Haplotype association analysis of discrete and continuous traits using mixture of regression models

We present a regression-based method of haplotype association analysis for quantitative and dichotomous traits in samples consisting of unrelated individuals. The method takes account of uncertain phase by initially estimating haplotype frequencies and obtaining the posterior probabilities of all possible haplotype combinations in each individual, then using these as weights in a finite mixture of regression models. Using this method, different combinations of marker loci can be modeled, to find a parsimonious set of marker loci that are most predictive and therefore most likely to be closely associated with the a quantitative trait locus. The method has the additional advantage of being able to use individuals with some missing genotype data, by considering all possible genotypes at the missing markers. We have implemented this method using the SNPHAP and Mx programs and illustrated its use on published data on idiopathic generalized epilepsy.

Investigation of promoter variants of the histamine 1 and 2 receptors in schizophrenia and clozapine response

We report the identification of four novel histamine 1 (H1-17-C/T, -974-C/A, -1023-A/G and -1536-G/C) and four novel histamine 2 promoter polymorphisms (H2-294-A/G, -592-A/G, -1018-G/A and -1077-G/A) which we have investigated for involvement in susceptibility to schizophrenia, and in clinical response to clozapine treatment. We identified a weak independent association between variants at the H1-1536-G/C locus and schizophrenia, where an excess of the H1-1536-C allele was observed amongst such patients (P = 0.036). However upon correction for multiple testing this relationship was no longer statistically significant. Similar investigation of the H2 receptor polymorphisms revealed association between genotype at the H2-1018-G/A locus and clinical response to clozapine treatment (P = 0.027), though upon correction for multiple testing this difference was no longer significant. We have concluded that the participation of these variants in the disorder is unlikely, particularly in view of their apparent lack of function and unlikely influence on receptor expression. However their nature alludes to the potential presence of other more important alterations further along these regions, where sequences encoding alternate promoters have recently been identified for each receptor that may yet be found to harbour such polymorphisms.

Antidepressants enhance glucocorticoid receptor function in vitro by modulating the membrane steroid transporters

1. Previous data demonstrate that the tricyclic antidepressant, desipramine, induces glucocorticoid receptor (GR) translocation from the cytoplasm to the nucleus in L929 cells and increases dexamethasone-induced GR-mediated gene transcription in L929 cells stably transfected with the mouse mammary tumour virus-chloramphenicol acetyltransferase (MMTV-CAT) reporter gene (LMCAT cells) (Pariante et al., 1997). 2. To extend these findings, the present study has investigated the effects of 24 h coincubation of LMCAT cells with dexamethasone and amitriptyline, clomipramine, paroxetine, citalopram or fluoxetine. 3. All antidepressants, except fluoxetine, enhanced GR-mediated gene transcription, with clomipramine having the greatest effect (10 fold increase). Twenty-four hours coincubation of cells with desipramine, clomipramine or paroxetine, also enhanced GR function in the presence of cortisol, but not of corticosterone. 4. It is proposed that these effects are due to the antidepressants inhibiting the L929 membrane steroid transporter, which actively extrudes dexamethasone and cortisol from the cell, but not corticosterone. This is further confirmed by the fact that clomipramine failed to enhance GR-mediated gene transcription in the presence of dexamethasone when the membrane steroid transporter was blocked by verapamil. 5. The membrane steroid transporters that regulate access of glucocorticoids to the brain in vivo, like the multiple drug resistance p-glycoprotein, could be a fundamental target for antidepressant action.

Dishevelled regulates the metabolism of amyloid precursor protein via protein kinase C/mitogen-activated protein kinase and c-Jun terminal kinase

Alzheimer's disease (AD) is a disorder of two pathologies: amyloid plaques, the core of which is a peptide derived from the amyloid precursor protein (APP), and neurofibrillary tangles composed of highly phosphorylated tau. Protein kinase C (PKC) is known to increase non-amyloidogenic alpha-secretase cleavage of APP, producing secreted APP (sAPPalpha), and glycogen synthase kinase (GSK)-3beta is known to increase tau phosphorylation. Both PKC and GSK-3beta are components of the wnt signaling cascade. Here we demonstrate that overexpression of another member of this pathway, dishevelled (dvl-1), increases sAPPalpha production. The dishevelled action on APP is mediated via both c-jun terminal kinase (JNK) and protein kinase C (PKC)/mitogen-activated protein (MAP) kinase but not via p38 MAP kinase. These data position dvl-1 upstream of both PKC and JNK, thereby explaining the previously observed dual signaling action of dvl-1. Furthermore, we show that human dvl-1 and wnt-1 also reduce the phosphorylation of tau by GSK-3beta. Therefore, both APP metabolism and tau phosphorylation are potentially linked through wnt signaling.

