Brain Cell Types Research Articles

An update on stem cell biology and engineering for brain development.

Two recent technologies, induced-pluripotent stem cells (iPSCs) and direct somatic reprogramming, have shown enormous potential for cell-based therapies against intractable diseases such as those that affect the central nervous system. Already, methods that generate most major cell types of the human brain exist. Whether the cell types are directly reprogrammed from human somatic cells or differentiated from an iPSC intermediate, the overview presented here demonstrates how these protocols vary greatly in their efficiencies, purity and maturation of the resulting cells. Possible solutions including micro-RNA switch technologies that purify target cell types are also outlined. Further, an update on the transition from 2D to 3D cultures and current organoid (mini-brain) cultures are reviewed to give the stem cell and developmental engineering communities an up-to-date account of the progress and future perspectives for modeling of central nervous system disease and brain development in vitro.

Sorting neurons from preserved brain tissue

Neuroscientists routinely store brain tissue samples in brain banks for future analysis. Being able to use cell-sorting techniques such as flow cytometry on this preserved tissue would allow researchers to study the effects of drugs, environmental factors, and diseases on specific brain cell types. However, it’s difficult to separate cells from chemically fixed, frozen tissue samples and prepare them for flow cytometry without causing damage. Now, Charles D. Nichols of the Louisiana State University Health Sciences Center New Orleans and colleagues have developed new protocols to overcome these limitations (ACS Chem. Neurosci. 2017, DOI: 10.1021/acschemneuro.6b00374). The researchers separated cells from human and rodent brain tissue samples—fixed using preservatives such as formalin, zinc, and paraformaldehyde—by passing liquefied frozen tissue through needles multiple times and applying an enzyme solution that cleaves chemical bonds between cells. They then fluorescently tagged the cells and passed cell...

Mathematical investigation of IP3-dependent calcium dynamics in astrocytes.

We study evoked calcium dynamics in astrocytes, a major cell type in the mammalian brain. Experimental evidence has shown that such dynamics are highly variable between different trials, cells, and cell subcompartments. Here we present a qualitative analysis of a recent mathematical model of astrocyte calcium responses. We show how the major response types are generated in the model as a result of the underlying bifurcation structure. By varying key channel parameters, mimicking blockers used by experimentalists, we manipulate this underlying bifurcation structure and predict how the distributions of responses can change. We find that store-operated calcium channels, plasma membrane bound channels with little activity during calcium transients, have a surprisingly strong effect, underscoring the importance of considering these channels in both experiments and mathematical settings. Variation in the maximum flow in different calcium channels is also shown to determine the range of stable oscillations, as well as set the range of frequencies of the oscillations. Further, by conducting a randomized search through the parameter space and recording the resulting calcium responses, we create a database that can be used by experimentalists to help estimate the underlying channel distribution of their cells.

Gray-level co-occurrence matrix analysis of several cell types in mouse brain using resolution-enhanced photothermal microscopy.

Qualifications of intracellular structure were performed for the first time using the gray-level co-occurrence matrix (GLCM) method for images of cells obtained by resolution-enhanced photothermal imaging. The GLCM method has been used to extract five parameters of texture features for five different types of cells in mouse brain; pyramidal neurons and glial cells in the basal nucleus (BGl), dentate gyrus granule cells, cerebellar Purkinje cells, and cerebellar granule cells. The parameters are correlation, contrast, angular second moment (ASM), inverse difference moment (IDM), and entropy for the images of cells of interest in a mouse brain. The parameters vary depending on the pixel distance taken in the analysis method. Based on the obtained results, we identified that the most suitable GLCM parameter is IDM for pyramidal neurons and BGI, granule cells in the dentate gyrus, Purkinje cells and granule cells in the cerebellum. It was also found that the ASM is the most appropriate for neurons in the basal nucleus.

Expression of Rac1 alternative 3′ UTRs is a cell specific mechanism with a function in dendrite outgrowth in cortical neurons

