Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

Coding variants represent many of the strongest associations between genotype and phenotype; however, they exhibit interindividual differences in effect, termed 'variable penetrance'. Here, we study how cis-regulatory variation modifies the penetrance of coding variants. Using functional genomic and genetic data from the Genotype-Tissue Expression Project (GTEx), we observed that in the general population, purifying selection has depleted haplotype combinations predicted to increase pathogenic coding variant penetrance. Conversely, in cancer and autism patients, we observed an enrichment of penetrance increasing haplotype configurations for pathogenic variants in disease-implicated genes, providing evidence that regulatory haplotype configuration of coding variants affects disease risk. Finally, we experimentally validated this model by editing a Mendelian single-nucleotide polymorphism (SNP) using CRISPR/Cas9 on distinct expression haplotypes with the transcriptome as a phenotypic readout. Our results demonstrate that joint regulatory and coding variant effects are an important part of the genetic architecture of human traits and contribute to modified penetrance of disease-causing variants.Peer reviewe

Methamphetamine-Induced Dopamine-Independent Alterations in Striatal Gene Expression in the 6-Hydroxydopamine Hemiparkinsonian Rats

Unilateral injections of 6-hydroxydopamine into the medial forebrain bundle are used extensively as a model of Parkinson's disease. The present experiments sought to identify genes that were affected in the dopamine (DA)–denervated striatum after 6-hydroxydopamine-induced destruction of the nigrostriatal dopaminergic pathway in the rat. We also examined whether a single injection of methamphetamine (METH) (2.5 mg/kg) known to cause changes in gene expression in the normally DA-innervated striatum could still influence striatal gene expression in the absence of DA. Unilateral injections of 6-hydroxydopamine into the medial forebrain bundle resulted in METH-induced rotational behaviors ipsilateral to the lesioned side and total striatal DA depletion on the lesioned side. This injection also caused decrease in striatal serotonin (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels. DA depletion was associated with increases in 5-HIAA/5-HT ratios that were potentiated by the METH injection. Microarray analyses revealed changes (± 1.7-fold, p<0.025) in the expression of 67 genes on the lesioned side in comparison to the intact side of the saline-treated hemiparkinsonian animals. These include follistatin, neuromedin U, and tachykinin 2 which were up-regulated. METH administration caused increases in the expression of c-fos, Egr1, and Nor-1 on the intact side. On the DA-depleted side, METH administration also increased the expression of 61 genes including Pdgf-d and Cox-2. There were METH-induced changes in 16 genes that were common in the DA-innervated and DA-depleted sides. These include c-fos and Nor-1 which show greater changes on the normal DA side. Thus, the present study documents, for the first time, that METH mediated DA-independent changes in the levels of transcripts of several genes in the DA-denervated striatum. Our results also implicate 5-HT as a potential player in these METH-induced alterations in gene expression because the METH injection also caused significant increases in 5-HIAA/5-HT ratios on the DA-depleted side

Retrograde Axonal-transport of Neurotensin in Rat Nigrostriatal Dopaminergic-neurons - Modulation During Aging and Possible Physiological-role

Biochemical and anatomical data are reported which demonstrate for the first time the existence of a retrograde axonal transport process for a neuropeptide, neurotensin, in rat brain. Neurotensin receptors are mainly located in the striatum on nerve terminals of the nigrostriatal dopaminergic pathway. Thus, the association of specific neurotensin receptors on a wen defined pathway provides an excellent model to investigate the existence of such a process. Two hours after the intrastriatal injection of iodinated neurotensin, radioactivity started to accumulate in the ipsilateral substantia nigra. The levels were maximal during the fourth hour. The appearance of this labelling was prevented by injection of a large excess of unlabelled neurotensin or of neurotensin 8-13, an active neurotensin fragment, but not by neurotensin 1-8 which had no affinity for neurotensin receptors. These results suggest that the appearance of radioactivity in the ipsilateral substantia nigra was dependent on the initial binding of this peptide to its receptors in the striatum. HPLC studies demonstrated that the radioactivity found in the substantia nigra corresponded to intact neurotensin and to degradation products of this peptide. Moreover, it has been shown that this retrograde transport was microtubule-dependent and occurred in dopaminergic nigrostriatal neurons. Light and electron microscopic data confirmed and extended the present results. Four and a half hours after intrastriatal injection of iodinated neurotensin, silver grains were mainly detected in dopaminergic perikarya of the substantia nigra pars compacta. The vast majority were associated with neuronal elements and their localization within cell bodies suggests that retrogradely transported neurotensin may be processed along a variety of intracellular pathways including those mediating recycling in the rough endoplasmic reticulum and degradation in lysosomes. However, the presence of silver grains over the nucleus, as well as the increase in tyrosine-hydroxylase mRNA expression in the ipsilateral substantia nigra 4 hr after intrastriatal injection of neurotensin support the concept that neurotensin alone, or associated with its receptor, might be involved in the regulation of gene expression. Finally, we have demonstrated that in old rats the quantity of retrogradely transported neurotensin was significantly decreased as compared to that observed in young adult rats. This retrograde axonal transport of a neuropeptide may represent, as already suggested for growth factors, an important dynamic process conveying information from nerve terminals to the cell body