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Biology subjects

Gomes, S.

Publications and source records attributed to Gomes, S..

7 recordsLinked to original sources

Serum albumin-fused interleukin-10 prevents neuroinflammation by promoting immunoregulation in the secondary lymphoid organs and limiting immune cell infiltration in the spinal cord

Interleukin-10 (IL-10) is a potent immunoregulatory cytokine that suppresses pro-inflammatory cytokine production, reduces antigen presentation by myeloid cells, promotes M2 macrophage polarization, and inhibits T cell activation. Despite these well-established immunoregulatory functions, efforts to harness recombinant IL-10 therapeutically have been limited by its short plasma half-life and poor retention in the secondary lymphoid organs (SLOs), key sites of autoreactive T cell priming in autoimmune disease. Previously, we engineered a fusion of serum albumin and IL-10 (SA-IL-10) with extended half-life and enhanced exposure in the SLOs following intravenous administration. Here, we integrate human transcriptomic analyses and a murine model of neuroinflammation, experimental autoimmune encephalomyelitis (EAE), to investigate how sustained IL-10 exposure in the SLOs modulates immune responses under inflammatory conditions. Human single-cell RNA sequencing analyses revealed reduced IL-10 expression alongside increased IL-10 receptor expression across multiple immune cell populations in treatment-naive patients with multiple sclerosis (MS), motivating the investigation of IL-10-based immunomodulatory strategies. Prophylactic SA-IL-10 administration prevented the development and progression of EAE with superior efficacy to wild type IL-10 and comparable protection to fingolimod, an FDA-approved MS therapy. Immunophenotyping of the SLOs revealed that SA-IL-10 suppressed pathogenic, antigen-specific ROR{gamma}t+ Foxp3- TH17 T cells, CD86+ M1-like macrophages, CD86+ dendritic cells, and pro-inflammatory cytokine production, while expanding immunoregulatory CD206+ M2-like macrophages and increasing the frequency of multiple checkpoint markers (CTLA-4, PD-1, TIGIT, ICOS) on GATA3+ Foxp3- TH2 cells. Despite the absence of direct central nervous system targeting, SA-IL-10 treatment also reduced the infiltration of macrophages, dendritic cells, and CD4+ T cells into the spinal cord. Repeated SA-IL-10 administration was well tolerated, as treated EAE mice gained significantly more body weight over the course of treatment compared to PBS- and WT IL-10-treated controls, and exhibited plasma biochemistry parameters comparable to control animals at study endpoint. Together, these findings demonstrate that increasing IL-10 exposure in the SLOs suppresses neuroinflammation by promoting immunoregulation.

immunology↗

Robust analytical methods for bis(monoacylglycero)phosphate profiling in health and disease

Bis(monoacylglycero)phosphate (BMP), a distinct anionic phospholipid predominantly found in late endosomes and lysosomes, plays a pivotal role in supporting lysosomal functions and maintaining metabolic homeostasis. Its impaired function is associated with an array of disorders, notably neurodegenerative diseases. However, the identification and quantitation of BMP remains difficult due to its structural similarity to isomer phosphatidylglycerol (PG), thus necessitating robust analytical methods for accurate and reliable BMP profiling. In this study, we present comprehensive liquid chromatography - tandem mass spectrometry (MS2) methodologies for the precise and systematic analysis of BMP species in biological samples. We detail LC/MS methods for both an untargeted Orbitrap mass spectrometer and a targeted triple quadrupole (QQQ) mass spectrometer. We utilize differences in polarity and structure to annotate BMPs and PGs based on retention time and positive mode MS2 fragmentation patterns, respectively. Further, we propose a new approach for overcoming common challenges in BMP profiling by leveraging the newly discovered biochemical function of CLN5 as the BMP synthase. Since genetic ablation of CLN5 leads to specific depletion of BMPs but not PGs, we use lipid extracts from CLN5 knockout (KO) and wild-type (WT) cells as biological standards to confidently annotate BMPs as targets with significantly low BMP Identification Index (BMPII), defined as BMPII = CLN5 KO / WT. We additionally propose the BMP enrichment score (BMPES) as a secondary validation metric, defined as lysosomal abundance of BMP / whole-cell abundance. Altogether, this approach constitutes a robust method for BMP profiling and annotation, furthering research into health and disease.

