DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.

Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as coprocessing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools. Here, we introduce fibertools, a state-of-the-art toolkit that features a semisupervised convolutional neural network for fast and accurate identification of m6A-marked bases using PacBio single-molecule long-read sequencing, as well as the coprocessing of long-read genetic and epigenetic data produced using either PacBio or Oxford Nanopore sequencing platforms. We demonstrate accurate DNA-m6A identification (>90% precision and recall) along >20 kilobase long DNA molecules with a ~1,000-fold improvement in speed. In addition, we demonstrate that fibertools can readily integrate genetic and epigenetic data at single-molecule resolution, including the seamless conversion between molecular and reference coordinate systems, allowing for accurate genetic and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.

P2X7 receptor-dependent increase in endocannabinoid 2-arachidonoyl glycerol production by neuronal cells in culture: Dynamics and mechanism.

BACKGROUND AND PURPOSE: Neurotransmission and neuroinflammation are controlled by local increases in both extracellular ATP and the endocannabinoid 2-arachidonoyl glycerol (2-AG). While it is known that extracellular ATP stimulates 2-AG production in cells in culture, the dynamics and molecular mechanisms that underlie this response remain poorly understood. Detection of real-time changes in eCB levels with the genetically encoded sensor, GRABeCB2.0, can address this shortfall. EXPERIMENTAL APPROACH: 2-AG and arachidonoylethanolamide (AEA) levels in Neuro2a (N2a) cells were measured by LC-MS, and GRABeCB2.0 fluorescence changes were detected using live-cell confocal microscopy and a 96-well fluorescence plate reader. KEY RESULTS: 2-AG and AEA increased GRABeCB2.0 fluorescence in N2a cells with EC50 values of 81 and 58 nM, respectively; both responses were reduced by the cannabinoid receptor type 1 (CB1R) antagonist SR141617 and absent in cells expressing the mutant-GRABeCB2.0. ATP increased only 2-AG levels in N2a cells, as measured by LC-MS, and induced a transient increase in the GRABeCB2.0 signal within minutes primarily via activation of P2X7 receptors (P2X7R). This response was dependent on diacylglycerol lipase ß activity, partially dependent on extracellular calcium and phospholipase C activity, but not controlled by the 2-AG hydrolysing enzyme, α/ß-hydrolase domain containing 6 (ABHD6). CONCLUSIONS AND IMPLICATIONS: Considering that P2X7R activation increases 2-AG levels within minutes, our results show how these molecular components are mechanistically linked. The specific molecular components in these signalling systems represent potential therapeutic targets for the treatment of neurological diseases, such as chronic pain, that involve dysregulated neurotransmission and neuroinflammation.

A pilot study investigating plasma pharmacokinetics and tolerance of oral capecitabine in carcinoma-bearing dogs.

BACKGROUND: Capecitabine is an oral prodrug of the active metabolite 5-fluorouracil, which has been used effectively in human colorectal, head and neck, and mammary carcinomas. Capecitabine has several properties that make it an attractive treatment option for dogs: (i) it is relatively inexpensive, (ii) it has a short half-life in humans, allowing for rapid plasma concentration changes to be achieved with dosage adjustments, (iii) it is effective for treating carcinomas in humans, for which there are no widely-effective oral chemotherapy options in dogs, and (iv) it is thought to preferentially target cancer cells due to different expression of thymidine phosphorylase, thereby decreasing the risk of off-target side effects. However, capecitabine has not been widely explored as a chemotherapy agent for dogs. The goal of this study was to determine the plasma disposition of capecitabine in dogs following a single oral dose and to document any adverse events associated with capecitabine administration over the course of 5 weeks. RESULTS: Capecitabine was well tolerated throughout the 5-week study period when administered to 5 dogs with naturally occurring carcinomas at 750 mg/m[Formula: see text] by mouth once daily for 14 consecutive days in a 3-week cycle. No dogs withdrew from the study due to adverse events or other causes. The median AUC[Formula: see text] was 890 h[Formula: see text]ng/ml (range 750-1100 h[Formula: see text]ng/ml); however, the maximum blood concentration and time to reach that concentration of capecitabine was highly variable after a single dose. CONCLUSIONS: Capecitabine appears well-tolerated as an oral chemotherapy agent for dogs with carcinomas, although individualized dosing may be necessary, and further studies are warranted.

