Genome-wide association meta-analysis of age at first cannabis use

BACKGROUND AND AIMS

Cannabis is one of the most commonly used substances among adolescents and young adults. Earlier age at cannabis initiation is linked to adverse life outcomes, including multi-substance use and dependence. This study estimated the heritability of age at first cannabis use and identified associations with genetic variants.

METHODS

A twin-based heritability analysis using 8055 twins from three cohorts was performed. We then carried out a genome-wide association meta-analysis of age at first cannabis use in a discovery sample of 24 953 individuals from nine European, North American and Australian cohorts, and a replication sample of 3735 individuals.

RESULTS

The twin-based heritability for age at first cannabis use was 38% [95% confidence interval (CI) = 19-60%]. Shared and unique environmental factors explained 39% (95% CI = 20-56%) and 22% (95% CI = 16-29%). The genome-wide association meta-analysis identified five single nucleotide polymorphisms (SNPs) on chromosome 16 within the calcium-transporting ATPase gene (ATP2C2) at P < 5E-08. All five SNPs are in high linkage disequilibrium (LD) (r2  > 0.8), with the strongest association at the intronic variant rs1574587 (P = 4.09E-09). Gene-based tests of association identified the ATP2C2 gene on 16q24.1 (P = 1.33e-06). Although the five SNPs and ATP2C2 did not replicate, ATP2C2 has been associated with cocaine dependence in a previous study. ATP2B2, which is a member of the same calcium signalling pathway, has been associated previously with opioid dependence. SNP-based heritability for age at first cannabis use was non-significant.

CONCLUSION

Age at cannabis initiation appears to be moderately heritable in western countries, and individual differences in onset can be explained by separate but correlated genetic liabilities. The significant association between age of initiation and ATP2C2 is consistent with the role of calcium signalling mechanisms in substance use disorders.

Effects of tetrahydrocannabinol on glucose uptake in the rat brain

Δ⁹-Tetrahydrocannabinol (THC) is the psychoactive component of the plant Cannabis sativa and acts as a partial agonist at cannabinoid type 1 and type 2 receptors in the brain. The goal of this study was to assess the effect of THC on the cerebral glucose uptake in the rat brain. 21 male Sprague Dawley rats (12-13 w) were examined and received five different doses of THC ranging from 0.01 to 1 mg/kg. For data acquisition a Focus 120 small animal PET scanner was used and 24.1-28.0 MBq of [¹⁸F]-fluoro-2-deoxy-d-glucose were injected. The data were acquired for 70 min and arterial blood samples were collected throughout the scan. THC, THC-OH and THC-COOH were determined at 55 min p.i. Nine volumes of interest were defined, and the cerebral glucose uptake was calculated for each brain region. Low blood THC levels of < 1 ng/ml (injected dose: ≤ 0.01 mg/kg) corresponded to an increased glucose uptake (6-30 %), particularly in the hypothalamus (p = 0.007), while blood THC levels > 10 ng/ml (injected dose: ≥ 0.05 mg/kg) coincided with a decreased glucose uptake (-2 to -22 %), especially in the cerebellar cortex (p = 0.008). The effective concentration in this region was estimated 2.4 ng/ml. This glucose PET study showed that stimulation of CB1 receptors by THC affects the glucose uptake in the rat brain, whereby the effect of THC is regionally different and dependent on dose - an effect that may be of relevance in behavioural studies.

Genome-wide association study of lifetime cannabis use based on a large meta-analytic sample of 32 330 subjects from the International Cannabis Consortium