biochemistry↗

Tagless LysoIP method for molecular profiling of lysosomal content in clinical samples

Lysosomes are implicated in a wide spectrum of human diseases including monogenic lysosomal storage disorders (LSDs), age-associated neurodegeneration and cancer. Profiling lysosomal content using tag-based lysosomal immunoprecipitation (LysoTagIP) in cell and animal models allowed major discoveries in the field, however studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the "tagless LysoIP method" to enable rapid enrichment of lysosomes, via immunoprecipitation, using the endogenous integral lysosomal membrane protein TMEM192, directly from clinical samples and human cell lines (e.g. induced Pluripotent Stem Cell (iPSCs) derived neurons). Isolated lysosomes are intact and suitable for subsequent multimodal omics analyses. To validate our approach, we employed the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells (PBMCs) derived from fresh blood from patients with CLN3 disease, a neurodegenerative LSD. Metabolic profiling of isolated lysosomes showed massive accumulation of glycerophosphodiesters (GPDs) in patients lysosomes. Interestingly, a patient with a milder phenotype and genotype displayed lower accumulation of lysosomal GPDs, consistent with their potential role as disease biomarkers. Altogether, the tagless LysoIP provides a framework to study native lysosomes from patient samples, identify novel biomarkers and discover human-relevant disease mechanisms.

cell biology↗

Engineered Flt3L Drives Tolerogenic State to Attenuate Anti-drug Antibody Responses

Immune reactions to protein drugs present substantial challenges to protein replacement for treating congenital diseases and metabolic deficiencies, due to the lack of endogenous tolerance or the protein drugs partial or total non-human origin. We sought to transiently modify the immune environment when the adaptive response to the drug antigen is mounted to lessen future reactions upon continued therapeutic treatment, without modifying the drug itself. Herein, we characterize a recombinant fusion of the cytokine Flt3L to serum albumin and describe a novel pathway of Flt3L-mediated immune regulation. We highlight reduced activation of dendritic cells (DC) as well as an increased frequency of DCs expressing LAP, a TGF-{beta} precursor. These effects in combination with low doses of the exogenous antigen led to less TH2 differentiation. This enabled a tolerance-biasing induction regimen to significantly decrease anti-drug antibodies upon repeated exposure to a clinically used, immunogenic fungal enzyme, rasburicase. This induction regimen reduced the Tfh compartment and increased Tfh cells expressing Foxp3 and PD-L1, suggesting a regulatory response. Overall, we introduce the use of a Flt3L variant as an induction therapeutic to modulate the innate immune response, thereby attenuating the adaptive reaction to antigenic protein drugs and addressing an unmet clinical need.