The differential expression of mRNAs containing tandem alternative 3′ UTRs, achieved by mechanisms of alternative polyadenylation and post-transcriptional regulation, has been correlated with a variety of cellular states. In differentiated cells and brain tissues there is a general use of distal polyadenylation signals, originating mRNAs with longer 3′ UTRs, in contrast with proliferating cells and other tissues such as testis, where most mRNAs contain shorter 3′ UTRs. Although cell type and state are relevant in many biological processes, how these mechanisms occur in specific brain cell types is still poorly understood. Rac1 is a member of the Rho family of small GTPases with essential roles in multiple cellular processes, including cell differentiation and axonal growth. Here we used different brain cell types and tissues, including oligodendrocytes, microglia, astrocytes, cortical and hippocampal neurons, and optical nerve, to show that classical Rho GTPases express mRNAs with alternative 3′ UTRs differently, by gene- and cell- specific mechanisms. In particular, we show that Rac1 originate mRNA isoforms with longer 3′ UTRs specifically during neurite growth of cortical, but not hippocampal neurons. Furthermore, we demonstrate that the longest Rac1 3′ UTR is necessary for driving the mRNA to the neurites, and also for neurite outgrowth in cortical neurons. Our results indicate that the expression of Rac1 longer 3′ UTR is a gene and cell-type specific mechanism in the brain, with a new physiological function in cortical neuron differentiation.

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain.

While RNA editing by A-to-I deamination is a requisite for neuronal function in humans, it is under-investigated in single cells. Here we fill this gap by analyzing RNA editing profiles of single cells from the brain cortex of living human subjects. We show that RNA editing levels per cell are bimodally distributed and distinguish between major brain cell types, thus providing new insights into neuronal dynamics.

T15 - A Novel Database Under Construction Featuring Spatiotemporal Expression Variations And Co-Expression Organization In Human Brain

Background Gene expression of specific genes change over a lifespan, and also vary by tissue or cell types. Such variations are critical for normal structure and functions of the human brain. Deviation from a normal range likely contributes to etiology and pathology of neuropsychiatric disorders. But such normal range has never been defined. Additionally, gene coexpression may reflect regulatory organization relationships among genes. We also considered that gene co-expression might guide complex connection variations in different brain regions and development stages. Changes of co-expression have also been implicated in multiple psychiatric disorders. To capture the variations of individual genes and related co-expression modules in normal human brains, we are developing a novel database, named Brain Gene Expression Database (BrainExDB), serving the needs of common reference data of normal expression levels, variations, and co-expression organizations. Methods We collected 15 brain regions and six cell types of 1,258 brain samples from existing public databases and our data, including the Gene Expression Omnibus database, ArrayExpress, Genotype-Tissue Expression project, Brain Cloud, and Stanley. Stringent quality control was applied to remove low-quality data. Both microarray and RNA-seq data have been included. For studies containing samples of different ages and different brain regions or cell types, data were partitioned by their spatiotemporal groups. All gene expression data were normalized into ranking orders to represent their expression levels so that different studies were comparable. Each gene was recorded for its average rank order and variance of expression by brain regions, cell types, and age ranges whichever available. Finally, we analyzed the data by the weighted gene co-expression network analysis to get the co-expression modules. The hub genes and members of co-expression modules were also databased for query. By comparing data across different studies, we will also identify marker genes that significantly differ by cell types, brain regions, age, and sex. Results We will build a human brain expression database featuring gene expression levels and variance in brain cells and regions throughout a lifespan. The database will provide the marker gene list of cell type-, brain region-, age-, and sex-specific genes. The database will also provide gene co-expression module data. Data can be queried by the list of genes, with filters for specific brain regions, cell types, age range, and sex. Discussion We are compiling the biggest datasets of human brain gene expression, aiming to develop reference data that can be used in studying gene expression changes in neuropsychiatric brains. For the time-being, its immediate value is to offer the comprehensive information about expression levels and variance of specific candidate genes in specific brain regions, cell types, age range, and sex. The stability and validity for predicting case states will need to be evaluated by subset data of those patient brains in the same data collection, and from other sources. Furthermore, the marker gene lists and co-expression modules can be used for gene set analyses, and deconvolution analysis of mixed data.

Gene Regulation As A Function of Epigenetic Marks (H3K4ME3, H3K27AC) And Cell Types (Neuronal And Non Neuronal Cells) In Human Brain

We developed a W/WOx-supported Ni catalyst for the diameter-controlled growth of single-walled carbon nanotubes (SWNTs) by chemical vapor deposition (CVD) valid for different substrates and broad growth conditions. The Ni nanoparticles anchored on W/WOx are well dispersed and show superior stability to high temperature. Under broad CVD windows of temperature and carbon feedstock supply conditions, SWNTs with narrow diameter distribution of ∼1.3 ± 0.1 nm can be steadily synthesized. This strategy also works well in the growth of surface lattice oriented SWNT arrays. The aligned SWNTs grown on ST-cut quartz show similar diameters to those obtained on silicon wafers.