Perceptions of the seriousness of major public health problems during the COVID-19 pandemic in seven middle-income countries.

INTRODUCTION: Public perception of the seriousness of the COVID-19 pandemic compared to six other major public health problems (alcoholism and drug use, HIV/AIDS, malaria, tuberculosis, lung cancer and respiratory diseases caused by air pollution and smoking, and water-borne diseases like diarrhea) is unclear. We designed a survey to examine this issue using YouGov's internet panels in seven middle-income countries in Africa, Asia, and Latin America in early 2022. METHODS: Respondents rank ordered the seriousness of the seven health problems using a repeated best-worst question format. Rank-ordered logit models allow comparisons within and across countries and assessment of covariates. RESULTS: In six of the seven countries, respondents perceived other respiratory illnesses to be a more serious problem than COVID-19. Only in Vietnam was COVID-19 ranked above other respiratory illnesses. Alcoholism and drug use was ranked the second most serious problem in the African countries. HIV/AIDS ranked relatively high in all countries. Covariates, particularly a COVID-19 knowledge scale, explained differences within countries; statistics about the pandemic were highly correlated with differences in COVID-19's perceived seriousness. CONCLUSIONS: People in the seven middle-income countries perceived COVID-19 to be serious (on par with HIV/AIDS) but not as serious as other respiratory illnesses. In the African countries, respondents perceived alcoholism and drug use as more serious than COVID-19. Our survey-based approach can be used to quickly understand how the threat of a newly emergent disease, like COVID-19, fits into the larger context of public perceptions of the seriousness of health problems.

We were curious what people in different countries thought about the seriousness of COVID-19 compared to other health problems. We designed a survey, and hired YouGov, a survey research firm, to administer it in seven countries in Africa, Asia, and Latin America in early 2022. Respondents answered the questions on their computer, tablets, or smart phones. Their answers revealed that in most countries respiratory illnesses were perceived to be a more serious problem than COVID-19. In Africa people felt that alcoholism and drug use were also more serious than COVID-19. These findings are important because they show that people still care about the health problems they were facing before the pandemic, which is useful information for healthcare providers.

Perampanel's forgiveness factor in a variable medication adherence paradigm in a rat model of chronic epilepsy.

BACKGROUND: Poor medication adherence contributes to increased morbidity and mortality in patients with epilepsy and may be under-addressed in clinical practice. Ethical concerns make it impossible to study the impact of medication nonadherence in clinical trials, but our previous work emphasizes the importance of using preclinical approaches to address these questions. With over 30 clinically available antiseizure medicines (ASM's), it remains an important question to understand the relationship between poor adherence and seizure incidence across mechanistically distinct ASM's, including the broad-spectrum ASM, perampanel (PER). METHODS: We formulated PER into chow pellets to deliver to rats in a 100% fully adherent or 50% variable nonadherent paradigm via our novel automated medication-in-food delivery system. Chronic oral dosing was initiated in male rats with chronic epilepsy while monitoring 24/7 for videoEEG evidence of seizures during a 4-week placebo baseline and 4-week treatment phase. PER concentrations were monitored in plasma at 1-week intervals and correlated with degree of seizure control. The relationship between missed doses and extended patterns of nonadherence were correlated with breakthrough seizures. RESULTS: Fully adherent rats demonstrated a median reduction in seizure frequency of 50%, whereas nonadherent rats had a median increase of 54%. Plasma concentrations of PER were stable over the 4-week treatment period in both fully adherent and nonadherent groups, with levels being twice as high in fully adherent animals. There was no correlation between a single missed dose or series of missed doses and the incidence of breakthrough seizures. However, those animals in the nonadherent group that received PER for every meal during a 24-h period had a reduced likelihood of seizure incidence. CONCLUSIONS: If our preclinical data is supported in the clinic, PER's favorable pharmacokinetic profile in humans, combined with a lowered risk of breakthrough seizures suggests that it may provide a certain forgiveness factor if a dose is missed within a 24-h window.