Cannabis is the most widely produced and consumed illicit psychoactive substance worldwide. Occasional cannabis use can progress to frequent use, abuse and dependence with all known adverse physical, psychological and social consequences. Individual differences in cannabis initiation are heritable (40-48%). The International Cannabis Consortium was established with the aim to identify genetic risk variants of cannabis use. We conducted a meta-analysis of genome-wide association data of 13 cohorts (N=32 330) and four replication samples (N=5627). In addition, we performed a gene-based test of association, estimated single-nucleotide polymorphism (SNP)-based heritability and explored the genetic correlation between lifetime cannabis use and cigarette use using LD score regression. No individual SNPs reached genome-wide significance. Nonetheless, gene-based tests identified four genes significantly associated with lifetime cannabis use: NCAM1, CADM2, SCOC and KCNT2. Previous studies reported associations of NCAM1 with cigarette smoking and other substance use, and those of CADM2 with body mass index, processing speed and autism disorders, which are phenotypes previously reported to be associated with cannabis use. Furthermore, we showed that, combined across the genome, all common SNPs explained 13-20% (P<0.001) of the liability of lifetime cannabis use. Finally, there was a strong genetic correlation (rg=0.83; P=1.85 × 10(-8)) between lifetime cannabis use and lifetime cigarette smoking implying that the SNP effect sizes of the two traits are highly correlated. This is the largest meta-analysis of cannabis GWA studies to date, revealing important new insights into the genetic pathways of lifetime cannabis use. Future functional studies should explore the impact of the identified genes on the biological mechanisms of cannabis use.

Genome-Wide Association Study of Behavioral Disinhibition in a Selected Adolescent Sample

Behavioral disinhibition (BD) is a quantitative measure designed to capture the heritable variation encompassing risky and impulsive behaviors. As a result, BD represents an ideal target for discovering genetic loci that predispose individuals to a wide range of antisocial behaviors and substance misuse that together represent a large cost to society as a whole. Published genome-wide association studies (GWAS) have examined specific phenotypes that fall under the umbrella of BD (e.g. alcohol dependence, conduct disorder); however no GWAS has specifically examined the overall BD construct. We conducted a GWAS of BD using a sample of 1,901 adolescents over-selected for characteristics that define high BD, such as substance and antisocial behavior problems, finding no individual locus that surpassed genome-wide significance. Although no single SNP was significantly associated with BD, restricted maximum likelihood analysis estimated that 49.3 % of the variance in BD within the Caucasian sub-sample was accounted for by the genotyped SNPs (p = 0.06). Gene-based tests identified seven genes associated with BD (p ≤ 2.0 × 10(-6)). Although the current study was unable to identify specific SNPs or pathways with replicable effects on BD, the substantial sample variance that could be explained by all genotyped SNPs suggests that larger studies could successfully identify common variants associated with BD.

Assembly of high-areal-density deuterium-tritium fuel from indirectly driven cryogenic implosions

The National Ignition Facility has been used to compress deuterium-tritium to an average areal density of ~1.0±0.1 g cm(-2), which is 67% of the ignition requirement. These conditions were obtained using 192 laser beams with total energy of 1-1.6 MJ and peak power up to 420 TW to create a hohlraum drive with a shaped power profile, peaking at a soft x-ray radiation temperature of 275-300 eV. This pulse delivered a series of shocks that compressed a capsule containing cryogenic deuterium-tritium to a radius of 25-35 μm. Neutron images of the implosion were used to estimate a fuel density of 500-800 g cm(-3).

Combining peer discussion with instructor explanation increases student learning from in-class concept questions

Use of in-class concept questions with clickers can transform an instructor-centered "transmissionist" environment to a more learner-centered constructivist classroom. To compare the effectiveness of three different approaches using clickers, pairs of similar questions were used to monitor student understanding in majors' and nonmajors' genetics courses. After answering the first question individually, students participated in peer discussion only, listened to an instructor explanation only, or engaged in peer discussion followed by instructor explanation, before answering a second question individually. Our results show that the combination of peer discussion followed by instructor explanation improved average student performance substantially when compared with either alone. When gains in learning were analyzed for three ability groups of students (weak, medium, and strong, based on overall clicker performance), all groups benefited most from the combination approach, suggesting that peer discussion and instructor explanation are synergistic in helping students. However, this analysis also revealed that, for the nonmajors, the gains of weak performers using the combination approach were only slightly better than their gains using instructor explanation alone. In contrast, the strong performers in both courses were not helped by the instructor-only approach, emphasizing the importance of peer discussion, even among top-performing students.

Backscatter measurements for NIF ignition targets (invited)

Backscattered light via laser-plasma instabilities has been measured in early NIF hohlraum experiments on two beam quads using a suite of detectors. A full aperture backscatter system and near backscatter imager (NBI) instrument separately measure the stimulated Brillouin and stimulated Raman scattered light. Both instruments work in conjunction to determine the total backscattered power to an accuracy of ∼15%. In order to achieve the power accuracy we have added time-resolution to the NBI for the first time. This capability provides a temporally resolved spatial image of the backscatter which can be viewed as a movie.

Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents

Cannabis is a major substance of abuse, and the gene encoding for the central cannabinoid receptor (CNR1) is a logical candidate gene for vulnerability toward developing symptoms of cannabis dependence. We studied four single-nucleotide polymorphisms (SNPs) in the CNR1 gene for association with having one or more symptoms of cannabis dependence in 541 adolescent subjects who had all tried cannabis five or more times. Cases (327) were defined as those who had tried marijuana and developed one or more symptoms, and controls (214) as those who had tried marijuana but developed no dependence symptoms. Cannabis dependence symptoms were assessed in these youth when they were 17 or older with the Composite International Diagnostic Interview--Substance Abuse Module. Univariate (single-marker) association tests demonstrated that SNP rs806380, located in intron 2 of the CNR1 gene, was significantly associated with developing one or more cannabis dependence symptoms, with the G allele having a protective effect (P < 0.02). This was consistent with the results of the global haplotype test (P < 0.01). One of the common haplotypes examined (present in 21% of the subjects) was significantly associated with a lower rate of having one or more cannabis dependence symptoms. Our findings provide evidence suggesting that a common CNR1 haplotype is associated with developing fewer cannabis dependence symptoms among adolescents who have experimented with cannabis.

Immunostimulation by bacterial components: II. Efficacy studies and meta-analysis of the bacterial extract OM-89

The bacterial extract OM-89 (Uro-Vaxom) consisting of immunostimulating components derived from 18 Escherichia coli strains is used for the treatment of recurrent urinary tract infections. We investigated in the mouse the immunogenicity of the bacterial extract after oral administration. After repeated administration of OM-89, a specific serum IgG and IgA response against a number of bacterial strains was obtained. Supernatants of cell cultures prepared from the urogenital tract of immunized mice also contained increased levels of strain specific IgG and IgA. We could show a bias towards a Th1 type immune response as indicated by increased IgG2a levels in sera, and increased IFNgamma levels in supernatants of spleen cells. These findings may contribute to an understanding of the therapeutic effect of Uro-Vaxom: the metaanalysis of several clinical studies confirmed that Uro-Vaxom constitutes an effective prophylaxis for urinary tract infections.

Molecular recognition of synthetic siderophore analogues: a study with receptor-deficient and fhu(A-B) deletion mutants of Escherichia coli

The biological activity of six synthetic siderophore analogues (two dihydroxamates, two trihydroxamates, one tetrahydroxamate and one 3-hydroxy-4(1H)pyridinone) has been studied in Escherichia coli, Morganella morganii 13 and Proteus mirabilis 8993 strains by using growth promotion tests. Various transport-deficient mutants of E. coli were used to study the route of entry into gram-negative bacteria. The results indicated that the synthetic hydroxamate compounds are transported via Fhu-mediated transport systems, although receptor specificity was low. This could be proven by using a delta (fhuA-B) E. coli mutant as a control in which growth promotion by natural hydroxamates was completely abolished, suggesting that a periplasmic binding-protein-dependent transport system (FhuB, C, D) is required for the transport of all synthetic ferric hydroxamate complexes. Although utilization of the synthetic hydroxamates was generally lower than that of the natural siderophores, differences in growth promotion could be detected. Highest activity was observed with the dihydroxamate DOCYDHAMA ligand which supported growth at concentrations < 1 mM. In comparison with other polyamino-polyhydroxamate ligands studied, this dihydroxamate ligand has an extra diamide backbone that could be important for the interaction with the receptors or with FhuD. The synthetic trihydroxamate and tetrahydroxamate ligands showed a relatively low siderophore activity. Studies with Proteus and Morganella in the presence of increasing bipyridyl concentrations showed a decreased growth promotion with the synthetic ferric hydroxamates, suggesting the involvement of a reduction step during iron mobilization or an increased toxicity of bipyridyl. This was not observed in the case of the 3-hydroxy-4(1H)pyridinone where bipyridyl had no effect.

