Mapping of deletion and translocation breakpoints in 1q44 implicates the serine/threonine kinase AKT3 in postnatal microcephaly and agenesis of the corpus callosum

Abstract

Deletions of chromosome 1q42-q44 have been reported in a variety of developmental abnormalities of the brain, including microcephaly (MIC) and agenesis of the corpus callosum (ACC). Here, we describe detailed mapping studies of patients with unbalanced structural rearrangements of distal 1q4. These define a 3.5-Mb critical region extending from RP11-80B9 to RP11-241M7 that we hypothesize contains one or more genes that lead to MIC and ACC when present in only one functional copy. Next, mapping of a balanced reciprocal t(1;13)(q44;q32) translocation in a patient with postnatal MIC and ACC demonstrated a breakpoint within this region that is situated 20 kb upstream of AKT3, a serine-threonine kinase. The murine orthologue Akt3 is required for the developmental regulation of normal brain size and callosal development. Whereas sequencing of AKT3 in a panel of 45 patients with ACC did not demonstrate any pathogenic variations, whole-mount in situ hybridization confirmed expression of Akt3 in the developing central nervous system during mouse embryogenesis. AKT3 represents an excellent candidate for developmental human MIC and ACC, and we suggest that haploinsufficiency causes both postnatal MIC and ACC.

Figures

Figure 1.

Brain-imaging abnormalities in patients with deletion 1q4, shown with T1-weighted midline sagittal (left column), T2-weighted low axial (middle column), and T2-weighted higher axial (right column) sequences in an unaffected 3-year-old child (LR06-130) (A–C) and in patients LR05-202 (D–F), LR06-076 (G–I), LR02-409 (J–L), and LR05-101 (M–O). In the normal scans, the corpus callosum is marked by an asterisk (*) (A and C), and the inferior margin of the vermis is marked by a solid white horizontal line at the level of the obex (A). In the images of the four patients, the corpus callosum is either absent (white arrows in panels D and M and two black arrows in panels F and O) or small with a narrow body and absent splenium (white arrow in panels G and J and single black arrow indicating absent posterior callosum in panels I and L). The cerebellar vermis is small in three patients who have the 1q4 deletion, with the inferior margin (dashed white lines in panels D, G, and J) located well above the level of the obex (solid white lines in panels D, G, and J). The vermis appears mildly small in the boy with the 1q;13q translocation, with a mildly reduced anterior-posterior diameter of the vermis resulting in an enlarged cisterna magna extending behind the cerebellum (M), even though the inferior vermis is located near the level of the obex (dashed and solid lines in panel M). The cerebellar hemispheres are normal (E, H, K, and N), and the fourth ventricle is normal (E, H, and N) or mildly enlarged (“4V” in panel K). Lower-resolution images of our other two patients (LP94-079 and LR04-249) are shown in figure 2.

Figure 2.

Brain-imaging abnormalities in patients with deletion 1q4, shown with head CT scan (A–C) or with T1-weighted midline sagittal (D) and T2-weighted axial (E and F) MRI sequences in patients LP94-079 (A–C) and LR04-249 (D–F). In patient LP94-079, the cortex appears thickened in the posterior frontal and perisylvian regions (white arrow[s] in panels A–C), suggesting PMG, although the resolution is low. The lateral ventricles are located in the normal position close to the midline (A and B), suggesting that the corpus callosum is normal. The cerebellar vermis is small, since it is not seen at the level of the low midbrain (white arrowhead in panel A), and a small skull defect is seen beneath an occipital cephalocele (white arrowhead in panel C). In LR04-249, gyral pattern is poorly developed, even for 35 wk gestation, and the corpus callosum is absent (white arrow in panel D and two black arrows in panel E). The cerebellar vermis is small, with the inferior margin (dashed line in panel D) well above the level of the obex (solid line in panel D).

Figure 3.

Precise delineation of chromosome rearrangements in distal 1q42-q44 in study patients. Deletion mapping of patients LR02-409 and LR05-202 defines a minimal deleted region of 1.25 Mb between BACs RP11-657L23 and RP1-241M7. This region is deleted in four patients, all of whom had ACC and MIC. Patient LP94-079 has a subtelomeric deletion that is distal to RP1-241M7 and had neither ACC or MIC. In patient LR05-101, the breakpoint of the t(1;13) balanced de novo translocation lies within this region and is situated with BAC clone RP11-351N5 and fosmid clone G248P89661B9. This is upstream of the first exon of AKT3.

Figure 4.

aCGH demonstrating deletions (arrows) in patients with the 1q4 deletion. Data are represented as the corrected log2 ratios between control and patient DNA. A, LR05-202. B, LR06-076. C, LR02-409. The distal region that is not deleted in LR06-076 is marked with an arrowhead.

Figure 5.

FISH mapping of patients LR05-101 (A) and LR02-409 (B–D). Analysis of LR05-101, who has a de novo 46,XY,t(1;13)(q44;q32) translocation, shows signals for fosmid G248P89661B9 (red) located on the normal and derived chromosomes 1, as well as on the derived chromosome 13. This confirms that it spans the breakpoint on chromosome 1q44. Analysis of LR02-409 with probes RP11-90B9 (green) and RP11-399B15 (red [B]) shows the distal inversion, since the position of the two probes is reversed on the two chromosome 1 homologs. The associated deletion inside the distal inversion is demonstrated by loss of RP11-553N16 (red [C]) and by loss of RP11-411G13 (green [D]) compared with RP11-438H8 (red [D]).