Gene signatures for intestinal and peripheral innate lymphoid cells in pigs reveal tissue-specific imprinting and similarities to human cells via single-cell RNA sequencing

Abstract

Abstract Intestinal innate lymphoid cells (iILCs) impact intestinal health outcomes, but study of iILCs in humans is limited. Human peripheral ILCs (pILCs) are easily obtained but may vary substantially from iILCs, thus requiring comparison of iILCs and pILCs to determine applicability of pILCs as surrogates to study iILC function. Pigs have anatomic, physiological, nutritional, and immune similarities to humans that are lacking in rodent models, making pigs a relevant biomedical model; however, ILCs are poorly defined in pigs. Single-cell RNA sequencing was performed to compare porcine iILCs to pILCs and determine potential similarities of porcine to human ILCs. Porcine pILCs matched porcine natural killer (NK) cell descriptions, while iILCs were annotated as group 1 and group 3 ILCs. Gene modules obtained independent of cell annotations were distilled to core signatures of genes most highly specific to pILCs, pan-iILCs, group 1 iILCs, and group 3 iILCs. The pILC signature included conventional NK cell genes, while the group 3 iILC signature included genes associated with type 3 immunity. Pan-iILC and group 1 iILC signatures included genes associated with tissue residency, cell activation, and metabolism, indicating tissue-specific, activation-associated imprinting. Gene profiles were used to develop in situ iILC detection methods, establishing group 1 iILCs were intraepithelial, while group 3 iILCs resided in lamina propria/gut-associated lymphoid tissue. Findings indicated iILCs were ILC subsets distinct from pILCs, thus opposing pILCs as surrogates to study iILC dynamics. Moreover, gene profiles and in situ locations of iILCs drew close parallels to human iILCs functions, supporting pigs as a biomedical model for iILC research. Research was supported by appropriated funds from USDA-ARS CRIS 5030-31320-004-00D, an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA). ORISE is managed by ORAU under DOE contract number DE-SC0014664. All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of USDA, ARS, DOE, or ORAU/ORISE. This research used resources provided by the SCINet project of the USDA ARS project number 0500-00093-001-00-D.