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.

Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as co-processing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools. Here, we introduce fibertools, a state-of-the-art toolkit that features a semi-supervised convolutional neural network for fast and accurate identification of m6A-marked bases using PacBio single-molecule long-read sequencing, as well as the co-processing of long-read genetic and epigenetic data produced using either PacBio or Oxford Nanopore sequencing platforms. We demonstrate accurate DNA-m6A identification (>90% precision and recall) along >20 kilobase long DNA molecules with a ~1,000-fold improvement in speed. In addition, we demonstrate that fibertools can readily integrate genetic and epigenetic data at single-molecule resolution, including the seamless conversion between molecular and reference coordinate systems, allowing for accurate genetic and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.

The Effects of Pregnancy on Amino Acid Levels and Nitrogen Disposition.

Limited data are available on the effects of pregnancy on the maternal metabolome. Therefore, the objective of this study was to use metabolomics analysis to determine pathways impacted by pregnancy followed by targeted confirmatory analysis to provide more powerful conclusions about metabolic alterations during pregnancy. Forty-seven pregnant women, 18-50 years of age were included in this study, with each subject serving as their own control. Plasma samples were collected between 25 and 28 weeks gestation and again ≥3 months postpartum for metabolomics analysis utilizing an HILIC/UHPLC/MS/MS assay with confirmatory targeted specific concentration analysis for 10 of the significantly altered amino acids utilizing an LC/MS assay. Principle component analysis (PCA) on metabolomics data clearly separated pregnant and postpartum groups and identified outliers in a preliminary assessment. Of the 980 metabolites recorded, 706 were determined to be significantly different between pregnancy and postpartum. Pathway analysis revealed three significantly impacted pathways, arginine biosynthesis (p = 2 × 10-5 and FDR = 1 × 10-3), valine, leucine, and isoleucine metabolism (p = 2 × 10-5 and FDR = 2 × 10-3), and xanthine metabolism (p = 4 × 10-5 and FDR = 4 × 10-3). Of these we focused analysis on arginine biosynthesis and branched-chain amino acid (BCAA) metabolism due to their clinical importance and interconnected roles in amino acid metabolism. In the confirmational analysis, 7 of 10 metabolites were confirmed as significant and all 10 confirmed the direction of change of concentrations observed in the metabolomics analysis. The data support an alteration in urea nitrogen disposition and amino acid metabolism during pregnancy. These changes could also impact endogenous nitric oxide production and contribute to diseases of pregnancy. This study provides evidence for changes in both the ammonia-urea nitrogen and the BCAA metabolism taking place during pregnancy.

How Does the Public Evaluate Vaccines for Low-Incidence, Severe-Outcome Diseases? A General-Population Choice Experiment.

BACKGROUND: Because immunizing large numbers of healthy people could be required to reduce a relatively small number of infections, disease incidence has a large impact on cost effectiveness, even if the infection is associated with very serious health outcomes. In addition to cost effectiveness, the US Advisory Committee on Immunization Practices requires evidence of stakeholders' values and preferences to help inform vaccine recommendations. This study quantified general-population preferences for vaccine trade-offs among disease severity, disease incidence, and other vaccine features. METHODS: We developed a best-practice discrete choice experiment survey and administered it to 1185 parents of children aged 12-23 years and 1203 young adults aged 18-25 years from a national opt-in consumer panel. The data were analyzed using exploded-logit latent-class analysis. RESULTS: Latent-class analysis identified two classes with similar relative-importance weights in both samples. One of the two classes represented about half the samples and had preferences consistent with well-structured, logically ordered, and acceptably precise stated-preference utility. Preferences for the other half of the samples were poorly defined over the ranges of vaccine and disease attributes evaluated. Both parents and young adults in the first class evaluated protection from a disease with 1 in 100 incidence and full recovery at home as having statistically the same preference utility as a disease with 1 in 1 million incidence requiring hospitalization and resulting in permanent deafness. CONCLUSIONS: The results suggest that vaccines that protect against low-incidence, severe-outcome diseases, provide 'peace of mind' benefits not captured by standard health-outcome metrics. The fact that half the respondents had poorly defined vaccine preferences is a reminder of the challenges of implementing patient-centric vaccine decision making.

