Biology subjects

Ramos, R. B.

Publications and source records attributed to Ramos, R. B..

8 recordsLinked to original sources

bioRxiv2026

A DMT1-dependent iron-endoplasmic reticulum-extracellular matrix axis regulates cancer cell invasion

Intracellular iron homeostasis is increasingly recognized as a regulator of cancer cell behavior, but how iron distribution influences extracellular matrix (ECM) organization and invasion remains poorly understood. Here, we show that loss of divalent metal transporter 1 (DMT1/SLC11A2) disrupts intracellular iron homeostasis and promotes cancer cell invasion through an iron-ER-ECM axis. In MDA-MB-231 cells, DMT1 knockout (KO) reduced total iron content but increased the labile iron pool (LIP) in both 2D and 3D culture models, indicating altered intracellular iron distribution. Across transcriptomic and phenotypic readouts, DMT1-dependent effects were more evident in 3D than in 2D models, with DMT1 KO inducing endoplasmic reticulum (ER) stress and impaired collagen/ECM organization. Functionally, the DMT1-loss phenotype was marked by reduced 2D motility, whereas in 3D spheroid models DMT1 KO cells displayed enhanced invasive outgrowth in both Matrigel and collagen matrices. Iron chelation further modulated this phenotype in a DMT1-dependent manner. Pharmacologic induction of ER stress phenocopied the loose spheroid architecture and invasive behavior, supporting ER stress as a mechanistic link between altered iron handling and ECM destabilization. Together, these findings identify intracellular iron distribution, rather than total iron abundance alone, as a determinant of ECM integrity and context-dependent cancer cell invasion. One Sentence Summary: Iron misrouting, not iron excess, drives ER stress and collagen failure that unleash invasion in triple-negative breast cancer.

cancer biology↗

bioRxiv2025

Lipid lowering alone fails to limit atherosclerosis progression and neutrophilic inflammation in middle-aged mice

While cholesterol lowering remains the cornerstone therapy for atherosclerosis and prevention of major adverse cardiovascular events, 33-50% of individuals on lipid-lowering therapy continue to exhibit elevated inflammation. Middle age (MA) represents a critical window for disease acceleration, underscoring a need to better understand non-resolving inflammation in this time frame. We rendered young (2 months) and MA mice (10 months) hypercholesterolemic with an AAV8-PCSK9 virus and fed a western diet (WD). Following 20 weeks on a WD, mice were switched to chow for 6 weeks to mimic lipid-lowering therapy. We found that MA atherosclerotic mice had increased plaque necrosis with increased circulating and bone marrow PMN compared to young mice. Upon lipid lowering, unlike in young mice, MA mice had increased necrosis, and reduced remodeling as well as increased circulating white blood cells and bone marrow hematopoietic stem cell progenitors (HSPCs). Circulating neutrophils correlated with necrosis in MA mice whereas young mice exhibited no correlation. Lipid lowered MA atherosclerotic mice had bone marrow HSPCs and neutrophils that exhibited a more activated phenotype relative to young. Elevated neutrophil-endothelial contacts were observed in the hippocampal vasculature of MA lipid lowered mice. While lipid lowering restrains atheroprogression in young, it is inadequate in MA, failing to reduce systemic inflammation and indicating the need for complementary therapies during this time frame.

immunology↗

bioRxiv2025

TRAP seq in 3D Angiogenesis Assays Reveals a Distinct Endothelial Translatome Associated with Early and Late Stages of Morphogenesis.

