Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico.

BACKGROUND: Preclinical models like cancer cell lines and patient-derived xenografts (PDXs) are vital for studying disease mechanisms and evaluating treatment options. It is essential that they accurately recapitulate the disease state of interest to generate results that will translate in the clinic. Prior studies have demonstrated that preclinical models do not recapitulate all biological aspects of human tissues, particularly with respect to the tissue of origin gene expression signatures. Therefore, it is critical to assess how well preclinical model gene expression profiles correlate with human cancer tissues to inform preclinical model selection and data analysis decisions. AIMS: Here we evaluated how well preclinical models recapitulate human cancer and non-diseased tissue gene expression patterns in silico with respect to the full gene expression profile as well as subsetting by the most variable genes, genes significantly correlated with tumor purity, and tissue-specific genes. METHODS: By using publicly available gene expression profiles across multiple sources, we evaluated cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. RESULTS: We found that using the full gene set improves correlations between preclinical model and tissue global gene expression profiles, confirmed that glioblastoma (GBM) PDX global gene expression correlation to GBM tumor global gene expression outperforms GBM cell line to GBM tumor global gene expression correlations, and demonstrated that preclinical models in our study often failed to reproduce tissue-specific expression. While including additional genes for global gene expression comparison between cell lines and tissues decreases the overall correlation, it improves the relative rank between a cell line and its tissue of origin compared to other tissues. Our findings underscore the importance of using the full gene expression set measured when comparing preclinical models and tissues and confirm that tissue-specific patterns are better preserved in GBM PDX models than in GBM cell lines. CONCLUSION: Future studies can build on these findings to determine the specific pathways and gene sets recapitulated by particular preclinical models to facilitate model selection for a given study design or goal.

Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico.

Preclinical models like cancer cell lines and patient-derived xenografts (PDXs) are vital for studying disease mechanisms and evaluating treatment options. It is essential that they accurately recapitulate the disease state of interest to generate results that will translate in the clinic. Prior studies have demonstrated that preclinical models do not recapitulate all biological aspects of human tissues, particularly with respect to the tissue of origin gene expression signatures. Therefore, it is critical to assess how well preclinical model gene expression profiles correlate with human cancer tissues to inform preclinical model selection and data analysis decisions. Here we evaluated how well preclinical models recapitulate human cancer and non-diseased tissue gene expression patterns in silico with respect to the full gene expression profile as well as subsetting by the most variable genes, genes significantly correlated with tumor purity, and tissue-specific genes by using publicly available gene expression profiles across multiple sources. We found that using the full gene set improves correlations between preclinical model and tissue global gene expression profiles, confirmed that GBM PDX global gene expression correlation to GBM tumor global gene expression outperforms GBM cell line to GBM tumor global gene expression correlations, and demonstrated that preclinical models in our study often failed to reproduce tissue-specific expression. While including additional genes for global gene expression comparison between cell lines and tissues decreases the overall correlation, it improves the relative rank between a cell line and its tissue of origin compared to other tissues. Our findings underscore the importance of using the full gene expression set measured when comparing preclinical models and tissues and confirm that tissue-specific patterns are better preserved in GBM PDX models than in GBM cell lines. Future studies can build on these findings to determine the specific pathways and gene sets recapitulated by particular preclinical models to facilitate model selection for a given study design or goal.

Canopy composition drives variability in urban growing season length more than the heat island effect.

The elevated heat of urban areas compared to their surroundings makes humid temperate cities a useful preview of future climate effects on natural forest phenology. The utility of this proxy rests on the expectation that trees in urban areas alter their phenology in response to warmer site conditions in spring and fall. However, it is possible that apparent lengthening of the growing season is instead governed by human-driven tree species selection and plant functional type (PFT; trees, shrubs, turfgrass) heterogeneity typical of managed landscapes. Without the use of highly spatially and temporally resolved remote sensing data, the roles of tree taxonomy and local site characteristics (e.g., impervious cover) in controlling phenology remain confounded. To understand the drivers of earlier start of season (SOS) and later end of season (EOS) among urban trees, we estimated individual tree phenology using >130 high-resolution satellite images per year (2018-2020) for ~10,000 species-labeled trees in Washington, DC. We found that species identity alone accounted for 4× more variability in the timing of SOS and EOS compared with a tree's planting location characteristics. Additionally, the urban mix of PFTs may be more responsible for apparent advances in SOS (by between 1.8 ± 1.3 and 3.5 ± 1.3 days) than heat per se. The results of this study caution against associating longer growing seasons in cities-observed in moderate to coarse resolution remote sensing imagery-to within-species phenological plasticity and demonstrate the power of high-resolution satellite data for tracking tree phenology in biodiverse environments.

Nucleic acid liquid biopsies in Alzheimer's disease: current state, challenges, and opportunities.