bioengineering↗

Genetic diversity of the pathogenic banana Fusarium wilt in northern Viet Nam

Fusarium is one of the most important fungal genera of plant pathogens that affect the cultivation of a wide range of crops. Agricultural losses caused by Fusarium oxysporum f. sp. cubense (Foc) have a direct effect on the income, subsistence and nourishment of thousands of smallholder farmers worldwide. In addition, also commercial growers are strongly affected. For Viet Nam, predictions on the impact of Foc for the future are dramatic with an estimated loss in banana production area of 8% within the next 5 years and up to 71% within the next 25 years. In the current study we applied a combined morphological - molecular approach to assess the taxonomic identity and phylogenetic position of the different Foc isolates that were collected in northern Viet Nam. In addition, we aim to estimate the proportion of the different Fusarium races that are infecting bananas in northern Viet Nam. The morphology of the isolates was investigated by growing the collected Fusarium isolates on four distinct nutritious media (PDA, SNA, CLA, and OMA). Molecular phylogenetic relationships were inferred by sequencing partial rpb1, rpb2 and tef1a genes and adding the obtained sequences into a large phylogenetic framework. The present study showed that Foc Race 1 is the most common strain in northern Viet Nam, causing 74% of all the infections. A more in-depth molecular characterization shows that of the Foc Race 1 infections, 92% are caused by Fusarium tardichlamydosporum and 8% by F. duoseptatum. Compared to Foc Race 1, Foc TR4 (represented by F. odoratissimum) account for only 10.5% of the Fusarium wilting in northern Viet Nam demonstrating that Foc TR4 is not yet a dominant strain in the region. Foc Race 2 infections of Vietnamese bananas also account for 10.5% of the Fusarium wilting in northern Viet Nam. One of the isolates cultured from diseased bananas collected in northern Viet Nam was phylogenetically not positioned within the F. oxysporum species complex (FOSC), but in contrast fell within the Fusarium fujikuroi species complex (FFSC). As a result, it is possible that a new pathogen for bananas has been found. Besides being present on several ABB Tay banana, Foc Race 1 was also found as pathogen on wild Musa lutea, showing the importance of wild bananas as possible sink for Foc.

evolutionary biology↗

Plant cheaters preferentially target arbuscular mycorrhizal fungi that are highly connected to mutualistic plants

O_LIHow antagonists - mycoheterotrophic plants that obtain carbon and soil nutrients from fungi - are integrated in the usually mutualistic arbuscular mycorrhizal networks is unknown. Here, we compare mutualistic and antagonistic plant associations with arbuscular mycorrhizal fungi and use network analysis to investigate fungal association preferences in the tripartite network. C_LIO_LIWe sequenced root tips from mutualistic and antagonistic plants in a tropical forest to assemble the combined tripartite network between mutualistic plants, mycorrhizal fungi, and antagonistic plants. We compared the fungal ecological similarity between mutualistic and antagonist networks, and searched for modules (an antagonistic and a mutualistic plant interacting with the same pair of fungi) to investigate whether pairs of fungi simultaneously linked to plant species from each interaction type were overrepresented throughout the network. C_LIO_LIAntagonistic plants interacted with approximately half the fungi detected in mutualistic plants. Antagonists were indirectly linked to any of the detected mutualistic plants, and fungal pairwise ecological distances were correlated in both network types. Moreover, pairs of fungi sharing the same antagonistic and mutualistic plant species occurred more often than expected by chance. C_LIO_LIWe hypothesize that the maintenance of antagonistic interactions is maximized by targeting well-linked mutualistic fungi, thereby minimizing the risk of carbon supply shortages. C_LI

ecology↗

FungalRoot: Global online database of plant mycorrhizal associations

O_LIThe urgent need to better understand profound impacts of mycorrhizas on functioning of terrestrial ecosystems, along with recent debates on resolving plant mycorrhizal associations, indicate that there is a great need for a comprehensive data of plant mycorrhizal associations able to support testing of ecological, biogeographic and phylogenetic hypotheses.\nC_LIO_LIHere present a database, FungalRoot, which summarizes publicly available data on plant mycorrhizal type and intensity of root colonization by mycorrhizal fungi, accompanied by rich meta-data. We collected and digitized data on plant mycorrhizal colonization intensity published until April 2019 in 9 globally most important languages. The data were assessed for quality and updated for plant taxonomy.\nC_LIO_LIThe FungalRoot database contains 36,303 species by site observations for 14,870 plant species, tripling the previously available amount in any compilation. The great majority of ectomycorrhizal and ericod mycorrhizal plants are trees and shrubs, 92% and 85% respectively. The majority of arbuscular mycorrhizal and of non-mycorrhizal plant species are herbaceous (50% and 70%).\nC_LIO_LIBesides acting as a compilation of referenced observations, our publicly available database provides a recommendation list of plant mycorrhizal status for ecological and evolutionary analyses to promote research on the links between above- and belowground biodiversity and functioning of terrestrial ecosystems.\nC_LI

ecology↗