Biology subjects

Pagel, R.

Publications and source records attributed to Pagel, R..

4 recordsLinked to original sources

bioRxiv2025

Compartment size and proliferation shape the murine T cell receptor repertoire in splenic T- and B cell zones during an immune response

The adaptive immune system recognizes billions of unique antigens using highly variable T cell receptors (TCRs). To what extent TCR features shape the spatial distribution of the TCR repertoire (TCR-R) within lymphoid organs remains unclear. Here, we compared the TCR-R composition in T cell zones (TCZ), B cell zones (BCZ), and germinal centers (GC) of the spleen by analyzing the complementarity-determining region 3 of the beta chain (CDR3{beta}) in microdissected splenic compartments from naive and immunized mice. While we found substantial differences in TCR-R composition between these compartments, these differences largely disappeared once the effects of compartment size and proliferation were accounted for: During steady state, the few T cells found in BCZs strongly resemble random subsets of those found in TCZs. After immunization, expanded clones started appearing in the TCZ at day 3 and later shifted to the BCZ. GCs harbored even further expanded clones that were grouped into clusters with high sequence similarity. TCR-R differences during the immune response were well explained by a Galton-Watson model of T cell proliferation, suggesting that this could be the central factor shaping the observed TCR-R differences. Similarly, while TCR length and closeness to germline appeared to differ between the compartments, our models of random distribution and proliferation explained these differences almost entirely. Hence, our findings suggest that splenic TCR-Rs are shaped predominantly by compartment size and proliferation rates rather than TCR sequence features. This would imply that quantitative assessment of TCR-R dynamics across heterogeneous spatial compartments during an immune response is only possible when these effects are explicitly accounted for.

immunology↗

bioRxiv2022

Machine learning analysis of the T cell receptor repertoire identifies sequence features that predict self-reactivity

The T cell receptor (TCR) determines the specificity and affinity for both foreign and self-peptides presented by MHC. It is established that self-pMHC reactivity impacts T cell function, but it has been challenging to identify TCR sequence features that predict T cell fate. To discern patterns distinguishing TCRs from naive CD4+ T cells with low versus high self-pMHC reactivity, we used data from 42 mice to train a machine learning (ML) algorithm that predicts self-reactivity directly from TCR{beta} sequences. This approach revealed that n-nucleotide additions and acidic amino acids weaken self-reactivity. We tested our ML predictions of TCR{beta} sequence self-reactivity using retrogenic mice. Extrapolating our analyses to independent datasets, we found high predicted self-reactivity for regulatory CD4+ T cells and low predicted self-reactivity for T cells responding to chronic infection. Our analyses suggest a potential trade-off between repertoire diversity and self-reactivity intrinsic to the architecture of a TCR repertoire.

immunology↗

bioRxiv2021

Colorectal cancer progression is potently reduced by a glucose-free, high-protein diet: comparison to anti-EGFR therapy

Background & AimsTo enable rapid proliferation, colorectal tumor cells up-regulate epidermal growth factor receptor (EGFR) signaling and perform high level of aerobic glycolysis, resulting in substantial lactate release into the tumor microenvironment and impaired anti-tumor immune responses. We hypothesized that an optimized nutritional intervention designed to reduce aerobic glycolysis of tumor cells may boost EGFR-directed antibody (Ab)-based therapy of pre-existing colitis-driven colorectal carcinoma (CRC). MethodsCRC development was induced by azoxymethane (AOM) and dextran sodium sulfate (DSS) administration to C57BL/6 mice. AOM/DSS treated mice were fed a glucose-free, high-protein diet (GFHPD) or an isoenergetic control diet (CD) in the presence or absence of i.p. injection of PBS, an irrelevant control mIgG2a or an anti-EGFR mIgG2a. Ex vivo, health status, tumor load, metabolism, colonic epithelial cell differentiation and immune cell infiltration were studied. Functional validation was performed in murine and human CRC cell lines MC-38 or HT29-MTX. ResultsAOM/DSS treated mice on GFHPD displayed reduced systemic glycolysis, resulting in improved tumoral energy homeostasis and diminished tumor load. Comparable but not additive to an anti-EGFR-Ab therapy, GFHPD was accompanied by enhanced tumoral differentiation and decreased colonic PD-L1 and splenic PD-1 immune checkpoint expression, presumably promoting intestinal barrier function and improved anti-tumor immune responses. In vitro, glucose-free, high-amino acid culture conditions reduced proliferation but improved differentiation of CRC cells in combination with down-regulation of PD-L1 expression. ConclusionWe here found GFHPD to metabolically reprogram colorectal tumors towards balanced OXPHOS, thereby improving anti-tumor T-cell responses and reducing CRC progression with a similar efficacy as EGFR-directed antibody therapy. SynopsisConsumption of glucose-free, high protein diet (GFHPD), comparable to EGFR-directed antibody-based therapy, efficaciously dampens colorectal tumor burden but does not have additive effects in combination with anti-EGFR therapy. GFHPD boosts amino acid metabolism, resulting in improved tumor differentiation and anti-tumor immune responses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/448354v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@e0c8fforg.highwire.dtl.DTLVardef@1abee36org.highwire.dtl.DTLVardef@a41e22org.highwire.dtl.DTLVardef@b678ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2017

Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones During an Immune Response

Immunological differences between hosts, such as diverse T-cell receptor (TCR) repertoires, are widely credited for reducing the risk of pathogen spread and adaptation in a population. Within-host immunological diversity might likewise be important for robust pathogen control, but to what extent naive TCR repertoires differ across different locations in the same host is unclear. T-cell zones (TCZs) in secondary lymphoid organs provide secluded micro-environmental niches. By harboring distinct TCRs, such niches could enhance within-host immunological diversity. On the other hand, rapid T cell migration is expected to dilute such diversity. Here, we combined tissue micro-dissection and deep sequencing of the TCR {beta} chain to examine the extent to which TCR repertoires differ between TCZs in murine spleens. In the absence of antigen, we found little evidence for differences between different TCZs of the same spleen. Yet, three days after immunization with sheep red blood cells, we observed a >10-fold rise in the number of clones that appeared to localize to individual zones. Remarkably, these differences largely disappeared at 4 days after immunization, when hallmarks of an ongoing immune response were still observed. These data suggest that in the absence of antigen, any repertoire differences observed between TCZs of the same host can largely be attributed to random clone distribution. Upon antigen challenge, segregated TCR compartments appear and disappear within days. Such \"transient mosaic\" dynamics could be an important barrier for pathogen adaptation and spread during an immune response.

immunology↗