Rakic, P. Evolution of the neocortex: a perspective from developmental biology. Nat. Rev. Neurosci. 10, 724–735 (2009).
Rakic, P. The radial edifice of cortical architecture: from neuronal silhouettes to genetic engineering. Brain Res. Rev. 55, 204–219 (2007).
Andrews, M. G., Subramanian, L., Salma, J. & Kriegstein, A. R. How mechanisms of stem cell polarity shape the human cerebral cortex. Nat. Rev. Neurosci. 23, 711–724 (2022).
Akula, S. K., Exposito-Alonso, D. & Walsh, C. A. Shaping the brain: the emergence of cortical structure and folding. Dev. Cell 58, 2836–2849 (2023).
Molnár, Z. et al. New insights into the development of the human cerebral cortex. J. Anat. 235, 432–451 (2019).
Casingal, C. R., Descant, K. D., & Anton, E. S. Coordinating cerebral cortical construction and connectivity: unifying influence of radial progenitors. Neuron https://doi.org/10.1016/j.neuron.2022.01.034 (2022).
Eze, U. C., Bhaduri, A., Haeussler, M., Nowakowski, T. J. & Kriegstein, A. R. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat. Neurosci. 24, 584–594 (2021).
Pebworth, M. P., Ross, J., Andrews, M., Bhaduri, A. & Kriegstein, A. R. Human intermediate progenitor diversity during cortical development. Proc. Natl Acad. Sci. USA 118, e2019415118 (2021).
Ma, S. et al. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science 377, eabo7257 (2022).
Stepien, B. K., Vaid, S. & Huttner, W. B. Length of the neurogenic period—a key determinant for the generation of upper-layer neurons during neocortex development and evolution. Front. Cell Dev. Biol. 9, 676911 (2021).
Hodge, R. D. et al. Conserved cell types with divergent features in human versus mouse cortex. Nature 573, 61–68 (2019).
Nakagawa, N. et al. Memo1-mediated tiling of radial glial cells facilitates cerebral cortical development. Neuron 103, 836–852 (2019).
Salussolia, C. L., Klonowska, K., Kwiatkowski, D. J. & Sahin, M. Genetic etiologies, diagnosis, and treatment of tuberous sclerosis complex. Annu. Rev. Genomics Hum. Genet. 20, 217–240 (2019).
Dibble, C. C. et al. TBC1D7 is a third subunit of the TSC1–TSC2 complex upstream of mTORC1. Mol. Cell 47, 535–546 (2012).
Vanclooster, S. et al. The research landscape of tuberous sclerosis complex-associated neuropsychiatric disorders (TAND)—a comprehensive scoping review. J. Neurodevel. Disord. 14, 13 (2022).
Girodengo, M., Ultanir, S. K. & Bateman, J. M. Mechanistic target of rapamycin signaling in human nervous system development and disease. Front. Mol. Neurosci. 15, 1005631 (2022).
Feliciano, D. M., Su, T., Lopez, J., Platel, J. C. & Bordey, A. Single-cell Tsc1 knockout during corticogenesis generates tuber-like lesions and reduces seizure threshold in mice. J. Clin. Invest. 121, 1596–1607 (2011).
Way, S. W. et al. Loss of Tsc2 in radial glia models the brain pathology of tuberous sclerosis complex in the mouse. Hum. Mol. Genet. 18, 1252–1265 (2009).
Magri, L. et al. Timing of mTOR activation affects tuberous sclerosis complex neuropathology in mouse models. Dis. Models Mech. 6, 1185–1197 (2013).
Magri, L. et al. Sustained activation of mTOR pathway in embryonic neural stem cells leads to development of tuberous sclerosis complex-associated lesions. Cell Stem Cell 9, 447–462 (2011).
Carson, R. P., Van Nielen, D. L., Winzenburger, P. A. & Ess, K. C. Neuronal and glia abnormalities in Tsc1-deficient forebrain and partial rescue by rapamycin. Neurobiol. Dis. 45, 369–380 (2012).
Onda, H. et al. Tsc2 null murine neuroepithelial cells are a model for human tuber giant cells, and show activation of an mTOR pathway. Mol. Cell. Neurosci. 21, 561–574 (2002).
Ess, K. C. et al. Expression profiling in tuberous sclerosis complex (TSC) knockout mouse astrocytes to characterize human TSC brain pathology. Glia 46, 28–40 (2004).
Mietzsch, U., McKenna, J. 3rd, Reith, R. M., Way, S. W. & Gambello, M. J. Comparative analysis of Tsc1 and Tsc2 single and double radial glial cell mutants. J. Comp. Neurol. 521, 3817–3831 (2013).