Birds of a feather sing together

Neuroscience How do birds know that a song that they hear is from a member of their own species, and how do they learn their songs in the first place? Araki et al. identified two types of brain cells involved in how finches learn their songs (see the Perspective by Tchernichovski and Lipkind). When zebra finches were raised by Bengalese finch foster parents, they learned a song whose morphology resembled that of their foster father. However, the temporal structure remained zebra finch–specific, suggesting that it is innate. Gadagkar et al. recorded activity in specific dopamine neurons in singing zebra finches while controlling perceived song quality with distorted auditory feedback. This distorted feedback represented worse performance than predicted and resulted in negative prediction errors. These findings suggest again that finches have an innate internal goal for their learned songs. Science , this issue p. [1282][1], p. [1234][2]; see also p. [1278][3] [1]: /lookup/doi/10.1126/science.aah6799 [2]: /lookup/doi/10.1126/science.aal3205 [3]: /lookup/doi/10.1126/science.aah6837

Mind the gap: Neural coding of species identity in birdsong prosody.

Juvenile songbirds learn vocal communication from adult tutors of the same species but not from adults of other species. How species-specific learning emerges from the basic features of song prosody remains unknown. In the zebra finch auditory cortex, we discovered a class of neurons that register the silent temporal gaps between song syllables and are distinct from neurons encoding syllable morphology. Behavioral learning and neuronal coding of temporal gap structure resisted song tutoring from other species: Zebra finches fostered by Bengalese finch parents learned Bengalese finch song morphology transposed onto zebra finch temporal gaps. During the vocal learning period, temporal gap neurons fired selectively to zebra finch song. The innate temporal coding of intersyllable silent gaps suggests a neuronal barcode for conspecific vocal learning and social communication in acoustically diverse environments.

Dopamine neurons encode performance error in singing birds.

Many behaviors are learned through trial and error by matching performance to internal goals. Yet neural mechanisms of performance evaluation remain poorly understood. We recorded basal ganglia-projecting dopamine neurons in singing zebra finches as we controlled perceived song quality with distorted auditory feedback. Dopamine activity was phasically suppressed after distorted syllables, consistent with a worse-than-predicted outcome, and was phasically activated at the precise moment of the song when a predicted distortion did not occur, consistent with a better-than-predicted outcome. Error response magnitude depended on distortion probability. Thus, dopaminergic error signals can evaluate behaviors that are not learned for reward and are instead learned by matching performance outcomes to internal goals.

MAPPING NEURONAL CELL TYPES USING INTEGRATIVE MULTI-SPECIES MODELING OF HUMAN AND MOUSE SINGLE CELL RNA SEQUENCING.

Mouse brain transcriptomic studies are important in the understanding of the structural heterogeneity in the brain. However, it is not well understood how cell types in the mouse brain relate to human brain cell types on a cellular level. We propose that it is possible with single cell granularity to find concordant genes between mouse and human and that these genes can be used to separate cell types across species. We show that a set of concordant genes can be algorithmically derived from a combination of human and mouse single cell sequencing data. Using this gene set, we show that similar cell types shared between mouse and human cluster together. Furthermore we find that previously unclassified human cells can be mapped to the glial/vascular cell type by integrating mouse cell type expression profiles.

Genetically dissecting P2rx7 expression within the central nervous system using conditional humanized mice

The purinergic P2X7 receptor (P2X7R) has attracted considerable interest as a potential target for various central nervous system (CNS) pathologies including affective and neurodegenerative disorders. To date, the distribution and cellular localization of the P2X7R in the brain are not fully resolved and a matter of debate mainly due to the limitations of existing tools. However, this knowledge should be a prerequisite for understanding the contribution of the P2X7R to brain disease. Here, we generated a genetic mouse model by humanizing the P2X7R in the mouse as mammalian model organism. We demonstrated its functionality and revealed species-specific characteristics of the humanized receptor, compared to the murine ortholog, regarding its receptivity to activation and modulation by 2′,3′-O-(benzoyl-4-benzoyl)-adenosine 5′-triphosphate (BzATP) and trifluoperazine (TFP). This humanized P2rx7 allele is accessible to spatially and temporally controlled Cre recombinase-mediated inactivation. In contrast to previously generated knockout (KO) mice, none of the described P2rx7 splice variants evade this null allele. By selective disruption and assessment of human P2RX7 expression in different brain regions and cell types, we were able to demonstrate that the P2X7R is specifically expressed in glutamatergic pyramidal neurons of the hippocampus. Also, P2X7R is expressed in major non-neuronal lineages throughout the brain, i.e., astrocytes, oligodendrocytes, and microglia. In conclusion, this humanized mouse model provides the means for detailed assessment of human P2X7R function in vivo including evaluation of agonists or antagonists. In addition, this conditional allele will enable future loss-of-function studies in conjunction with mouse models for CNS disorders.

