CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications

Abstract 105: Sex Difference in Brain Energy Metabolism After Electronic Cigarette Vape Exposure May Contribute to Worsened Stroke Injury in Rats

Abstract only Introduction: Electronic cigarettes (EC) are battery-powered nicotine delivery devices that have gained popularity as alternatives to tobacco cigarettes for young smokers and smokers trying to cease. Because of its relative novelty, our understanding about the effects of EC vaping on stroke outcome is limited. Here we aim to investigate the effects of EC on energy metabolism in the brain and on stroke outcome in animals of both sexes. Methods: Female and male Sprague-Dawley rats (2-3 months old; n=8) were randomly assigned to either air or EC vapor (5% nicotine Juul pods) exposure for 16 nights using the EcigAero-TM Aerosol Exposure Apparatus. After the exposure period, the rats were divided into two cohorts. The brains were collected from the first cohort of rats for unbiased metabolomic (Metabolon Inc.) or Western blot analysis. The second cohort underwent transient middle cerebral artery occlusion (tMCAO; 90 min) or sham surgery and was survived for 21 days. During the post-tMCAO/sham survival, cognition was assessed using the Morris water maze followed by brain collection for histopathological analysis. Results: Metabolomic analysis showed substantial changes in glycolytic metabolites in EC-exposed female rats in relation to air controls, implying altered brain energetics. In EC-exposed female animals, a significant increase (p<0.05) in glucose, glucose 6-phosphate, fructose-6-phosphate, and fructose 1-6 diphosphate was noted compared to air controls. However, such changes were not seen in EC-exposed male rats. Quantification of infarct volume demonstrated that, compared to air rats, EC-exposed rats displayed a significantly increased infarct volume in female rats while showing a trend of increase in male rats. In female rats, infarct volumes were 86 ± 19 mm 3 and 151 ± 25 mm 3 for air and EC groups, respectively, a significant difference (p<0.05). In the male rat air group, tMCAO resulted in an infarct volume of 80 ± 37 mm 3 , while EC yielded 130 ± 38 mm 3 . Behavioral testing showed worsened post-stroke cognitive outcome in EC groups compared to air groups in rats of both sexes. Conclusion: EC vape exposure, even for as short as two weeks, impacts glucose metabolism and worsens post-stroke cognitive deficits in female more than male rats

Post-stroke whole body vibration therapy alters the cerebral transcriptome to promote ischemic tolerance in middle-aged female rats

Low-frequency whole body vibration (WBV; 40 Hz) therapy after stroke reduces ischemic brain damage, motor, and cognitive deficits in middle-aged rats of both sexes. However, the underlying mechanisms responsible for WBV induced ischemic protections remain elusive. In the current study, we hypothesize that post-stroke WBV initiates transcriptional reprogramming in the cortex of middle-aged female rats which is responsible for the observed reduced stroke consequences. Middle-aged female Sprague-Dawley rats that remained in constant diestrus (reproductively senescent) were randomized to either sham or transient middle cerebral artery occlusion (tMCAO; 90 min) surgery. A day after induction of tMCAO, animals received either WBV or no-WBV treatment for 15 min twice a day for five days for a week. Post-treatment, cortical tissue was analyzed for gene expression using RNA sequencing (RNAseq) and gene enrichment analysis via Enrichr. The RNAseq data analysis revealed significant changes in gene expression due to WBV therapy and the differentially expressed genes are involved in variety of biological processes like neurogenesis, angiogenesis, excitotoxicity, and cell death. Specifically, observed significant up-regulation of 116 and down-regulation of 258 genes after WBV in tMCAO exposed rats as compared to the no-WBV group. The observed transcriptional reprogramming will identify the possible mechanism(s) responsible for post-stroke WBV conferred ischemic protection and future studies will be needed to confirm the role of the genes identified in the current study. •Post-stroke whole body vibration (WBV) therapy improves stroke outcomes in rats.•WBV alters the cortical transcriptome.•WBV enhances genes linked to neurogenesis, angiogenesis, and synaptic plasticity.•WBV downregulates genes related to inflammation and cell death

Impact of Electronic Cigarette Vaping on Cerebral Ischemia: What We Know So Far

Electronic cigarettes (ECs) are battery-powered nicotine delivery devices that have rapidly gained popularity and attention globally. ECs work by heating a liquid to produce an aerosol that usually contains nicotine, flavoring compounds, and other chemicals, which are inhaled during vaping. EC aerosols are depicted to contain a lower number and overall quantity of harmful toxicants than conventional cigarettes (CCs). However, emerging research indicates that EC aerosols contain harmful ingredients including ultrafine particles, volatile organic compounds, and heavy metals. One common ingredient found in both CCs and ECs is nicotine, which has been shown to be both highly addictive and toxic. Particularly relevant to our current review, there is an enormous amount of literature that shows that smoking-derived nicotine exacerbates ischemic brain damage. Therefore, the question arises: will EC use impact the outcome of stroke? ECs are highly popular and relatively new in the market; thus, our understanding about the long-term effects of EC use on brain are lacking. The current review strives to extrapolate the existing understanding of the nicotine-induced effects of conventional smoking on the brain to the possible effects that ECs may have on the brain, which may ultimately have a potential for adverse stroke risk or severity

