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The brain has innate immune myeloid cells (including microglia and border-associated macrophages) that have dynamic roles in homeostasis and the response to tissue injury and infection. Given the ability of brain myeloid cells to sense a variety of environmental cues, several studies have investigated their roles in neurodegenerative disease onset and progression. But, the impact of fetal myeloid cells on neurodevelopmental disorders is relatively unexplored in comparison. We used two mouse models of neurodevelopmental disorders to uncover the impact of fetal myeloid cell immunity to both normal and abnormal brain development. We found that an inflammatory lytic form of cell death, termed pyroptosis, in microglia may be required for establishing certain normal behavioral circuits. With genetic deficiency in the pyroptosis pathway, or upon pharmacological inhibition thereof, mice have attention-deficit/hyperactivity disorder (ADHD)-like behavior changes. Using the maternal immune activation (MIA) model of autism spectrum disorder (ASD), we identified a fetal myeloid responder population, likely to be border-associated macrophages, which directly sense MIA challenge. Thus, we learned that fetal immunity, mediated by myeloid cells, has important consequences for brain formation. Disruption or activation of these roles may constitute an upstream arm in neurodevelopmental disorder etiology.

The house mouse, Mus musculus , is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life., Competing Interests: Competing Financial Interests Statement J.S. is a scientific advisory board member, consultant and/or co-founder of Scale Biosciences, Prime Medicine, Cajal Neuroscience, Guardant Health, Maze Therapeutics, Camp4 Therapeutics, Phase Genomics, Adaptive Biotechnologies, Sixth Street Capital and Pacific Biosciences. C.T. is a co-founder of Scale Biosciences. All other authors declare no competing interests.

In situ hybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed 'pSABER', for the amplification of ISH signals in cell and tissue systems. pSABER decorates the in situ target with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.