Biology subjects

Gomez Toledo, A.

Publications and source records attributed to Gomez Toledo, A..

6 recordsLinked to original sources

bioRxiv2025

Multi-omic analysis reveals the unique glycan landscape of the blood-brain barrier glycocalyx

The blood-brain barrier (BBB) glycocalyx is the dense layer of glycans and glycoconjugates that coats the luminal surface of the central nervous system (CNS) vasculature. Despite being the first point of contact between the blood and brain, not much is known about the BBB glycocalyx. Here, we performed a multi-omic investigation of the BBB glycocalyx which revealed a unique glycan landscape characterized by enrichment of sialic acid, chondroitin sulfate, and hyaluronan. We found that the BBB glycocalyx was thicker than glycocalyces in the peripheral vasculature and that hyaluronan was the major contributor to its ultrastructure. Using endothelial RNA sequencing, we found potential genetic determinants for these differences, including BBB enrichment of genes involved in sialic acid addition and peripheral enrichment of Tmem2 and Hyal2, the only known cell-surface hyaluronidases. Glycocalyx degradation and increases in vascular permeability are widely associated with inflammation. However, we found that the BBB glycocalyx remains largely unchanged in neuroinflammation during the experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis and that its degradation is not sufficient to alter BBB permeability in health. Moreover, we showed that CNS endothelial sialic acid removal delays onset of EAE, indicating that BBB glycocalyx sialic acid may contribute to the progression of neuroinflammation. These findings underscore the unique and robust nature of the BBB glycocalyx and provide targets and tools for future studies into its role in health and neuroinflammation.

molecular biology↗

bioRxiv2025

Cumulating MS Signal enables polyclonal antibody analysis

Unraveling the complexities of protein systems via Mass Spectrometry (MS), particularly polyclonal antibodies, demands innovative analytical strategies. Here, we introduce the cumulative MS score (cMS), a novel mathematical framework that transcends traditional spectrum-matching, integrating MS evidence across multiple sample injections to achieve robust de novo peptide sequencing annotation. This approach, shifting from isolated spectrum analysis to a holistic MS signal-based methodology, was rigorously evaluated and validated across diverse sample types and experimental conditions. We applied this framework to characterize a complex polyclonal antibody mixture of Streptococcus pyogenes M1 protein binders derived from intravenous immunoglobulin (IVIG), revealing predominant variable heavy (VH) and light (VL) chain subgroups consistent with established genetic studies. Furthermore, we successfully identified conserved complementarity-determining region (CDR) features and predicted stable antibody-antigen interactions through molecular dynamics simulations, demonstrating the methods potential for dissecting intricate antibody responses. This work establishes a powerful alternative to conventional tandem mass spectrometry MS/MS data analysis, enabling deeper insights into protein systems and paving the way for targeted therapeutic development.

bioinformatics↗

bioRxiv2024

Multiplex genome editing eliminates the Warburg Effect without impacting growth rate in mammalian cells

The Warburg effect is ubiquitous in proliferative mammalian cells, including cancer cells, but poses challenges for biopharmaceutical production, as lactate accumulation inhibits cell growth and protein production. Previous efforts to eliminate lactate production via knockout have failed in mammalian bioprocessing since lactate dehydrogenase has proven essential. However, here we eliminated the Warburg effect in Chinese hamster ovary (CHO) and HEK293 cells by simultaneously knocking out lactate dehydrogenase and regulators involved in a negative feedback loop that typically inhibits pyruvate conversion to acetyl-CoA. In contrast to long-standing assumptions about the role of aerobic glycolysis, Warburg-null cells maintain wildtype growth rate while producing negligible lactate. Further characterization of Warburg-null CHO cells showed a compensatory increase in oxygen consumption, a near total reliance on oxidative metabolism, and higher cell densities in fed-batch cell culture. These cells remained amenable for production of diverse biotherapeutic proteins, reaching industrially relevant titers and maintaining product glycosylation. Thus, the ability to eliminate the Warburg effect is an important development for biotherapeutic production and provides a tool for investigating a near-universal metabolic phenomenon.