Organization of human and mouse skeletal myosin heavy chain gene clusters is highly conserved

Myosin heavy chains (MyHCs) are highly conserved ubiquitous actin-based motor proteins that drive a wide range of motile processes in eukaryotic cells. MyHC isoforms expressed in skeletal muscles are encoded by a multigene family that is clustered on syntenic regions of human and mouse chromosomes 17 and 11, respectively. In an effort to gain a better understanding of the genomic organization of the skeletal MyHC genes and its effects on the regulation, function, and molecular genetics of this multigene family, we have constructed high-resolution physical maps of both human and mouse loci using PCR-based marker content mapping of P1-artificial chromosome clones. Genes encoding six MyHC isoforms have been mapped with respect to their linear order and transcriptional orientations within a 350-kb region in both human and mouse. These maps reveal that the order, transcriptional orientation, and relative intergenic distances of these genes are remarkably conserved between these species. Unlike many clustered gene families, this order does not reflect the known temporal expression patterns of these genes. However, the conservation of gene organization since the estimated divergence of these species (approximately 75-110 million years ago) suggests that the physical organization of these genes may be significant for their regulation and function.

Chromosome 18 breakpoint in t(11;18)(q21;q21) translocation associated with MALT lymphoma is proximal to BCL2 and distal to DCC

The t(11;18)(q21;q21) translocation has recently been identified as a recurring chromosomal abnormality in a subset of extranodal marginal zone B-cell lymphoma, a low-grade lymphoma of mucosa-associated lymphoid tissue (MALT). Neither the 11q21 nor the 18q21 breakpoints have been characterized by molecular genetic analysis. As a prelude to isolation of the gene(s) involved in this translocation, we have mapped the 18q21 breakpoint region by fluorescence in situ hybridization (FISH) of YAC and PAC clones. We mapped 37 YACs assigned to a 29-cM region within the chromosomal band 18q21. Using nine of these YACs in single- and/or dual-color FISH to analyze three cases of MALT lymphomas with the t(11;18)(q21;q21) translocation, we localized the breakpoints within a 1.6-Mb nonchimeric YAC (938E1). This YAC is useful for the detection of the translocation in metaphase and in interphase cells. A nonchimeric YAC contig of an 8-cM region around the breakpoint comprising nine YACs and a PAC contig of YAC 938E1 were constructed, which enabled the refinement of the breakpoint region in the proximal region of the YAC within a <820-kb segment. This breakpoint is proximal to the BCL2 locus and distal to DCC and DPC4 loci in chromosomal band 18q21.

CONTIG EXPLORER: interactive marker-content map assembly

In STS-content mapping of a region, multiple optimal or near-optimal putative orders of markers exist. Determining which of the markers in this region can be placed reliably on the physical map of the chromosome and which markers lack sufficient evidence to be placed requires software that facilitates exploratory sensitivity analysis and interactive reassembly with different subsets of the imput data and that also assists the evaluation of any arbitrary (user-specified) marker order. We describe CONTIG EXPLORER, a package for interactive assembly of STS-content maps that provides the user with various ways of performing such analyses, thereby facilitating the design of laboratory experiments aimed at reducing ambiguity in STS order. We then compare the output of CONTIG EXPLORER with two other assembly programs, SEGMAP and CONTIGMAKER, for a region of chromosome 12p between 21 and 38 cM on the sex-averaged CEPH/Généthon linkage map.

Localization of the human achaete-scute homolog gene (ASCL1) distal to phenylalanine hydroxylase (PAH) and proximal to tumor rejection antigen (TRA1) on chromosome 12q22-q23

ASCL1, the human achaete-scute homolog, is a helix-loop-helix transcription factor that was previously assigned to chromosome 12 using a rodent-human somatic hybrid panel. We now placed this gene on a yeast artificial chromosome contig encompassing position 119 cM of the Généthon genetic map between the two genes phenylalanine hydroxylase (PAH) and tumor rejection antigen 1 (TRA1). We also localized ASCL1 in the 12q22-q23 cytogenetic interval by using fluorescence in situ hybridization.

