Abstract: Aspects of the disclosure relate to the finding that certain modeling of single-cell RNA-sequencing (scRNA-seq) data can provide cell profiles of the analyzed cell population. Certain aspects use algorithms including topic modeling, burst modeling, and data integration to determine the profiles. To apply RNA velocity to more general systems, including immune response studies, aspects herein concern a new approach that can infer the cells and genes associated with distinct active processes via probabilistic topic modeling and uses the results to estimate process-specific velocity parameters.

Abstract: Interleukin (IL)-33 is a critical regulator of allergic airway inflammation in the lung and is released by stressed or damaged epithelial cells. Here, Applicants show that alveolar macrophages regulate epithelial alarmin expression via CLEC-2 (C-type Lectin-like Receptor-2), which binds to PDPN (podoplanin). Therefore, CLEC-2/PDPN interactions are critical for regulating type 2 immunity in the lung and modulating expression of the epithelial alarmin IL-33. Methods are disclosed for therapeutic and screening applications. Novel therapeutic targets in alveolar macrophages and epithelial cells are disclosed.

Abstract: The present invention provides novel compositions and methods based on the discovery of the mechanisms and gene expression programs associated with homeostatic ILC2s and proinflammatory ILC2s that drive tissue inflammation. Molecular cues were identified that modulate ILC responses to alarmins using single-cell RNA-sequencing (scRNA-seq) profiles of lung-resident ILCs at steady state and after in vivo stimulation. The neuropeptide CGRP and the CGRP receptor were identified as expressed on ILC2s. Treatment with CGRP reduces allergic lung inflammation and reduces the proliferation and expansion of ILC2 cells. The results demonstrate that CGRP signaling strongly modulates ILC2 responses and highlights the importance of neuro-immune crosstalk in allergic inflammatory responses at mucosal surfaces.

Abstract: Computational and functional analysis identified the neuropeptide receptor Nmur1 as selectively expressed on Type 2 innate lymphoid cells (ILC2s). While both IL-33 and IL-25 promote ILC activation in vivo, IL-33 induces robust ILC proliferation, whereas ILCs activated with IL-25 do not proliferate as robustly and up-regulate Nmur1 expression. Treatment with neuromedin U (NMU), the neuropeptide ligand of Nmur1, had little effect on its own. Co-administration of IL-25 with NMU, however, dramatically amplified allergic lung inflammation and induced the proliferation and expansion of specific ILC2 subsets, characterized by a molecular signature unique to pro-inflammatory ILC2s. The results demonstrate that Nmur1 signaling strongly modulates IL-25-mediated ILC2 responses, resulting in highly proliferative pro-inflammatory ILCs, and highlights the importance of neuro-immune crosstalk in allergic inflammatory responses at mucosal surfaces.