Alzheimer's disease (AD) is the most common neurodegenerative disease and affects persons of all races, ethnic groups, and sexes. The disease is characterized by neuronal loss leading to cognitive decline and memory loss. There is no cure and the effectiveness of existing treatments is limited and depends on the time of diagnosis. The long prodromal period, during which patients' ability to live a normal life is not affected despite neuronal loss, often leads to a delayed diagnosis because it can be mistaken for normal aging of the brain. In order to make a substantial impact on AD patient survival, early diagnosis may provide a greater therapeutic window for future therapies to slow AD-associated neurodegeneration. Current gold standards for disease detection include magnetic resonance imaging and positron emission tomography scans, which visualize amyloid ß and phosphorylated tau depositions and aggregates. Liquid biopsies, already an active field of research in precision oncology, are hypothesized to provide early disease detection through minimally or non-invasive sample collection techniques. Liquid biopsies in AD have been studied in cerebrospinal fluid, blood, ocular, oral, and olfactory fluids. However, most of the focus has been on blood and cerebrospinal fluid due to biomarker specificity and sensitivity attributed to the effects of the blood-brain barrier and inter-laboratory variation during sample collection. Many studies have identified amyloid ß and phosphorylated tau levels as putative biomarkers, however, advances in next-generation sequencing-based liquid biopsy methods have led to significant interest in identifying nucleic acid species associated with AD from liquid tissues. Differences in cell-free RNAs and DNAs have been described as potential biomarkers for AD and hold the potential to affect disease diagnosis, treatment, and future research avenues.

Considerations and challenges for sex-aware drug repurposing.

Sex differences are essential factors in disease etiology and manifestation in many diseases such as cardiovascular disease, cancer, and neurodegeneration [33]. The biological influence of sex differences (including genomic, epigenetic, hormonal, immunological, and metabolic differences between males and females) and the lack of biomedical studies considering sex differences in their study design has led to several policies. For example, the National Institute of Health's (NIH) sex as a biological variable (SABV) and Sex and Gender Equity in Research (SAGER) policies to motivate researchers to consider sex differences [204]. However, drug repurposing, a promising alternative to traditional drug discovery by identifying novel uses for FDA-approved drugs, lacks sex-aware methods that can improve the identification of drugs that have sex-specific responses [7, 11, 14, 33]. Sex-aware drug repurposing methods either select drug candidates that are more efficacious in one sex or deprioritize drug candidates based on if they are predicted to cause a sex-bias adverse event (SBAE), unintended therapeutic effects that are more likely to occur in one sex. Computational drug repurposing methods are encouraging approaches to develop for sex-aware drug repurposing because they can prioritize sex-specific drug candidates or SBAEs at lower cost and time than traditional drug discovery. Sex-aware methods currently exist for clinical, genomic, and transcriptomic information [1, 7, 155]. They have not expanded to other data types, such as DNA variation, which has been beneficial in other drug repurposing methods that do not consider sex [114]. Additionally, some sex-aware methods suffer from poorer performance because a disproportionate number of male and female samples are available to train computational methods [7]. However, there is development potential for several different categories (i.e., data mining, ligand binding predictions, molecular associations, and networks). Low-dimensional representations of molecular association and network approaches are also especially promising candidates for future sex-aware drug repurposing methodologies because they reduce the multiple hypothesis testing burden and capture sex-specific variation better than the other methods [151, 159]. Here we review how sex influences drug response, the current state of drug repurposing including with respect to sex-bias drug response, and how model organism study design choices influence drug repurposing validation.

Genetic variation among populations of, and evidence of deep divergence within, the Rio Grande Chirping Frog, Eleutherodactylus campi (Anura: Eleutherodactylidae).

Herein we report the first molecular assessment of intra-species genetic variation and interrelationships within the Rio Grande Chirping frog, Eleutherodactylus campi. We analyzed 548 base pairs of 16S rRNA gene for 71 ingroup individuals belonging to the genus Eleutherodactylus (including 42 E. campi sampled from 15 localities in the United States and Mexico) and four outgroup samples. By unveiling two highly divergent and geographically structured clades within E. campi this study provides a novel phylogenetic placement of E. campi populations north and south of the Rio Grande Valley as sister groups to each other. The observed level of genetic divergence between these two clades (5.8%) is, on average, comparable to or greater than the levels of divergence found between several currently valid amphibian species pairs. Estimates of Time to Most Common Ancestor (TMRCA) indicate that the phylogeographic split between the two E. campi clades may have occurred 7.6 MYA (i.e., late Miocene), consistent with the geologic history of southwestern North America. The study also confirms that south Texas served as the source population for populations of E. campi in its introduced range (i.e., Alabama, Louisiana, and Texas). Overall, this molecular study indicates that E. campi consists of two deeply divergent lineages corresponding to its populations north and south of Rio Grande Valley. These results suggest that the recovered lineages may represent independent species and thereby highlight the need for further research to clarify their status.

Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics.

Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.

Efficacy and safety of biofilm dispersal by glycoside hydrolases in wounds.

Novel anti-biofilm and dispersal agents are currently being investigated in an attempt to combat biofilm-associated wound infections. Glycoside hydrolases (GHs) are enzymes that hydrolyze the glycosidic bonds between sugars, such as those found within the exopolysaccharides of the biofilm matrix. Previous studies have shown that GHs can weaken the matrix, inducing bacterial dispersal, and improving antibiotic clearance. Yet, the number of GH enzymes that have been examined for potential therapeutic effects is limited. In this study, we screened sixteen GHs for their ability to disperse mono-microbial and polymicrobial biofilms grown in different environments. Six GHs, α-amylase (source: A. oryzae), alginate lyase (source: various algae), pectinase (source: Rhizopus sp.), amyloglucosidase (source: A. niger), inulinase (source: A. niger), and xylanase (source: A. oryzae), exhibited the highest dispersal efficacy in vitro. Two GHs, α-amylase (source: Bacillus sp.) and cellulase (source: A. niger), used in conjunction with meropenem demonstrated infection clearing ability in a mouse wound model. GHs were also effective in improving antibiotic clearance in diabetic mice. To examine their safety, we screened the GHs for toxicity in cell culture. Overall, there was an inverse relationship between enzyme exposure time and cellular toxicity, with twelve out of sixteen GHs demonstrating some level of toxicity in cell culture. However, only one GH exhibited harmful effects in mice. These results further support the ability of GHs to improve antibiotic clearance of biofilm-associated infections and help lay a foundation for establishing GHs as therapeutic agents for chronic wound infections.

Anatomical entrapment of the dorsal scapular and long thoracic nerves, secondary to brachial plexus piercing variation.

Circumscapular pain is a frequent complaint in clinical practice. The dorsal scapular and long thoracic nerves course through the neck, where they may become entrapped between or within adjacent scalene muscles. Additionally, a high frequency of brachial plexus "piercing" variants have recently been documented, and it is unclear how they influence branching patterns distally along the brachial plexus. In the project reported here we strived to identify and quantify variations in dorsal scapular nerve and long thoracic nerve secondary to brachial plexus piercing variation. Ninety brachial plexuses from human cadavers (45 female/45 male) were evaluated to identify nerve branching patterns, specifically piercing versus non-piercing variants in the brachial plexus roots and nerves. Anatomical entrapment of the dorsal scapular nerve and long thoracic nerve was found in high frequencies (60.8% and 44.6%, respectively). Anomalous brachial plexus piercing variants were associated with higher frequencies of distal nerve branches also coursing through the scalene musculature, and there was a statistically significant correlation between brachial plexus and long thoracic nerve piercings (p = 0.027). Anatomical entrapment of nerves within scalene musculature is common and may be causative factors for idiopathic circumscapular pain, dorsalgia, and dysfunction of scapulohumeral rhythm. This study revealed a link between anatomical arrangement of the brachial plexus and occurrence of long thoracic nerve entrapment, which may lead to a series of cascading neurologic effects in which affected individuals may suffer from increased incidence of thoracic outlet syndrome and long thoracic nerve entrapment resulting in additional symptoms of interscapular pain and compromised shoulder mobility.

Prevalence of vitamin D deficiency among healthy infants and toddlers.

OBJECTIVES: To determine the prevalence of vitamin D deficiency and to examine whether 25-hydroxyvitamin D (25OHD) concentration varies as a function of skin pigmentation, season, sun exposure, breastfeeding, and vitamin D supplementation. DESIGN: Cross-sectional sample. SETTING: Urban primary care clinic. PARTICIPANTS: Healthy infants and toddlers (N = 380) who were seen for a routine health visit. OUTCOME MEASURES: Primary outcomes were serum 25OHD and parathyroid hormone levels; secondary measures included data on sun exposure, nutrition, skin pigmentation, and parental health habits. Wrist and knee radiographs were obtained for vitamin D-deficient participants. RESULTS: The prevalence of vitamin D deficiency (< or =20 ng/mL) was 12.1% (44 of 365 participants), and 146 participants (40.0%) had levels below an accepted optimal threshold (< or =30 ng/mL). The prevalence did not vary between infants and toddlers or by skin pigmentation. There was an inverse correlation between serum 25OHD and parathyroid hormone levels (infants: r = -0.27, P < .001; toddlers: r = -0.20, P = .02). In multivariable models, breastfeeding without supplementation among infants and lower milk intake among toddlers were significant predictors of vitamin D deficiency. In vitamin D-deficient participants, 3 participants (7.5%) exhibited rachitic changes on radiographs, whereas 13 (32.5%) had evidence of demineralization. CONCLUSIONS: Suboptimal vitamin D status is common among otherwise healthy young children. Predictors of vitamin D status vary in infants vs toddlers, information that is important to consider in the care of these young patients. One-third of vitamin D-deficient participants exhibited demineralization, highlighting the deleterious skeletal effects of this condition.