Physical mapping of the human ELA1 gene between D12S361 and D12S347 on chromosome 12q13

ELA1, the pancreatic elastase 1 gene, is conserved in mammalian genomes. ELA1 was previously mapped to chromosome 12 using a panel of mouse-human somatic cell hybrids. We now report the physical and cytogenetic localization of the ELA1 gene. On the physical map, ELA1 is adjacent to the polymorphic marker AFMa283yg1 and between D12S361 and D12S347. Using fluorescence in situ hybridization, we determined that ELA1 maps to 12q13.

A second-generation YAC contig map of human chromosome 12

Human chromosome 12 constitutes approximately 4.5% of the human genome and has an estimated size of 135 million base pairs (Mb). We have started to construct a high-resolution physical map of chromosome 12 as overlapping yeast artificial chromosomes (YACs), using as a foundation the first-generation physical map of this chromosome covers nearly 102 Mb of DNA and includes 426 highly polymorphic, monomorphic and gene-based markers. We also mapped 119 of the YACs, most of which are part of the physical map, by cytogenetic methods. Thus the map integrates genetic, physical and cytogenetic data and provides information about the organization of this chromosome and will help in the localization and cloning of disease-related genes. The strategy used here to generate the chromosome-12 map could be applied for the rapid construction of physical and expression maps for other human chromosomes.

Unequal homologous recombination of human DNA on a yeast artificial chromosome

We examined unequal homologous DNA recombination between human repetitive DNA elements located on a yeast artificial chromosome (YAC) and transforming plasmid molecules. A plasmid vector containing an Alu element, as well as a sequence identical to a unique site on a YAC, was introduced into yeast and double recombinant clones analyzed. Recombination occurs between vector and YAC Alu elements sharing as little as 74% identity. The physical proximity of an Alu element to the unique DNA segment appears to play a significant role in determining the frequency with which that element serves as a recombination substrate. In addition, cross-over points of the recombination reaction are largely confined to the ends of the repetitive element. Since a similar distribution of crossover sites occurs during unequal homologous recombination in human germ and somatic tissue, we propose that similar enzymatic processes may be responsible for the events observed in our system and in human cells. This suggests that further examination of the enzymology of unequal homologous recombination of human DNA within yeast may yield a greater understanding of the molecular events which control this process in higher eukaryotes.

p27Kip1: chromosomal mapping to 12p12-12p13.1 and absence of mutations in human tumors

The p27Kip1 gene codes for a cyclin-dependent kinase inhibitor implicated in G1 arrest by transforming growth factor beta, cell-cell contact, agents that elevate cyclic AMP, and the growth-inhibitory drug rapamycin. p27 binds to and inhibits complexes formed by cyclin E-cdk2, cyclin A-cdk2, and cyclin D-cdk4. The involvement of p27 in the negative regulation of cell proliferation suggests that it may also function as a tumor suppressor gene. Using a combination of somatic cell hybrid panels and fluorescence in situ hybridization p27Kip1 has been mapped to the short arm of chromosome 12 at the 12p12-12p13.1 boundary, reported to harbor deletions and rearrangements in leukemia and mesotheliomas. In order to assess potential p27Kip1 gene alterations, we have screened a total of 147 human primary solid tumors and found no detectable cancer-specific mutations. These results argue that the often observed loss of antimitogenic transforming growth factor beta responsiveness in human cancer cells is not due to structural defects in p27Kip1.

Organization of the human keratin type II gene cluster at 12q13

Keratin proteins constitute intermediate filaments and are the major differentiation products of mammalian epithelial cells. The epithelial keratins are classified into two groups, type I and type II, and one member of each group is expressed in a given epithelial cell differentiation stage. Mutations in type I and type II keratin genes have now been implicated in three different human genetic disorders, epidermolysis bullosa simplex, epidermolytic hyperkeratosis, and epidermolytic palmoplantar keratoderma. Members of the type I keratins are mapped to human chromosome 17, and the type II keratin genes are mapped to chromosome 12. To understand the organization of the type II keratin genes on chromosome 12, we isolated several yeast artificial chromosomes carrying these keratin genes and examined them in detail. We show that eight already known type II keratin genes are located in a cluster at 12q13, and their relative organization reflects their evolutionary relationship. We also determined that a type I keratin gene, KRT18, is located next to its partner, KRT8, in this cluster. Careful examination of the cluster also revealed that there may be a number of additional keratin genes at this locus that have not been described previously.