Support for regulation versus compliance: Face masks during COVID-19.

Objectives: Wearing masks could still be one of the few non-pharmaceutical interventions for controlling the pandemic. There are people who wear them and people who don't, but this framing is overly simplistic. We aim to chart the contradictions in attitudes and behavior regarding mask wearing and describe the messaging challenge that these generate. Study design: Our data come from a survey administered to a nationally representative sample of 2000 respondents from the YouGov panel of US households in August-September 2020. Methods: Respondents were asked whether they wear a facemask when they go outside their home since the COVID-19 epidemic began and whether they support or oppose your municipal government passing mask wearing regulation. We also collected respondents' demographic and economic characteristics, knowledge regarding the facts of COVID-19 and political ideology. Results: A substantial majority of Americans (60%) both favor a masking requirement and are themselves wearing masks, while 13% oppose a mask mandate and do not wear masks. In contrast, 17% of Americans oppose a mask mandate but are currently wearing one, while 10% do not wear a mask but favor a mask mandate. These two groups are distinctively different from one another and the other groups in their socioeconomic characteristics, risk perception and political beliefs. Conclusions: Our study offers a better understanding of the mismatch between mask wearing behavior and attitude toward the mask mandate, which will help the public health authorities to devise policies regarding mask wearing as an effective intervention to manage the pandemic.

Who should get the scarce ICU bed? The US public's view on triage in the time of COVID-19.

OBJECTIVE: To determine the relative importance members of the US public place on different patient attributes in triage decisions about who should receive the last available intensive care unit (ICU) bed. METHODS: A discrete choice experiment was conducted with a nationally representative sample of 2000 respondents from the YouGov internet panel of US households. Respondents chose which of three hypothetical patients with COVID-19 should receive an ICU bed if only one were available. The three patients differed in age, gender, Alzheimer's-like disability and probability of survival if the patient received the ICU bed. An experimental design varied the values of the four attributes of the three hypothetical patients with COVID-19 that a respondent saw in four choice tasks. RESULTS: The most important patient attribute to respondents was the probability the patient survives COVID-19 if they get the ICU bed (OR CI: 4.41 to 6.91). There was heterogeneity among different age groups of respondents about how much age of the patient mattered. Respondents under 30 years of age were more likely to choose young patients and old patients, and less likely to select patients aged 40-60 years old. For respondents in the age group 30-49 years old, as the age of the patient declined, their preference for saving the patient declined modestly in a linear fashion. CONCLUSIONS: Respondents favoured giving the last ICU bed available to the patient with the highest probability of surviving COVID-19. Public opinion suggests a simple guideline for physician choices based on likelihood of survival as opposed to the number of life-years saved. There was heterogeneity among respondents of different age groups for allocating the last ICU bed, as well as to the importance of the patient having an Alzheimer's-like disability (where religion of the respondent is important) and the gender of the patient (where the gender and racial identity are important).

Do Extremely Low Gestational Age Neonates Regulate Iron Absorption via Hepcidin?

