Biology subjects

Chambers, B.

Publications and source records attributed to Chambers, B..

6 recordsLinked to original sources

bioRxiv2026

Immune repertoire profiling reveals extensive clonal expansion of T and B cells in CXCL9-rich niches in sinonasal cancer

Sinonasal cancer (SNC) is a rare and aggressive head and neck cancer with limited therapeutic options and an incompletely defined immune microenvironment. Although histopathology remains central to clinical tumor evaluation, immune profiling typically requires tissue dissociation and therefore loses the spatial relationships that shape antitumor immunity. Here, we combined single-cell RNA-sequencing approaches, spatial transcriptomics and Spatial V(D)J, a technique we recently pioneered, to analyse the cellular, spatial, and clonal architecture of SNC. We found that SNC tumors were marked by a robust T cell infiltration, including substantial proportions of classical tissue resident memory (TRM) and exhausted (TExh) CD8+ T cells. This inflamed phenotype was accompanied by an immense infiltration of suppressive regulatory T (Treg) cells, which differentiated towards a Tbet+CXCR3+ phenotype. Spatially, expanded Treg, CD8 T and B cell clones concentrated within specialized peritumoral immune niches enriched for cancer-associated fibroblasts, CXCL9 tumor-associated macrophages and LAMP3IDO1 dendritic cells. T cell clones occupying these niches were clonally related to those infiltrating epithelial tumor regions, linking lymphoid hubs to the broader tumor immune response. Together, these data identify SNC as an inflamed but highly immunoregulatory tumor type and reveal a spatially organized clonal architecture in which suppressive and cytotoxic lymphocyte states coexist within CXCL9 myeloid niches.

immunology↗

bioRxiv2023

A simple method to genetically differentiate invasive F1 Typha hybrids (T. x glauca) and advanced-generation/backcrossed hybrids from parent species (T. latifolia and T. angustifolia) in eastern Canada and northeastern USA

A widespread Typha (cattail) hybrid zone in southeastern Canada and northeastern USA comprises T. latifolia, T. angustifolia, and their hybrid T. x glauca. In this region the hybrid is considered invasive because of its detrimental impacts on wetlands and biodiversity. Researchers and managers are increasingly interested in tracking and controlling the spread of the invasive hybrid, but this can be hampered by challenges in differentiating taxa: while the parent species and F1 hybrids can often be identified from morphological characteristics, advanced-generation and backcrossed hybrids can be common, and these have obscured morphological distinctions among taxa. Here we present five species-specific genetic markers that differentiate T. latifolia, T. angustifolia, F1 hybrids, and advanced-generation/backcrossed hybrids. Unlike the pre-existing species-specific microsatellite markers, these markers require only PCR or PCR followed by a restriction enzyme digest, and can be visualized on an agarose gel. As a result, they require less specialized equipment than existing species-specific markers, and should therefore be useful for a larger group of practitioners. Future use of these markers could include monitoring range expansions, assessing the outcomes of restoration programs, and avoiding the unnecessary elimination of native Typha.

molecular biology↗

bioRxiv2022

Jagged1 overexpression on T cells induces thymic regulatory T cells leading to thymic involution

We previously described a mouse model, tg66, with a severe defect resulting in diminished thymic size and complete involution by early adulthood. In the current study, we identified overexpression of Jagged1 as a mechanism for the alterations in thymic development in tg66 mice. T cells in the tg66 thymus were skewed towards CD8+ T cells, and within the CD4+ T cell compartment there was an over-representation of Foxp3+ cells. Regulatory Foxp3+ T cells (Tregs) isolated from tg66 mice had increased ST2 and CD103 expression. These Tregs could suppress proliferation to the same extent as conventional Tregs. Corroborating these results, tg66 mice were resistant to experimental induction of neuroinflammation in a common animal model for multiple sclerosis (EAE). Using bone marrow chimeras, we recorded a stark reduction in the number of thymocytes and a corresponding increase in Tregs in the thymus of mice receiving tg66 bone marrow. Conversely, through blocking Jagged1, the number of thymocytes was significantly increased, being concomitantly associated with a drop in the frequency of Tregs. We conclude that Tregs may play a role in thymic involution and could explain early thymic involution or loss as it is observed in diseases of thymic atrophy such as Down syndrome.