Endothelial cells (ECs) are often a minority cell type in a tissue, limiting the utility of bulk sequencing approaches. Single cell sequencing lacks sensitivity and requires disruptive tissue digestion techniques. TRAP seq (Translating Ribosome Affinity Purification) or "RiboTag" has been used to overcome these limitations. Multicellular co-culture systems allow primary ECs to differentiate and undergo tubular morphogenesis in cell culture, however similar limitations exist with these in vitro assays, as ECs are under-represented by as much as a factor of 10 in many assays. We sought to use TRAP seq to better understand the gene expression landscapes that drive these morphogenic events. We found TRAP seq selectively enriches for endothelial RNA in two distinct co-culture paradigms, in both the planar and fibrin bead co-culture assays. Intriguingly, the use of this technology in vitro, revealed distinct gene expression changes in blood vessel development and in the mitotic cell cycle, with genes unique to early and late phases of morphogenesis. It is widely accepted that expression of the NOTCH signaling pathway is a regulator of angiogenesis in vivo. Correspondingly, we found that a large number of NOTCH related genes relevant to endothelial cell biology, were changing across this morphogenic process, underpinning the importance and utility of this technology in 3D multicellular cultures that model in vivo environments.

cell biology↗

bioRxiv2024

A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice

Sepsis-associated encephalopathy (SAE) is a common manifestation in septic patients that is associated with increased risk of long-term cognitive impairment. SAE is driven, at least in part, by brain endothelial dysfunction in response to systemic cytokine signaling. However, the mechanisms driving SAE and its consequences remain largely unknown. Here, we performed translating ribosome affinity purification and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge. LPS induced a strong acute transcriptional response in the brain endothelium that partially correlates with the whole brain transcriptional response and suggested an endothelial-specific hypoxia response. Consistent with a crucial role for IL-6, loss of the main regulator of this pathway, SOCS3, leads to a broadening of the population of genes responsive to LPS, suggesting that an overactivation of the IL-6/JAK/STAT3 pathway leads to an increased transcriptional response that could explain our prior findings of severe brain injury in these mice. To identify any potential sequelae of this acute response, we performed brain TRAP-seq following a battery of behavioral tests in mice after apparent recovery. We found that the transcriptional response returns to baseline within days post-challenge. Despite the transient nature of the response, we observed that mice that recovered from the endotoxemic shock showed mild, sex-dependent cognitive impairment, suggesting that the acute brain injury led to sustained, non-transcriptional effects. A better understanding of the transcriptional and non-transcriptional changes in response to shock is needed in order to prevent and/or revert the devastating consequences of septic shock. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/583191v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@19515borg.highwire.dtl.DTLVardef@2c307dorg.highwire.dtl.DTLVardef@12393f9org.highwire.dtl.DTLVardef@c7d795_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Fatty acid metabolism in neutrophils promotes lung damage and bacterial replication during tuberculosis.

Mycobacterium tuberculosis (Mtb) infection triggers a significant influx of neutrophils to the lungs, which is linked to tuberculosis (TB) severity. The mechanism by which Mtb infection induces neutrophillic inflammation remains unclear. Using a clinically relevant and hypervirulent Mtb strain from the W-Beijing family, HN878, we found that genes related to both glycolysis and fatty acid metabolism are upregulated in the lung neutrophils of susceptible mice. Similar effects in gene expression were observed in rabbits, and humans with pulmonary TB compared to healthy controls. Inhibiting glycolysis with 2-deoxy D-glucose (2-DG) exacerbated disease pathology, while fatty acid oxidation (FAO) inhibitor Etomoxir (ETO) improved outcomes by reducing weight loss, immunopathology, and bacterial replication within neutrophils in genetically susceptible mice. Notably, ETO reduced neutrophil production in the bone marrow and their recruitment to the lungs. ETO specifically restrained the recruitment of Ly6Glow/dim immature neutrophil population, which is elevated during disease progression and harbors the bulk of bacilli. In a transwell setup, we demonstrated that ETO dose-dependently inhibited neutrophil chemotaxis towards infected macrophages. In summary, our research highlights the crucial role of fatty acid metabolism in regulating neutrophilic inflammation during TB and provides a rationale for targeting immunometabolism of neutrophils for potential TB treatment.