OBJECTIVES: To evaluate whether extremely preterm infants regulate iron status via hepcidin. STUDY DESIGN: In this retrospective analysis of infants from the Preterm Epo Neuroprotection (PENUT) Trial, urine hepcidin (Uhep) normalized to creatinine (Uhep/UCr) was evaluated among infants randomized to erythropoietin (Epo) or placebo. RESULTS: The correlation (r) between Uhep/UCr and serum markers of iron status (ferritin and zinc protoporphyrin-to-heme ratio [ZnPP/H]) and iron dose was assessed. A total of 243 urine samples from 76 infants born at 24-276/7 weeks gestation were analyzed. The median Uhep/UCr concentration was 0.3, 1.3, 0.4, and 0.1 ng/mg at baseline, 2 weeks, 4 weeks, and 12 weeks, respectively, in placebo-treated infants. The median Uhep/UCr value in Epo-treated infants were not significantly different, with the exception of the value at the 2-week time point (median Uhep/UCr, 0.1 ng/mg; P < .001). A significant association was seen between Uhep/UCr and ferritin at 2 weeks (r = 0.63; P < .001) and at 4 weeks (r = 0.41; P = .01) and between Uhep/UCr and ZnPP/H at 2 weeks (r = -0.49; P = .002). CONCLUSIONS: Uhep/UCr values correlate with serum iron markers. Uhep/UCr values vary over time and are affected by treatment with Epo, suggesting that extremely preterm neonates can regulate hepcidin and therefore their iron status. Uhep is suppressed in extremely preterm neonates, particularly those treated with Epo.

Pharmacologic therapy for engraftment arrhythmia induced by transplantation of human cardiomyocytes.

Heart failure remains a significant cause of morbidity and mortality following myocardial infarction. Cardiac remuscularization with transplantation of human pluripotent stem cell-derived cardiomyocytes is a promising preclinical therapy to restore function. Recent large animal data, however, have revealed a significant risk of engraftment arrhythmia (EA). Although transient, the risk posed by EA presents a barrier to clinical translation. We hypothesized that clinically approved antiarrhythmic drugs can prevent EA-related mortality as well as suppress tachycardia and arrhythmia burden. This study uses a porcine model to provide proof-of-concept evidence that a combination of amiodarone and ivabradine can effectively suppress EA. None of the nine treated subjects experienced the primary endpoint of cardiac death, unstable EA, or heart failure compared with five out of eight (62.5%) in the control cohort (hazard ratio = 0.00; 95% confidence interval: 0-0.297; p = 0.002). Pharmacologic treatment of EA may be a viable strategy to improve safety and allow further clinical development of cardiac remuscularization therapy.

Collaborative management of the Grand Ethiopian Renaissance Dam increases economic benefits and resilience.

The landscape of water infrastructure in the Nile Basin is changing with the construction of the Grand Ethiopian Renaissance Dam. Although this dam could improve electricity supply in Ethiopia and its neighbors, there is a lack of consensus between Ethiopia, Sudan, and Egypt on the dam operation. We introduce a new modeling framework that simulates the Nile River System and Egypt's macroeconomy, with dynamic feedbacks between the river system and the macroeconomy. Because the two systems "coevolve" throughout multi-year simulations, we term this a "coevolutionary" modeling framework. The framework is used to demonstrate that a coordinated operating strategy could allow the Grand Ethiopian Renaissance Dam to help meet water demands in Egypt during periods of water scarcity and increase hydropower generation and storage in Ethiopia during high flows. Here we show the hydrological and macroeconomic performance of this coordinated strategy compared to a strategy that resembles a recent draft proposal for the operation of the dam discussed in Washington DC.

Repeated isolation of an antibiotic-dependent and temperature-sensitive mutant of Pseudomonas aeruginosa from a cystic fibrosis patient.

