Single-cell transcriptional analysis reveals naïve helper ILC-like cells in zebrafish

Abstract

Innate lymphoid cells (ILCs) are important mediators of the immune response and homeostasis in barrier tissues of mammals. However, the existence and function of ILCs in other vertebrates is poorly understood. Here, we use single-cell RNA sequencing to generate a comprehensive atlas of zebrafish lymphocytes during tissue homeostasis and following immune challenge. We profiled 14,080 individual cells from the gut of wild-type zebrafish, as well as of rag1-deficient fish which lack T and B cells, and discovered diverse populations of helper ILC-like cells. Unexpectedly, fish displayed a rorc-positive, naïve subset that established a Type 3 or Type 2 response only upon immune challenge. Specifically, naïve ILC-like cells expressed il22 and tnfa following exposure to inactivated bacteria, or il13 following exposure to helminth extract. Cytokine-producing ILC-like cells express a specific repertoire of novel immune-type receptors, likely involved in recognition of environmental cues. We identified additional novel markers of zebrafish ILCs and generated a cloud repository for their in-depth exploration.

A Population of Injury-Responsive Lymphoid Cells Expresses mpeg1.1 in the Adult Zebrafish Heart

“…However, we also provide new evidence that mpeg1.1 + cells harness a transcriptional profile of NKL cells. The presence of NK and NKL cells in zebrafish has been determined by the identification of orthologs of mammalian NK-specific genes, namely novel immunetype receptors and NK lysins, by single-cell sequencing and morphological studies (22,23,51,52). However, functional studies of these cells have not yet been performed.…”

“…Furthermore, the discovery that zebrafish hematopoiesis is strikingly similar to that of mammalian systems (20)(21)(22)(23)(24), including the establishment of a sophisticated adaptive immune system by 3 wk postfertilization, has opened up new avenues of investigation in adult zebrafish (21,25). The recent characterization of zebrafish T lymphocytes (26), B lymphocytes (20,27), and innate lymphoid cells such as NK cells (23) has demonstrated that the function and organization of immune cell populations share many similarities to their mammalian counterparts. Combined with their regenerative capacity, the adult zebrafish therefore provides a unique model system to characterize the complex inflammatory processes that govern natural regeneration in vertebrates.…”

Innate lymphoid cells, mediators of tissue homeostasis, adaptation and disease tolerance

“…ILC populations were found that expressed the signature transcription factors T‐bet, RORγt, or GATA‐3. They were present in rag1 −/− fish and showed no signs of recombination at the TCR or BCR gene locus . ILC were also present, although in smaller numbers, in wildtype fish.…”

“…While mammalian ILCs are mainly activated by cytokines, zebrafish ILCs express low levels of cytokine receptors and express high levels of “novel immune‐type receptors” (NITR), considered functional orthologs of mammalian NK receptors (NKR). Nitr9, one of the few activating NITR, is exclusively expressed by the “bi‐potent” ILC2/3 population . Finally, scRNA‐seq revealed an ILC population that could be an LTi ancestor because of the co‐expression of LTα ( tnfb ) and rorc .…”

“…Unexpectedly, fish displayed a Rorc‐positive ILC subset that established a type 3 or type 2 response depending on the microbial trigger. Such Rorc + ILC from the zebrafish gut responded to the stimulation with bacterial antigens with IL‐22 and TNF production, whereas helminth extract induced IL‐13 production and increased GATA‐3 expression . This “bi‐potent” population will need to be further characterized to resolve its degree of heterogeneity and its lineage relationship.…”