optimal, three suboptimal) in a randomized crossover design, performing WM and control tasks. The optimal stimulation improved WM performance by the final session, with no improvement observed in the control task. Additionally, the decoder output predicted behavioral performance on the WM task, both during the TMS/fMRI and neuromodulation sessions. These findings show that neural network-guided closed-loop neuromodulation can improve TMS effectiveness, marking a step forward in personalized brain stimulation. HIGHLIGHTSO_LIClosed-loop TMS guided by real-time brain decoding enhances post-stimulation behavioral effects. C_LIO_LIIndividualized functional connectivity networks enable targeted neuromodulation C_LIO_LIOptimal stimulation boosted working memory performance over sub-optimal C_LIO_LIBrain decoder readouts predicted behavioral performance C_LI

neuroscience↗

bioRxiv2025

Patagonian fjords/channels vs. open ocean: phytoplankton molecular diversity in Southern Chilean coast

Environmental filtering hypothesis studies have revealed immense diversity of microorganisms across oceans; however, these studies are scarce along the Southeast Pacific coast. In this work, we describe the molecular diversity of phytoplankton communities from two biogeographic areas with contrasting oceanographic characteristics, namely fjords and channels versus the open Pacific Ocean (36{degrees}S to 53{degrees}S). Both areas have seen an increase in the frequency and intensity of Harmful Algal Bloom events (HABs). Using a molecular approach based on metabarcoding of the SSU ribosomal gene, we retrieve micro-phytoplankton diversity, community composition, and biogeographical patterns. The ASVs assigned to Dinophyceae and Bacillariophyta classes show differences in richness and dominance between both studied areas. The diversity pattern described in this work shows a higher harmful potential in fjord/channel areas versus the open ocean, which provides grounds for future studies about the factors triggering temporal variations in phytoplankton communities within these two contrasting environments.

ecology↗

bioRxiv2024

Local Synthesis of Reticulon-1C Lessens the Outgrowth of Injured Axons by Controlling Spastin Activity

The regenerative potential of developing cortical axons depends on intrinsic mechanisms, such as axon-autonomous protein synthesis, that are still not fully understood. An emerging factor in this regenerative response is the bi-directional interplay between microtubule dynamics and the axonal endoplasmic reticulum (ER). We hypothesize that locally synthesized ER proteins regulate microtubule dynamics and the regeneration of cortical axons. RNA data-mining identified the ER-shaping protein Reticulon-1 as a relevant candidate across eight axonal transcriptomes. Using microfluidic chambers, we demonstrate that local knockdown of Reticulon-1 synthesis increases the outgrowth of injured cortical axons while reducing their distal tubulin levels. Furthermore, we show by live-cell imaging that axonal Reticulon-1 knockdown restores the microtubule growth rate and track length modified by injury. Interestingly, local inhibition of the microtubule- severing protein Spastin prevents the axonal knockdown-mediated effects over outgrowth and tubulin levels. We demonstrate that the Reticulon-1C isoform is locally synthesized within axons and support its isoform-specific role in attenuating Spastin-mediated microtubule severing. These findings uncover a mechanism by which axonal protein synthesis finely controls microtubule dynamics and outgrowth upon injury.

neuroscience↗

bioRxiv2024

Deepening biomedical research training: Community-Building Wellness Workshops for Post-Baccalaureate Research Education Program (PREP) Trainees

ProblemAll trainees, especially those from historically minoritized backgrounds, experience stresses that may reduce their continuation in science, technology, engineering, math, and medicine (STEMM) careers. The Johns Hopkins University School of Medicine is one of [~]45 institutions with a National Institutes of Health funded Postbaccalaureate Research Education Program (PREP) that provides mentoring and a year of fulltime research to prepare students from historically excluded groups for graduate school. Having experienced the conflation of stresses during the COVID-19 pandemic and related shutdown, we realized our program lacked a component that explicitly helped PREP Scholars recognize and cope with non-academic stresses (financial, familial, social, mental) that might threaten their confidence and success as scientists and future in STEMM. InterventionWe developed an early-intervention program to help Scholars develop life-long skills to become successful and resilient scientists. We developed a year-long series comprised of 9 workshops focused on community, introspection, financial fitness, emotional intelligence, mental health, and soft-skills. We recruited and compensated a cohort of PhD students and postdoctoral fellows to serve as Peer Mentors, to provide a community and the safest space for Scholars to discuss personal concerns. Peer Mentors were responsible for developing and facilitating these Community-Building Wellness Workshops (CBWW). ContextCBWW were created and exectued as part of the larger PREP program. Workshops included a PowerPoint presentation by Peer Mentors that featured several case studies that prompted discussion and provided time for small-group discussions between Scholars and Peer Mentors. We also included pre- and post-work for each workshop. These touch-points helped Scholars cultivate the habit of introspection. ImpactThe CBWW exceeded our goals. Both Peer Mentors and Scholars experienced strong mutual support, and Scholars developed life-long skills. Notably, several Scholars who had been experiencing financial, mental or mentor-related stress immediately brought this to the attention of program leadership, allowing early and successful intervention. At the completion of CBWW, PREP Scholars reported implementing many workshop skills into practice, were reshaping their criteria for choosing future mentors, and evaluating career decisions. Strikingly, Peer Mentors found they also benefitted from the program as well, suggesting a potential larger scope for the role of CBWW in academia. Lessons LearnedPeer Mentors were essential in creating a safe supportive environment that facilitated discussions, self-reflection, and self-care. Providing fair compensation to Peer Mentors for their professional mentoring and teaching contributions was essential and contributed meaningfully to the positive energy and impact of this program.