BACKGROUND: Bacteria adapt to survive and grow in different environments. Genetic mutations that promote bacterial survival under harsh conditions can also restrict growth. The causes and consequences of these adaptations have important implications for diagnosis, pathogenesis, and therapy. OBJECTIVES: We describe the isolation and characterization of an antibiotic-dependent, temperature-sensitive Pseudomonas aeruginosa mutant chronically infecting the respiratory tract of a cystic fibrosis (CF) patient, underscoring the clinical challenges bacterial adaptations can present. METHODS: Respiratory samples collected from a CF patient during routine care were cultured for standard pathogens. P. aeruginosa isolates recovered from samples were analysed for in vitro growth characteristics, antibiotic susceptibility, clonality, and membrane phospholipid and lipid A composition. Genetic mutations were identified by whole genome sequencing. RESULTS: P. aeruginosa isolates collected over 5 years from respiratory samples of a CF patient frequently harboured a mutation in phosphatidylserine decarboxylase (psd), encoding an enzyme responsible for phospholipid synthesis. This mutant could only grow at 37°C when in the presence of supplemented magnesium, glycerol, or, surprisingly, the antibiotic sulfamethoxazole, which the source patient had repeatedly received. Of concern, this mutant was not detectable on standard selective medium at 37°C. This growth defect correlated with alterations in membrane phospholipid and lipid A content. CONCLUSIONS: A P. aeruginosa mutant chronically infecting a CF patient exhibited dependence on sulphonamides and would likely evade detection using standard clinical laboratory methods. The diagnostic and therapeutic challenges presented by this mutant highlight the complex interplay between bacterial adaptation, antibiotics, and laboratory practices, during chronic bacterial infections.

Understanding and managing new risks on the Nile with the Grand Ethiopian Renaissance Dam.

When construction of the Grand Ethiopian Renaissance Dam (GERD) is completed, the Nile will have two of the world's largest dams-the High Aswan Dam (HAD) and the GERD-in two different countries (Egypt and Ethiopia). There is not yet agreement on how these dams will operate to manage scarce water resources. We elucidate the potential risks and opportunities to Egypt, Sudan and Ethiopia by simulating the filling period of the reservoir; a new normal period after the reservoir fills; and a severe multi-year drought after the filling. Our analysis illustrates how during filling the HAD reservoir could fall to levels not seen in recent decades, although the risk of water shortage in Egypt is relatively low. The new normal will benefit Ethiopia and Sudan without significantly affecting water users in Egypt. Management of multi-year droughts will require careful coordination if risks of harmful impacts are to be minimized.

Risk of Breast Cancer Associated with Estrogen DNA Adduct Biomarker.

BACKGROUND: It is biologically plausible that genotoxic estrogens, namely estrogen DNA adducts (EDA), have a role in breast cancer development. Support comes from three prior studies that reported elevated concentrations of EDA relative to estrogen metabolites and conjugates (EDA:EMC) in women with breast cancer relative to control women. METHODS: In postmenopausal women in the Women's Health Initiative (WHI), EDA:EMC in 191 controls was compared with findings in 194 prediagnosis urine samples from breast cancer cases. EDA:EMC determinations were by mass spectrometry as previously described, and logistic regression was employed to estimate ORs. RESULTS: EDA:EMC did not differ in breast cancer cases compared with controls overall [0.93 (95% confidence interval, 0.71-1.23)], with a mean (SD) of 2.3 (0.8) and 2.4 (1.1) in cases and controls, respectively. Similarly, the ratio did not differ when examined by estrogen receptor or recency of biospecimen collection prior to breast cancer. CONCLUSIONS: Despite the demonstrated genotoxic properties of certain catechol estrogens resulting in EDAs, this analysis did not provide evidence for an increased breast cancer risk in relation to an elevated EDA:EMC. IMPACT: This analysis, conducted prospectively within postmenopausal women in the WHI study, suggests that a strong association between EDA:EMC and breast cancer could be ruled out, as this study was powered to detect an OR of 2.2 or greater.

Forecasts of mortality and economic losses from poor water and sanitation in sub-Saharan Africa.

This paper presents country-level estimates of water, sanitation and hygiene (WASH)-related mortality and the economic losses associated with poor access to water and sanitation infrastructure in sub-Saharan Africa (SSA) from 1990 to 2050. We examine the extent to which the changes that accompany economic growth will "solve" water and sanitation problems in SSA and, if so, how long it will take. Our simulations suggest that WASH-related mortality will continue to differ markedly across countries in sub-Saharan Africa. In many countries, expected economic growth alone will not be sufficient to eliminate WASH-related mortality or eliminate the economic losses associated with poor access to water and sanitation infrastructure by 2050. In other countries, WASH-related mortality will sharply decline, although the economic losses associated with the time spent collecting water are forecast to persist. Overall, our findings suggest that in a subset of countries in sub-Saharan Africa (e.g., Angola, Niger, Sierra Leone, Chad and several others), WASH-related investments will remain a priority for decades and require a long-term, sustained effort from both the international community and national governments.

