Biology subjects

Andrade, M. S.

Publications and source records attributed to Andrade, M. S..

4 recordsLinked to original sources

bioRxiv2026

High-dimensional spatial proteomics and novel machine learning pipeline identifies disease specific renal damage states

Lupus nephritis (LuN) and renal allograft rejection (RAR) manifest inflammation and fibrosis that ultimately lead to kidney failure. To quantitatively assess spatial injury patterns, we collected high dimensional spatial proteomics data from 23 LuN, 33 RAR, and 8 kidney control (KC) biopsies. We developed a computational pipeline to segment and classify tubules, capillaries, and glomeruli in whole-slide images using three trained neural networks (Renal Damage diagnosis, RDDx). RDDx achieved high accuracy and generalizability, reliably identifying small capillaries and differentiating tubular and vascular inflammation in kidney tissues. Both LuN and RAR showed reduced tubular and capillary areas with expanded interstitial space. LuN displayed patchy clusters of stressed and inflamed tubules, whereas RAR exhibited diffuse injury. Within RAR, T cell-mediated rejection (TCMR) showed intense tubulitis while antibody-mediated rejection (ABMR) featured proliferating and inflamed capillaries near atrophic tubules. RDDx quantitative metric outputs correlated with histopathological scores, highlighting their reproducibility and clinical relevance. Stressed tubules in mildly inflamed LuN biopsies suggested they were a sensitive injury marker, while proliferating capillaries revealed microvascular remodeling in ABMR. These findings indicated RDDx can identify and quantify damage mechanisms specific to each renal disease thus facilitating future mechanistic studies and therapeutic target discovery.

immunology↗

bioRxiv2025

Comparative ScRNA-Seq Profiling of Antigen-Specific CD4+ T cells in Semi-Allogeneic Transplantation and Pregnancy Reveals Intersecting Signatures of Rejection and Tolerance

Transplantation of allogeneic organs requires lifelong immunosuppression to prevent rejection. Prior sensitization and resultant memory T cells are barriers to achieving successful transplant tolerance. In reproductive immunology by contrast, pregnancy represents a spontaneous model of tolerance where the semi-allogeneic fetus evades rejection even in multiparous or rejection-sensitized mothers. CD8+ T cell phenotypes of tolerance and rejection have been previously reported in transplant and pregnancy, but the transcriptional states of donor and fetus-specific CD4+ T cells remain poorly defined. Here, we performed Single-cell RNA-sequencing on endogenous, antigen-specific CD4+ T cells across models of allogeneic heart transplants and naive or paternal skin-sensitized pregnancy. We identified expanded T follicular helper (Tfh) and non-follicular effectors in transplant rejection absent in tolerance. Naive pregnancy resulted in a modest expansion of effector clusters with transcriptional quiescence that mirrored virgin mice. Successful sensitized pregnancy resulted in expanded Tfh clusters consistent with increased fetal-specific antibodies and limited non-Tfh effector responses. Most striking were the extensive changes imposed on donor-specific Foxp3pos regulatory T cells (Tregs) resulting in the co-clustering together with Foxp3neg T conventional cells (Tconvs) in transplant tolerance and the emergence of a Foxp3neg Type I Regulatory cluster observed in pregnancy of sensitized dams. Finally, we showed that these transcriptomes were relevant and enriched in human datasets of health and disease respectively. Thus, the context-dependent signatures of antigen-specific CD4+ T cells provide new insights into their divergent responses to allogeneic conflict at the intersection of transplant and reproductive immunology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/663404v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1b30a86org.highwire.dtl.DTLVardef@17820cforg.highwire.dtl.DTLVardef@1b1fbeaorg.highwire.dtl.DTLVardef@11ff17_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Fast surveillance response and genome sequencing reveals the circulation of a new Yellow Fever Virus sublineage in 2021, in Minas Gerais, Brazil