scientific communication and education↗

bioRxiv2020

Potent Neutralizing Monoclonal Antibodies Directed to Multiple Epitopes on the SARS-CoV-2 Spike

The SARS-CoV-2 pandemic rages on with devasting consequences on human lives and the global economy1,2. The discovery and development of virus-neutralizing monoclonal antibodies could be one approach to treat or prevent infection by this novel coronavirus. Here we report the isolation of 61 SARS-CoV-2-neutralizing monoclonal antibodies from 5 infected patients hospitalized with severe disease. Among these are 19 antibodies that potently neutralized the authentic SARS-CoV-2 in vitro, 9 of which exhibited exquisite potency, with 50% virus-inhibitory concentrations of 0.7 to 9 ng/mL. Epitope mapping showed this collection of 19 antibodies to be about equally divided between those directed to the receptor-binding domain (RBD) and those to the N-terminal domain (NTD), indicating that both of these regions at the top of the viral spike are immunogenic. In addition, two other powerful neutralizing antibodies recognized quaternary epitopes that are overlapping with the domains at the top of the spike. Cryo-electron microscopy reconstructions of one antibody targeting RBD, a second targeting NTD, and a third bridging two separate RBDs revealed recognition of the closed, "all RBD-down" conformation of the spike. Several of these monoclonal antibodies are promising candidates for clinical development as potential therapeutic and/or prophylactic agents against SARS-CoV-2.

microbiology↗

bioRxiv2019

Herpes Simplex Virus type 1 Inflammasome Activation in Human Macrophages is Dependent on NLRP3, ASC, and Caspase-1

The pro-inflammatory cytokines interleukin (IL)-1{beta} and IL-18 are products of activation of the inflammasome, an innate sensing system, and important in the pathogenesis of herpes simplex type 1 (HSV-1). The release of IL-18 and IL-1{beta} from monocytes/macrophages is critical for protection from HSV-1 based on animal models of encephalitis and genital infection, yet if and how HSV-1 activates inflammasomes in human macrophages is unknown. To investigate this, we utilized both primary human monocyte derived macrophages and human monocytic cell lines (THP-1 cells) with various inflammasome components knocked-out. We found that HSV-1 activates inflammasome signaling in pro-inflammatory primary human macrophages. Additionally, HSV-1 inflammasome activation is dependent on nucleotide-binding domain and leucine-rich repeat-containing receptor 3 (NLRP3), apoptosis-associated speck-like molecule containing a caspase recruitment domain (ASC), and caspase-1, but not on absent in melanoma 2 (AIM2), or gamma interferon-inducible protein 16 (IFI16). Ultraviolet irradiation of HSV-1 enhanced inflammasome activation, demonstrating that viral replication suppresses inflammasome activation. These results confirm that HSV-1 is capable of activating the inflammasome in human macrophages through an NLRP3 dependent process and that the virus has an NLRP3 specific mechanism to inhibit inflammasome activation in monocytes and macrophages.\n\nAuthor SummaryThe inflammasome is a multi-protein complex that forms in response to pathogens and cellular damage. Active inflammasomes recruit pro-caspase-1 via ASC and cleave the cytokine precursors pro-IL-1{beta} and pro-IL-18 into mature IL-1{beta} and IL-18. These cytokines serve to activate other immune cells that either repair the damage or attempt to clear the invading pathogen. Upon activation, the inflammasome also promotes an inflammatory form of cell death called pyroptosis. Herpes simplex virus type 1 (HSV-1) is a common human pathogen that can cause cold sores, genital ulcers, encephalitis, and blindness. HSV-1 infection leads to induction of IL-1{beta} and IL-18, but whether it is capable of activating inflammasomes in macrophages, which play a role in severe forms of HSV-1 infection, was unclear. Here, we infected both primary human macrophages and a macrophage/monocytic cell line, THP-1 cells, with HSV-1. We found that HSV-1 does activate inflammasome signaling in macrophages in a process dependent on NLRP3, ASC, and caspase-1. This is important because it illustrates the mechanism by which HSV-1 infection leads to inflammasome activation in macrophages, known to be crucial for protection from severe disease in mouse models.

microbiology↗