23 24 25 26 27 2 ABSTRACT 28 29During the development of the cerebral cortex, neurons are generated directly from radial glial cells 30 or indirectly via basal progenitors. The balance between these division modes determines the 31 number and types of neurons formed in the cortex thereby affecting cortical functioning. Here, we 32 investigate the role of primary cilia in this process. We show that a mutation in the ciliary gene Inpp5e 33 leads to a transient increase in direct neurogenesis and subsequently to an overproduction of layer 34 V neurons in newborn mice. Loss of Inpp5e also affects ciliary structure coinciding with increased 35 Akt and mTOR signalling and reduced Gli3 repressor levels. Genetically re-storing Gli3 repressor 36 rescues the decreased indirect neurogenesis in Inpp5e mutants. Overall, our analyses reveal how 37 primary cilia determine neuronal subtype composition of the cortex by controlling direct vs indirect 38 neurogenesis. These findings have implications for understanding cortical malformations in 39 ciliopathies with INPP5E mutations.40 41 101 rescues the decreased formation of basal progenitors. Taken together, these findings implicate the 102 primary cilium in controlling the decision of RGCs to either undergo direct neurogenesis or to form 103 basal progenitors, thereby governing the neuronal subtype composition of the cerebral cortex. 104 105 5 RESULTS 106 107 Inpp5e embryos show mild telencephalic patterning defects 108 Controlling the balance between direct and indirect neurogenesis in the developing cerebral 109 cortex is mediated by cell-cell signaling (Cardenas et al., 2018) and is hence likely to involve the 110 primary cilium. To investigate potential ciliary roles, we started characterizing cortical stem cell 111 development in embryos mutant for the Inpp5e gene which has a prominent role in ciliary signaling 112 and stability. Mutations in ciliary genes have previously been found to result in telencephalon 113 patterning defects, most notably in a ventralisation of the dorsal telencephalon and/or in defects at 114 the corticoseptal (CSB) and pallial/subpallial boundaries (PSPB) (Ashique et al., 2009; Besse et al., 115 2011; Willaredt et al., 2008). Therefore, we first considered the possibility that such early patterning 116 defects may be present in Inpp5e mutant embryos and could affect cortical stem cell development. 117 In situ hybridization and immunofluorescence analyses of E12.5 control and Inpp5e embryos 118 revealed no obvious effect on the expression of dorsal and ventral telencephalic markers at the 119 corticoseptal boundary (SupFig. 1). In contrast, the pallial/subpallial boundary was not well defined 120 with a few scattered Pax6+ and Dlx2 expressing cells on the wrong side of the boundary, i.e. in the 121 subpallium and pallium, respectively (SupFig. 1). Moreover, the hippocampal anlage appeared 122 smaller and disorganized with low level and diffuse expression of cortical hem markers (SupFig. 2), 123 consistent with known roles of Wnt/-catenin and...