Goto, J. et al. Regulable neural progenitor-specific Tsc1 loss yields giant cells with organellar dysfunction in a model of tuberous sclerosis complex. Proc. Natl Acad. Sci. USA 108, E1070–E1079 (2011).
Man, A. et al. The genetics of tuberous sclerosis complex and related mTORopathies: current understanding and future directions. Genes 15, 332 (2024).
Winden, K. D., Ebrahimi-Fakhari, D. & Sahin, M. Abnormal mTOR activation in autism. Annu. Rev. Neurosci. 41, 1–23 (2018).
Mühlebner, A. et al. Specific pattern of maturation and differentiation in the formation of cortical tubers in tuberous sclerosis complex (TSC): evidence from layer-specific marker expression. J. Neurodevelop. Disord. 8, 9 (2016).
Catlett, T. S. et al. RHOA signaling defects result in impaired axon guidance in iPSC-derived neurons from patients with tuberous sclerosis complex. Nat. Commun. 12, 2589 (2021).
Martin, K. R. et al. The genomic landscape of tuberous sclerosis complex. Nat. Commun. 8, 15816 (2017).
Meng, D., Frank, A. R. & Jewell, J. L. mTOR signaling in stem and progenitor cells. Development 145, dev152595 (2018).
Park, S. M. et al. Brain somatic mutations in mTOR disrupt neuronal ciliogenesis, leading to focal cortical dyslamination. Neuron 99, 83–97 (2018).
Schrötter, S. et al. The non-essential TSC complex component TBC1D7 restricts tissue mTORC1 signaling and brain and neuron growth. Cell Rep. 39, 110824 (2022).
Kim, M. et al. Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia. Nat. Neurosci. 24, 799–809 (2021).
Beattie, R. et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron 94, 517–533 (2017).
Zong, H., Espinosa, J. S., Su, H. H., Muzumdar, M. D. & Luo, L. Mosaic analysis with double markers in mice. Cell 121, 479–492 (2005).
Loo, L. et al. Single-cell transcriptomic analysis of mouse neocortical development. Nat. Commun. 10, 134 (2019).
Li, M. et al. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362, eaat7615 (2018).
Nowakowski, T. J. et al. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science 358, 1318–1323 (2017).
SFARI Gene. Human Gene Module. SFARI Gene https://gene.sfari.org/database/human-gene/ (2025).
Andrews, M. G., Subramanian, L. & Kriegstein, A. R. mTOR signaling regulates the morphology and migration of outer radial glia in developing human cortex. eLife 9, e58737 (2020).
Pollen, A. A. et al. Molecular identity of human outer radial glia during cortical development. Cell 163, 55–67 (2015).
Fietz, S. A. et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc. Natl Acad. Sci. USA 109, 11836–11841 (2012).
Florio, M. et al. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science 347, 1465–1471 (2015).
Polioudakis, D. et al. A single-cell transcriptomic atlas of human neocortical development during mid-gestation. Neuron 103, 785–801 (2019).
Zhang, Y. et al. An rNA sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J. Neurosci. 34, 11929–11947 (2014).
Zhang, Y. et al. Purification and characterization of progenitor and mature human astrocytes reveals transcriptional and functional differences with mouse. Neuron 89, 37–53 (2016).
Ferrari, K. J. et al. Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Mol. Cell 53, 49–62 (2014).
Riising, E. M. et al. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol. Cell 55, 347–360 (2014).
van Arensbergen, J. et al. Genome-wide mapping of autonomous promoter activity in human cells. Nat. Biotechnol. 35, 145–153 (2017).
Tie, F. et al. CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 136, 3131–3141 (2009).
Pasini, D. et al. Characterization of an anatgonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of the Polycomb group target genes. Nucleic Acid Res. 38, 4958–4969 (2010).
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Ziller, M. J. et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 518, 355–359 (2015).
Albert, M. et al. Epigenome profiling and editing of neocortical progenitor cells during development. EMBO J. 36, 2642–2658 (2017).
Reilly, S. K. et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 347, 1155–1160 (2015).
Won, H. et al. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature 538, 523–527 (2016).
Armand, E. J., Li, J., Xie, F., Luo, C. & Mukamel, E. A. Single-cell sequencing of brain cell transcriptomes and epigenomes. Neuron 109, 11–26 (2021).
Mangan, R. J. et al. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell 185, 4587–4603 (2022).
de la Torre-Ubieta, L. et al. The dynamic landscape of open chromatin during human cortical neurogenesis. Cell 172, 289–295 (2018).
