---
title: "RNA-seq Time Course Identifies Late B Cell Infiltration in Cerebral Toxoplasmosis"
id: "frontiers-in-immunology-17-temporal-rna-seq-analysis-reveals-previously-uncharacterized-b-cell"
canonical_url: "https://medichelpline.com/clinical-feed/frontiers-in-immunology-17-temporal-rna-seq-analysis-reveals-previously-uncharacterized-b-cell"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "Frontiers in Immunology"
source_url: "https://www.frontiersin.org/articles/10.3389/fimmu.2026.1885764"
published_at: "2026-10-12T00:00:00.000Z"
evidence_level: "Journal Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# RNA-seq Time Course Identifies Late B Cell Infiltration in Cerebral Toxoplasmosis
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/frontiers-in-immunology-17-temporal-rna-seq-analysis-reveals-previously-uncharacterized-b-cell
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** Frontiers in Immunology
- **Source URL:** [Original Journal Publication](https://www.frontiersin.org/articles/10.3389/fimmu.2026.1885764)
- **Published At:** 2026-10-12T00:00:00.000Z
- **Evidence Rating:** Journal Feed
## Executive GIST (TL;DR)
- The article title reports a temporal **RNA-seq** analysis that identified previously uncharacterized **B cell** infiltration during late chronic **cerebral toxoplasmosis**. Short and direct: RNA sequencing over time was used and a new cellular signature was observed. - The source text available to this rewrite does not include experimental details. The authors’ specific sequencing protocol, time points sampled, animal or human cohort characteristics, and analytic pipelines were not reported in the provided source material. - The title implies a longitudinal design (temporal), which suggests sequential sampling or staged observations. The exact temporal intervals and number of samples were not provided by the source. - The finding described centers on late chronic disease. The source did not supply definitions for “late” or “chronic” stages, so clinical or temporal thresholds remain unspecified. - No quantitative results, statistical measures, or gene lists were present in the supplied content. The source did not report effect sizes, p-values, or differentially expressed genes in the excerpt provided. - The title signals a novel or previously uncharacterized immune cell population (B cells) within the brain during chronic infection; the source did not report immunohistochemistry, flow cytometry, or functional validation methods in the text available here. - The available material lacks stated implications, mechanistic experiments, or translational recommendations. The source did not provide downstream experiments linking B cell infiltration to neuropathology, protection, or therapy. - Key unanswered questions remain: which B cell subtypes infiltrate, whether they are antigen-specific, how they arrive in the CNS, and whether their presence alters parasite control or host damage. The source did not report data addressing these topics. - Readers should consult the full Frontiers in Immunology article for methods, sample sizes, gene-level results, and validation; those elements were not present in the provided source content. - In short: the title communicates a time-resolved transcriptional study that detected B cell infiltration late in chronic cerebral toxoplasmosis, but the supplied text omitted all supporting experimental and analytic detail required for clinical interpretation.
## Clinical Analysis & Structured Key Points
Frontiers | Temporal RNA-seq analysis reveals previously uncharacterized B cell infiltration during late chronic cerebral toxoplasmosis ORIGINAL RESEARCH article Front. Immunol. , 12 October 2026 Sec. Parasite Immunology Volume 17 - 2026 | https://doi.org/10.3389/fimmu.2026.1885764 Published in Frontiers in Immunology Parasite Immunology 7 impact factor 11.3 citescore Part of a Research Topic Inflammation and immune modulation induced by parasitic infection 53k views 29 articles Editor & Reviewers Edited by S A Silvia Amaral Gonçalves Da-Silva Reviewed by P M Priscilla Miranda Henriques M H Mohammad Hossein Banabazi Outline Figures and Tables Figure 1 View in article Figure 2 View in article Figure 3 View in article ORIGINAL RESEARCH article Front. Immunol. , 12 October 2026 Sec. Parasite Immunology Volume 17 - 2026 | https://doi.org/10.3389/fimmu.2026.1885764 Temporal RNA-seq analysis reveals previously uncharacterized B cell infiltration during late chronic cerebral toxoplasmosis G T Gabriel Targino 1 I A Iasmin Aparecida Cunha Araújo 1 A L Anna Laura de Jesus Gomes 1 D E Duarte Eduardo Pereira 1 V M Valdemir Moreira 1 P C Paulo Czarnewski 2 † * N M Neide Maria