Mapping of the 12q12-q22 region with respect to tumor translocation breakpoints

The consistent involvement of the region 12q13-q15 in numerous human tumors speaks in favor of the presence of genes that may contribute to oncogenesis. Mapping genes within this region of chromosome 12 is a necessary step toward the identification of those that play a role in this process. We have undertaken a multiplex analysis using translocation breakpoint mapping to order from the centromere to the telomere a series of 24 loci from the region 12q12-q22. Thirteen adipose tissue tumors with seven different chromosome changes involving the long arm of chromosome 12 (12q) were used. Since most of these loci are genes or anonymous DNA segments largely available to the scientific community, this map should be useful for investigation of genetic disorders associated with chromosome 12q. While these breakpoints were used as natural landmarks to order groups of loci, this work has positioned them more accurately, leading to a better chromosomal definition of the translocations than the one derived from standard cytogenetic studies.

Induced transcription of the mouse beta-globin transcription unit in erythroleukemia cells. Time-course of induction and of changes in chromatin structure

The transcription of the beta-globin genes in mouse erythroleukemia cells has been examined by hybridizing labeled RNA obtained from isolated nuclei after chain elongation in the presence of [alpha-32P]UTP. There is induction of at least 30-fold of beta maj globin transcription after cells are treated with either dimethylsulfoxide or hexamethylene bisacetamide. The induction requires 36 to 48 hours to be maximal, during which time the cells double about three to four times. During this time, a site in the beta maj DNA region becomes hypersensitive to DNase. The development of this hypersensitive site is co-ordinate with the transcriptional increase. The induced transcripts in the beta-globin region are alpha-amanitin-sensitive (and therefore are RNA polymerase II products). An examination of weak transcriptional signals to DNA fragments upstream of the beta maj globin gene in uninduced mouse erythroleukemia cells and in cells that do not make globin is also reported. The low level of hybridization to the upstream regions in uninduced erythroleukemia cells, in L cells (a fibroblast) and in a strain of erythroleukemia cells that no longer make globin are not equally sensitive to alpha-amanitin as in the induced signal. These experiments help define the inducible transcription unit for beta maj globin mRNA production.

Structural genes of the mouse major urinary protein are on chromosome 4

The major urinary proteins (MUPs) of mouse are a family of at least three major proteins which are synthesized in the liver of all strains of mice. The relative levels of synthesis of these proteins with respect to each other in the presence of testosterone is regulated by the Mup-a locus located on chromosome 4. In an effort to determine the mechanism of this regulation in molecular terms, a cDNA clone containing most of the coding region of a MUP protein has been isolated and identified by partial DNA sequence analysis. Using a combination of hybridization analysis and somatic cell genetics, the structural gene family has been unambiguously mapped to mouse chromosome 4. These data suggest that Mup-a regulation operates in a cis fashion and that models proposing trans regulation of MUP protein synthesis are unlikely.

Transcriptional control in the production of liver-specific mRNAs

cDNA clones complementary to liver mRNA were prepared and used to determine transcription rates of specific genes in isolated nuclei from liver, brain, and hepatoma cells. The cDNA sequences complementary to mRNA found only (or mainly) in the liver hybridize to labeled nuclear RNA only from liver nuclei. It appears that transcriptional events are primarily responsible for the synthesis of these, and perhaps most, tissue-specific moderately abundant mRNAs.

Heavy-metal tolerance in algae isolated from contaminated lakes near Sudbury, Ontario

Chemical analyses of lake waters in the Sudbury smelting area indicated abnormally high levels of metals, especially of copper and nickel. Two of the algal isolates from these contaminated lakes, a Scenedesmus species and a Chlorella species, were chosen for study. Their growth, as determined by cell number, was tested under controlled conditions in defined media. Nutrient conditions, pH, and concentration in solution of copper and nickel were used as variables in bioassays. In comparison with laboratory strains of similar algae, in medium with no chelate (ethylenediaminetetraacetic acid) the isolated lake strains were found to be tolerant of the heavy metals nickel (Scenedesmus) and copper (Scenedesmus and Chlorella). The patterns of response to metals in solution differed markedly between laboratory and lake strains. The ecological implications are considered.