Deverman, B. E. & Patterson, P. H. Cytokines and CNS development. Neuron 64, 61–78 (2009).
Choi, G. B. et al. The maternal interleukin-17a pathway in mice promotes autism-like phenotypes in offspring. Science 351, 933–939 (2016).
Kalish, B. T. et al. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat. Neurosci. 24, 204–213 (2021).
Kwon, H.-K., Choi, G. B. & Huh, J. R. Maternal inflammation and its ramifications on fetal neurodevelopment. Trends Immunol. 43, 230–244 (2022).
Cowardin, C. A. et al. Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy. Nat. Rev. Gastroenterol. Hepatol. 20, 223–237 (2023).
Knuesel, I. et al. Maternal immune activation and abnormal brain development across CNS disorders. Nat. Rev. Neurol. 10, 643–660 (2014).
Vuong, H. E. et al. The maternal microbiome modulates fetal neurodevelopment in mice. Nature 586, 281–286 (2020).
Breach, M. R. & Lenz, K. M. Sex differences in neurodevelopmental disorders: a key role for the immune system. Curr. Top. Behav. Neurosci. 62, 165–206 (2023).
Moffitt, J. R. et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl Acad. Sci. USA 113, 11046–11051 (2016).
Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods 19, 1634–1641 (2022).
Ruan, X. et al. Progenitor cell diversity in the developing mouse neocortex. Proc. Natl Acad. Sci. USA 118, e2018866118 (2021).
Borrett, M. J. et al. Single-cell profiling shows murine forebrain neural stem cells reacquire a developmental state when activated for adult neurogenesis. Cell Rep. 32, 108022 (2020).
Marin, O., Anderson, S. A. & Rubenstein, J. L. Origin and molecular specification of striatal interneurons. J. Neurosci. 20, 6063–6076 (2000).
Hrvatin, S. et al. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat. Neurosci. 21, 120–129 (2018).
Morabito, S., Reese, F., Rahimzadeh, N., Miyoshi, E. & Swarup, V. hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. Cell Rep. Methods 3, 100498 (2023).
Fu, J. M. et al. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat. Genet. 54, 1320–1331 (2022).
Farah, E. N. et al. Spatially organized cellular communities form the developing human heart. Nature 627, 854–864 (2024).
Alcamo, E. A. et al. Satb2 regulates callosal projection neuron identity in the developing cerebral cortex. Neuron 57, 364–377 (2008).
Gu, W.-L. et al. Chondroitin sulfate proteoglycans regulate the growth, differentiation and migration of multipotent neural precursor cells through the integrin signaling pathway. BMC Neurosci. 10, 128 (2009).
Vasistha, N. A. et al. Maternal inflammation has a profound effect on cortical interneuron development in a stage and subtype-specific manner. Mol. Psychiatry 25, 2313–2329 (2020).
Chen, Q. et al. CXCR7 mediates neural progenitor cells migration to CXCL12 independent of CXCR4. Stem Cells 33, 2574–2585 (2015).
Meyrath, M. et al. The atypical chemokine receptor ACKR3/CXCR7 is a broad-spectrum scavenger for opioid peptides. Nat. Commun. 11, 3033 (2020).
Sánchez-Alcañiz, J. A. et al. Cxcr7 controls neuronal migration by regulating chemokine responsiveness. Neuron 69, 77–90 (2011).
Wang, Y. et al. CXCR4 and CXCR7 have distinct functions in regulating interneuron migration. Neuron 69, 61–76 (2011).
Bauer, S., Kerr, B. J. & Patterson, P. H. The neuropoietic cytokine family in development, plasticity, disease and injury. Nat. Rev. Neurosci. 8, 221–232 (2007).
Heinrich, P. C. et al. Principles of interleukin (IL)-6-type cytokine signalling and its regulation. Biochem. J. 374, 1–20 (2003).
Williams, J. L., Holman, D. W. & Klein, R. S. Chemokines in the balance: maintenance of homeostasis and protection at CNS barriers. Front. Cell Neurosci. 8, 154 (2014).
Trettel, F., Di Castro, M. A. & Limatola, C. Chemokines: key molecules that orchestrate communication among neurons, microglia and astrocytes to preserve brain function. Neuroscience 439, 230–240 (2020).
Estes, M. L. & McAllister, A. K. Maternal immune activation: implications for neuropsychiatric disorders. Science 353, 772–777 (2016).
Hall, M. B., Willis, D. E., Rodriguez, E. L. & Schwarz, J. M. Maternal immune activation as an epidemiological risk factor for neurodevelopmental disorders: considerations of timing, severity, individual differences, and sex in human and rodent studies. Front. Neurosci. 17, 1135559 (2023).
McEwan, F., Glazier, J. D. & Hager, R. The impact of maternal immune activation on embryonic brain development. Front. Neurosci. 17, 1146710 (2023).
Yu, D. et al. Microglial GPR56 is the molecular target of maternal immune activation-induced parvalbumin-positive interneuron deficits. Sci. Adv. 8, eabm2545 (2022).
Shin Yim, Y. et al. Reversing behavioural abnormalities in mice exposed to maternal inflammation. Nature 549, 482–487 (2017).
Lubin, J.-B. et al. Arresting microbiome development limits immune system maturation and resistance to infection in mice. Cell Host Microbe 31, 554–570 (2023).
Koren, O., Konnikova, L., Brodin, P., Mysorekar, I. U. & Collado, M. C. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat. Rev. Gastroenterol. Hepatol. 21, 35–45 (2024).
Ruiz-Triviño, J., Álvarez, D., Cadavid, J., Á, P. & Alvarez, A. M. From gut to placenta: understanding how the maternal microbiome models life-long conditions. Front. Endocrinol. 14, 1304727 (2023).
Kim, S. et al. Maternal gut bacteria promote neurodevelopmental abnormalities in mouse offspring. Nature 549, 528–532 (2017).
Kim, E. et al. Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells. Immunity 55, 145–158 (2022).
Hurkacz, M., Dobrek, L. & Wiela-Hojeńska, A. Antibiotics and the nervous system—which face of antibiotic therapy is real, Dr. Jekyll (neurotoxicity) or Mr. Hyde (neuroprotection)? Molecules 26, 7456 (2021).
Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA 116, 19490–19499 (2019).
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291 (2019).
Chen, Y., Chen, L., Lun, A. T. L., Baldoni, P. L. & Smyth, G. K. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Res. 53, gkaf018 (2025).
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
Jin, S., Plikus, M. V. & Nie, Q. CellChat for systematic analysis of cell−cell communication from single-cell and spatially resolved transcriptomics. Nat Protoc. 20, 180–219 (2025).
Raudvere, U. et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 47, W191–W198 (2019).
Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87–D92 (2020).
McFarlane, L., Truong, V., Palmer, J. S. & Wilhelm, D. Novel PCR assay for determining the genetic sex of mice. Sex. Dev. 7, 207–211 (2013).