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Human intellectual disability genes form conserved functional modules in Drosophila.

Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L, Galy A, van Bokhoven H, Habermann B, Brunner HG, Zweier C, Verstreken P, Huynen MA, Schenck A - PLoS Genet. (2013)

Bottom Line: Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development.Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved.The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands.

ABSTRACT
Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

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Histological analysis of Drosophila ID gene knockdown eyes with ERG defects.(A) Wildtype pattern of an ommatidia array in a transversal section of a control retina. Arrowhead: pigment cells (A′) Longitudinal section of a single ommatidium, lens to the top. The horizontal line and asterisk mark the level of the transversal section in all other panels. Dark structures (A, A′) are rhabdomeres, the photosensitive domains of Photoreceptors (PRs). (B) Schematic drawing of PR 1–7 in their typical stereotype pattern. PR cytoplasms in light grey. R: rhabdomeres. (C–I) A selection of histological sections of Drosophila ID gene knockdown eyes. Corresponding human gene names are indicated. Genes that have not previously been associated with histological phenotypes are highlighted in bold. The novelty of these data is discussed in Table S2. (C,C′) Transversal and longitudinal sections reveal a TBCE mutant phenotype of developmental origin. Arrowheads: bulky rhabdomeres, arrows: mis-positioned PR8s. (D–F) and genes indicated to their right: neurodegeneration in several ID conditions. Arrows in D point to black photoreceptor cytoplasms, arrowheads to single lost PRs/rhabdomeres. Massive loss of PRs can be seen in panels E and F. (G–I) and genes indicated to their right: structurally intact photoreceptors. Genotypes are provided in Table S1B.
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pgen-1003911-g003: Histological analysis of Drosophila ID gene knockdown eyes with ERG defects.(A) Wildtype pattern of an ommatidia array in a transversal section of a control retina. Arrowhead: pigment cells (A′) Longitudinal section of a single ommatidium, lens to the top. The horizontal line and asterisk mark the level of the transversal section in all other panels. Dark structures (A, A′) are rhabdomeres, the photosensitive domains of Photoreceptors (PRs). (B) Schematic drawing of PR 1–7 in their typical stereotype pattern. PR cytoplasms in light grey. R: rhabdomeres. (C–I) A selection of histological sections of Drosophila ID gene knockdown eyes. Corresponding human gene names are indicated. Genes that have not previously been associated with histological phenotypes are highlighted in bold. The novelty of these data is discussed in Table S2. (C,C′) Transversal and longitudinal sections reveal a TBCE mutant phenotype of developmental origin. Arrowheads: bulky rhabdomeres, arrows: mis-positioned PR8s. (D–F) and genes indicated to their right: neurodegeneration in several ID conditions. Arrows in D point to black photoreceptor cytoplasms, arrowheads to single lost PRs/rhabdomeres. Massive loss of PRs can be seen in panels E and F. (G–I) and genes indicated to their right: structurally intact photoreceptors. Genotypes are provided in Table S1B.

Mentions: Internal eye architecture and the state of photoreceptors were monitored in order to obtain further insights into the cellular basis of the identified neurophysiological defects. Each wild-type ommatidium contains eight photoreceptors, organized in a stereotypical pattern (Figure 3A,B). Histological sections of ERG-defective Drosophila ID conditions detected a number of phenotypes (Figure 3, Table S1B). For example, knockdown of TBCE/tbce, implicated in hypoparathyroidism-retardation-dysmorphism syndrome, showed structural defects of developmental origin. R8 photoreceptors, normally located underneath photoreceptor 7, failed to be maintained in their appropriate proximal position and thus appeared in distal sections (Figure 3C). Moreover, rhabdomere extension towards the retina base, a process taking place during pupal development, failed in the majority of ommatidia (Figure 3C′) leading to distally accumulated “bulky” rhabdomeres (Figure 3C). This defect has recently been associated with regulators of the actin cytoskeleton that are linked to ID [23], [24]. In contrast, RNAi against several ERG defective Drosophila ID genes, including PEX7, ARFGEF2 and PAFAH1B1 caused neuronal degeneration of variable degrees, identifying a role for the encoded proteins in neuronal maintenance (Figure 3D–F). Thirteen of 21 ERG defective Drosophila ID conditions, including NKX2-1, PRPS1 and ATP6V0A2 knockdown animals, showed intact and properly organized photoreceptors (Figure 3G–I). Some of these conditions showed darker photoreceptor cytoplasm or pigment cell abnormalities (Figure 3G–I and Table S1B).


