Charting the Cannabis plant chemical space with computational metabolomics
Ontology highlight
ABSTRACT: Leaf and flower extracts of Cannabis strains Amnesia haze (80% C.sativa and 20% C.indica) and Royal dutch cheese (70% C.indica and 30% C.sativa).
Project description:Leaf and flower extracts of Cannabis strains Amnesia haze (80% C.sativa and 20% C.indica) and Royal dutch cheese (70% C.indica and 30% C.sativa).
Project description:In this study, we evaluated the common proteomic profile, as well as, the exclusively deregulated proteins in ON cells from healthy controls cannabis users (HC/c), SCZ patients non-cannabis users (SCZ/nc) and SCZ patients cannabis users (SCZ/c) as compared to healthy controls non-cannabis users (HC/nc). Moreover, we investigated quantitative and functional differences between HC/c and SCZ, and we characterized the distinct effect of cannabis in SCZ comparing SCZ/nc and SCZ/c.
Project description:Role of alternative polyadenylation (APA) in rat brain after vaporized cannabis plant matter (CPM) exposure remains largely undetermined. Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternative polyadenylation events responsible for dominantly down-regulates APA expression on Glutamatergic Transcripts in rats after CPM Exposure.
Project description:Cannabis use has been controversial, largely having been designated a controlled substance over the last century. The link between cannabis smoking and disease pathogenesis may best be explored through DNA methylation, an epigentic mechanism. We investigated the relationship between epigenetic age and cannabis smoking in participants within the Canadian Cohort of Obstructive Lung Disease (CanCOLD) cohort (n=93) (ClinicalTrials.gov identifier NCT00920348). Blood samples were profiled for DNA methylation using the Illumina MethylationEPIC BeadChipv1 at two separate laboratories and the blood epigenetic age of each sample was calculated using the Clock Foundation tool (https://dnamage.clockfoundation.org). An ANOVA was used to identify differences in the age acceleration residuals associated with cannabis smoking status (never, former, and current), adjusted for chronological age, sex, body mass index (BMI), batch, cigarette smoking status, and the first two principal components of blood cell proportions. Our observations indicated that current cannabis smoking and higher joint-years exposure are associated with epigenetic age acceleration; cessation, however, may help to normalize in part this age acceleration.
Project description:Even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills. In this work, publicly available gene expression datasets have been analyzed giving rise to a total of 40,224 gene expression profiles within different Cannabis tissues/developmental stages. The resource here proposed will provide researchers with a starting point for future investigations of Cannabis sativa.
Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
Project description:Medical cannabis has been increasingly prescribed for a range of conditions including epilepsy, chronic neuropathic pain, and chemotherapy-induced nausea and vomiting. The benefits and possible adverse events of medical-grade cannabis products vary between patients, suggesting that genetics may play a role in the pharmacokinetics of the cannabinoids, yet regulatory restrictions have led to limited clinical studies. This study is aimed at identifying a genetic signature that is predictive of the pharmacokinetics of tetrahydrocannabinol (THC), the principal intoxicating chemical compound derived from cannabis. We have identified 55 variants among 38 genes that were overrepresented in either the Low-THC or High-THC groups.
Project description:Population-based studies show cannabis use doubles the risk of developing schizophrenia especially when use occurs in early adolescence (prior to age 15). However, the cause-and-effect mechanisms are largely unknown. To investigate the effect of cannabis on brain maturation and relation to the development of psychosis-like behaviours in adulthood, we treated young adolescent mice with vehicle or cannabis extract once a day for 2 weeks between postnatal days 14 and 28, and then collected hippocampal tissue for microarray analysis 12 weeks later. We identify a total of 78 differentially expressed genes (25 upregulated and 53 downregulated; p<0.05, fold change ± 1.2) and validate increases in dopamine D2 receptor (Drd2) and fatty acid amide hydrolase (Faah). Changes in Faah expression were limited to the hippocampus however Drd2 also increased in striatum but not prefrontal cortex or amygdala. When tested in adulthood with a behavioural panel relevant to schizophrenia, cannabis-treated mice displayed lower anxiety in the elevated zero-maze, decreased social preference, increased social novelty preference, mild cognitive impairments in a spatial version of the novel object recognition task and absence of latent inhibition when compared to vehicle controls. Adolescent treatment with cannabis extract thus lead to long-lasting changes in gene expression within the hippocampus which together result in behavioural deficits consistent with the negative and positive symptoms of schizophrenia.