immunology↗

bioRxiv2023

Computational Assessment on Catalytic Activity of PET Hydrolase

BackgroundPET hydrolase from Ideonella sakaiensis might provide a response for PET accumulation in the environment. In this project some previously studied mutations were implemented and their performance was evaluated via computational methods with tools such as Modeller, HADDOCK, PyMOL and Gromacs. One possible mutation that could lead to improved catalytic activity was proposed. ResultsPET hydrolase DM S209F W130H and I179 provide interesting binding results with studied ligands, however a solution that combines both mutations does not seem viable, since the binding cleft becomes occluded. Following the same rationale, the triple mutant S209F W130H I179Q is proposed but instead leaves space in the binding cleft for ligand to enter and might bond with the oxygen at the ester group. The experiments conducted with triple mutant S209F W130H I179Q failed to beat HADDOCK score for DM, however its experimental results could still increase PET degradation. Results from surface charge may indicate an increase in stability and binding affinity for the protein. ConclusionsAmong models implemented, DM S209F W130H seems the best model studied regarding BHET or PET binding. Despite Protein Engineering is a complex process, computational tools might provide a way of studying binding sites of hypothetical proteins. Supplementary informationSupplementary data is available in annexes.

bioinformatics↗

bioRxiv2023

Gene Expression and Physiological traits in Mice

BackgroundGene expression regulates several complex traits observed. In this study, datasets comprising of transcriptome information and clinical traits regarding fat composition and vitals were analyzed via several statistical methods in order to find relations between genes and clinical outcomes. ResultsBiological big data is diverse and numerous, which makes for a complex case study and difficulties to stablish a metric. Histological data with semi-quantitative scores proved unreliable to correlate with other vitals, such as cholesterol composition, which complicates prediction of clinical outcomes. A composition of vitals, turned out to be a better variable for regression and factors for gene analysis. Several genes were found to be statistically significant after statistical analysis by ANOVA regarding the progressive categories of the preferred clinical variable. ConclusionsANOVA is proposed as a method for genetic information retrieval in order to extract biological meaning from RNA seq or microarray data, accounting for multiple classes of target variables. It Provides a reliable statistical method to associate genes or clusters of genes with particular traits. Supplementary informationSupplementary data are available in annexes.

genomics↗

bioRxiv2022

Regulation of endothelial DNA methylation by the sustained response to IL-6

Endothelial dysfunction is a critical factor in promoting organ failure during septic shock. Organ dysfunction during shock increases the risk of long-term sequelae in survivors through mechanisms that remain unknown. We postulated that vascular dysfunction during shock contributes to the long-term morbidity post shock through transcriptional and epigenetic changes within the endothelium. As we have previously demonstrated that IL-6/JAK/STAT3 signaling in endothelial cells contributes to the inflammatory response following endotoxin, we performed cross-omics analyses on kidney endothelium from acute endotoxin-challenged mice lacking or not the JAK/STAT3 inhibitor SOCS3. This analysis revealed significant DNA methylation changes upon proinflammatory signaling that was significantly associated with transcriptional activity through AP1, STAT, and IRF families, suggesting a mechanism driving transcription-induced gene-specific methylation changes. In vitro, we demonstrated that IL-6 induces similar changes in DNA methylation. Specific genes showed DNA methylation changes in response to an IL-6+R challenge, and consistently, changes in their expression levels by 72 hours of IL-6+R treatment. Further, changes in the endothelial methylome remain in place for prolonged periods in absence of IL-6, suggesting that this cytokine may elicit transcriptional changes long after the resolution of inflammation. Also, demonstrated that DNA methylation changes could directly alter the expression of these genes and that STAT3 activation had a causal role in this transcriptional response. Our findings provide evidence for a critical role for IL-6 signaling in regulating shock-induced epigenetic changes and sustained endothelial activation, offering a new therapeutic target to limit vascular dysfunction and prevent long-term organ damage. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/502384v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@453cbdorg.highwire.dtl.DTLVardef@196b50dorg.highwire.dtl.DTLVardef@1487180org.highwire.dtl.DTLVardef@113a9ee_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