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Purpose/background: A weight-based dosing approach of 20-30 mg/kg per day of valproic acid (VPA) has been shown to achieve rapid attainment of mood symptom control. Due to interindividual pharmacokinetic variability, therapeutic drug monitoring may be a useful tool to avoid VPA toxicity. Limited research exists on the impact of patient body weight on VPA pharmacokinetic profiles. This analysis aims to explore the correlation between steady-state serum levels of VPA and weight-based dosing strategies, including total body weight (TBW), ideal body weight (IBW), and adjusted body weight (AdjBW), between obese and nonobese patients., Methods/procedures: This single-center, retrospective, observational cohort analysis evaluated weight-based dosing of VPA in obese and nonobese patients admitted to inpatient psychiatry at a large academic medical center between July 1, 2017, and July 1, 2022., Findings/results: This analysis included 93 obese and 93 nonobese patients. No significant difference in median VPA serum concentrations was observed between groups ( P = 0.82). However, the obese group received a lower median weight-based dose (15.6 mg/kg) compared with the nonobese group (19.5 mg/kg, P < 0.001). A stronger correlation was found between VPA dose and therapeutic serum levels in the obese group compared with the nonobese group regardless of weight-based dosing strategy. Dosing with AdjBW in obese patients most closely approximated dosing with TBW in nonobese patients., Implications/conclusions: In obese patients, our analysis suggests dosing VPA using AdjBW may be considered as the preferred dosing strategy over IBW or TBW to minimize toxicity risk. Further research is needed with larger sample sizes and diverse patient populations to confirm these findings., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Mathematics is presented in a variety of font types across materials (e.g., textbooks, online problems); however, little is known about the effects of font type on students' mathematical performance. Undergraduate students ( N  = 121) completed three mathematical tasks in a one-hour online session in one of three font conditions: Times New Roman ( n  = 45), Kalam ( n  = 41), or handwriting ( n  = 35). We examined whether font type impacted students' performance, as measured by accuracy and response time, on the Perceptual Math Equivalence Task, error identification task, and equation-solving task. Compared to students in the Kalam and handwriting conditions, students in the Times New Roman condition were less accurate on the Perceptual Math Equivalence Task in which they judged whether two expressions were equivalent or not equivalent. We did not find differences between conditions in performance on error identification and equation-solving tasks. The findings have implications for research and practice. Specifically, researchers and educators may choose font types in which they present mathematics information with consideration, as font types may impact students' mathematical processing and performance., Competing Interests: Conflict of interestNone., (© The Author(s), under exclusive licence to Springer Nature Singapore Pte Ltd. 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Objective: Post-operative ileus (POI) is a common and potentially serious complication after surgery. We assessed the incidence and identified predictors of POI in older surgical patients., Design: A retrospective observational study., Setting: University of California-San Francisco electronic medical record data., Participants: Opioid-naïve, noncancer patients, aged 65 and older, who underwent elective surgery in the period 2017-2019., Exposure: Administration of opioid analgesics per day of hospitalization in opioid naïve patients., Main Outcomes Measure: Incidence of POI and likelihood of developing POI., Results: In the study period, 3 percent of opioid naïve patients developed POI. Patients with POI used on average 197.1 oral morphine equivalents (OMEs) per day of hospitalization compared to 82.5 OME in patients without POI (p = 0.013). Yet, there were not statistically significant differences in post-operative pain scores between patients with and without POI. General surgery (p = 0.0031), length of surgery (p = 0.0031), and hospital length of stay (p < 0.0001) were significant predictors of the risk for developing POI. Adjusted inpatient administration of more than 90 OME per day of hospitalization was associated with a four times greater risk for developing POI (p = 0.016). Developing POI was associated with 6.5 (95 percent confidence interval: 5.2-7.8) additional days of hospitalization among patients who developed POI compared to patients who did not develop POI (p < 0.0001)., Conclusions: Adjusted inpatient administration of more than 90 OME significantly increased the risk for developing POI in opioid-naïve older patients. Developing POI after surgery significantly increased the hospital length of stay. Optimizing inpatient administration of opioids may prevent opioid use-related POI and longer hospitalizations.