Yellow fever virus (YFV) exhibits a sylvatic cycle of transmission involving wild mosquitoes and non-human primates (NHP). In Brazil, YFV is endemic in the Amazon region, from where waves of epidemic expansion towards other Brazilian states eventually occur. During such waves, the virus usually follows the route from North to the Central-West and Southeast Brazilian regions. Amidst these journeys, outbreaks of Yellow Fever (YF) in NHPs, with spillovers to humans have been observed. In the present work, we describe a surveillance effort encompassing the technology of smartphone applications and the coordinated action of several research institutions and health services that succeeded in the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021, followed by genome sequencing in an interval of only ten days. Samples from two NHPs (one of the species Alouatta caraya in the municipality of Icarai de Minas and the other of the species Callithrix penicillata in the municipality of Ubai) were collected and the presence of YFV was confirmed by RT-qPCR. We generated three near-complete by Nanopore sequencer MinION. Phylogenetic analysis revealed that all viral genomes recovered are equal and related to lineage South America 1, clustering with a genome detected in the Amazon region (Para state) in 2017. These findings reveal the occurrence of a new wave of viral expansion in MG, six years after the beginning of the major outbreak in the state, between 2015-2018. No human cases were reported to date, showing the importance of coordinated work between local surveillance based on available technologies and support laboratories to ensure a quick response and implementation of contingency measures towards avoiding the occurrence of YF cases in humans.

molecular biology↗

bioRxiv2019

Direct visualization of membrane-spanning pores formed by a Leishmania amazonensis pore-forming cytolysin, as probed by atomic force microscopy

We have previously shown that Leishmania amazonensis produces and secretes a cytolysin that lyses membranes of mammalian cells, including macrophages, its host cell. Using the patch-clamp technique, we have previously demonstrated that the mechanism by which this cytolysin rupture macrophages plasma membrane is by pore formation, which lead us to name it leishporin. While we have characterized leishporin in several aspects, its molecular identity is still unknown. Its behavior suggests that leishporin is, or depend on, a protein, but recent results also suggests that a non-protein molecule is involved in cell lysis. Although the patch-clamp has undeniably revealed that L. amazonensis extracts generates pores in macrophages, these structures have not been spotted on cell membranes, which prompted us to several questions: 1) What is the appearance of leishporin-induced pores? Is it similar to that of other described pores? 2) Do these pores physically span lipid bilayers? 4) Are their directly-measured sizes compatible with those previously suggested by patch-clamp? 5) Do these pores fuse with one another, enlarging in size, as suggested by our previous reports? In the present work, we have used two membrane models, erythrocytes and liposomes, to visualize pores induced by the cytolysin on parasite extracts. Leishporin-mediated lysed erythrocytes or liposomes were analyzed by atomic force microscopy (AFM), which allowed us to visualize multiple membrane-spanning pores of variable diameters, ranging from 25 to 230 nm. They do not resemble to protein-formed pores, but rather, to pores made by small molecules such as lipids or peptides, as also visualized by AFM. Our results suggest that the maximum size for individual pores formed by leishporin is around 32 nm, but indicate that they are prone to coalesce, originating large membrane damages that leads to cell collapse, what seems to be a unique property among pore-forming cytolysins.\n\nAuthor summaryOne of the mechanisms whereby a cell can be destroyed is by punching holes into their membranes. Through these holes, due to differences in osmolarity between the outside and the inside of a cell, water flows towards the cytoplasm causing plasma membrane ruptures, which damages or lyses cells. We have previously described in the protozoan parasite Leishmania amazonensis one of such activities. Using an electrophysiology technique, we have found that parasite extracts lyse cells by making pores on their membranes. However these pores were not directly visualized so far. In this report, using a high-resolution-type scanning microscopy, the atomic force microscopy, we showed in red blood cells membranes and artificial lipid membranes (liposomes) the physical aspect of the pores we described earlier. We observed that these pores are circular-shaped structures with variable diameters, ranging from 25 to 230 nm that span the whole thickness of both types of membranes. We verified that L. amazonensis extracts-mediated pores resemble to pores formed by lipids or peptides and not by pores formed by proteins and that they may fuse with one another forming larger holes.

microbiology↗