[Show abstract][Hide abstract] ABSTRACT: Adult neurogenesis, the lifelong production of new neurons in the adult brain, is under complex genetic control but many of the genes involved remain to be identified. In this study, we have integrated publicly available gene expression data from the BXD and CXB recombinant inbred mouse lines to discover genes co-expressed in the adult hippocampus with Nestin, a common marker of the neural precursor cell population. In addition, we incorporated spatial expression information to restrict candidates to genes with high differential gene expression in the hippocampal dentate gyrus. Incorporating data from curated protein-protein interaction databases revealed interactions between our candidate genes and those already known to be involved in adult neurogenesis. Enrichment analysis suggested a link to the Wnt/β-catenin pathway, known to be involved in adult neurogenesis. In particular, our candidates were enriched in targets of Lef1, a modulator of the Wnt pathway. In conclusion, our combination of bioinformatics approaches identified six novel candidate genes involved in adult neurogenesis; Amer3, Eya3, Mtdh, Nr4a3, Polr2a, and Tbkbp1. Further, we propose a role for Lef1 transcriptional control in the regulation of adult hippocampal precursor cell proliferation.
Frontiers in Neuroscience 12/2014; 8:418. DOI:10.3389/fnins.2014.00418 · 3.70 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Exercise stimulates cellular brain plasticity by extending the pool of proliferating neural precursor cells in the adult hippocampus. This effect has been investigated extensively, but the most immediate cellular effect induced by exercise that results in this acute increase in the number of cycling cells remained unclear. In the developing brain as well as adult pathological models, cell cycle alterations have a major influence on the balance between proliferative and neurogenic divisions. In this study we investigated whether this might also apply to the acute physiological pro-neurogenic stimulus of physical exercise in adulthood. Do changes in cell cycle precede the measurable increase in proliferation? After 5 days of voluntary wheel running, however, we measured only a very small, statistically not significant acceleration in cell cycle, which could not quantitatively explain the observed increase in proliferating cells after exercise. Thus, at this acute stage, changes at the level of cell cycle control is not the primary causal mechanism for the expansion of the precursor cell population, although with time after the stimulus changes in cell cycle of the entire population of labeled cells might be the result of the expanded pool of cells that have progressed to the advanced neurogenic stages with shorter cell cycle length.
Frontiers in Neuroscience 10/2014; 8:314. DOI:10.3389/fnins.2014.00314 · 3.70 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This study builds on the findings that physical activity, such as wheel running in mice, enhances cell proliferation and neurogenesis in the adult hippocampus of the common mouse strain C57BL/6, and that the baseline level of neurogenesis varies by strain, being considerably lower in DBA/2. Because C57BL/6 and DBA/2 are important as the parental strains of the BXD recombinant inbred cross which allows the detection of genetic loci regulating phenotypes such as adult neurogenesis, we performed the current study to investigate the gene x environment interactions regulating neurogenesis. At equal distances and times run DBA/2J mice lacked the acute increase in precursor cell proliferation known from C57BL/6. In DBA/2J proliferation even negatively correlated with the distance run. This was neither due to a stress response (to running itself or single housing) nor differences in estrous cycle. DBA/2 animals exhibited a delayed and weaker pro-neurogenic response with a significant increase in numbers of proliferating cells first detectable after more than a week of wheel running. The proliferative response to running was transient in both strains, the effect being undetectable by 6 weeks. There was also a small transient increase in the production of new neurons in DBA/2J, although these extra cells did not survive. These findings indicate that the comparison between C57BL/6 and DBA/2, and by extension the BXD genetic reference population derived from these strains, should provide a powerful tool for uncovering the complex network of modifier genes affecting the activity-dependent regulation of adult hippocampal neurogenesis. More generally, our findings also describe how the external physical environment interacts with the internal genetic environment to produce different responses to the same behavioral stimuli.