Abstract TMP111: Electronic Cigarette Exposure Exacerbates Ischemic Stroke Outcome Via Altered Neurotransmitter Metabolism In Rats Of Both Sexes

Byline: Hari Pradhyumnan, Neurology, Univ of Miami, Miami, FL; Shahil H Patel, Neurology, Univ of Miami, Miami, FL; Ofelia Furones-Alonso, Neurological Surgery, Univ of Miami, Miami, FL; Helen Bramlett, Neurological Surgery, Univ of Miami, Miami, FL; Ami P Raval, Neurology, Univ of Miami, Miami, FL Introduction: Smoking is a preventable risk factor for stroke and battery-operated nicotine delivery systems known as electronic cigarettes (EC) are popular. EC vapes aerosolize a mix of nicotine and chemicals forming harmful toxicants such as formaldehyde hemiacetal. Our understanding about effects of EC vaping on stroke outcome is limited. This study investigated effects of EC on global metabolic signature and stroke outcome in animals of both sexes. Methods: Sprague-Dawley rats (2-3 months old; n=8) of both sexes were randomly assigned either to air or EC vapor (5% nicotine Juul pods) exposure using the EcigAero-TM Aerosol Exposure Apparatus. Rats were exposed to air/EC for 16 nights. Per night, rats were exposed to 16 episodes of EC vapor. Each episode consisted of 2 seconds of Juul puffs followed by 8 seconds of air over the period of 8 minutes. After 16 days, the rats were divided into two cohorts. The first cohort of rats exposed to EC/Air was tested for cognitive capacities using the Morris water maze (WM) followed by brain collection for unbiased metabolomic (Metabolon Inc.) or Western blot analysis. The second cohort of rats exposed to EC/Air was subjected to transient middle cerebral artery occlusion (tMCAO; 90 min) or sham surgery and survived for 15-21 days. During the post-tMCAO survival, rats were tested for cognition using WM followed by brain collection for histopathological analysis. Results: Metabolomic analysis indicated that EC exposure resulted in significant increases (pëñ0.05) in phenylalanine and tryptophan metabolites, and both increases (pëñ0.05) and decreases (pëñ0.05) in histamine and tyrosine metabolites in the brains of female and male rats. Western blotting of rate-limiting enzymes in respective NT pathways corroborated the metabolomic data. Behavioral testing indicated worsened cognitive outcome in EC groups compared to air groups in rats of both sexes. Conclusion: EC vape exposure, even for as short as 2 weeks, impacts the metabolism of NT, induces cognitive deficits and worsens stroke outcomes in young male and female rats. Future studies investigating the impact of EC withdrawal on NT metabolism are needed to understand how long the deleterious effects of EC vaping persist in the brain.Academi

Abstract WP213: The Effect Of Nicotine Withdrawal On Stroke Outcome In Female Rats

Byline: Shahil H Patel, Neurology, Univ of Miami Miller Sch of Medicine, Miami, FL; Isabel Saul; Kunjan R Dave; Miguel A Perez-Pinzon; Ami P Raval Significance: Smoking-derived nicotine (N) is known to synergistically magnify the risk and severity of cerebral ischemia in females. Most importantly, smoking is the one preventable risk factor and giving up smoking reduces the risk for cerebral ischemia. However, how long the harmful effects of N on the brain persist after women stop smoking is unknown. In a laboratory study using an animal model of cerebral ischemia, we demonstrated that N alters brain energy metabolism and thus exacerbates ischemic brain damage. Therefore, the current study aims to investigate how long after N withdrawal (NW) N toxicity on brain energy metabolism persists and its impact on stroke outcomes in female rats. Methods: Female Sprague-Dawley rats (n=8/group) were randomly exposed to either saline or N (4.5 mg/kg) for 16-21 days after which point, they were withdrawn from N exposure and able to recover for 0, 15, or 30 days. These rats were then randomly assigned to either have their cortical tissue collected for global metabolomic (Metabolon Inc) and Western blot analysis or undergo a sham surgery or transient middle-cerebral artery occlusion (tMCAO; 90 min). Post-stroke cognition was tested with contextual fear conditioning at month following tMCAO, subsequently the brains were collected for infarct quantification. Results: Analysis of the metabolomics data revealed an increase in carbohydrate metabolites in the 30-day NW group when compared to the N-exposed group, suggesting persistence of N toxicity in the brain. Furthermore, fear conditioning data revealed a significantly lower freezing time in all NW groups when compared to the saline group implying that spatial memory deficits persist even after 30 days of NW. Lastly, the observed infarct volume was 26%(p<0.05), 25%(p<0.05), and 16%(p<0.05) higher in the 0, 15, and 30 day NW groups respectively, when compared to the saline group. Conclusion: Even after 30 days of NW, N-induced global metabolomic changes in the brain persist and may be responsible for increased ischemic brain damage as well as cognitive deficits in female rats.Academi

