Sequential Transcriptional Programs of Tissue Residency Drive Human Uterine NK Cell Development

Abstract

The idea of tissue resident immune populations is a concept extending to the innate lymphocyte population of NK cells. One such population of tissue resident NK cell is decidual natural killer cells, which are critical for pregnancy success but the origin and development of these cells in the human uterus remain unclear. Here we use various single-cell approaches to identify the transcriptional programs governing uterine NK cell development in humans. These analyses suggest a developmental continuum from immature CD56bright precursors in the blood through a putative endometrial founder NK cell to mature tissue resident NK cells. Our work identifies a role for sequential programs of tissue residency in the differentiation of these cells, as differentiating trNK cells acquire early and late transcriptional programs of residency which coincide with acquisition of unique non-cytotoxic effector programs. Notably, we identified early residency programs in human endometrial trNK by expression of NR4A2, AP-1 transcription factors, and other immediate early response genes that were shared with CD8 tissue resident memory T cells in mice, suggesting conservation of transcriptional programs of early tissue residency programs across species and cell types. Late residency programs were guided by TGFβ, which promoted expression of various integrins and trNK subset diversification within the non-pregnant endometrium. Altogether, these data identify the molecular foundations for endometrial trNK heterogeneity and suggest that the uterine NK diversity observed during pregnancy is established before embryo implantation and intimately tied to residency programming.

Inhibition of NFAT promotes loss of tissue resident uterine natural killer cells and attendant pregnancy complications in humans

“…6C). trNK2 subsets had intermediate expression of both gene modules, suggesting an intermediate transcriptional state between trNK1 and trNK3 cells, in line with prior results ( 56 ). Notably, trNK2 and trNK3 subsets were distinguished from trNK1s in part by increased expression of the developmental module composed of AP-1 transcription factors (i.e., developmental module 2) (Fig.…”

“…To investigate the mechanism of NK loss in UTx recipients, we first determined whether the NK cell reduction in UTx affected all uterine NK subsets equally. Consistent with prior studies ( 54–56 ), we identified two major populations of endometrial NK cells which could be distinguished by differential expression of NCAM1 and FCGR3A (Fig. 1A and 4A) as well as transcriptional programs governing tissue residency and cytotoxic effector function (Fig.…”

“…4, D and E). Because uterine trNKs are transcriptionally and functionally heterogeneous ( 56, 59, 60 ), we next determined if all trNK subsets were reduced in UTx or whether the trNK defect was limited to specific trNK subsets. After identification of canonical trNK subsets by expression of decidual NK signatures (Fig.…”

“…are not only expressed early after tissue entry but are required for tissue residence ( 65 ). Moreover, prior work investigating human uterine NK development has suggested that a similar transcriptional program of early tissue adaptation is upregulated in early endometrial immigrants after arrival from the blood ( 56 ). We thus tested the hypothesis that trNKs were reduced in UTx due to defective expression of this early developmental program (EDP) that is conserved between species and cell types (table S2).…”

“…are not only expressed early after tissue entry but are required for tissue residence (65). Moreover, prior work investigating human uterine NK development has suggested that a similar transcriptional program of early tissue adaptation is upregulated in early endometrial immigrants after arrival from the blood (56).…”