Biology subjects

Simoes, I.

Publications and source records attributed to Simoes, I..

3 recordsLinked to original sources

bioRxiv2025

A Proteomics-Based Comparison of Host Responses to Spotted Fever Group Rickettsia in Endothelial Cells

Spotted fever group (SFG) Rickettsia species are obligate intracellular bacteria with a tropism for endothelial cells (ECs), where they initiate pathogenesis leading to rickettsial vasculitis. However, how endothelial cells sense and respond to infection by Rickettsia species of differing pathogenic potential remains poorly defined. In this study, we conducted a comparative analysis of four SFG Rickettsia species - R. africae, R. parkeri, R. massiliae, and R. montanensis - using high-throughput label-free SWATH/DIA-MS/MS in human HUVEC/TERT2 cells. Our results revealed distinct intracellular growth dynamics that correlated with known virulence profiles: the more pathogenic R. africae and R. parkeri replicated more efficiently, while the non-pathogenic R. montanensis failed to replicate. Proteomic profiling uncovered both shared and species-specific host responses, with a marked induction of proteins associated with type I interferon (IFN-I) signaling, particularly in response to R. africae and R. parkeri. Proteins typically involved in antiviral immunity, such as RIG-I, ISG15, IFITs, MX1, MX2, and OAS family members, were significantly accumulated, suggesting activation of cytosolic nucleic acid sensing pathways upon infection with pathogenic rickettsiae. ISGylation levels, however, remained low and varied depending on the species, pointing to complex regulatory mechanisms. Comparison with previous quantitative proteomics data in THP-1 macrophages revealed a conserved interferon signature, while also highlighting cell-type-specific responses. Overall, our findings demonstrate that endothelial cells activate innate immune pathways typically associated with antiviral defense upon Rickettsia infection. These immune signatures may serve as potential indicators of pathogenic potential and provide a foundation for identifying biomarkers and therapeutic targets in rickettsial diseases.

microbiology↗

bioRxiv2021

Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages

OBJECTIVEA key event in atherogenesis is the formation of lipid-loaded macrophages, lipidotic cells, which exhibit irreversible accumulation of undigested modified low-density lipoproteins in lysosomes. This event culminates with the loss of cell homeostasis, inflammation and cell death. In this study we propose to identify the chemical etiological factors and understanding the molecular and cellular mechanisms responsible for the impairment of lysosome function in macrophages. APPROACH AND RESULTSUsing shotgun lipidomics we have discovered that a family of oxidized lipids (cholesteryl hemiesters, ChE), end products of oxidation of polyunsaturated cholesteryl esters, occurs at higher concentrations in the plasma of two cohorts of cardiovascular disease patients than in the plasma of a control cohort. Macrophages exposed to the most prevalent ChE, cholesteryl hemiazelate (ChA) exhibit lysosome enlargement, peripheral lysosomal positioning, lysosome dysfunction and lipidosis which are irreversible. The transcriptomic profile of macrophages exposed to ChA indicates that the lysosome pathway is deeply affected and is well correlated with lysosome phenotypic and functional changes. Interestingly, the dysfunctional peripheral lysosomes are more prone to fuse with the plasma membrane, secreting their undigested luminal content into the extracellular milieu with potential consequences to the pathology. CONCLUSIONWe identify ChA not only as one of the molecules involved in the etiology of irreversible lysosome dysfunction culminating with lipidosis but also as a promoter of exocytosis of the dysfunctional lysosomes. The latter event is a new mechanism that may be important in the pathogenesis of atherosclerosis.

cell biology↗

bioRxiv2018

A generic normalization method for proper quantification in untargeted proteomics screening

The label-free quantitative mass spectrometry methods, in particular, the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using other methods). Therefore, the proposed strategy is able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids analyses) or by enrichment approaches (such as immunopurifications). Moreover, this approach corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.

biochemistry↗