Haplotype transmission disequilibrium and evidence for linkage of the CHRNA7 gene region to schizophrenia in Southern African Bantu families

Recent reports have strongly linked markers near the alpha-7 nicotinic cholinergic receptor subunit gene on human chromosome 15q13-q14 to a sensory gating deficit common in schizophrenics, and have shown positive though non-significant results linking this region to the primary phenotype of schizophrenia in a sample of North American families. We therefore tested for linkage between markers in this region of chromosome 15q and schizophrenia in a sample of 15 multiply affected and 5 single case families with schizophrenia drawn from the Bantu-speaking black population of South Africa. An initial replication using markers from the original study gave an affected-only LOD score maximum of 1.08 under a recessive model at Theta=0.00 for D15S1360, a dinucleotide polymorphism found on the same YAC as the alpha-7 receptor gene. Nonparametric affected-only multipoint analysis gave a Z-score of 1. 29, P=0.098, for D15S1360, and Z=1.45, p=0.075 for D15S118. We then increased the resolution of the map with an extended set of 20 markers. Again, two peaks were observed, with NPL scores of 1.81, p=0.037, at D15S1043 and 1.79 at D15S1360 and 1.80 at D15S1010, both p=0.037. Transmission disequilibrium testing of data from D15S1360 gave an allele-wise and genotype-wise chi(2) of 6.59, 2 df, p=0.037. Haplotype transmission disequilibrium testing using a restricted allele and haplotype set from D15S1043 and D15S1360 gave a global chi(2) of 10.647, 4 df, P=0.007, and a maximum chi(2) of 6.567, 1 df, P=0.004 for excess transmission of the 1.2 haplotype into affected offspring. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:196-201, 2000.

Molecular cloning of human GABABR1 and its tissue distribution

GABABR1 clones were isolated from a human cerebellum library. The human sequence is very similar to rat GABABR1 with the cDNAs sharing 91.3% sequence identity and the receptors sharing 98.6% amino acid sequence identity. Northern blotting has shown that the receptor is brain-specific with a widespread distribution throughout the brain but none detected in the spinal cord.

Immunohistochemical localisation of mGluR7 protein in the rodent and human cerebellar cortex using subtype specific antibodies

Metabotropic glutamate receptors (mGluRs) are a heterogeneous family of G protein coupled receptors that are linked to multiple second messenger systems to regulate neuronal excitability and synaptic transmission. To characterise the protein expression of the two mGluR7 receptor splice variants in human and rat cerebellar cortex, antibodies specific to mGluR7 were generated. Antibodies were raised against a glutathione-S-transferase fusion protein containing amino acid residues located in the extracellular domain common to both the human and rat mGluR7 splice variants. These antibodies specifically detected human mGluR7a in mammalian cells transfected with this receptor. In agreement with mGluR7 in situ hybridisation studies, immunohistochemistry performed at the light microscope level revealed that mGluR7 protein expression occurred most prominently in a particular population of nerve cells common to both the human and rat, located within the cerebellar cortex of gray matter contained within transverse folia. Moreover, strong mGluR7-like immunoreactivity was seen in Purkinje cell body cytoplasm of the Purkinje cell layer. In the most superficial cerebellar cortical layer, the molecular layer, immunostaining was observed in Purkinje cell associated proximal and distal dendritic trees. No detectable labelling was evident in intrinsic deep cerebellar nuclei known to contain GABAergic terminals of projecting Purkinje cell axons. These data are suggestive of a post-synaptic location of mGluR7 in this central nervous system structure. In the rodent, additional non-Purkinje cells thought to represent inhibitory interneurones were labelled at all levels in the molecular layer. mGluR7-like immunoreactivity was not associated with glial cells.

Localization of mGluR4 protein in the rat cerebral cortex and hippocampus

The cellular distribution of the rat metabotropic glutamate receptor type 4 (mGluR4) was examined in the adult rat cerebral cortex and hippocampus. Antibodies were raised against amino acid residues located in the extracellular amino terminal domain that is common to both the mGluR4a and mGluR4b splice variants, and used for an immunohistochemical investigation. The affinity-purified antibodies on immunoblot analysis specifically detected mGluR4 protein in transfected mammalian cells, showing no cross-reactivity with other members of the mGluR family. At the light microscope level intense mGluR4-like immunoreactivity was detected in the CA2 region of Ammon's horn in the hippocampus. In the cerebral cortex numerous non-pyramidal cells were strongly immunolabelled.