Treatment of hypovitaminosis D in infants and toddlers.

CONTEXT: Hypovitaminosis D appears to be on the rise in young children, with implications for skeletal and overall health. OBJECTIVE: The objective of the study was to compare the safety and efficacy of vitamin D2 daily, vitamin D2 weekly, and vitamin D3 daily, combined with supplemental calcium, in raising serum 25-hydroxyvitamin D [25(OH)D] and lowering PTH concentrations. DESIGN: This was a 6-wk randomized controlled trial. SETTING: The study was conducted at an urban pediatric clinic in Boston. SUBJECTS: Forty otherwise healthy infants and toddlers with hypovitaminosis D [25(OH)D < 20 ng/ml] participated in the study. INTERVENTIONS: Participants were assigned to one of three regimens: 2,000 IU oral vitamin D2 daily, 50,000 IU vitamin D2 weekly, or 2,000 IU vitamin D3 daily. Each was also prescribed elemental calcium (50 mg/kg.d). Infants received treatment for 6 wk. MAIN OUTCOME MEASURES: Before and after treatment, serum measurements of 25(OH)D, PTH, calcium, and alkaline phosphatase were taken. RESULTS: All treatments approximately tripled the 25(OH)D concentration. Preplanned comparisons were nonsignificant: daily vitamin D2 vs. weekly vitamin D2 (12% difference in effect, P = 0.66) and daily D2 vs. daily D3 (7%, P = 0.82). The mean serum calcium change was small and similar in the three groups. There was no significant difference in PTH suppression. CONCLUSIONS: Short-term vitamin D2 2,000 IU daily, vitamin D2 50,000 IU weekly, or vitamin D3 2,000 IU daily yield equivalent outcomes in the treatment of hypovitaminosis D among young children. Therefore, pediatric providers can individualize the treatment regimen for a given patient to ensure compliance, given that no difference in efficacy or safety was noted among these three common treatment regimens.

Cardiovascular changes during induced emotion: an application of lang's theory of emotional imagery.

Studies of emotion have provided occasional support for physiological differentiation of affective states; however, the evidence has been inconsistent. The aims of the present study were to investigate cardiovascular changes associated with relived experiences of happiness, sadness, anger, fear, and disgust and to examine the utility of methods designed to optimize the induction of emotional responses. Thirty-four undergraduates who scored 0.5 sd above the mean on Larsen and Diener's Affect Intensity Measure described their most intense experiences of five emotions. These descriptions were then used to induce those emotions while blood pressure and other hemodynamic measures were monitored. Systolic blood pressure, diastolic blood pressure, and stroke volume differentiated among emotions. The results support the suggestion that cardiovascular activity differentiates emotional states and provide some insight into the physiological adjustments subserving such effects. The study demonstrates a method that may be applied to studies of discrete emotions.

Injuries and use of protective equipment among college in-line skaters.

In-line skating injuries and protective gear use were explored in a sample of college students (n = 217). A minority of respondents wore protective gear. One third of skaters had experienced at least one minor injury, and a smaller percentage had experienced fractures or head injuries. Most minor injuries occurred during the first 1-2 times skating, while more serious injuries tended to occur after at least 50 times on in-line skates. Psychosocial predictors of protective gear use were explored. Four major Health Belief Model constructs (perceived barriers to wearing gear, perceived susceptibility to injury, perceived severity of injury, and perceived benefits of wearing gear) were significant predictors of protective gear use. The Health Belief Model, tested using regression and structural equation modelling, predicted gear typically worn, frequency of gear use, and injuries received while in-line skating. Implications for increasing protective gear use are described.

Youth beliefs and knowledge about the risks of drinking while pregnant.

Because no published studies of young persons' knowledge and awareness of fetal alcohol syndrome are available, the awareness and beliefs about drinking while pregnant in several large samples of young persons ages 13-20 are examined. Approximately 81 percent of the entire sample that completed questionnaires in school surveys believe that drinking alcohol while pregnant can definitely harm the fetus, although males and younger persons are less likely to believe in this risk. A substantial proportion of respondents believe that occasional heavy use is not harmful and suggest a safe level of drinking that is higher than the Surgeon General's abstinence recommendations. Only 72 percent have heard of fetal alcohol syndrome, and more than one-third incorrectly report that it describes a baby born addicted to alcohol, that the syndrome can be inherited, and that it can be cured. As in prior studies of adults, beliefs about drinking while pregnant are inconsistent with the Surgeon General's recommendations. Implications for increasing the awareness of the risk of drinking while pregnant are discussed.