Biology subjects

Morgan, D. M.

Publications and source records attributed to Morgan, D. M..

6 recordsLinked to original sources

bioRxiv2024

Interferon-γ signaling in eosinophilic esophagitis has implications for epithelial barrier function and programmed cell death.

ObjectiveEosinophilic esophagitis (EoE) is a chronic esophageal inflammatory disorder characterized by eosinophil-rich mucosal inflammation and tissue remodeling. Transcriptional profiling of esophageal biopsies has previously revealed upregulation of type I and II interferon (IFN) response genes. We aim to unravel interactions between immune and epithelial cells and examine functional significance in esophageal epithelial cells. Design We investigated epithelial gene expression from EoE patients using single-cell RNA sequencing and a confirmatory bulk RNA-sequencing experiment of isolated epithelial cells. The functional impact of interferon signaling on epithelial cells was investigated using in vitro organoid models. ResultsWe observe upregulation of interferon response signature genes (ISGs) in the esophageal epithelium during active EoE compared to other cell types, single-cell data, and pathway analyses, identified upregulation in ISGs in epithelial cells isolated from EoE patients. Using an esophageal organoid and air-liquid interface models, we demonstrate that IFN-{gamma} stimulation triggered disruption of esophageal epithelial differentiation, barrier integrity, and induced apoptosis via caspase upregulation. We show that an increase in cleaved caspase-3 is seen in EoE tissue and identify interferon gamma (IFNG) expression predominantly in a cluster of majority-CD8+ T cells with high expression of CD69 and FOS. ConclusionThese findings offer insight into the interplay between immune and epithelial cells in EoE. Our data illustrate the relevance of several IFN-{gamma}-mediated mechanisms on epithelial function in the esophagus, which have the potential to impact epithelial function during inflammatory conditions. Key MessagesWhat is already known about this topic: O_LIThe transcriptome of esophageal biopsy tissue reproducibly distinguishes eosinophilic esophagitis from histologically normal tissue, with evidence of mixed inflammatory signals. C_LIO_LIInterferon response signature genes are elevated in EoE biopsy tissue compared to controls, suggesting T1 in addition to T2 cytokine signaling within EoE mucosa. C_LI What this study adds: O_LIWe observe reproducible, robust upregulation of interferon signature genes in esophageal epithelium, and we confirm that esophageal epithelium expresses functional IFN-a and IFN-{gamma} receptors. C_LIO_LIIFN-{gamma} treatment of epithelial organoids has several detrimental effects, including decreased proliferation, organoid formation, and increased caspase activation. C_LIO_LIAnalysis of single-cell RNA-sequencing data from of EoE biopsy tissue during active disease and remission identified that a CD8+ population expressing high levels of FOS, ITGAE, and ITGA1 expresses high levels of IFNG C_LI How this study might affect research, practice, or policy: O_LIWe identify esophageal epithelium as the cellular source for interferon response gene signature in EoE and a CD8+ tissue-resident memory T-cell population was the main source of IFNG. C_LIO_LIFurther mechanistic studies are required to identify how non-T2 signaling mechanisms like IFN-{gamma} signaling contribute to EoE pathogenesis, and if this pathway can be targeted as an adjunctive therapy for EoE. C_LI

immunology↗

bioRxiv2023

Differentiation and Expansion of Tumor-Infiltrating T Cell Clonotypes Occurs in the Spleen Following Immune Checkpoint Blockade

Immune checkpoint blockade (ICB) enhances tumor-reactive T cell responses against cancer, leading to long-term tumor control and survival in a fraction of patients. Given the increasingly recognized complexity of T cell differentiation that occurs in response to chronic antigen stimulation, it remains unclear precisely which T cell differentiation states are critical for the response to ICB, as well as the anatomic sites at which ICB-mediated reinvigoration of these T cells occurs. We used paired single-cell RNA and T cell receptor (TCR) sequencing to profile endogenous, tumor-reactive CD8+ T cells isolated from tumors, tumor-draining lymph nodes, and spleens of mice treated with ICB. We identified an intermediate-exhausted population of T cells in the spleen which underwent the greatest expansion in response to ICB and gave rise to the majority of tumor-infiltrating clonotypes. Increasing concentrations of antigen in the spleen perturbed the differentiation of this phenotype towards a divergent exhausted_KLR state, resulting in reduced numbers of tumor-infiltrating T cells and blunted ICB efficacy. Likewise, an analogous population of exhausted_KLR CD8+ T cells in matched human tumor and blood samples and exhibited diminished tumor-trafficking ability. These data demonstrate that the spleen is a critical anatomic site for coordinating the differentiation of tumor-infiltrating clonotypes and their expansion in response to ICB.

immunology↗

bioRxiv2023

Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) - defining features that confer antigen specificity to B cells - remain limited, especially from widely-used 3'-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3'-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination.

immunology↗

bioRxiv2022

Eradication of tumors with pre-existing antigenic heterogeneity by vaccine-mediated co-engagement of CAR T and endogenous T-cells

Chimeric Antigen Receptor (CAR) T-cell therapy can be effective in treating human cancer but loss of the antigen recognized by the CAR poses a major obstacle. Here, we report an approach for vaccine boosting CAR T-cells, which triggers engagement of the endogenous immune system to circumvent antigen-negative tumor escape. Vaccine-boosted CAR T-cells promoted dendritic cell (DC) recruitment to tumors, increased tumor antigen uptake by DCs, and elicited priming of endogenous anti-tumor T-cells (antigen spreading). This process was accompanied by a shift in toward oxidative phosphorylation in CAR T-cells and was critically dependent on CAR-T-derived IFN-{gamma}. Antigen spreading induced by vaccine-boosted CAR-T enabled a proportion of complete responses even when the initial tumor was 50% CAR-antigen-negative, and heterogenous tumor control was further enhanced by genetically amplifying CAR-T IFN-{gamma} expression. Thus, CAR T-cell-derived IFN-{gamma} plays a critical role in promoting antigen spreading, and vaccine boosting provides a clinically-translatable strategy to drive such responses against solid tumors.

immunology↗

bioRxiv2022

Identification of highly cross-reactive mimotopes for a public T cell response in murine melanoma

While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often unknown what antigens are being recognized by T cells or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet showed modest survival benefit in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and generation of mimotopes which can induce robust functional T cell responses that are cross-reactive to the endogenous antigen across multiple individuals.

immunology↗

bioRxiv2022

WAT3R: Recovery of T-Cell Receptor Variable Regions From 3' Single-Cell RNA-Sequencing

SummaryDiversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of and {beta} chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3-biased single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3 scRNA-seq is not available. Here we present an analysis pipeline to process TCR variable regions enriched from 3 scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells (PBMCs) from a healthy donor and detect TCR sequences in a high proportion of single T-cells. Detection of TCR sequences is negligible in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T-cells than other T-cell types, indicating an association between T-cell clonotypes and differentiation states. Availability and implementationThe Workflow for Association of T-cell receptors from 3 single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r), and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number pending).

immunology↗