Mutations in mitochondrial enzyme GPT2 cause metabolic dysfunction and neurological disease with developmental and progressive features

Mutations that cause neurological phenotypes are highly informative with regard to mechanisms governing human brain function and disease. We report autosomal recessive mutations in the enzyme glutamate pyruvate transaminase 2 (GPT2) in large kindreds initially ascertained for intellectual and developmental disability (IDD). GPT2 [also known as alanine transaminase 2 (ALT2)] is one of two related transaminases that catalyze the reversible addition of an amino group from glutamate to pyruvate, yielding alanine and α-ketoglutarate. In addition to IDD, all affected individuals show postnatal microcephaly and ∼80% of those followed over time show progressive motor symptoms, a spastic paraplegia. Homozygous nonsense p.Arg404* and missense p.Pro272Leu mutations are shown biochemically to be loss of function. The GPT2 gene demonstrates increasing expression in brain in the early postnatal period, and GPT2 protein localizes to mitochondria. Akin to the human phenotype, Gpt2-null mice exhibit reduced brain growth. Through metabolomics and direct isotope tracing experiments, we find a number of metabolic abnormalities associated with loss of Gpt2. These include defects in amino acid metabolism such as low alanine levels and elevated essential amino acids. Also, we find defects in anaplerosis, the metabolic process involved in replenishing TCA cycle intermediates. Finally, mutant brains demonstrate misregulated metabolites in pathways implicated in neuroprotective mechanisms previously associated with neurodegenerative disorders. Overall, our data reveal an important role for the GPT2 enzyme in mitochondrial metabolism with relevance to developmental as well as potentially to neurodegenerative mechanisms.National Institute of Neurological Diseases and Stroke (U.S.) (R01NS035129)United States. National Institutes of Health (R21TW008223)National Cancer Institute (U.S.) (R01CA157996

Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks

DNA microarrays are powerful tools for comparing gene expression profiles from closely related organisms. However, a single microarray design is frequently used in these studies. Therefore, the levels of certain transcripts can be grossly underestimated due to sequence differences between the transcripts and the arrayed DNA probes. Here, we seek to improve the sensitivity and specificity of oligonucleotide microarray-based gene expression analysis by using genomic sequence information to predict the hybridization efficiency of orthologous transcripts to a given microarray. To test our approach, we examine hybridization patterns from three Escherichia coli strains on E.coli K-12 MG1655 gene expression microarrays. We create electronic mask files to discard data from probes predicted to have poor hybridization sensitivity and specificity to cDNA targets from each strain. We increased the accuracy of gene expression analysis and identified genes that cannot be accurately interrogated in each strain using these microarrays. Overall, these studies provide guidelines for designing effective electronic masks for gene expression analysis in organisms where substantial genome sequence information is available

Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Abstract Background Genetic studies in autism have pinpointed a heterogeneous group of loci and genes. Further, environment may be an additional factor conferring susceptibility to autism. Transcriptome studies investigate quantitative differences in gene expression between patient-derived tissues and control. These studies may pinpoint genes relevant to pathophysiology yet circumvent the need to understand genetic architecture or gene-by-environment interactions leading to disease. Methods We conducted alternate gene set enrichment analyses using differentially expressed genes from a previously published RNA-seq study of post-mortem autism cerebral cortex. We used three previously published microarray datasets for validation and one of the microarray datasets for additional differential expression analysis. The RNA-seq study used 26 autism and 33 control brains in differential gene expression analysis, and the largest microarray dataset contained 15 autism and 16 control post-mortem brains. Results While performing a gene set enrichment analysis of genes differentially expressed in the RNA-seq study, we discovered that genes associated with mitochondrial function were downregulated in autism cerebral cortex, as compared to control. These genes were correlated with genes related to synaptic function. We validated these findings across the multiple microarray datasets. We also did separate differential expression and gene set enrichment analyses to confirm the importance of the mitochondrial pathway among downregulated genes in post-mortem autism cerebral cortex. Conclusions We found that genes related to mitochondrial function were differentially expressed in autism cerebral cortex and correlated with genes related to synaptic transmission. Our principal findings replicate across all datasets investigated. Further, these findings may potentially replicate in other diseases, such as in schizophrenia

Additional file 9: of Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Table S7. DAVID functional annotation clustering analysis of Voineagu et al. downregulated genes. Using the genes downregulated in autism cerebral cortex from Voineagu et al., DAVID functional annotation clustering was performed to generate groups of enriched gene sets. The top 5 clusters had several gene sets related to mitochondrial function. (XLSX 49 kb

Additional file 4: of Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Table S3. DAVID functional annotation clustering analysis of Parikshak et al. downregulated genes. Using the genes downregulated in autism cerebral cortex from Parikshak et al., DAVID functional annotation clustering was performed to generate groups of enriched gene sets. (XLSX 134 kb

Additional file 1: of Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Figure S1. Venn diagram depicting the overlap of participants between the RNA-seq dataset and the three microarray datasets analyzed in this study. See the “Participants” section under the “Methods” section for more information on each study. Both autism and control subjects are included in the Venn diagram. (PDF 176 kb

Additional file 5: of Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Table S4. Synapse pathway and mitochondria pathway genes. The mitochondria pathway genes were downregulated in autism cerebral cortex in Parikshak et al. and were members of the GO “Mitochondrion” term. The synapse pathway genes were also downregulated in Parikshak et al. and were members of the UniProt “Synapse” term. All genes in the synapse pathway and in the related “M12” module from Voineagu et al. [17] were excluded from the mitochondria pathway. (XLSX 16 kb