Silva 1 † * 1. Laboratory of Immunopathology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil 2. Precisium AI, Solna, Sweden Article metrics View details Abstract Chronic toxoplasmosis begins when tachyzoites cross the blood–brain barrier and enter the Central Nervous System (CNS). There, they differentiate into bradyzoites, which persist in tissue cysts. Here, we investigate changes in host gene expression in the mouse brain by RNA sequencing at different time points during chronic toxoplasmosis. We show a conserved gene expression pattern caused by the infection, primarily associated with cytotoxic immune responses against the parasite and neuronal degeneration, regardless of the time point. Surprisingly, we observed that genes associated with B cell function continuously increased over time, whilst cytotoxic responses decreased. Immunoglobulin gene expression and IgA staining showed that B cells were absent from healthy brains. Following infection, they accumulated near penetrating vessels and infiltrated the brain parenchyma. Additionally, these plasma cells produced T. gondii -specific IgA. Our results show a previously unrecognized expansion of brain B cells in late chronic toxoplasmosis. Introduction Toxoplasma gondii is a neurotropic pathogen with worldwide distribution. In humans, the estimated global seroprevalence of Toxoplasma gondii infection is 25.7% ( 1 ). In vitro , T. gondii can grow in human astrocytes, neurons ( 2 ), and microglia ( 3 ). Studies of primary mouse brain cultures demonstrated that T. gondii can infect neurons, astrocytes, microglia, and oligodendrocytes ( 4 , 5 ). Mouse in vivo studies showed that T. gondii primarily infects neurons ( 6 ). The interferon-γ-dependent immune responses control the rapid parasite growth in the acute phase of infection. Thus, the parasite disseminates to different tissues and differentiates into semidormant cysts mainly within muscle cells and neurons, where they persist for life in the infected host ( 7 ). Before effective antiretroviral therapy, T. gondii was the most common cause of encephalitis in AIDS patients due to the recrudescence of latent chronic infection ( 8 ). However, it remains a health problem if prophylaxis is not provided to seropositive individuals who experience antiretroviral therapy failure ( 9 ). Toxoplasmic encephalitis can also develop in other immunosuppressive conditions, such as those following organ transplantation or occurring in patients with cancer receiving immunosuppressive therapy ( 10 ). T. gondii triggers innate immunity by inducing IL-12 production by macrophages, dendritic cells, and neutrophils. This promotes NK, CD4, and CD8 T cell activation and interferon gamma (IFN-γ) production, which restrict parasite growth ( 11 ). Adaptive immunity to Toxoplasma depends on both CD4 and CD8 T cells, with the latter playing a dominant role in controlling chronic infection. Although CD8 T cells play an important effector role in controlling chronic infection, their maintenance depends on help from CD4 T cells ( 12 ). Related to B cells, their protective role has not been extensively studied; however, studies utilizing B cell-deficient mice have shown that antibodies may function protectively in vivo by blocking tachyzoite infection of host cells ( 13 ). Several meta-analyses have linked T. gondii infection with cognitive and neuropsychiatric disorders, including bipolar disorder, schizophrenia ( 14 ), obsessive-compulsive disorder, epilepsy ( 15 ), and Alzheimer’s disease ( 16 ). However, these associations remain controversial. In mice, chronic T. gondii infection also induces behavioral alterations ( 17 ). Nevertheless, findings from both human and mouse studies remain controversial, with some studies showing correlations between neuropsychiatric disorders and T. gondii infection and others showing no such correlations ( 18 ). Thus, the interaction between T. gondii and the central nervous system, and the consequences of this interaction, are not completely understood. Genome-wide transcriptomic profiling provides an unbiased approach to studying normal and pathological conditions. Previous studies have described the transcriptomic changes in the brain during T. gondii infection ( 19 – 21 ), primarily focusing on comparisons against healthy controls or contrasting acute versus chronic infection. In the present study, we performed a detailed longitudinal analysis of differentially expressed genes in the brains of chronically T. gondii -infected mice compared with uninfected mice. We describe the temporal changes in gene expression that occur during chronification of infection, highlighting the unexpected detection of