Biology subjects

Nogueira, F. C. S.

Publications and source records attributed to Nogueira, F. C. S..

9 recordsLinked to original sources

bioRxiv2026

Sample Preparation and Homology-Driven Search Shape the First Holobiont Proteome of the Marine Sponge Viles ophiraphidites (formerly Topsentia ophiraphidites)

Marine sponges are holobionts of host cells, extracellular matrix and dense microbial communities, and most lack reference proteomes. Viles ophiraphidites (formerly Topsentia ophiraphidites), a Brazilian demosponge, is represented in UniProtKB by a single protein. The study had two phases. In phase 1, four sample preparation workflows were compared on two specimens in 42 nLC-MS/MS runs: urea/thiourea in-solution digestion, acetone precipitation, S-Trap and GeLC-MS/MS. Every run was analysed with FragPipe and with a homology-driven pipeline that adds three layers to a rescored Sage search: the proteome of the closest sequenced relative (Halichondria panicea), MS-BLAST style alignment of de novo sequence tags, and error-tolerant interpretation of tag flanks. In phase 2, the selected workflow, S-Trap, was applied to four specimens in 12 runs. Both strategies ranked the workflows identically ({rho} = 0.98). S-Trap gave the deepest and most specimen independent proteome, with about 2,100 protein groups per specimen and an 8% difference between specimens, against 21-39% for the other workflows. The homology-driven layers raised assigned non-contaminant spectra by 21.3% in phase 1 and 26.8% in phase 2. They contributed 1,969 protein groups found only by homology and agreed with the database search on 99.5-99.9% of shared spectra. The proteome comprises 4,294 protein groups: 42% sponge and 58% bacterial or archaeal, the latter dominated by Poribacteria. It includes Nitrospira nitrite oxidoreductase detected in every run. The four phase-2 specimens had a similar composition (Bacteria 51-64% and Porifera 35-48% of peptides, Poribacteria alone 27-33%), whereas the two specimens stored long-term in ethanol at 4{degrees}C, which also differed in collection site and storage history, yielded four to five times less evidence than the frozen ones, even though reduction and alkylation had not been effective in the two frozen specimens. S-Trap combined with homology-driven search is a robust strategy for proteomics of non-model holobionts.

biochemistry↗

bioRxiv2025

Proteome Complexity Scales with Architecture in Human Neural Models

Mass-spectrometry-based proteomics enables high-throughput identification and quantification of proteins, providing molecular insight into neural development and cellular organization. Applying this approach to in vitro systems of increasing architectural complexity, we compared immortalized monolayer cell lines with two tissue-like neural models. Here, we present a comparative proteomic analysis of three human neural models: SH-SY5Y neuroblastoma cells (2D), neurospheres, and cerebral organoids. Protein profiling revealed a stepwise increase in molecular complexity, with enhanced detection of neural-related proteins linked to axon guidance, synapse formation, and GTPase signaling. This trend was most pronounced in tissue-like models, underscoring their suitability for studying neuronal maturation and circuit assembly. Functional enrichment analyses showed progressive acquisition of neurodevelopmental programs, including synaptic vesicle cycling, presynaptic organization, neurotransmitter regulation, and late-stage gliogenesis, accompanied by increased expression of astrocytic and oligodendrocytic markers. Kinase diversity also increased across models, reaching up to 210 regulatory kinases in organoids, many implicated in neural development and degeneration. Gene set enrichment for neurological pathways mirrored this trend, aligning proteomic complexity with disease relevance. Regional brain mapping further indicated that organoids most closely recapitulate the protein architecture of the human CNS. Together, these findings demonstrate that tissue-like neural models provide richer proteomic landscapes that approximate in vivo brain biology and support the application of integrative proteomics in neuroscience and translational research.

neuroscience↗

bioRxiv2025

A fast TMT-based proteomic workflow reveals neural enrichment in neurospheres of hiPSC-derived neural stem cells

Three-dimensional (3D) neural spheroids, or neurospheres, generated from human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs) more accurately recapitulate the microenvironmental cues of neural tissue compared to traditional two-dimensional (2D) monolayers. However, comparative omics-based characterizations of these models remain limited. Here, we present a streamlined and scalable TMT-based quantitative proteomics workflow to contrast the proteomic landscapes of hiPSC-derived NSCs cultured in 2D monolayers versus 3D neurospheres. A total of 1,576 proteins were identified in an unfractionated LC-MS/MS of 68 minutes, with 542 showing significant differential abundance between groups. Neurospheres exhibited enrichment in neural-related pathways, such as synaptic signaling, neurotrophin signaling, cytoskeletal organization and vesicle trafficking, while monolayers enriched for multipotency features, such as general metabolic activity. Cell-type enrichment analyses confirmed increased neuronal identity in neurospheres, including elevated levels of markers associated with neuronal maturation. Our results demonstrate that 3D culture of NSCs induces a proteomic shift toward a more mature neural phenotype. This rapid, multiplexed proteomic approach enables high-content molecular profiling suitable for drug screening and personalized medicine applications. SignificanceThe present work contributes to the molecular and biological understanding of iPSC-derived neurospheres by exploring the proteome of this model. Neurospheres are a culture model of great potential and applicability in neurobiology research and personalized medicine, which still lacks a robust omic characterization. By studying neurospheres, we also work with a 3D culture model generated in vitro, avoiding the use of primary neural cells culture and animal models. Our fast method is relevant to single-cell proteomics, personalized medicine and screening assays.