immunology↗

bioRxiv2021

Stimulation with mycobacterial glycolipids and PPD reveals different innate immune response profiles in active and latent TB

Upon infection with Mycobacterium tuberculosis (Mtb) the host immune response might clear the bacteria, control its growth leading to latent tuberculosis (LTB), or fail to control its growth resulting in active TB (ATB). There is however no clear understanding of the features underlying a more or less effective response. Mtb glycolipids are abundant in the bacterial cell envelope and modulate the immune response to Mtb, but the patterns of response to glycolipids are still underexplored. To identify the CD45+ leukocyte activation landscape induced by Mtb glycolipids in peripheral blood of ATB and LTB, we performed a detailed assessment of the immune response of PBMCs to the Mtb glycolipids lipoarabinomannan (LAM) and its biosynthetic precursor phosphatidyl-inositol mannoside (PIM), and PPD. At 24 h and 5 days of stimulation, cell profiling and secretome analysis was done using mass cytometry and high-multiplex immunoassay. PIM mainly affected antigen-presenting cells to produce both proinflammatory (IL-2, IL-6, IL-17A, TNF- and GM-CSF), and IL-4 and IL-10 cytokines, but not IFN-{gamma}. LAM triggered a similar, albeit weaker, response. By contrast, PPD induced an increase in IFN-{gamma}-producing cells. Moreover, PPD also led to increased numbers of IL-2, IL-6, IL-10, IL-17A, TNF- and GrzB-producing cells. Treatment with an anti-TLR2 antibody led to partial inhibition of PIM-induced IL-6 production in myeloid cells, suggesting that PIM induces IL-6 production through TLR2. Expansion of monocyte subsets in response to PIM or LAM was reduced in both ATB and LTB as compared to healthy controls, suggesting a hyporesponsive/tolerance pattern in Mtb-infected individuals.

immunology↗

bioRxiv2021

FOXO1 and FOXO3 cooperatively regulate innate lymphoid cell development

The natural killer (NK) and non-cytotoxic innate lymphoid cells (ILC) lineages play vital role in the regulation of the immune system. Yet understanding of mechanisms controlling NK/ILC development remains incomplete. The evolutionary conserved FOXO family of forkhead transcription factors are critical regulators of cellular processes. We found that the loss of FOXO1 and FOXO3 together caused impaired activation of the NK gene expression program and reduced ETS binding already at the common lymphoid progenitor (CLP) level and a block at the ILC progenitor (ILCP) to NK progenitor transition. FOXO controlled NK cell maturation in organ specific manner and their ability to respond to IL-15. At the ILCP level, disruption of the ILC lineage specific gene programs was associated with broad perturbation of the generation of the non-cytotoxic ILC subsets. We concluded that FOXO1 and FOXO3 cooperatively regulate ILC lineage specification at the progenitor level as well as the generation of mature ILCs.

cell biology↗

bioRxiv2020

NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding

Machine reading is essential for unlocking valuable knowledge contained in the millions of existing biomedical documents. Over the last two decades 1,2, the most dramatic advances in machine-reading have followed in the wake of critical corpus development3. Large, well-annotated corpora have been associated with punctuated advances in machine reading methodology and automated knowledge extraction systems in the same way that ImageNet 4 was fundamental for developing machine vision techniques. This study contributes six components to an advanced, named-entity analysis tool for biomedicine: (a) a new, Named-Entity Recognition Ontology (NERO) developed specifically for describing entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine; (b) detailed guidelines for human experts annotating hundreds of named-entity classes; (c) pictographs for all named entities, to simplify the burden of annotation for curators; (d) an original, annotated corpus comprising 35,865 sentences, which encapsulate 190,679 named entities and 43,438 events connecting two or more entities; (e) validated, off-the-shelf, named-entity recognition automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.

systems biology↗