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Developmental regulation of gliogenesis in the mammalian CNS is incompletely understood, in part due to a limited repertoire of lineage-specific genes. We used Aldh1l1-GFP as a marker for gliogenic radial glia and later-stage precursors of developing astrocytes and performed gene expression profiling of these cells. We then used this dataset to identify candidate transcription factors that may serve as glial markers or regulators of glial fate. Our analysis generated a database of developmental stage-related markers of Aldh1l1+ cells between murine embryonic day 13.5-18.5. Using these data we identify the bZIP transcription factor Nfe2l1 and demonstrate that it promotes glial fate under direct Sox9 regulatory control. Thus, this dataset represents a resource for identifying novel regulators of glial development.

Developmental regulation of gliogenesis in the mammalian CNS is incompletely understood, in part due to a limited repertoire of lineage-specific genes. We used Aldh1l1-GFP as a marker for gliogenic radial glia and later-stage precursors of developing astrocytes and performed gene expression profiling of these cells. We then used this dataset to identify candidate transcription factors that may serve as glial markers or regulators of glial fate. Our analysis generated a database of developmental stage-related markers of Aldh1l1+ cells between murine embryonic day 13.5-18.5. Using these data we identify the bZIP transcription factor Nfe2l1 and demonstrate that it promotes glial fate under direct Sox9 regulatory control. Thus, this dataset represents a resource for identifying novel regulators of glial development.

Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease.

Proper neurological function in humans requires precise control of levels of the epigenetic regulator methyl CpG-binding protein 2 (MeCP2). MeCP2 protein levels are low in fetal brains, where the predominant MECP2 transcripts have an unusually long 3' untranslated region (UTR). Here, we show that miR-483-5p, an intragenic microRNA of the imprinted IGF2, regulates MeCP2 levels through a human-specific binding site in the MECP2 long 3' UTR. We demonstrate the inverse correlation of miR-483-5p and MeCP2 levels in developing human brains and fibroblasts from Beckwith-Wiedemann syndrome patients. Importantly, expression of miR-483-5p rescues abnormal dendritic spine phenotype of neurons overexpressing human MeCP2. In addition, miR-483-5p modulates the levels of proteins of the MeCP2-interacting corepressor complexes, including HDAC4 and TBL1X. These data provide insight into the role of miR-483-5p in regulating the levels of MeCP2 and interacting proteins during human fetal development.

Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next-generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene coexpression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes coexpressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a window through which to view the foundation of uniquely human cognitive capacities.

BACKGROUND: Genomic datasets generated by new technologies are increasingly prevalent in disparate areas of biological research. While many studies have sought to characterize relationships among genomic features, commensurate efforts to characterize relationships among biological samples have been less common. Consequently, the full extent of sample variation in genomic studies is often under-appreciated, complicating downstream analytical tasks such as gene co-expression network analysis. RESULTS: Here we demonstrate the use of network methods for characterizing sample relationships in microarray data generated from human brain tissue. We describe an approach for identifying outlying samples that does not depend on the choice or use of clustering algorithms. We introduce a battery of measures for quantifying the consistency and integrity of sample relationships, which can be compared across disparate studies, technology platforms, and biological systems. Among these measures, we provide evidence that the correlation between the connectivity and the clustering coefficient (two important network concepts) is a sensitive indicator of homogeneity among biological samples. We also show that this measure, which we refer to as cor(K,C), can distinguish biologically meaningful relationships among subgroups of samples. Specifically, we find that cor(K,C) reveals the profound effect of Huntingtons disease on samples from the caudate nucleus relative to other brain regions. Furthermore, we find that this effect is concentrated in specific modules of genes that are naturally co-expressed in human caudate nucleus, highlighting a new strategy for exploring the effects of disease on sets of genes. CONCLUSIONS: These results underscore the importance of systematically exploring sample relationships in large genomic datasets before seeking to analyze genomic feature activity. We introduce a standardized platform for this purpose using freely available R software that has been designed to enable iterative and interactive exploration of sample networks.