Molecular characterization and localization of human metabotropic glutamate receptor type 3

A human brain cDNA library was screened using amplified human metabotropic glutamate receptor (mGluR) cDNA sequences as probes. The resulting clones included one containing the complete coding sequence of mGluR3. This sequence has 90% DNA sequence identity with rat mGluR3 and the predicted protein sequence has 97% identity. The mGluR3 cDNA was transfected in Chinese hamster ovary (CHO) cells. Stimulation of the expressed receptor by (2S,3S,4S)-alpha-(carboxycyclopropyl) glycine (L-CCG-I) resulted in a reduction of forskolin-stimulated cyclic AMP (cAMP) with EC50 values of 0.15-0.3 microM. A specific probe from the human mGluR3 clone was used to hybridise to Northern blots of mRNA from various human tissues and different brain regions. The mGluR3 mRNA is brain-specific, and is expressed in all the brain regions represented on the blot. In-situ hybridization studies on human brain sections confirmed this widespread distribution with expression in neurones in the cerebral cortex, caudate-putamen, thalamus and cerebellum.

Human metabotropic glutamate receptor type 7: molecular cloning and mRNA distribution in the CNS

Human metabotropic glutamate receptor type 7 (mGluR7) cDNA clones were isolated from a medulla cDNA library. The sequence, which includes a polymorphism, has 92% DNA sequence identity with rat mGluR7 and the predicted protein sequence has 99% identity. In-situ hybridization studies on human brain sections showed that mGluR7 mRNA has a widespread distribution with highest levels in the hippocampal formation, cerebral cortex and cerebellum.

Molecular characterization and localization of human metabotropic glutamate receptor type 4

Oligonucleotides of consensus sequences from rat metabotropic glutamate receptor (mGluR) genes were synthesized and used to amplify human DNA by the polymerase chain reaction (PCR). Five unique human sequences homologous to these rat receptor genes were isolated including mGluR4. A human cerebellum cDNA library was screened using this amplified mGluR4 sequence as a probe and yielded clones which between them contained the complete coding sequence for human mGluR4. The coding sequence is very similar to the equivalent rat gene (90% DNA sequence identity and 97% predicted protein sequence identity). The mGluR4 cDNA was transfected in Chinese hamster ovary (CHO) cells and stable clonal cell lines were isolated. Stimulation of the expressed receptor by L-2-amino-4-phosphonobutyrate (L-AP4), L-glutamate or (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid (1S,3R-ACPD) resulted in a reduction of forskolin-stimulated cyclic AMP (cAMP) with EC50 values of 0.2, 13 and 90 microM respectively. Quisqualate had little effect at concentrations up to 1 mM. In Northern blots mGluR4 mRNA appears to be brain-specific, and shows a distinct distribution (excluding the cerebellum), being expressed in the thalamus, hypothalamus and caudate nucleus. In situ hybridization studies on human brain sections confirmed this general pattern of distribution. The strongest mGluR4 mRNA signal was found in the cerebellar granule cells consistent with the reported distribution of mGluR4 in the rat brain. The major difference from the rat brain is the presence in the human brain of mGluR4 mRNA in the caudate nucleus and putamen.

Translational fusions with fragments of the trpE gene improve the expression of a poorly expressed heterologous gene in Escherichia coli

A series of plasmids expressing fusions between the trpE gene product, anthranilate synthase component I and the major immunogen (VP1) of foot and mouth disease virus were constructed such that increasing amounts of the 3' end of trpE were deleted. Deletions removing up to 70% of trpE had little effect on the quantity of fusion protein expressed, while the number of molecules appeared to increase. Larger deletions led to a steady decrease in both the quantity of fusion protein produced and in the number of molecules. This is consistent with trpE being responsible for the high levels of expression of VP1 by its gene product stabilizing VP1 against proteolytic degradation. Some out-of-frame deletion mutants were also produced. All deletion mutants in one wrong reading frame expressed low levels of two VP1-containing polypeptides. This observation is interpreted as being due to re-initiation of translation at a site inside the VP1 sequence which is activated by local termination of translation.