bioinformatics↗

bioRxiv2024

Evidence that the monoamine oxidase B (MAO-B) plays a central role in the inotropic dysfunction induced by genetic deletion of the Mas-related-G protein-coupled receptor D (MrgD) in mice

The renin-angiotensin system (RAS) plays a critical role in the regulation of the cardiovascular system. The Mas-related G protein receptor member D (MrgD) is the receptor of alamandine, and both are components of the RAS noncanonical arm. Alamandine/MrgD induces vasodilation, anti-inflammatory, anti-fibrotic and anti-oxidative effects. In contrast, Mrgd gene deletion leads to a remarkable dilated cardiomyopathy (DCM) in mice. Here, we aimed to investigate the molecular mechanisms of DCM triggered by the deletion of MrgD in the left ventricle and isolated ventricular cardiomyocytes from 8-12 weeks old mice using phosphoproteomics. Our findings revealed an increased oxidative stress not caused by angiotensin II/AT1 hyperactivation but instead due to the up-regulation of the monoamine oxidase B (MAO-B), leading to a higher catabolism of dopamine and epinephrine in the MrgD-KO cardiac tissues. The oxidative environment induced by MAO-B hyperactivation seems to be the cause of the observed alteration in ionic dynamics - altered Ca2+ transient and Na+/K+-ATPase activity - leading to altered resting membrane potential (RMP) and decreased contraction of MrgD-KO cardiomyocytes. In addition, cardiac Troponin-I phosphorylation, and Titin dephosphorylation seem to contribute to the contractile dysfunction observed in MrgD-KO. The treatment of cardiomyocytes from MrgD-KO mice with the MAO-B inhibitor Pargyline reverted the observed impaired contraction, corroborating the hypothesis that MAO-B hyperactivation is, at least partially, the cause of the failing heart observed in MrgD-KO mouse. The findings reported here provide important insights into the pathogenesis of heart failure and suggest a potential therapeutic target (MrgD activation) for managing failing hearts.

physiology↗

bioRxiv2022

Candidate proteins associated with popping expansion capacity of popcorn

The mechanical resistance of the popcorn pericarp has a positive and direct relationship to its expansion volume. It allows enough time for the endosperm to gelatinize completely before its extravasation. Expansion is a polygenic trait that has been extensively studied. However, no records in the literature indicate proteins that directly affect pericarp thickness and integrity. Therefore, the present work aimed to identify candidate pericarp proteins associated with the expansion capacity of popcorn kernels using the shotgun proteomic approach. The analyses were carried out in the pericarp of two popcorn inbred lines, P11 (expansion volume of 30 mL g-1) and P16 (expansion volume of 14 mL g-1), in two developmental stages (15 and 25 DAP). A total of 803 non-redundant proteins were identified. Most of them were involved in key processes associated with pericarp development and thickening. Two candidate proteins stood out among the differentially abundant proteins. Peroxidase was up-accumulated in P11/25 DAP (high popping expansion) and was 1.498 times more abundant in this inbred line, while xyloglucan endotransglucosylase/hydrolase was more abundant in P16 (low popping expansion) in both developmental stages. Thus, the peroxidase protein increases expandability, whereas xyloglucan endotransglucosylase/hydrolase decreases it, even though its specific role has not been elucidated. These proteins should be further investigated, as they may be used to improve expansion capacity in popcorn breeding programs.

genomics↗

bioRxiv2022

Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants

The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.

biochemistry↗

bioRxiv2022

Interspecies isobaric labeling-based quantitative proteomics reveals protein changes in the ovary of Aedes aegypti co-infected with ZIKV and Wolbachia