AbstractBackgroundGenomic datasets generated by new technologies are increasingly prevalent in disparate areas of biological research. While many studies have sought to characterize relationships among genomic features, commensurate efforts to characterize relationships among biological samples have been less common. Consequently, the full extent of sample variation in genomic studies is often under-appreciated, complicating downstream analytical tasks such as gene co-expression network analysis.ResultsHere we demonstrate the use of network methods for characterizing sample relationships in microarray data generated from human brain tissue. We describe an approach for identifying outlying samples that does not depend on the choice or use of clustering algorithms. We introduce a battery of measures for quantifying the consistency and integrity of sample relationships, which can be compared across disparate studies, technology platforms, and biological systems. Among these measures, we provide evidence that the correlation between the connectivity and the clustering coefficient (two important network concepts) is a sensitive indicator of homogeneity among biological samples. We also show that this measure, which we refer to as cor(K,C), can distinguish biologically meaningful relationships among subgroups of samples. Specifically, we find that cor(K,C) reveals the profound effect of Huntington’s disease on samples from the caudate nucleus relative to other brain regions. Furthermore, we find that this effect is concentrated in specific modules of genes that are naturally co-expressed in human caudate nucleus, highlighting a new strategy for exploring the effects of disease on sets of genes.ConclusionsThese results underscore the importance of systematically exploring sample relationships in large genomic datasets before seeking to analyze genomic feature activity. We introduce a standardized platform for this purpose using freely available R software that has been designed to enable iterative and interactive exploration of sample networks.

In many applications, one is interested in determining which of the properties of a network module change across conditions. For example, to validate the existence of a module, it is desirable to show that it is reproducible (or preserved) in an independent test network. Here we study several types of network preservation statistics that do not require a module assignment in the test network. We distinguish network preservation statistics by the type of the underlying network. Some preservation statistics are defined for a general network (defined by an adjacency matrix) while others are only defined for a correlation network (constructed on the basis of pairwise correlations between numeric variables). Our applications show that the correlation structure facilitates the definition of particularly powerful module preservation statistics. We illustrate that evaluating module preservation is in general different from evaluating cluster preservation. We find that it is advantageous to aggregate multiple preservation statistics into summary preservation statistics. We illustrate the use of these methods in six gene co-expression network applications including 1) preservation of cholesterol biosynthesis pathway in mouse tissues, 2) comparison of human and chimpanzee brain networks, 3) preservation of selected KEGG pathways between human and chimpanzee brain networks, 4) sex differences in human cortical networks, 5) sex differences in mouse liver networks. While we find no evidence for sex specific modules in human cortical networks, we find that several human cortical modules are less preserved in chimpanzees. In particular, apoptosis genes are differentially co-expressed between humans and chimpanzees. Our simulation studies and applications show that module preservation statistics are useful for studying differences between the modular structure of networks. Data, R software and accompanying tutorials can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ModulePreservation.

Dosimetry provides information linking environmental exposures to sites of deposition, removal from these sites, and translocation of deposited materials. Dosimetry also aids in extrapolating laboratory animal and in vitro data to humans. Recent progress has shed light on: properties of particles in relation to their fates in the body; influence of age, gender, body size, and lung diseases on inhaled particle doses; particle movement to the brain via the olfactory nerves; and particle deposition hot spots in the respiratory tract. Ultrafine size has emerged as an important dosimetric characteristic. Particle count, composition, and surface properties are recognized as potentially important toxicology-related considerations. Differences in body size influence airway sizes, inhaled particle deposition, specific ventilation, and specific doses (e.g. per unit body mass). Related to body size, age, gender, species, and strain are also dosimetric considerations. Diseases, such as chronic obstructive pulmonary disease (COPD) and bronchitis, produce uneven doses within the respiratory tract. Traditional concepts of the translocation and clearance of deposited particles have been challenged. Ultrafine particles can translocate to the brain via olfactory nerves, and from the lung to other organs. The clearance rates of particles from tracheobronchial airways are slowed by respiratory tract infections, but newer evidence implies that slow particle clearance from this region also exists in healthy lungs. Finally, hot spots of particle deposition are seen in hollow models, lung tissue, and dosimetric simulations. Local doses to groups of epithelial cells can be much greater than those to surrounding cells. The new insights challenge dosimetry scientists.