Human intellectual disability genes form conserved functional modules in Drosophila.

Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L, Galy A, van Bokhoven H, Habermann B, Brunner HG, Zweier C, Verstreken P, Huynen MA, Schenck A - PLoS Genet. (2013)

Histological analysis of Drosophila ID gene knockdown eyes with ERG defects.(A) Wildtype pattern of an ommatidia array in a transversal section of a control retina. Arrowhead: pigment cells (A′) Longitudinal section of a single ommatidium, lens to the top. The horizontal line and asterisk mark the level of the transversal section in all other panels. Dark structures (A, A′) are rhabdomeres, the photosensitive domains of Photoreceptors (PRs). (B) Schematic drawing of PR 1–7 in their typical stereotype pattern. PR cytoplasms in light grey. R: rhabdomeres. (C–I) A selection of histological sections of Drosophila ID gene knockdown eyes. Corresponding human gene names are indicated. Genes that have not previously been associated with histological phenotypes are highlighted in bold. The novelty of these data is discussed in Table S2. (C,C′) Transversal and longitudinal sections reveal a TBCE mutant phenotype of developmental origin. Arrowheads: bulky rhabdomeres, arrows: mis-positioned PR8s. (D–F) and genes indicated to their right: neurodegeneration in several ID conditions. Arrows in D point to black photoreceptor cytoplasms, arrowheads to single lost PRs/rhabdomeres. Massive loss of PRs can be seen in panels E and F. (G–I) and genes indicated to their right: structurally intact photoreceptors. Genotypes are provided in Table S1B.
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pgen-1003911-g003: Histological analysis of Drosophila ID gene knockdown eyes with ERG defects.(A) Wildtype pattern of an ommatidia array in a transversal section of a control retina. Arrowhead: pigment cells (A′) Longitudinal section of a single ommatidium, lens to the top. The horizontal line and asterisk mark the level of the transversal section in all other panels. Dark structures (A, A′) are rhabdomeres, the photosensitive domains of Photoreceptors (PRs). (B) Schematic drawing of PR 1–7 in their typical stereotype pattern. PR cytoplasms in light grey. R: rhabdomeres. (C–I) A selection of histological sections of Drosophila ID gene knockdown eyes. Corresponding human gene names are indicated. Genes that have not previously been associated with histological phenotypes are highlighted in bold. The novelty of these data is discussed in Table S2. (C,C′) Transversal and longitudinal sections reveal a TBCE mutant phenotype of developmental origin. Arrowheads: bulky rhabdomeres, arrows: mis-positioned PR8s. (D–F) and genes indicated to their right: neurodegeneration in several ID conditions. Arrows in D point to black photoreceptor cytoplasms, arrowheads to single lost PRs/rhabdomeres. Massive loss of PRs can be seen in panels E and F. (G–I) and genes indicated to their right: structurally intact photoreceptors. Genotypes are provided in Table S1B.
Mentions: Internal eye architecture and the state of photoreceptors were monitored in order to obtain further insights into the cellular basis of the identified neurophysiological defects. Each wild-type ommatidium contains eight photoreceptors, organized in a stereotypical pattern (Figure 3A,B). Histological sections of ERG-defective Drosophila ID conditions detected a number of phenotypes (Figure 3, Table S1B). For example, knockdown of TBCE/tbce, implicated in hypoparathyroidism-retardation-dysmorphism syndrome, showed structural defects of developmental origin. R8 photoreceptors, normally located underneath photoreceptor 7, failed to be maintained in their appropriate proximal position and thus appeared in distal sections (Figure 3C). Moreover, rhabdomere extension towards the retina base, a process taking place during pupal development, failed in the majority of ommatidia (Figure 3C′) leading to distally accumulated “bulky” rhabdomeres (Figure 3C). This defect has recently been associated with regulators of the actin cytoskeleton that are linked to ID [23], [24]. In contrast, RNAi against several ERG defective Drosophila ID genes, including PEX7, ARFGEF2 and PAFAH1B1 caused neuronal degeneration of variable degrees, identifying a role for the encoded proteins in neuronal maintenance (Figure 3D–F). Thirteen of 21 ERG defective Drosophila ID conditions, including NKX2-1, PRPS1 and ATP6V0A2 knockdown animals, showed intact and properly organized photoreceptors (Figure 3G–I). Some of these conditions showed darker photoreceptor cytoplasm or pigment cell abnormalities (Figure 3G–I and Table S1B).

Bottom Line: Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development.Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved.The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands.

ABSTRACT
Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

Show MeSH
Related in: MedlinePlus