Zika is a vector-borne disease caused by an arbovirus (ZIKV) and overwhelmingly transmitted by Ae. aegypti. This disease is linked to adverse fetal outcomes, mostly microcephaly in newborns, and other clinical aspects such as acute febrile illness and neurologic complications, for example, Guillain-Barre syndrome. One of the actual most promising strategies to mitigate arbovirus transmission involves releasing Ae. aegypti mosquitoes carrying the maternally inherited endosymbiont bacteria Wolbachia pipientis. The presence of Wolbachia is associated with a reduced susceptibility to arboviruses and a fitness cost in mosquito life-history traits as fecundity and fertility. However, the mechanisms by which Wolbachia influences metabolic pathways leading to differences in egg production remains poorly known. To investigate the impact of co-infections on the reproductive tract of the mosquito, we applied an isobaric labeling-based quantitative proteomic strategy to investigate the influence of Wolbachia wMel and ZIKV infection in Ae. aegypti ovaries. To the best of our knowledge, this is the most complete proteome of Ae. aegypti ovaries reported so far, with a total of 3,913 proteins identified, also,were able to quantify a total of 1,044 Wolbachia proteins in complex sample tissue of Ae. aegypti ovary.. Furthermore, we discuss proteins and pathways altered in Ae. aegypti during ZIKV infections, Wolbachia infections, co-infection Wolbachia/ZIKV, and compared with no infection, focusing on immune and reproductive aspects of Ae. aegypti. The modified aspects were mostly related to the immune priming enhancement by Wolbachia presence and the modulation of the Juvenile Hormone pathway caused by both microorganisms infection. HighlightsO_LIProteome changes in Ae. aegypti, Wolbachia, and ZIKV interactions C_LIO_LIA great diversity of Wolbachia proteins were quantified in Ae. aegypti ovary C_LIO_LIJuvenile Hormone pathway is modulated by both infections C_LIO_LIWolbachia enhances Ae. aegypti immune priming mechanism C_LIO_LIZIKV unsettles host immune response by reducing antimicrobial peptides production C_LIO_LICoinfection triggers oxidative stress and a lack of vitellogenin precursors C_LI

biochemistry↗

bioRxiv2021

Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres

Axon guidance is required for the establishment of brain circuits. Whether much of the molecular basis of axon guidance is known from animal models, the molecular machinery coordinating axon growth and pathfinding in humans remains to be elucidated. The use of induced pluripotent stem cells (iPSC) from human donors has revolutionized in vitro studies of the human brain. iPSC can be differentiated into neuronal stem cells which can be used to generate neural tissue-like cultures, known as neurospheres, that reproduce, in many aspects, the cell types and molecules present in the brain. Here, we analyzed quantitative changes in the proteome of neurospheres during differentiation. Relative quantification was performed at early time points during differentiation using iTRAQ-based labeling and LC-MS/MS analysis. We identified 6,438 proteins, from which 433 were downregulated and 479 were upregulated during differentiation. We show that human neurospheres have a molecular profile that correlates to the fetal brain. During differentiation, upregulated pathways are related to neuronal development and differentiation, cell adhesion, and axonal guidance whereas cell proliferation pathways were downregulated. We developed a functional assay to check for neurite outgrowth in neurospheres and confirmed that neurite outgrowth potential is increased after 10 days of differentiation and is enhanced by increasing cyclic AMP levels. The proteins identified here represent a resource to monitor neurosphere differentiation and coupled to the neurite outgrowth assay can be used to functionally explore neurological disorders using human neurospheres as a model.

neuroscience↗

bioRxiv2020

Comprehensive quantitative proteome analysis of Aedes aegypti identifies proteins and pathways involved in Wolbachia pipientis and Zika virus interference phenomenon

Zika virus is a global public health emergency due to its association with microcephaly, Guillain-Barre syndrome, neuropathy, and myelitis in children and adults. A total of 87 countries have had evidence of autochthonous mosquito-borne transmission of Zika virus, distributed across four continents, and no antivirus therapy or vaccines are available. Therefore, several strategies have been developed to target the main mosquito vector, Aedes aegypti, to reduce the burden of different arboviruses. Among such strategies, the use of the maternally-inherited endosymbiont Wolbachia pipientis has been applied successfully to reduce virus susceptibility and decrease transmission. However, the mechanisms by which Wolbachia orchestrate resistance to ZIKV infection remain to be elucidated. In this study, we apply isobaric labeling quantitative mass spectrometry-based proteomics to quantify proteins and identify pathways altered during ZIKV infection; Wolbachia infection; co-infection with Wolbachia/ZIKV in the Ae. aegypti heads and salivary glands. We show that Wolbachia regulates proteins involved in ROS production, regulates humoral immune response, and antioxidant production. The reduction of ZIKV polyprotein in the presence of Wolbachia in mosquitoes was determined by mass spectrometry and corroborates the idea that Wolbachia helps to block ZIKV infections in Ae. aegypti. The present study offers a rich resource of data that may help to elucidate mechanisms by which Wolbachia orchestrate resistance to ZIKV infection in Ae. aegypti, and represents a step further on the development of new targeted methods to detect and quantify ZIKV and Wolbachia directly in complex tissues. HighlightsO_LIThe abundance of ZIKV polyprotein is reduced in the presence of Wolbachia C_LIO_LIShotgun proteomics quantifies ZIKV and Wolbachia proteins directly in tissues C_LIO_LIWolbachia regulates proteins involved in ROS production C_LIO_LIWolbachia regulates humoral immune response and antioxidant production C_LIO_LIMetabolism and detoxification processes were associated with mono infections C_LI

biochemistry↗