Abstract Background Since human brain tissue is often unavailable for transcriptional profiling studies, blood expression data is frequently used as a substitute. The underlying hypothesis in such studies is that genes expressed in brain tissue leave a transcriptional footprint in blood. We tested this hypothesis by relating three human brain expression data sets (from cortex, cerebellum and caudate nucleus) to two large human blood expression data sets (comprised of 1463 individuals). Results We found mean expression levels were weakly correlated between the brain and blood data (r range: [0.24,0.32]). Further, we tested whether co-expression relationships were preserved between the three brain regions and blood. Only a handful of brain co-expression modules showed strong evidence of preservation and these modules could be combined into a single large blood module. We also identified highly connected intramodular "hub" genes inside preserved modules. These preserved intramodular hub genes had the following properties: first, their expression levels tended to be significantly more heritable than those from non-preserved intramodular hub genes (p < 10-90); second, they had highly significant positive correlations with the following cluster of differentiation genes: CD58, CD47, CD48, CD53 and CD164; third, a significant number of them were known to be involved in infection mechanisms, post-transcriptional and post-translational modification and other basic processes. Conclusions Overall, we find transcriptome organization is poorly preserved between brain and blood. However, the subset of preserved co-expression relationships characterized here may aid future efforts to identify blood biomarkers for neurological and neuropsychiatric diseases when brain tissue samples are unavailable.

The use of respiratory tract dosimetry predictions to estimate the desired aerosol exposure concentration required for a specific target deposited dose in animal inhalation studies has been hindered by: (1) a lack of species/strain specific quantitative respiratory tract anatomy; and (2) verification by comparison of calculated and experimentally measured deposited doses. Using recent literature on tracheobronchial and pulmonary respiratory tract anatomy, dosimetry predictions for the Balb/c mouse were compared with deposited doses for 0.5, 1.0, and 2.0 micrometer diameter aerosols in a newly available nose-only exposure system. Spatial and temporal aerosol port to port uniformity of this nose-only exposure system was within ± 10% of the mean. Dosimetry predictions were in agreement with the measured mean deposited doses for the aerosols tested. © 2009 Taylor & Francis Group, LLC.

Genome-wide expression profiling has aided the understanding of the molecular basis of neuronal diversity, but achieving broad functional insight remains a considerable challenge. Here, we perform the first systems-level analysis of microarray data from single neuronal populations using weighted gene co-expression network analysis to examine how neuronal transcriptome organization relates to neuronal function and diversity. We systematically validate network predictions using published proteomic and genomic data. Several network modules of co-expressed genes correspond to interneuron development programs, in which the hub genes are known to be critical for interneuron specification. Other co-expression modules relate to fundamental cellular functions, such as energy production, firing rate, trafficking, and synapses, suggesting that fundamental aspects of neuronal diversity are produced by quantitative variation in basic metabolic processes. We identify two transcriptionally distinct mitochondrial modules and demonstrate that one corresponds to mitochondria enriched in neuronal processes and synapses, whereas the other represents a population restricted to the soma. Finally, we show that galectin-1 is a new interneuron marker, and we validate network predictions in vivo using Rgs4 and Dlx1/2 knockout mice. These analyses provide a basis for understanding how specific aspects of neuronal phenotypic diversity are organized at the transcriptional level.

