The essential role of centrosomal NDE1 in human cerebral cortex neurogenesis

Abstract

We investigated three families whose offspring had extreme microcephaly at birth and profound mental retardation. Brain scans and postmortem data showed that affected individuals had brains less than 10% of expected size (≤10 standard deviation) and that in addition to a massive reduction in neuron production they displayed partially deficient cortical lamination (microlissencephaly). Other body systems were apparently unaffected and overall growth was normal. We found two distinct homozygous mutations of NDE1, c.83+1G>T (p.Ala29GlnfsX114) in a Turkish family and c.684_685del (p.Pro229TrpfsX85) in two families of Pakistani origin. Using patient cells, we found that c.83+1G>T led to the use of a novel splice site and to a frameshift after NDE1 exon 2. Transfection of tagged NDE1 constructs showed that the c.684_685del mutation resulted in a NDE1 that was unable to localize to the centrosome. By staining a patient-derived cell line that carried the c.83+1G>T mutation, we found that this endogeneously expressed mutated protein equally failed to localize to the centrosome. By examining human and mouse embryonic brains, we determined that NDE1 is highly expressed in neuroepithelial cells of the developing cerebral cortex, particularly at the centrosome. We show that NDE1 accumulates on the mitotic spindle of apical neural precursors in early neurogenesis. Thus, NDE1 deficiency causes both a severe failure of neurogenesis and a deficiency in cortical lamination. Our data further highlight the importance of the centrosome in multiple aspects of neurodevelopment.

Figure 1

Clinical Details of Research Families (A) The pedigrees of families A, B, and C. The closest consanguineous links between family members are shown; affected individuals are filled-in shapes and unaffected sibling existence is marked as a lozenge. Number and gender of unaffected siblings is undisclosed to protect privacy. (B) Pictures of affected children. (Right) A sagittal plane image of the computed tomography brain scan of an affected child at 4 years old. (C) Magnetic resonance images of an affected child at 2 years old. Axial, coronal, and sagittal MR images show severe microcephaly with cortical simplification, agenesis of the corpus callosum, and a hypoplastic cerebellum. The upper three panels show a control for comparison. Photographically inverted T2 images are shown.

Figure 2

Discovery of Mutations in NDE1 (A) Linkage strategy employed for families A and B. As previously published, an ExcludeAR analysis is based on the principle that by excluding regions of nonlinkage, any chromosomal region that remains must contain the locus of interest. It detects heterozygous or homozygous but discordant results for each consecutive SNP and allows the detection of significant shared regions of concordant homozygosity in up to four affected family members. The output plot for family A is shown on the left and depicts the five concordant homozygous regions of significant size that were found. On the right, an illustration of Chromosome 16 shows the largest concordant region in family A and where it overlaps with a homozygous region found in family B. NDE1 is within this defined linkage region. (B) Exome sequencing results. Exome sequencing demonstrates a G to T substitution in NDE1. Across the top of the figure is the wild-type (WT) sequence orientated 5′ to 3′ relative to NDE1. The wild-type G base mutated in the family is shown in green in the reference sequence (red arrow). Beneath this are the reads from the affected child from family C. The canonical splice donor site is shown in the red box. The depth of coverage across the variant was 17×, and all of the reads showed the substitution. (C) Sequencing of mRNA extracted from family C lymphocytes. The two electropherograms depict the wild-type (top panel) and affected child (bottom panel) sequences as derived from mRNA sequencing. Called nucleotides are depicted above the electropherogram, and above this the codon is defined and translated into amino acids. The affected child in family C bears a homozygous c.83+1G>T mutation, and the red colon in the called nucleotides of this child shows that one base has been lost from the NDE1 mRNA. The codon amino acid track shows amino acid 28 of mutated NDE1 remains an arginine, but thereafter the frame shift causes the introduction of a novel sequence of 113 amino acids followed by a premature termination codon (p.Ala29GlnfsX114) (Figure S4).

Figure 3

NDE1, NDE1, and Family Mutations (A) NDE1 shown 5′ to 3′ with an untranslated exon 1 within a CpG island is shown in green and followed by eight coding exons (shown in black) and the 3′ UTR terminating in a single polyadenylation signal (shown in red). The size of the exons relative to one another is shown as is the position of the two homozygous mutations found at the donor site of exon 2 in family C (c.83+1G>T) and in exon 6 in families A and B (c.684_685del). (B) An illustration of the NDE1 protein is shown with its two defined and evolutionarily conserved domains shown in shades of gray (top). In the center is the predicted protein deriving from the c.684_685del mutation, with loss of almost all of NUDE_C domain and the substitution with a novel peptide sequence of 84 amino acids. At the bottom is the predicted protein deriving from the c.83+1G>T mutation with loss of both known domains and the addition of 113 novel amino acids. The novel amino acid additions to NDE1 have no homology to known proteins or protein domains. (C) NDE1 construct engineering. The three constructs made to investigate the c.684_685del mutation are shown. At the top, we have the wild-type protein tagged with GFP, designated GFP-NDE1. In the middle is the expected protein product of the mutation with the novel peptide sequence tagged with GFP, designated NDE1-M. At the bottom is a construct made with a stop codon at position 227, thus creating a protein truncated for the NUDE_C domain tagged with GFP, designated NDE1-MSTOP.