Ziffra, R. S. et al. Single-cell epigenomics reveals mechanisms of human cortical development. Nature 598, 205–213 (2021).
Wang, L. et al Molecular and cellular dynamics of the developing human neocortex. Nature https://doi.org/10.1038/s41586-024-08351-7 (2025).
Liang, D. et al. Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. Nat. Neurosci. 24, 941–953 (2021).
Larson, M. H. et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat. Protoc. 8, 2180–2196 (2013).
Stein, J. L. et al. A quantitative framework to evaluate modeling of cortical development by neural stem cells. Neuron 83, 69–86 (2014).
Velasco, S. et al. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature 570, 523–527 (2019).
Namba, T. et al. Human-specific ARHGAP11B acts in mitochondria to expand neocortical progenitors by glutaminolysis. Neuron 105, 867–881 (2020).
Patowary, A. et al. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 384, eadh7688 (2024).
Eichmüller, O. L. et al. Amplification of human interneuron progenitors promotes brain tumors and neurological defects. Science 375, eabf5546 (2022).
Blair, J. D., Hockemeyer, D. & Bateup, H. S. Genetically engineered human cortical spheroid models of tuberous sclerosis. Nat. Med. 24, 1568–1578 (2018).
Li, T. L. et al. mTORC1 activation drives astrocyte reactivity in cortical tubers and brain organoid models of TSC. Preprint at bioRxiv https://doi.org/10.1101/2025.02.28.640914 (2025).
Pollen, A. A. et al. Establishing cerebral organoids as models of human-specific brain evolution. Cell 176, 743–756 (2019).
Chung, C. et al. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat. Genet. 55, 209–220 (2023).
Wamsley, B. et al. Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics. Science 384, eadh2602 (2024).
Martin, P. et al. TSC2 loss in neural progenitor cells suppresses translation of ASD/NDD-associated transcripts in an mTORC1- and MNK1/2-reversible fashion. Preprint at bioRxiv https://doi.org/10.1101/2024.06.04.597393 (2024).
Mills, J. D. et al. Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. Sci. Rep. 7, 8089 (2017).
Iwata, R. et al. Mitochondria metabolism sets the species-specific tempo of neuronal development. Science 379, eabn4705 (2023).
Diaz-Cuadros, M. et al. Metabolic regulation of species-specific developmental rates. Nature 613, 550–557 (2023).
McLean, C. et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471, 216–219 (2011).
Benito-Kwiecinski, S. et al. An early cell shape transition drives evolutionary expansion of the human forebrain. Cell 184, 2084–2102 (2021).
Kwiatkowski, D. J. et al. A mouse model of TSC1 reveals sex-dependent lethality from liver hemangiomas, and up-regulation of p70S6 kinase activity in Tsc1 null cells. Hum. Mol. Genet. 11, 525–534 (2002).
Hernandez, O., Way, S., McKenna, J. 3rd & Gambello, M. J. Generation of a conditional disruption of the Tsc2 gene. Genesis 45, 101–106 (2007).
Guo, H. et al. Specificity and efficiency of Cre-mediated recombination in Emx1-Cre knock-in mice. Biochem. Biophys. Res. Commun. 273, 661–665 (2000).
Pimeisl, I. M. et al. Generation and characterization of a tamoxifen-inducible EomesCreER mouse line. Genesis 51, 725–733 (2013).
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
Hippenmeyer, S. Dissection of gene function at clonal level using mosaic analysis with double markers. Front. Biol. 8, 557–568 (2013).
Srivastava, A., Malik, L., Smith, T., Sudbery, I. & Patro, R. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biol. 20, 65 (2019).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
Tiberi, S., Crowell, H. L., Samartsidis, P., Weber, L. M. & Robinson, M. D. distinct: a novel approach to differential distribution analyses. Ann. Appl. Stat. 17, 1681–1700 (2023).
Phipson, B. et al. propeller: testing for differences in cell type proportions in single cell data. Bioinformatics 38, 4720–4726 (2022).
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
Konopka, G. et al. Modeling the functional genomics of autism using human neurons. Mol. Psychiatry 17, 202–214 (2012).
Brien, A. O. & Bailey, T. L. GT-Scan: identifying unique genomic targets. Bioinformatics 30, 2673–2675 (2014).
Hansen, D. V., Rubenstein, J. L. & Kriegstein, A. R. Deriving excitatory neurons of the neocortex from pluripotent stem cells. Neuron 70, 645–660 (2011).
Smith, J. R. et al. Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm. Dev. Biol. 313, 107–117 (2008).