Animal models are essential for understanding the fates and effects of inhaled materials, because invasive methods are frequently necessary to provide the desired information. Because of the variability in humans of particle deposition, clearance, and effects, numerous animal models have been used in inhalation studies. Furthermore, humans are not typical mammals in some ways that affect inhalation phenomena. Humans have less fur, longer gestation and life times, simplified nasal structure, and symmetric bronchial branching in relation to other mammals. However, experience, plus the genetic similarity among mammals, underpins the use of animal models. Mammals are varied with respect to their inhaled particle deposition and clearance phenomena. Total inhaled aerosol deposition probability versus particle-size curves are qualitatively similar for various mammals of similar body mass, despite airway anatomy differences. However, more species variation is seen in regional particle deposition curves, complicating aerosol study design. The rates of clearance of deposited slowly dissolving particles are animal species dependent, apparently due to differences in gross, subgross, and cellular respiratory tract biology. Clearance rates for rapidly dissolving particles are not strongly species dependent. Inhalation toxicology studies require several animal species. Rodents are among the most frequently used, but for studies of lung development, diseases, exercise, etc., and for extrapolation to humans, larger mammals are also needed. Fortunately, the research database, and excellent monographs on inhalation phenomena provide ample guidance for study design.

Toxicological evaluations of flavor chemicals for use in inhalation products that utilize heat for aerosol generation are complicated because of the potential effect heat may have on the flavor chemical. The objective was to develop a thermal degradation technique to screen flavor chemicals as part of a toxicological testing program for their potential use in ENDS formulations. Based upon published data for acetaldehyde, acrolein, and glycidol from ENDS products (common thermal degradants of propylene glycol and glycerin), the pyrolizer temperature was adjusted until a similar ratio of acetaldehyde, acrolein, and glycidol was obtained from a 60/40 ratio (v/v) of glycerin/propylene glycol via GC/MS analysis. For each of 90 flavor chemicals, quantitative measurements of acetaldehyde, acrolein, and glycidol, in addition to semiquantitative non-targeted analysis tentatively identifying chemicals from thermal degradation, were obtained. Twenty flavor chemicals transferred at greater than 99% intact, another 26 transferred at greater than 95% intact, and another 15 flavor chemicals transferred at greater than 90% intact. Most flavor chemicals resulted in fewer than 10–12 tentatively identified thermal degradants. The practical approach to the thermal degradation of flavor chemicals provided useful information as part of the toxicological evaluation of flavor chemicals for potential use in ENDS formulations. [ABSTRACT FROM AUTHOR]

A unique adult human mouth/throat physical model has been developed to study e-cigarette aerosol dynamics during inhalation. The 3D printed physical model was created from the CT scan of a 28 yr. old healthy male. Internal walls of the physical model were lined with a thin layer of cotton gauze that can be saturated with water to replicate the high relative humidity conditions in a human Oral/Pharyngeal cavity. Aerosol hygroscopic growth and deposition inside the physical model from a cartomizer style e-cigarette using a prototype e-liquid formulation was determined by measuring cumulative aerosol mass from five puffs (gravimetric) and for individual constituents (propylene glycol, glycerol, and nicotine) from a single puff (GC/MS analysis). Measurements were taken at constant temperature of 37 °C under both wet and dry inner wall conditions for a for a 3-sec. 55 mL puff. The condition of holding aerosol inside the physical model without airflow for a duration of 3-sec. was also included. For the same puffing conditions of 3-sec puff of 55 mL and a 3-sec. puff hold time, dry wall conditions resulted in a mean aerosol mass loss of 20.9 ± 3.8%, while the total aerosol mass was increased by 150.9 ± 19% under wet wall condition when compared to total aerosol mass entering the physical model entrance. The dramatic increase is due to water vapor uptake by the aerosol particles when flowing through the wetted physical model. Aerosol evolution of individual chemical constituent analysis appeared to vary as a function of volatility. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to present a method for estimating particle doses that may be used to reconcile particle deposition doses used in in vitro toxicology studies with in vivo exposure levels. The focus is on the tracheobronchial (TB) tree of heavily exposed individuals. A review of the factors that influence inhaled particle deposition doses in environmental exposures leads to the identification of cases in which greater than average TB tree doses are received. Exercising individuals and those with chronic obstructive pulmonary disease not only inhale increased volumes of air but they also may have uneven ventilation that leads to greater than average particle deposition doses per unit of TB tree surface area. In addition, deposition hot spots, as occur at airway bifurcations, will greatly increase the particle exposures of target cells in the TB tree. Three particle exposure scenarios are proposed, and the average and local doses to the TB epithelium are calculated. When various factors that enhance particle doses (enhancement factors, or EFs) in vivo are considered, substantial particle doses may be justified for in vitro tissue culture studies that use TB target cells, such as epithelial cell cultures. The use of such EFs is intended to improve in vitro dosing with particles. Although the exposure of cells in vitro cannot fully replicate the complexity of in vivo exposures, it is possible to calculate toxicologically relevant doses that may define adverse health effects in potentially sensitive human populations. Local groups of TB cells in high-dose individuals are predicted to receive particle doses that are 3000-25,000 times higher than the doses averaged over the entire TB region.

