Unconventional intraepithelial gut T cells: the TCR says it all

Rarity: discovering rare cell populations from single-cell imaging data

MOTIVATION

Cell type identification plays an important role in the analysis and interpretation of single-cell data and can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we can list all cell types and their respective marker genes a priori, while unsupervised clustering algorithms look for groups of cells with similar expression properties. This property permits the identification of both known and unknown cell populations, making unsupervised methods suitable for discovery. Success is dependent on the relative strength of the expression signature of each group as well as the number of cells. Rare cell types therefore present a particular challenge that is magnified when they are defined by differentially expressing a small number of genes.

RESULTS

Typical unsupervised approaches fail to identify such rare subpopulations, and these cells tend to be absorbed into more prevalent cell types. In order to balance these competing demands, we have developed a novel statistical framework for unsupervised clustering, named Rarity, that enables the discovery process for rare cell types to be more robust, consistent, and interpretable. We achieve this by devising a novel clustering method based on a Bayesian latent variable model in which we assign cells to inferred latent binary on/off expression profiles. This lets us achieve increased sensitivity to rare cell populations while also allowing us to control and interpret potential false positive discoveries. We systematically study the challenges associated with rare cell type identification and demonstrate the utility of Rarity on various IMC datasets.

AVAILABILITY AND IMPLEMENTATION

Implementation of Rarity together with examples is available from the Github repository (https://github.com/kasparmartens/rarity).

Fetal Thymic Organ Culture and Negative Selection

Negative selection removes potentially harmful T cell precursors from the conventional T cell pool. This process can involve the induction of apoptosis, anergy, receptor editing, or deviation into a regulatory T cell lineage. As such, this process is essential for the health of an organism through its contribution to central and peripheral tolerance. While a great deal is known about the process, the precise mechanisms that regulate these various forms of negative selection are not clear. Numerous models exist with the potential to address these questions in vitro and in vivo. This chapter describes fetal thymic organ culture methods designed to analyze the signals that determine these unique cell fates.

The dephosphorylation of FADD at S191 induces an excessive expansion of TCRαβ+ IELs in the intestinal mucosa

Intestinal intraepithelial lymphocytes (IELs) play a crucial role in host defence against pathogens in the intestinal mucosa. The development of intestinal IELs is distinct from peripheral T lymphocytes and remains elusive. Fas-associated protein with death domain (FADD) is important for T cell development in the thymus. Here we describe a novel function of FADD in the IEL development. FADD (S191A), a mouse FADD mutant at Ser191 to Ala mimicking constitutively unphosphorylated FADD, promoted a rapid expansion of TCRαβ⁺ IELs, not TCRγδ⁺ IELs. Mechanism investigation indicated that the dephosphorylation of FADD was required for cell activation mainly in TCRαβ⁺ CD8⁺ T cells. Consistently, FADD (S191A) as dephosphorylated FADD led to a high NF-κB activation in the TCR-dependent cell expansion. In addition, The FADD (S191A)-induced abnormal IEL populations resulted in the increased incidence and severity of colitis in mice. In summary, FADD signalling is involved in the intestinal IEL development and might be a regulator for intestinal mucosal homeostasis.

The Immune Barrier of Porcine Uterine Mucosa Differs Dramatically at Proliferative and Secretory Phases and Could Be Positively Modulated by Colonizing Microbiota

Endometrial immune response is highly associated with the homeostatic balance of the uterus and embryo development; however, the underlying molecular regulatory mechanisms are not fully elucidated. Herein, the porcine endometrium showed significant variation in mucosal immunity in proliferative and secretory phases by single-cell RNA sequencing. The loose arrangement and high motility of the uterine epithelium in the proliferative phase gave opportunities for epithelial cells and dendritic cells to cross talk with colonizing microbial community, guiding lymphocyte migration into the mucosal and glandular epithelium. The migrating lymphocytes were primarily NK and CD8⁺ T cells, which were robustly modulated by the chemokine signaling. In the secretory phase, the significantly strengthened mechanical mucosal barrier and increased immunoglobulin A alleviated the migration of lymphocytes into the epithelium when the neuro-modulation, mineral uptake, and amino acid metabolism were strongly upregulated. The noticeably increased intraepithelial lymphocytes were positively modulated by the bacteria in the uterine cavity. Our findings illustrated that significant mucosal immunity variation in the endometrium in the proliferative and secretory phases was closely related to intraepithelial lymphocyte migration, which could be modulated by the colonizing bacteria after cross talk with epithelial cells with higher expressions of chemokine.

CD8αα TCRαβ Intraepithelial Lymphocytes in the Mouse Gut

The epithelium of the mouse small intestine harbors an abundant CD8αα(+)TCRαβ(+) intraepithelial lymphocyte (IEL) population. This unique IEL subset is a self-reactive population that requires exposure to self-agonists for selection in the thymus, similarly to other regulatory T cell populations. After leaving the thymus, these cells directly seed the intestinal epithelium, which provides a unique combination of cellular interactions together with cytokines, nutrients, and antigens that guide the lineage-specific differentiation and function of these IELs. For instance, epithelial cells and nearby immune cells secrete a number of cytokines, including interleukin-15 (IL-15), IL-7, and transforming growth factor-β, resulting in an assortment of cellular responses, including activation of master transcription factors, cell proliferation, and cytokine secretion. Recent advances have also highlighted the importance of diet-derived substances and commensal metabolites, such as the aryl hydrocarbon receptor ligands and vitamin D, in controlling the survival and gene expression of CD8αα(+)TCRαβ(+) IELs. Furthermore, these cells function in the epithelium and require constant communication between cells in the form of cell-to-cell contacts. These interactions tune the antigen sensitivity of the TCR and maintain the quiescence of the CD8αα(+)TCRαβ(+) IELs. Finally, we discuss how these cells might contribute to tolerance and immunopathological responses in the gut. Therefore, an increased understanding of CD8αα(+)TCRαβ(+) IELs in the gut will help us understand how these cells participate in immune regulation and protection.