Transposable elements (TEs) are mobile genetic elements that make up a large fraction of mammalian genomes. While select TEs have been co-opted in host genomes to have function, the majority of these elements are epigenetically silenced by DNA methylation in somatic cells. However, some TEs in mice, including the Intracisternal A-particle (IAP) subfamily of retrotransposons, have been shown to display interindividual variation in DNA methylation. Recent work has revealed that IAP sequence differences and strain-specific KRAB zinc finger proteins (KZFPs) may influence the methylation state of these IAPs. However, the mechanisms underlying the establishment and maintenance of interindividual variability in DNA methylation still remain unclear. Here, we report that sequence content and genomic context influence the likelihood that IAPs become variably methylated. IAPs that differ from consensus IAP sequences have altered KZFP recruitment that can lead to decreased KAP1 recruitment when in proximity of constitutively expressed genes. These variably methylated loci have a high CpG density, similar to CpG islands, and can be bound by ZF-CxxC proteins, providing a potential mechanism to maintain this permissive chromatin environment and protect from DNA methylation. These observations indicate that variably methylated IAPs escape silencing through both attenuation of KZFP binding and recognition by ZF-CxxC proteins to maintain a hypomethylated state., Competing Interests: KC, AL, CT, ML, MB, JP, DS No competing interests declared, (© 2021, Costello et al.)

Endogenous retroviruses (ERVs) are ancient viral elements that have accumulated in the genome through retrotransposition events. Although they have lost their ability to transpose, many of the long terminal repeats (LTRs) that originally flanked full-length ERVs maintain the ability to regulate transcription. While these elements are typically repressed in somatic cells, they can function as transcriptional enhancers and promoters when this repression is lost. Epstein-Barr virus (EBV), which transforms primary B cells into continuously proliferating cells, is a tumor virus associated with lymphomas. We report here that transformation of primary B cells by EBV leads to genome-wide activation of LTR enhancers and promoters. The activation of LTRs coincides with local DNA hypomethylation and binding by transcription factors such as RUNX3, EBF1, and EBNA2. The set of activated LTRs is unique to transformed B cells compared with other cell lines known to have activated LTRs. Furthermore, we found that LTR activation impacts the B cell transcriptome by up-regulating transcripts driven by cryptic LTR promoters. These transcripts include genes important to oncogenesis of Hodgkin lymphoma and other cancers, such as HUWE1/HECTH9 These data suggest that the activation of LTRs by EBV-induced transformation is important to the pathology of EBV-associated cancers. Altogether, our results indicate that EBV-induced transformation of B cells alters endogenous retroviral element activity, thereby impacting host gene regulatory networks and oncogenic potential., (© 2018 Leung et al.; Published by Cold Spring Harbor Laboratory Press.)

Vertical sleeve gastrectomy (VSG) produces sustainable weight loss, remission of type 2 diabetes (T2D), and improvement of nonalcoholic fatty liver disease (NAFLD). However, the molecular mechanisms underlying the metabolic benefits of VSG have remained elusive. According to our previous results, diet-induced obesity induces epigenetic modifications to chromatin in mouse liver. We demonstrate here that VSG in C57BL/6J wild-type male mice can reverse these chromatin modifications and thereby impact the expression of key metabolic genes. Genes involved in lipid metabolism, especially omega-6 fatty acid metabolism, are up-regulated in livers of mice after VSG while genes in inflammatory pathways are down-regulated after VSG. Consistent with gene expression changes, regulatory regions near genes involved in inflammatory response displayed decreased chromatin accessibility after VSG. Our results indicate that VSG induces global regulatory changes that impact hepatic inflammatory and lipid metabolic pathways, providing new insight into the mechanisms underlying the beneficial metabolic effects induced by VSG.

Background: Functional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation, and variation in chromatin accessibility across individuals has been linked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained. Furthermore, the processes through which the variation of chromatin accessibility contributes to phenotypic diversity remain poorly understood., Results: We profiled chromatin accessibility in liver from seven strains of mice with phenotypic diversity in response to a high-fat/high-sucrose (HF/HS) diet and identified reproducible chromatin variation across the individuals. We found that sites of variable chromatin accessibility were more likely to coincide with particular classes of transposable elements (TEs) than sites with common chromatin signatures. Evolutionarily younger long interspersed nuclear elements (LINEs) are particularly likely to harbor variable chromatin sites. These younger LINEs are enriched for binding sites of immune-associated transcription factors, whereas older LINEs are enriched for liver-specific transcription factors. Genomic region enrichment analysis indicates that variable chromatin sites at TEs may function to regulate liver metabolic pathways. CRISPR-Cas9 deletion of a number of variable chromatin sites at TEs altered expression of nearby metabolic genes. Finally, we show that polymorphism of TEs and differential DNA methylation at TEs can both influence chromatin variation., Conclusions: Our results demonstrate that specific classes of TEs show variable chromatin accessibility across strains of mice that display phenotypic diversity in response to a HF/HS diet. These results indicate that chromatin variation at TEs is an important contributor to phenotypic variation among populations.

Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain-dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with a high fat diet remains in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of diet-induced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J mice are associated with specific transcription factors and histone post-translational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

Investigations into the genomic landscape of histone modifications in heterochromatic regions have revealed histone H3 lysine 9 dimethylation (H3K9me2) to be important for differentiation and maintaining cell identity. H3K9me2 is associated with gene silencing and is organized into large repressive domains that exist in close proximity to active genes, indicating the importance of maintenance of proper domain structure. Here we show that nickel, a nonmutagenic environmental carcinogen, disrupted H3K9me2 domains, resulting in the spreading of H3K9me2 into active regions, which was associated with gene silencing. We found weak CCCTC-binding factor (CTCF)-binding sites and reduced CTCF binding at the Ni-disrupted H3K9me2 domain boundaries, suggesting a loss of CTCF-mediated insulation function as a potential reason for domain disruption and spreading. We furthermore show that euchromatin islands, local regions of active chromatin within large H3K9me2 domains, can protect genes from H3K9me2-spreading-associated gene silencing. These results have major implications in understanding H3K9me2 dynamics and the consequences of chromatin domain disruption during pathogenesis.

Background: The formation of chromatin domains is an important step in lineage commitment. In human hematopoietic stem and progenitor cells (HSPCs), G9a/GLP-dependent H3K9me2 chromatin territories form de novo during lineage specification and are nucleated at punctate sites during lineage commitment. Here, we examined the patterning of G9a/GLP-dependent H3K9me2 in HSPCs and the consequences for chromatin structure., Results: We profiled chromatin accessibility across the genome of HSPCs treated with either a small molecule inhibitor of G9a/GLP or DMSO. We observed that chromatin accessibility is dramatically altered at the regions of H3K9me2 nucleation. We have characterized the regions of H3K9me2 nucleation, with our analysis revealing that H3K9me2 is nucleated in HSPCs at CpG islands (CGIs) and CGI-like sequences across the genome. Our analysis furthermore revealed a bias of H3K9me2 nucleation towards regions with low rates of C- > T deamination, which typically lack DNA methylation. Lastly, we examined the interaction of H3K9me2 and DNA methylation and determined that chromatin accessibility changes upon loss of H3K9me2 are dependent on the presence of DNA methylation., Conclusions: These results indicate that H3K9me2 nucleation is established at specific sequences that have base composition similar to CGIs. Our results furthermore indicate that H3K9me2 nucleation leads to local changes in chromatin accessibility and that H3K9me2 and DNA methylation work synergistically to regulate chromatin accessibility.

Metabolic diseases result from multiple genetic and environmental factors. We report here that one manner in which environmental factors can contribute to metabolic disease progression is through modification to chromatin. We demonstrate that high fat diet leads to chromatin remodeling in the livers of C57BL/6J mice, as compared with mice fed a control diet, and that these chromatin changes are associated with changes in gene expression. We further show that the regions of greatest variation in chromatin accessibility are targeted by liver transcription factors, including HNF4α, CCAAT/enhancer-binding protein α (CEBP/α), and FOXA1. Repeating the chromatin and gene expression profiling in another mouse strain, DBA/2J, revealed that the regions of greatest chromatin change are largely strain-specific and that integration of chromatin, gene expression, and genetic data can be used to characterize regulatory regions. Our data indicate dramatic changes in the epigenome due to diet and demonstrate strain-specific dynamics in chromatin remodeling., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)

Rationale: Misregulation of angiotensin II (Ang II) actions can lead to atherosclerosis and hypertension. Evaluating transcriptomic responses to Ang II in vascular smooth muscle cells (VSMCs) is important to understand the gene networks regulated by Ang II, which might uncover previously unidentified mechanisms and new therapeutic targets., Objective: To identify all transcripts, including novel protein-coding and long noncoding RNAs, differentially expressed in response to Ang II in rat VSMCs using transcriptome and epigenome profiling., Methods and Results: De novo assembly of transcripts from RNA-sequencing revealed novel protein-coding and long noncoding RNAs (lncRNAs). The majority of the genomic loci of these novel transcripts are enriched for histone H3 lysine-4-trimethylation and histone H3 lysine-36-trimethylation, 2 chromatin modifications found at actively transcribed regions, providing further evidence that these are bonafide transcripts. Analysis of transcript abundance identified all protein-coding and lncRNAs regulated by Ang II. We further discovered that an Ang II-regulated lncRNA functions as the host transcript for miR-221 and miR-222, 2 microRNAs implicated in cell proliferation. Additionally, small interfering RNA-mediated knockdown of Lnc-Ang362 reduced proliferation of VSMCs., Conclusions: These data provide novel insights into the epigenomic and transcriptomic effects of Ang II in VSMCs. They provide the first identification of Ang II-regulated lncRNAs, which suggests functional roles for these lncRNAs in mediating cellular responses to Ang II. Furthermore, we identify an Ang II-regulated lncRNA that is responsible for the production of 2 microRNAs implicated in VSMC proliferation. These newly identified noncoding transcripts could be exploited as novel therapeutic targets for Ang II-associated cardiovascular diseases.