T cell development and selection are coordinated in the thymus by a specialized niche of diverse stromal populations. Although much progress has been made over the years in identifying the functions of the different cell types of the thymic stromal compartment, there is no comprehensive characterization of their diversity and heterogeneity. Here we combined massively parallel single-cell RNA-sequencing, spatial mapping, chromatin profiling and gene targeting to characterize de novo the entire stromal compartment of the mouse thymus. We identified dozens of cell states, with thymic epithelial cells (TECs) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient in Pou2f3, a master regulator of tuft cells, have complete and specific depletion of mTEC IV cells, which results in increased levels of thymus-resident type-2 innate lymphoid cells. Overall, our study provides a comprehensive characterization of the thymic stroma and identifies a new tuft-like TEC population, which is critical for shaping the immune niche in the thymus.
Antibacterial drugs are among the most common medications used by pregnant women. While medical literature generally defines nitrofurantoin as an antibiotic that is safe for use during the first trimester of pregnancy, new concerns about a possible association between congenital malformations following exposure to nitrofurantoin during the first trimester of pregnancy have recently surfaced. To address these concerns, we conducted a large population-based retrospective cohort study to assess this possible association (including cases of medical terminations of pregnancy or stillbirth) and congenital malformations. A computerized database for medications dispensed to pregnant women in southern Israel was linked with records from the district hospital. Associations between exposure to nitrofurantoin during the first trimester and major malformations were assessed. Our research included a total of 105,492 pregnancies, 1,112 of which involved pregnancy terminations for medical reasons. A total of 1,329 infants and abortuses had been exposed to nitrofurantoin during the first trimester of pregnancy. Exposure to nitrofurantoin was not associated with increased risk of major malformations in general (adjusted OR = 0.85, 95% CI 0.67-1.08) or with specific malformations. First trimester exposure to nitrofurantoin was not associated with increased risk for total major congenital malformations or with specific malformations.
While no association was found between fetal exposure to nitrofurantoin and major malformation in cohort studies, there was a slight but significant teratogenic risk in case-control studies, which are more sensitive to adverse effects.
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