bioengineering↗

bioRxiv2023

Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow

Most individuals maintain circulating antibodies against various pathogenic bacteria as a consequence of previous exposures. However, it remains unclear to what extent these antibodies contribute to host protection. This knowledge gap is linked to the need for better methods to characterize antimicrobial polyclonal antibodies, including their antigen and epitope repertoires, subclass distribution, glycosylation status, and effector functions. Here, we showcase a generic mass spectrometry-based strategy that couples systems antigenomics and systems serology to characterize human antibodies directly in clinical samples. The method is based on automated affinity purification workflows coupled to an integrated suite of high-resolution MS-based quantitative, structural- and glyco-proteomics readouts. We focused on Streptococcus pyogenes (Group A Streptococcus; GAS), a major human pathogen still awaiting an approved vaccine. Our methodology reveals that both healthy and GAS infected individuals have circulating Immunoglobulin G (IgG) against a subset of genomically conserved streptococcal proteins, including numerous toxins and virulence factors. The antigen repertoire targeted by these antibodies was relatively constant across healthy individuals, but considerably changed in GAS bacteremia. Detailed analysis of the antigen-specific IgG indicates inter-individual variation regarding titers, subclass distributions, and Fc-signaling capacity, but not in epitope and Fc-glycosylation patterns. Importantly, we show that the IgG subclass has a major impact on the ability of GAS-antibodies to trigger immune signaling, in an antigen- and Fc receptor-specific fashion. Overall, these results uncover exceeding complexity in the properties of GAS-specific IgG, and showcase our methodology as high-throughput and flexible workflow to understand adaptive immune responses to bacterial pathogens. Significance statementMost people develop polyclonal antibodies against bacterial pathogens during infections but their structural and functional properties are poorly understood. Here, we showcase a combined systems antigenomics and systems serology strategy to quantify key antibody properties directly in clinical samples. We applied this method to characterize polyclonal antibody responses against Streptococcus pyogenes, a major human pathogen. We mapped the antigen and epitope landscape of anti-streptococcal antibodies circulating in healthy adult plasma, and their changes during blood infections. We further demonstrate the analytical power of our approach to resolve individual variations in the structure and effector functions of antigen-specific antibodies, including a dependency between immunoglobulin subclass and Fc-signaling capacity.

immunology↗

bioRxiv2023

Release of extracellular matrix components after human traumatic brain injury

Most research on the evolution of damage after traumatic brain injury (TBI) focuses on cellular effects, but the analysis of human tissue slices and animal research have shown that TBI causes concomitant damage in the extracellular matrix, which can play a significant role in both short-term consequences such as edema, and late effects such as post-traumatic epilepsy (PTE). To test the hypothesis that traumatic brain injury (TBI) in human patients causes disruption of sulfated glycosaminoglycan (sGAG) in the extracellular matrix, we measured levels of these substances in the ventricular cerebrospinal fluid (CSF) in patients with severe TBI in the acute post-injury period, along with concomitant levels in blood and urine. We assessed whether levels corresponded to parenchymal injury load, distance of traumatic brain lesions from the ventricle, presence of polytrauma, or host demographic factors. MethodsSamples of CSF, blood, and urine were obtained within 72 hours of injury in patients who received external ventricular drains as part of their treatment of severe TBI, and levels of chondroitin and heparan sGAGs were measured, along with their disaccharide constituents. Basic demographic information, presence and severity of polytrauma, brain injury load based on imaging findings, and distance of radiologically visible parenchymal injury from the ventricle were analyzed for correlation with total subtype sGAG levels in each patient. ResultsLevels were measured in 14 patients ranging in age from 17-90 years. CSF sGAG levels were variable among patients, and sGAG levels were higher in plasma than in CSF and variable in urine. Patients with polytrauma had non-significantly higher blood sGAG compared to patients with isolated head injury. Subcategories of CSF sGAG levels correlated with distance from the ventricle of parenchymal injury but not with brain injury load, which may reflect rapid metabolism in the parenchyma, contamination by blood, or bulk directional CSF flow from the ventricle to the subarachnoid space. ConclusionThis study is the first to measure sGAG levels in ventricular CSF and also provides the first measurements in patients with TBI. Damage to the extracellular matrix may play a major role in acute and chronic injury sequelae, and these data demonstrate elevation locally of intracranial sGAGS after severe TBI and also suggest rapid local metabolism of these breakdown products. The consequences of extracellular matrix breakdown may provide unique therapeutic and preventive avenues to mitigate post-injury sequelae.

neuroscience↗

bioRxiv2021

Vascular proteome responses precede organ dysfunction in sepsis

Vascular dysfunction and organ failure are two distinct, albeit highly interconnected clinical outcomes linked to morbidity and mortality in human sepsis. The mechanisms driving vascular and parenchymal damage are dynamic and display significant molecular crosstalk between organs and tissues. Therefore, assessing their individual contribution to disease progression is technically challenging. Here, we hypothesize that dysregulated vascular responses predispose the organism to organ failure. To address this hypothesis, we have evaluated four major organs in a murine model of S. aureus sepsis by combining in vivo labeling of the endothelial proteome, data-independent acquisition (DIA) mass spectrometry, and an integrative computational pipeline. The data reveal, with unprecedented depth and throughput, that a septic insult evokes organ-specific proteome responses that are highly compartmentalized, synchronously coordinated, and significantly correlated with the progression of the disease. Vascular proteome changes were found to precede bacterial invasion and leukocyte infiltration into the organs, as well as to precede changes in various well-established cellular and biochemical correlates of systemic coagulopathy and tissue dysfunction. Importantly, our data suggests a potential role for the vascular proteome as a determinant of the susceptibility of the organs to undergo failure during sepsis.

immunology↗