β-Hydroxybutyrate in the Brain: One Molecule, Multiple Mechanisms.

β-Hydroxybutyrate (βOHB), a ketone body, is oxidised as a brain fuel. Although its contribution to energy metabolism in the healthy brain is minimal, it is an interesting metabolite which is not only oxidised but also has other direct and collateral effects which make it a molecule of interest for therapeutic purposes. In brain βOHB can be produced in astrocytes from oxidation of fatty acids or catabolism of amino acids and is metabolised in the mitochondria of all brain cell types although uptake across the blood brain barrier is a metabolic control point. βOHB possesses an intrinsic high heat of combustion, making it an efficient mitochondrial fuel, where it can alter the NAD+/NADH and Q/QH2 couples and reduce production of mitochondrial reactive oxygen species. It can directly interact as a signalling molecule influencing opening of K+ channels and regulation of Ca2+ channels. βOHB is an inhibitor of histone deacetylases resulting in upregulation of genes involved in protection against oxidative stress and regulation of metabolism. It interacts with an inflammasome in immune cells to reduce production of inflammatory cytokines and reduce inflammation. Use of βOHB as an efficient neurotherapeutic relies on increasing blood βOHB levels so as to encourage entry of βOHB to the brain. While use of βOHB as a sole therapeutic is currently limited, with employment of a ketogenic diet a more widely used approach, recent development and testing of esterified forms of βOHB have shown great promise, with the approach elevating plasma βOHB while allowing consumption of normal diet. An improved understanding of the mechanisms by which βOHB acts will allow better design of both diet and supplemental interventions.

Circulating Insulin-Like Growth Factor I Regulates Its Receptor in the Brain of Male Mice.

The role of IGF-1 and its receptor (IGF-1R) in brain pathology is still unclear. Thus, either reduction of IGF-IR or treatment with IGF-1, two apparently opposite actions, has proven beneficial in brain diseases such as Alzheimer's dementia. A possible explanation of this discrepancy is that IGF-1 down-regulates brain IGF-1R levels, as previously seen in a mouse Alzheimer's dementia model. We now explored whether under normal conditions IGF-1 modulates its receptor. We first observed that in vitro, IGF-1 reduced IGF-1R mRNA levels in all types of brain cells including neurons, astrocytes, microglia, endothelial cells, and oligodendrocytes. IGF-1 also inhibited its own expression in neurons and brain endothelium. Next, we analyzed the in vivo actions of IGF-1. Because serum IGF-1 can enter the brain, we injected mice with IGF-1 ip. As soon as 1 hour after the injection, decreased hippocampal IGF-1 levels were observed, followed by increased IGF-1 and IGF-1R mRNAs 6 hours later. Because environmental enrichment (EE) stimulates the entrance of serum IGF-1 into the brain, we analyzed whether a physiological entrance of IGF-1 also produced changes in brain IGF-1R. Stimulation of IGF-1R by EE triggered a gradual decrease in hippocampal IGF-1 levels. After 6 hours of EE exposure, IGF-1 levels reached a significant decrease in parallel with increased IGF-1R expression. After longer times, IGF-1R mRNA levels returned to baseline. Thus, under nonpathological conditions, IGF-1 regulates brain IGF-1R. Because baseline IGF-1R levels are rapidly restored, a tight control of brain IGF-1R expression seems to operate under physiological conditions.

Cell- and region-specific expression of depression-related protein p11 (S100a10) in the brain.

ABSTRACTP11 (S100a10), a member of the S100 family of proteins, has widespread distribution in the vertebrate body, including in the brain, where it has a key role in membrane trafficking, vesicle secretion, and endocytosis. Recently, our laboratory has shown that a constitutive knockout of p11 (p11‐KO) in mice results in a depressive‐like phenotype. Furthermore, p11 has been implicated in major depressive disorder (MDD) and in the actions of antidepressants. Since depression affects multiple brain regions, and the role of p11 has only been determined in a few of these areas, a detailed analysis of p11 expression in the brain is warranted. Here we demonstrate that, although widespread in the brain, p11 expression is restricted to distinct regions, and specific neuronal and nonneuronal cell types. Furthermore, we provide comprehensive mapping of p11 expression using in situ hybridization, immunocytochemistry, and whole‐tissue volume imaging. Overall, expression spans multiple brain regions, structures, and cell types, suggesting a complex role of p11 in depression. J. Comp. Neurol. 525:955–975, 2017. © 2016 Wiley Periodicals, Inc.