A Perspective on Hormonal Contraception Usage in Central Nervous System Injury

Naturally occurring life stages in women are associated with changes in the milieu of endogenous ovarian hormones. Women of childbearing age may be exposed to exogenous ovarian hormone(s) due to their use of varying combinations of estrogen and progesterone hormones-containing oral contraceptives (OC; also known as "the pill"). If women suffer central nervous system (CNS) injury such as spinal cord injury (SCI) and traumatic brain injury (TBI) during their childbearing age, they are likely to retain their reproductive capabilities and may use OC. Many deleterious side effects of long-term OC use have been reported, such as aberrant blood clotting and endothelial dysfunction which consequently increase the risk of myocardial infarction, venous thromboembolism, and ischemic brain injury. Although controversial, studies have suggested that OC use is associated with neuropsychiatric ramifications, including uncontrollable mood swings and poorer cognitive performance. Our understanding about how the combination of endogenous hormones and OC-conferred exogenous hormones affect outcomes after CNS injuries remains limited. Therefore, understanding the impact of OC use on CNS injury outcomes needs further investigation to reveal underlying mechanisms, promote reporting in clinical or epidemiological studies, and raise awareness of possible compounded consequences. The goal of the current review is to discuss the impacts of CNS injury on endogenous ovarian hormones and vice-versa, as well as the putative consequences of exogenous ovarian hormones (OC) on the CNS to identify potential gaps in our knowledge to consider for future laboratory, epidemiological, and clinical studies

Electronic Cigarette Vape Exposure Exacerbates Post-Ischemic Outcomes in Female but Not in Male Rats

Nicotine-containing electronic cigarette (EC) vaping has become popular worldwide, and our understanding of the effects of vaping on stroke outcomes is elusive. Using a rat model of transient middle cerebral artery occlusion, the current exploratory study aims to evaluate the sex-dependent effects of EC exposure on brain energy metabolism and stroke outcomes.Adult Sprague-Dawley rats of both sexes were randomly assigned to air/EC vapor (5% nicotine Juul pods) exposure for 16 nights, followed by randomization into 3 cohorts. The first cohort underwent exposure to air/EC preceding randomization to transient middle cerebral artery occlusion (90 minutes) or sham surgery, followed by survival for 21 days. During the survival period, rats underwent sensorimotor and Morris water maze testing. Subsequently, brains were collected for histopathology. A second cohort was exposed to air/EC after which brains were collected for unbiased metabolomics analysis. The third cohort of animals was exposed to air/EC and received transient middle cerebral artery occlusion/sham surgery, and brain tissue was collected 24 hours later for biochemical analysis.In females, EC significantly increased (<0.05) infarct volumes by 94% as compared with air-exposed rats, 165±50 mmin EC-exposed rats, and 85±29 mmin air-exposed rats, respectively, while in males such a difference was not apparent. Morris water maze data showed significant deficits in spatial learning and working memory in the EC sham or transient middle cerebral artery occlusion groups compared with the respective air groups in rats of both sexes (<0.05). Thirty-two metabolites of carbohydrate, glycolysis, tricarboxylic acid cycle, and lipid metabolism were significantly altered (≤0.05) due to EC, 23 of which were specific for females. Steady-state protein levels of hexokinase significantly decreased (<0.05) in EC-exposed females; however, these changes were not seen in males.Even brief EC exposure over 2 weeks impacts brain energy metabolism, exacerbates infarction, and worsens poststroke cognitive deficits in working memory more in female than male rats

The Impact of Nicotine along with Oral Contraceptive Exposure on Brain Fatty Acid Metabolism in Female Rats

Smoking-derived nicotine (N) and oral contraceptive (OC) synergistically exacerbate ischemic brain damage in females, and the underlying mechanisms remain elusive. In a previous study, we showed that N + OC exposure altered brain glucose metabolism in females. Since lipid metabolism complements glycolysis, the current study aims to examine the metabolic fingerprint of fatty acids in the brain of female rats exposed to N+/&minus;OC. Adolescent and adult Sprague&ndash;Dawley female rats were randomly (n = 8 per group) exposed to either saline or N (4.5 mg/kg) +/&minus;OC (combined OC or placebo delivered via oral gavage) for 16&ndash;21 days. Following exposure, brain tissue was harvested for unbiased metabolomic analysis (performed by Metabolon Inc., Morrisville, NC, USA) and the metabolomic profile changes were complemented with Western blot analysis of key enzymes in the lipid pathway. Metabolomic data showed significant accumulation of fatty acids and phosphatidylcholine (PC) metabolites in the brain. Adolescent, more so than adult females, exposed to N + OC showed significant increases in carnitine-conjugated fatty acid metabolites compared to saline control animals. These changes in fatty acyl carnitines were accompanied by an increase in a subset of free fatty acids, suggesting elevated fatty acid &beta;-oxidation in the mitochondria to meet energy demand. In support, &beta;-hydroxybutyrate was significantly lower in N + OC exposure groups in adolescent animals, implying a complete shunting of acetyl CoA for energy production via the TCA cycle. The reported changes in fatty acids and PC metabolism due to N + OC could inhibit post-translational palmitoylation of membrane proteins and synaptic vesicle formation, respectively, thus exacerbating ischemic brain damage in female rats