A mobile whole-body exposure system was developed for exposing mice to concentrated ambient particulate matter smaller than 2.5 microm in mass median aerodynamic diameter (MMAD). Each 20-L exposure cage was designed to hold 9 mice within individual compartments. This allowed for transport and subsequent exposure. Airflow mixing and the potential for stagnant areas within the compartments were modeled using computational fluid dynamic modeling (CFD). CFD analysis showed no stagnant areas and good mixing throughout the exposure cage. The actual performance of the exposure system was determined for 0.5 to 2.0 microm diameter aerosols by measuring (1) uniformity of aerosol distribution and (2) particle deposition in the tracheobronchial and pulmonary regions of mice exposed in the system. A 0.6-microm MMAD (GSD=2.0) cigarette smoke aerosol was used to experimentally measure the uniformity of aerosol distribution to the nine individual compartments. The average data from three runs showed no statistically significant difference among individual compartments. Particle deposition efficiency in adult male BALB/c mice was measured after exposure (30 min) in the system using monodisperse fluorescent polystyrene latex particles (0.5, 1, and 2 microm aerodynamic diameter). The measured deposition efficiency in this mobile exposure system for the combined tracheobronchial and pulmonary regions of the adult male BALBc mice was 21% for 0.5 microm, 11% for 1.0 microm, and 6.5% for 2.0 microm particles. These deposition efficiencies are similar to those reported for mice exposed in a nose-only exposure system, which indicates that particle losses to animal fur and exposure system surfaces were acceptable.

Strain- and variety-related differences in responses of mice have been reported for a variety of inhaled particulate and gaseous materials. It is important to understand the potential contributions to such responses of differences in delivered doses to the respiratory tract as well as differences in biochemical processes. Deposition doses of inhaled particles are influenced by several factors, including airway anatomy, ventilation, and particle characteristics. Tracheobronchial airway morphometry for airway generations 1-6 of the BALB/c mouse was generated using replica lung casts prepared in situ. Measurements were performed on two groups: control and ovalbumin-sensitized male BALB/c mice. These measurements were compared with previously published airway morphometry of male B6C3F(1) mice. Sensitization did not significantly change measured airway dimensions in the BALB/c mouse. However, the two mouse varieties had significant differences in airway anatomy. The differences found in airway anatomy between mouse varieties correlated with differences in body length and chest circumference. Particle deposition predictions for both varieties of mice were performed for unit density spherical particles from 0.1 to 10 microm in diameter at two ventilation rates using a published aerosol dosimetry computer code. Particle deposition in the proximal tracheobronchial tree ranged up to 3 times greater for the BALB/c mouse for a 2 microm particle diameter and high ventilation rate. These differences in predicted particle deposition suggest that observed strain and variety differences in response to inhaled particulate matter may be in part due to differences in delivered doses to the respiratory tract.

The purpose of this paper is to review the application of mathematical models of inhaled particle deposition to people of various ages. The basic considerations of aerosol physics, biological characteristics and model structure are presented along with limitations inherent in modern modeling techniques. Application of the models to children and senescent adults has been largely based on extrapolating anatomical and physiological data from young adults to match the changes observed during growth and aging. Sample results are included for total particle deposition and deposition in the bronchial and pulmonary regions. The models proposed provide particle deposition predictions that are consistent with the scant measurements available. The models discussed appear to be on firm theoretical grounds, but they are largely limited in application to simple aerosols and average individuals. Also, additional validation of the computational predictions is needed.