immunoglobulin transcripts in late chronic infection. Validation experiments confirmed the recruitment of IgA+ B cells into CNS tissue during chronic toxoplasmosis. Results Exploration of cerebral toxoplasmosis by RNA sequencing To characterize the temporal dynamics of gene expression in the brain during chronic infection without bias, we first analyzed a public dataset, GSE117504 ( 22 ) ( Figure 1a ). It encompasses a comprehensive collection of transcriptomic data derived from experimental cerebral toxoplasmosis, providing a valuable resource for understanding the intricate molecular mechanisms underpinning this complex disease. It comprises a diverse array of samples representing various time points during infection. Notably, the dataset exhibited robust data quality, as evidenced by over 20 million reads per sample ( Supplementary Figure S1A ) and consistently stable relative log expression (RLE) values after count normalization ( Supplementary Figure S1B ). These results indicate that GSE117504 has high overall sample quality, with no strong batch effects detected. Figure 1 Analysis of bulk RNA sequencing data of chronic cerebral toxoplasmosis. The RNA-seq dataset from GSE117504 ( 22 ) was generated using the CBA/J mouse strain (three mice per group). (A) Schematic illustration of the experimental design used for collecting brain samples from infected and uninfected mice under chronic toxoplasmosis. Time points are indicated with two to three mice per group. (B) Principal component analysis of all samples, highlighting the separation of infected samples (squares) from controls (circles) and the infection duration (color gradient). (C) Volcano plot for the conserved signature under infection across all time points, showing significantly up- (red) and downregulated genes (blue). Genes with a −log10( p -value) above 2 and log2(FC) above ± 1 (dashed lines) are considered significant. A few selected genes are highlighted. (D) Functional gene set analysis for up- and downregulated genes using Gene Ontology. Together, these analyses show that chronic T. gondii infection induces a robust and persistent immune transcriptional program while simultaneously suppressing genes associated with neuronal function. Terms with a −log10( p -value) above 2 (dashed lines) are considered significant. Next, we computed gene-wise variance on the normalized counts to identify genes, without bias, whose expression may vary over time and with infection status ( Supplementary Figure S1C ). The top 500 variable genes were selected for unsupervised dimensionality reduction via principal component analysis (PCA) for visualization and data exploration ( Figure 1B ). This analysis revealed a distinct segregation of samples primarily driven by infection status along the first principal component (PC1), which accounted for over 80% of all variation in the dataset. In contrast, the duration of infection was the main driver of separation along the second principal component (PC2), with about 5% of the variance explained ( Figure 1B ). This compelling separation strongly implies the pivotal role played by infection in shaping the intricate molecular landscape associated with cerebral toxoplasmosis and suggests that the chronic infection is not homogeneous. To further dissect the effect of infection and distinguish it from the effect of infection duration, we employed a generalized linear model (GLM) with edgeR ( 23 ), a flexible statistical method that allows the effects of infection and time to be separated. In other words, GLMs consider the gene expression of any given gene to be a combination of the effects of the variables (in this case, infection and time). We modeled the gene expression as the complete interaction between the infection status and the time points, including all interactions of the infection at different days of infection: With this approach, we identified more than 2,500 differentially expressed genes (DEGs) in infected brains versus uninfected controls, regardless of the time of infection ( Figure 1C ). This large number of infection-induced DEGs is consistent with the PCA results, in which infection contributed the most to PC1. The upregulated gene cluster was notably associated with pathways involved in cytokine signaling ( Il12b , Tnf , Il18rap ), type 1 immune response ( Nkg7 , Oas1a , Isg15 , Cd8a/b , Stat1 , Irf7 ), response to microbial stimuli ( Reg3g , Cd74 , Tnf ), and cell chemotaxis ( Cxcl9 , Cxcl11 , Ccr2 , Ccl12 , Cxcr3 ), providing insight into the complex host immune response to cerebral toxoplasmosis ( Figure 1D ). Conversely, the downregulated genes were associated with pathways governing synaptic structure ( Cbln3 , Cbln1 ), chemical synaptic transmission ( Glra1 , Gabra6 , Mpz , Chrna6 , Cbln1 ), and neuronal development ( Foxa1 , Neurod4 , Lhx1 , Lhx5 ), suggesting potential disruptions in neuronal signaling pathways induced by the infection ( Figure 1D ). The complete list of differentially expressed genes and pathway enrichment analyses is provided in Supplementary Tables S1 , S2 . These findings provide insight into the complex interplay between the host immune response and neurophysiological alterations in the context of cerebral toxoplasmosis. B cell-related genes are enriched in late chronic cerebral toxoplasmosis Having identified the top DEGs driven by T. gondii infection using the GLM, we next investigated the heterogeneity of chronic infection, as reflected in PC2 previously described ( Figure 1B ). We therefore computed differential expression across time points, including samples from early chronic infection (days 21 and 28) and late chronic infection (days 90 and 180). Compared with day 21, when the first tachyzoites arrive and start colonizing the brain ( 24 ), samples from day 28 showed only a handful of genes differentially expressed (11 upregulated and three downregulated) ( Figure 2A ). Surprisingly, samples from days 90 and 180 of infection showed much larger numbers of DEGs, including both up- and downregulated genes ( Figure 2A ). We also noted that many of the genes identified across the time points were significantly dysregulated, although to different extents. These include genes related to reduced mitotic spindle activity ( Cdc20 , Cenpf , Nuf2 , Bub1b , Ttk ) and diminished T cell immunity ( Trbc1 , Nkg7 , Cd3g , Cd3e , Cd3d ) and NK cytotoxicity ( Il21 , Ncr1 , Klrk1 , Klrc2 , Klrd1 , Klrc1 ) ( Supplementary Figure S2 ). These results highlight that, after the early chronification phase (around days 21 to 28), the abundance of T cells and other immune cells decreased. This pattern is in line with the interconversion of tachyzoites to bradyzoites and parasite evasion and immune response ( 25 ) and with the regulation of early mitotic activity during bradyzoite differentiation ( 26 ). Figure 2 B cell dynamics in the brain during chronic T. gondii infection. The RNA-seq dataset from GSE117504 ( 22 ) was generated using the CBA/J mouse strain (three mice per group). (A) Volcano plots for genes that are differentially expressed at each time point, compared with mice at day 21 of infection. Selected up- and downregulated genes are shown. (B) Heatmap for all genes temporally affected by the infection, which were clustered into seven distinct gene modules (m1–m7). The color represents the scaled gene expression across samples ( Z -score). (C) Temporal expression trend and gene set analysis for selected gene modules m3 and m5. Each dot represents the normalized expression of a gene within the gene module for each sample group. (D) Immunohistochemistry staining for IgA in the mouse brain at 30 days of infection (BALB/c strain). These results identify a progressive enrichment of B cell-associated genes during late chronic infection and experimentally confirm the presence of IgA+ B cells within the infected brain parenchyma. The region delimited by the dashed gray line represents the choroid plexus. Scale bars represent 200, 40, and 5 µm. Boxplots represent the fifth, 25th, 50th, 75th, and 95th quantiles, respectively. Among genes upregulated on days 90 and 180 of infection, genes associated with B cell function were identified, including B-cell differentiation ( Mzb1 , Cd79a/b ), class-switched antibody chains ( Igha , Ighe , Ighga , Ighg2c , Jchain ), and several B cell receptor genes ( Igkv , Ighv , Igkc , Ighc ) ( Figures 2A, B ). These findings are particularly surprising because, to the best of our knowledge, B cell expansion or migration to the brain during T. gondii infection appears to be a previously unrecognized phenomenon. Similar phenomena have been reported in other pathologies, particularly when Cxrc3 and Cxcl9 are produced in the brain, promoting B cell diapedesis ( 27 ). In fact, both of these molecules were among the top DEGs found in chronically infected brains ( Figure 1C ). B cells migrate to the brain in late chronic infection We next decided to investigate further whether the findings above could be driven purely by natural aging of the brain or by the maturation of the immune response during T. gondii infection. To this end, we selected all genes differentially expressed at any given time point and clustered them into temporally coherent gene modules ( Figures 2B, C ; Supplementary Figure S3 ). Among these modules, three stood out: a module enriched for genes involved in the T cell