Maternal intra-epithelial lymphocytes support lactogenesis and offspring fitness

Breastfeeding is an obligatory requirement of mammalian survival. This fundamental process is associated with the remodeling of maternal physiology including the transformation of mammary gland into milk-secreting organ. While adaptive immunity has been associated with the broad control of host physiology, how maternal immunity contributes to organismal remodeling during pregnancy including mammary gland remodeling and function remains largely unknown. Here, we show that maternal adaptive immunity plays a critical role in shaping lactogenesis. Specifically, physiological adaptation to pregnancy is associated with thymic involution and paradoxical enrichment in intraepithelial lymphocyte precursors that no longer migrate to the gut but preferentially accumulate within the mammary gland. Within this compartment the precursors develop as T-bet expressing lymphocytes accumulating within the mammary epithelium in an IL-15 dependent manner. Mammary intra-epithelial lymphocytes control milk production by favoring differentiation of both contractile and milk-secreting cells, thereby affecting offspring fitness. Altogether, this work uncovers a previously unappreciated contribution of the maternal adaptive immune system in organismal remodeling during pregnancy associated with mammary gland development and function. To identify whether mammary unconventional intra-epithelial lymphocytes regulate mammary epithelial and basal cell differentiation, we performed scRNA-seq on mammary epithelial-myoepithelial and lymphoid cells along with bulk RNA-Seq on CD8 beta+ T-cells and DN (double negative) NK1.1+ lymphocytes in mice. The number of libraries sequenced is one for mammary epithelial-myoepithelial scRNA-seq, four for lymphoid scRNA-seq, three for each of the bulk RNA-Seq samples derived from CD8 beta+ T-cells and DN NK1.1+ lymphocytes. The scRNA-seq libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled RNA libraries into individual mice for downstream analysis, whereas the lymphoid cells were also used for generating T cell receptor (VDJ region) sequencing libraries for characterizing the immune repertoire landscape.