Structure-Activity Relationships for CYP4B1 Bioactivation of 4-Ipomeanol Congeners: Direct Correlation between Cytotoxicity and Trapped Reactive Intermediates.

Cytochrome P450 4B1 (CYP4B1) has been explored as a candidate enzyme in suicide gene systems for its ability to bioactivate the natural product 4-ipomeanol (IPO) to a reactive species that causes cytotoxicity. However, metabolic limitations of IPO necessitate discovery of new "pro-toxicant" substrates for CYP4B1. In the present study, we examined a series of synthetically facile N-alkyl-3-furancarboxamides for cytotoxicity in HepG2 cells expressing CYP4B1. This compound series maintains the furan warhead of IPO while replacing its alcohol group with alkyl chains of varying length (C1-C8). Compounds with C3-C6 carbon chain lengths showed similar potency to IPO (LD50 ≈ 5 µM). Short chain analogs (<3 carbons) and long chain analogs (>6 carbons) exhibited reduced toxicity, resulting in a parabolic relationship between alkyl chain length and cytotoxicity. A similar parabolic relationship was observed between alkyl chain length and reactive intermediate formation upon trapping of the putative enedial as a stable pyrrole adduct in incubations with purified recombinant rabbit CYP4B1 and common physiological nucleophiles. These parabolic relationships reflect the lower affinity of shorter chain compounds for CYP4B1 and increased ω-hydroxylation of the longer chain compounds by the enzyme. Furthermore, modest time-dependent inhibition of CYP4B1 by N-pentyl-3-furancarboxamide was completely abolished when trapping agents were added, demonstrating escape of reactive intermediates from the enzyme after bioactivation. An insulated CYP4B1 active site may explain the rarely observed direct correlation between adduct formation and cell toxicity reported here.

Quantitative analysis of chondroitin sulfate disaccharides from human and rodent fixed brain tissue by electrospray ionization-tandem mass spectrometry.

Chondroitin sulfates (CS) are long, negatively charged, unbranched glycosaminoglycan (GAG) chains attached to CS-proteoglycan (CSPG) core proteins that comprise the glycan component in both loose interstitial extracellular matrices (ECMs) and in rigid, structured perineuronal net (PNN) scaffolds within the brain. As aberrant CS-PNN formations have been linked to a range of pathological states, including Alzheimer's disease (AD) and schizophrenia, the analysis of CS-GAGs in brain tissue at the disaccharide level has great potential to enhance disease diagnosis and prognosis. Two mass-spectrometry (MS)-based approaches were adapted to detect CS disaccharides from minute fixed tissue samples with low picomolar sensitivity and high reproducibility. The first approach employed a straightforward, quantitative direct infusion (DI)-tandem mass spectrometry (MS/MS) technique to determine the percentages of Δ4S- and Δ6S-CS disaccharides within the 4S/6S-CS ratio, while the second used a comprehensive liquid chromatography (LC)-MS/MS technique to determine the relative percentages of Δ0S-, Δ4S-, Δ6S-, Δ4S6S-CS and Δ2S6S-CS disaccharides, with internal validation by full chondroitin lyase activity. The quantitative accuracy of the five primary biologically relevant CS disaccharides was validated using a developmental time course series in fixed rodent brain tissue. We then analyzed the CS disaccharide composition in formalin-fixed human brain tissue, thus providing the first quantitative report of CS sulfation patterns in the human brain. The ability to comprehensively analyze the CS disaccharide composition from fixed brain tissue provides a means with which to identify alterations in the CS-GAG composition in relation to the onset and/or progression of neurological diseases.