Figure 4

Determining the Consequence of the NDE1 Mutations (A) The c.684_685del mutation prevents mutant NDE1 from localizing to the centrosome. The top four images of the panel show a representative HeLaM cell transfected with NDE1-GFP. On the left, NDE1 tagged with GFP is directly visualized in green. The two middle images show γ-tubulin in red, a constitutional marker of the centrosome, and α-tubulin in white. The merged image on the right shows the colocalization of NDE1 and γ-tubulin at the centrosome. The middle panel of four images shows the results after transfection with the NDE1-M construct. No centrosome localization could be found in any transfected cells (n > 200); instead aggregates formed within the more heavily transfected cells. In the bottom panel, we show the results obtained with NDE1-MSTOP construct; despite good levels of transfection, no NDE1 signal was seen at the centrosome, and aggregates were rarely seen. The scale bar indicates 10 μm. (B) Subcellular localization of mutant NDE1 in patient from family C (individual C.V-1 in Figure 1) and wild-type control-derived lymphoblastoid cell line. We can see colocalization of NDE1 (green) with γ-tubulin (red) in the control but not in the patient cell line.

Figure 5

Expression of NDE1 in the Mammalian Brain (A) NDE1 expression in a CS23 human embryo head. We performed in situ hybridization by using a riboprobe to NDE1 on a sagittal section of a human embryo. Darker red staining shows expression (see Figure S7 for control probe study). The black arrow indicates NDE1 expression in the neuroepithelium of the developing cerebral cortex, and the blue arrow indicates expression of the developing cerebellum in the neuroepithelium. The green star shows the mouth and hence the front of the face. (B) A composite of two consecutively cut 10 μm sections through the developing cerebral cortex neuroepithelium. In the upper panel, dark red eosin and hematoxylin staining shows the structure of the neuroepithelium. The lower panel shows the results of NDE1 riboprobe in situ hybridization. Only cells within the neuroepithelium are stained. See Figure S7 for control probe study.

Figure 6

Immunohistochemical Analysis of E13 Mouse and CS22 Human Brains (A) The upper set of four panels from a mouse indicate Nde1 (in red); Sox2 (in green) showing neuroepithelial cells; γ-tubulin (in white) showing centrosomes; and the merged image (on the right) including DAPI, showing DNA in blue. Nde1 is expressed at the apical rim (left and bottom) and more diffusely in the developing cortical plate (right and top). Immunohistochemical analysis of a CS22 human brain showing the cerebral cortex. This period of development is closest to E13 in mice. The color scheme is as above. NDE1 expression is marked in the neuroepithelium (left and bottom), and there is almost no expression in the subventricular zone (running left top to bottom right), whereas there is expression in the developing cortical plate (top right). Note that the subventricular zone is more developed in humans than in mice at the stages examined. Furthermore, the processing of the mouse embryonic brain can be better controlled to allow far greater clarity, particularly of microtubule-related proteins and structures, than in the human brain. Therefore, subcellular localization is likely to be less precise in our human studies than in mouse studies. The scale bar indicates 10 μm. (B) Magnified image of mouse E13 and human CS22 neuroepithelium, clearly showing NDE1 cytoplasmic dots in apical mitotic precursors. Single, thin arrows indicate examples of apical neural precursor cells undergoing mitosis with a pair of centrosomes on either side of a DNA metaphase plate. The scale bar indicates 10 μm. (C) Examination of Nde1 localization at the centrosome in apical neural epithelial cells. Nde1 is shown in red; DAPI shows DNA in blue; and Nestin, an apical progenitor cell marker, is shown in green; and γ-tubulin, a centrosome marker, is shown in white. The apical membrane of the neuroepithelial cells face the ventricle (the empty black space at the bottom). The white arrow dissects a representative centrosome for which we conducted an intensity profile analysis. The x-y graph below plots distance (defined by the path crossed by the arrow) on the x axis, and signal intensity on the y axis. The channels correspond respectively to Nestin (green, ChS1-T1), Nde1 (red, ChS1-T2), DNA (blue, ChS1-T3), and γ-tubulin (white, ChS1-T4). The intensity for both the white (γ-tubulin) and red (Nde1) channels reach a peak at the same point in the path defined by the arrow, whereas that for Nestin does not. We conclude that Nde1 is expressed at the centrosome of apical neural precursor cells where it colocalizes with γ-tubulin. The scale bar indicates 10 μm.

Figure 7

Subcellular Localization of NDE1 in NEP and HeLa Cells (A) Representative NEP cells in interphase, prophase, and metaphase. Clear centrosomal staining is present during both interphase and prophase. In metaphase, NDE1 decorates the mitotic spindle. Cells were stained with antibodies against NDE1 (red); γ-tubulin (green), as a centrosome marker; α-tubulin (white), as a microtubule marker; and DNA (blue) stained with DAPI. The scale bars indicate 10 μm. (B) NDE1 localization during metaphase in HeLa and NEP cells. NDE1 localizes to the centrosomes in HeLa cells, whereas it is present on the mitotic spindle in NEP cells. The scale bars indicate 10 μm.