Mutations in the small GTPase gene RAB39B are responsible for X-linked mental retardation associated with autism, epilepsy, and macrocephaly

Abstract

Human Mental Retardation (MR) is a common and highly heterogeneous pediatric disorder affecting around 3% of the general population; at least 215 X-linked MR (XLMR) conditions have been described, and mutations have been identified in 83 different genes, encoding proteins with a variety of function, such as chromatin remodeling, synaptic function, and intracellular trafficking. The small GTPases of the RAB family, which play an essential role in intracellular vesicular trafficking, have been shown to be involved in MR. We report here the identification of mutations in the small GTPase RAB39B gene in two male patients. One mutation in family X (D-23) introduced a stop codon seven amino acids after the start codon (c.21C > A; p.Y7X). A second mutation, in the MRX72 family, altered the 5' splice site (c.215+1G > A) and normal splicing. Neither instance produced a protein. Mutations segregate with the disease in the families, and in some family members intellectual disabilities were associated with autism spectrum disorder, epileptic seizures, and macrocephaly. We show that RAB39B, a novel RAB GTPase of unknown function, is a neuronal-specific protein that is localized to the Golgi compartment. Its downregulation leads to an alteration in the number and morphology of neurite growth cones and a significant reduction in presynaptic buttons, suggesting that RAB39B is required for synapse formation and maintenance. Our results demonstrate developmental and functional neuronal alteration as a consequence of downregulation of RAB39B and emphasize the critical role of vesicular trafficking in the development of neurons and human intellectual abilities.

Figure 1

RAB39B Mutations in Family X (D-23) and MRX72 (A and B) The upper panels show the corresponding sequence from a normal individual; the lower panels are from the patients. Arrows indicate the mutations. Sequence numbers refer to the human RAB39B cDNA (NM_171998). (C) Immunoblot analysis performed on 30 μg of total protein extracted from HeLa cells transfected with pFLAG-RAB39B constructs containing the wild-type RAB39B cDNA (WT), family X (D-23) mutated cDNA, or MRX72 cDNA. The 24-kDa band corresponds to FLAG-RAB39B fusion protein, and the 51-kDa band corresponds to beta-tubulin. MOCK: cells transfected with pCMV2-FLAG. NT: cells not transfected. (D) Pedigree of family X (D-23). (E) Pedigree of MRX72. Black squares indicate males with mental retardation, dotted circles indicate carrier females, and open symbols indicate unaffected individuals. Asterisks indicate family members who have been sequenced in this study.

Figure 2

Expression Analysis on Different Human and Mouse Tissues (A) Expression of RAB39B transcript in different human tissues. (B) Expression of Rab39b transcript in mouse tissues. (C) Expression profile of Rab39b and Rab39a in mouse total brain during post-natal (P) development (from P1 to P180; for each age point, n = 8). Data were expressed as Rab39b or Rab39a expression normalized to Histone-H3 (2^{-ΔCt(Rab39b–H3)}) (±SE).

Figure 3

Rab39b Is Specifically Expressed in Neurons (A) In situ hybridization analysis of Rab39b on P90 mouse brain. Light-microscopic images showing the distribution of Rab39b mRNA in 20 μm mouse brain sagittal sections. Anti-sense (A) and sense (B) Rab39b probe. (C–F) Enlargements of specific regions: CC, cerebral cortex; CbC, cerebellar cortex; Hi, hippocampus; OB, olfactory bulb; T, thalamus; S, subiculum; CA1 and CA3, fields of the hippocampus; DG, dentate gyrus; PL, Purkinje layer; and Mi, mitral cells. Scale bars represent 2 mm (A and B) and 0.1 mm (C–F). (G) Rab39b expression normalized to Histone-H3 (2^{-ΔCt(Rab39b–H3)}) in neuronal cell types. P2 mouse cerebral cortices were dissected, dissociated in trypsin medium, and plated. Different neuronal cell types were prepared as described.Rab39b is specifically expressed in neuronal precursors and neurons.

Figure 4

RAB39B Intracellular Localization in Mouse Hippocampal Neurons Neurons were transduced at 3 DIV with pCCL-RAB39B lentiviral particles (green) at an MOI of 1 and analyzed at 7 DIV. The major colocalization was with GM130 (cis-Golgi) and GIANTIN (Golgi complex), VAMP4 and SYNTAXIN16 (STX16)—involved in trafficking from the cell surface to the trans-Golgi network (TGN)—and SYNTAXIN13 (STX13) and RAB11, which are present in recycling endosomes. No colocalization was observed with the adaptor protein 2 (AP2). The scale bar represents 10 μm.

Figure 5

RAB39B Is Involved in Neurite Differentiation Hippocampal neurons were transduced with lentiviral particles containing shRab39b and shScramble at an MOI of 1. The downregulation of the endogenous Rab39b RNA level was quantified at 3 DIV by qRT-PCR, and 40% reduction was observed in shRab39b-transduced neurons. (A) There was a significant difference (p = 0.005) in the mean number of growth cones (GCs) at each neurite terminal (±SE) in shRab39b neurons (3.1 ± 0.1) versus shScramble neurons (3.8 ± 0.1) (mean ± SEM). (B) There was a significant difference (p = 0.05) in the mean area of GCs (±SE) in shRab39b neurons versus shScramble neurons (38.7 ± 2.8 [mean ± SEM] and 30.8 ± 2.4, respectively). (C) TRITC-Phalloidin immunostaining revealed altered GC morphology (enlargement of GC morphology in right panel). The scale bar represents 10 μm. (D) For Sholl analysis, as a measure of neuronal differentiation, a mask of concentric circles 5 μm apart was created and superimposed on neuronal cells. The first 10 μm from the center of the mask corresponds to the neuronal cell body. Repeated-measures ANOVA revealed significant differences between treatments, where F (1,147) = 6.6, p = 0.01, and between treatment and Sholl category (μm from the cell body), where F (1,5) = 2.3, p = 0.04. Factorial ANOVA for each Sholl category revealed a significant p value for 30 μm [F (1,147) = 9.3, p = 0.003], 35 μm [F (1,147) = 7.6, p = 0.006], and 40 μm [F (1,147) = 7.2; p = 0.007]. ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001. Data are expressed as means ±SE.

Figure 6

RAB39B Localizes to Golgi-Derived Vesicles (A) Hippocampal neurons transduced immediately after being plated with pCCL-RAB39B lentiviral particles at an MOI of 1 and immunostained at 3 DIV. TRITC-Phalloidin and anti-Tuj1 immunostaining revealed that RAB39B occupied a region similar to that of the GC actin domain. (B) A partial colocalization was observed with GIANTIN, as a marker for the Golgi-derived vesicles, as shown by the arrows in the enlargement in the merged right panel. The scale bar represents 10 μm.

Figure 7

RAB39B Is Involved in Synapse Formation Hippocampal neurons were transduced immediately after being plating with shRab39b and shScramble lentiviral particles at an MOI of 1. The downregulation of the endogenous Rab39b RNA level was quantified at 7 DIV by qRT-PCR, and 70% reduction was observed in shRab39b-transduced neurons. (A and B) SYNAPSIN1 immunostaining and quantification showed a 49% reduction in the SYN1 pre-synaptic compartment on shRab39b compared to shScramble neurons. (C) FM4-64-positive labeling showed a 40% reduction for shRab39b neurons compared to shScramble. The scale bar represents 10 μm. ^∗∗∗p < 0.001. Data are expressed as means ±SE.