immune response (m6), a module enriched for B cell signatures and activation (m5), and a module enriched for the control of cell division (m3) ( Figure 2C ). Importantly, only module m2 showed an expression pattern enriched in 180-day-old mice (regardless of infection status), suggesting a gene network associated with senescence/maturation. Conversely, modules m1 and m7 showed decreased or nearly absent expression only at day 180, regardless of infection status. However, none of these modules (m1, m2, and m7) showed significant pathway enrichment ( Supplementary Figure S3 ). Module m4 also showed a gene expression trend that decreased over time regardless of infection status, with genes associated with cranial skeletal development and neuronal maturation. These findings are in line with previous studies showing that molecular development in the brain ( 28 ) and structural ( 29 ) development peak at around 30–60 days of age and decline thereafter. The B cell module m5 had no genes detected in uninfected mice, suggesting that B cell expansion is a phenomenon triggered by inflammation ( Figure 2C ). Thus, we sought to directly verify whether IgA+ B cells are indeed present in the tissue as early as day 30 of infection, a time point commonly used for the study of chronic toxoplasmosis. In fact, staining for IgA+ cells in the brain of infected mice at 30 d.p.i. showed that B cells were found primarily near the vessels of the pia mater ( Figure 2D ) but could also infiltrate the parenchyma ( Figure 2D ). Quantification of IgA+ cells in the healthy brain showed little to no detection of B cells ( Figure 2D ), further corroborating the RNA-seq results regarding the near absence of B cells in the healthy brain. We observed that IgA+ cells were located throughout the sections and were not grouped into inflammatory foci or tertiary lymphoid structures, consistent with our hypothesis that IgA+ cells migrate to the tissue rather than arise from local expansion of tissue-resident B cells. It is plausible that B cells at day 180 might be transcriptionally distinct from those found at day 30, but this distinction could be further characterized in future studies using single-cell sequencing. In summary, we showed through quantification of B cell transcripts in an RNA-seq dataset and direct detection of IgA+ cells in the brain that B cells are nearly absent from the healthy brain and can infiltrate the cerebral parenchyma during infection. These IgA-positive cells are experts in producing specific- T. gondii antibodies To get an idea of whether this IgA is protective against infection, we evaluated the specificity and levels of IgA in the brain and systemically in two mouse strains, susceptible C57BL/6 and resistant BALB/c, to T. gondii infection. Female and male C57BL/6 mice showed severe inflammation in the brain, which was characterized by vascular cuffing, inflammatory foci in the parenchyma, and inflammatory cell infiltration in the meninges, while the lesions in the brain of BALB/c mice were milder ( Figure 3A ). Both mouse strains showed IgA+ cells in the parenchyma ( Figure 3B ), and these cells produced T. gondii -specific IgA, which was higher in susceptible mice than in resistant mice, although the difference did not reach statistical significance ( Figure 3C ). Interestingly, both mouse strains produced specific IgA systematically, whose levels showed an opposite pattern to those observed in the brain ( Figure 3D ). These data suggest that brain-specific IgA does not appear to protect the brain of C57BL/6 mice against infection and inflammation. Figure 3 Both infected C57BL/6 and BALB/c mouse strains showed IgA+ cells in the brain and specific IgA in serum samples following infection. Animals were infected by the intraperitoneal route, and on day 30 of infection, the brain and serum samples were collected, and specific IgA was analyzed by ELISA. (A) Inflammatory score and photomicrographs of infected brains (H&E staining). Inflammatory foci (arrowheads), vascular cuffing (black arrows), inflammatory cells in the meninges (large arrow), and a cyst-like structure (white arrow) were observed in the parenchyma of infected animals. (B) IgA+ cells detected by immunostaining. (C) T. gondii -specific IgA antibodies in the brain homogenate and (D) serum samples detected by ELISA. Although both mouse strains exhibited IgA+ cells in the brain, susceptible C57BL/6 mice developed more severe neuropathology, indicating that the presence of IgA+ cells alone is insufficient to prevent brain inflammation. Data are representative of one of two independent experiments with five mice per gro
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