Zika virus infection during the period of maximal brain growth causes microcephaly and corticospinal neuron apoptosis in wild type mice.

Zika virus (ZIKV) infection in pregnant women has been established as a cause of microcephaly in newborns. Here we test the hypothesis that neurodevelopmental stages when the brain is undergoing rapid growth are particularly vulnerable to the effects of ZIKV infection. We injected ZIKV intracranially into wild type C57BL/6 mice at two different time points: early postnatal development, when the brain is growing at its maximal rate, and at weaning, when the brain has largely reached adult size. Both time points showed widespread immunoreactivity for ZIKV and cleaved caspase 3 (CC3, a marker of apoptosis) throughout the brain. However, in early postnatal ZIKV injected mice, some brain areas and cell types display particularly large increases in apoptosis that we did not observe in older animals. Corticospinal pyramidal neurons, a cell type implicated in human microcephaly associated with ZIKV infection, are an example of one such cell type. Proliferating cells in the ventricular zone stem cell compartment are also depleted. These findings are consistent with the hypothesis that periods of rapid brain growth are especially susceptible to neurodevelopmental effects of ZIKV infection, and establish a valuable model to investigate mechanisms underlying neurodevelopmental effects of ZIKV infection and explore candidate therapeutics.

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types.

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1062-5) contains supplementary material, which is available to authorized users.

Oxidative damage and chemokine production dominate days before immune cell infiltration and EAE disease debut.

BackgroundMultiple sclerosis is widely accepted as an inflammatory disease. However, studies indicate that degenerative processes in the CNS occur prior to inflammation. In the widely used animal model experimental autoimmune encephalomyelitis (EAE), we investigated the significance of degenerative processes from mitochondrial membrane potentials, reactive oxidative species, cell death markers, chemokines, and inflammatory cell types in brain, spinal cord, and optic nerve tissue during the effector phase of the disease, before clinical disease was evident.MethodsSixty-two rats were placed in eight groups, n = 6 to 10. Four groups were immunized with spinal cord homogenate emulsified in complete Freund’s adjuvant (one served as EAE group), three groups were immunized with complete Freund’s adjuvant only, and a control group was injected with phosphate buffered saline only. Groups were sacrificed 3, 5, 7, or 12–13 days after the intervention and analyzed for early signs of CNS degeneration.ResultsLoss of mitochondrial membrane potential and oxidative changes was observed days before clinical disease debut at day 9.75 ± 0.89. The early mitochondrial changes were not associated with cytochrome C release, cleavage of caspases 9 (38/40 kDa) and 3 (17/19 kDa), and cleavage of PARP (89 kDa) or spectrin (120/150 kDa), and apoptosis was not initiated. Axonal degeneration was only present at disease onset. Increases in a range of cytokines and chemokines were observed systemically as a consequence of immunization with complete Freund’s adjuvant, whereas the encephalitogenic emulsion induced an upregulation of the chemokines Ccl2, Ccl20, and Cxcl1, specifically in brain tissue, 7 days after immunization.ConclusionFive to seven days after immunization, subtle decreases in the mitochondrial membrane potential and an increased reactive oxygen species burden in brain tissue were observed. No cell death was detected at these time-points, but a specific expression pattern of chemokines indicates activity in the CNS, several days before clinical disease debut.

Glucocorticoids in the management of peritumoral brain edema: a review of molecular mechanisms.

Peritumoral brain edema (PTBE) is mediated by blood-brain barrier breakdown. PTBE results from interstitial vasogenic brain edema due to vascular endothelial growth factor and other inflammatory products of brain tumors. Glucocorticoids (GCs) are the mainstay for treatment of PTBE despite significant systemic side effects. GCs are thought to affect multiple cell types in the edematous brain. Here, we review preclinical studies of GC effects on edematous brain and review mechanisms underlying GC action on tumor cells, endothelial cells, and astrocytes. GCs may reduce tumor cell viability and suppress vascular endothelial growth factor (VEGF) production in tumor cells. Modulation of expression and distribution of tight junction proteins occludin, claudin-5, and ZO-1 in endothelial cells likely plays a central role in GC action on endothelial cells. GCs may also have an effect on astrocyte angiopoietin production and limited effect on astrocyte aquaporin. A better understanding of these molecular mechanisms may lead to the development of novel therapeutics for management of PTBE with a better side effect profile.