PLoS ONE 12/2013; 8(12):e83797. DOI:10.1371/journal.pone.0083797 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Adult hippocampal neurogenesis is to a large degree controlled at the level of cell survival, and a number of potential mediators of this effect have been postulated. Here, we investigated the small heat shock protein Hspb8, which, because of its pleiotropic prosurvival effects in other systems, was considered a particularly promising candidate factor. Hspb8 is, for example, found in plaques of Alzheimer disease but exerts neuroprotective effects. We found that expression of Hspb8 increased during differentiation in vitro and was particularly associated with later stages (48 –96 h) of differentiation. Gain-of-function and loss-of-function experiments supported the hypothesis that Hspb8 regulates cell survival of new neurons in vitro. In the dentate gyrus of adult mice in vivo, lentiviral overexpression of Hspb8 doubled the surviving cells and concomitantly promoted differentiation and net neurogenesis without affecting precursor cell prolifer-ation. We also discovered that the truncated form of the crystallin domain of Hspb8 was sufficient to affect cell survival and neuronal differentiation in vitro and in vivo. Precursor cell experiments in vitro revealed that Hspb8 increases the phosphorylation of Akt and suggested that the prosurvival effect can be produced by a cell-autonomous mechanism. Analysis of hippocampal Hspb8 expression in mice of 69 strains of the recombinant inbred set BXD revealed that Hspb8 is a cis-acting gene whose expression was associated with clusters of transcript enriched in genes linked to growth factor signaling and apoptosis. Our results strongly suggest that Hspb8 and its -crystallin domain might act as pleiotropic prosurvival factor in the adult hippocampus.
The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 03/2013; 33((13)):5785-5796. DOI:10.1523/JNEUROSCI.6452-11.2013 · 6.75 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gene WFS1 encodes a protein with unknown function although its functional deficiency causes different neuropsychiatric and neuroendocrine syndromes. In the present study, we aimed to find the functional networks influenced by the time-dependent silencing of WFS1 in HEK cells. We performed whole genome gene expression profiling (Human Gene 1.0 ST Arrays) in HEK cells 24, 48, 72 and 96 hours after transfection with three different WFS1 siRNAs. In order to verify silencing we performed quantitative RT-PCR and western blot analysis. Analysis was conducted in two ways. First we analyzed the overall effect of the siRNA treatment on the gene expression profile. As a next step we performed time-course analysis separately for different siRNAs and combined for all siRNAs. Quantitative RT-PCR and western blot analysis confirmed clear silencing of the expression of WFS1 after 48 hours. Significant (FDR value less than 10%) changes in the expression of eleven genes was identified with most of these genes being related to the mitochondrial dysfunction and apoptosis. Time-course analysis confirmed significant correlations between WFS1 silencing and changes in the expression profiles of several genes. The pathways that were influenced significantly by WFS1 silencing were related to mitochondrial damage and neurodegenerative diseases. Our findings suggest a role of WSF1 gene in cell survival and its involvement in degenerative diseases.
[Show abstract][Hide abstract] ABSTRACT: Genetic basis of complex traits including behavioral phenotypes are often studied in animal (such as rodent) sets of the recombinant inbred (RI) strains. This study evaluated hippocampus-dependent learning in the active place avoidance, referred here to as Carousel maze, in the HXB/BXH recombinant inbred (RI) strains (N = 30) derived from SHR/Ola and BN-Lx/Cub strains.Methods
The Carousel maze involves avoidance of a stable unmarked sector on a slowly rotating circular arena. Moreover, we recorded the open-field behavior and beam-walking performance in the RI set.ResultsWe observed large inter-strain variability in the carousel arena performance and analysis of within/between-strain variances suggested a significant heritability. We have analyzed possible genetic determinants of this parameter using a web-based tool www.genenetwork.org. We detected no significant QTL for learning, suggesting that learning in HXB/BXH RI strains is determined by many loci rather than oligogenetically. From previously published phenotypes, we observed significant correlations of maximum time avoided on the final reversal session with several metabolic and cardiovascular traits. Maximum time avoided on the final reversal session also showed two suggestive QTLs and a significant QTL for locomotor activity. Several correlations with cardiovascular traits were detected.ConclusionsA more detailed elaboration of behavioral parameters including further QTL mapping and also analysis of covariance of multiple parameters from the Carousel maze and open-field test with physiological traits and gene expression will contribute to understanding of regulatory genetic relationships between these phenotypes.
European Psychiatry 12/2012; 27:1. DOI:10.1016/S0924-9338(12)74548-0 · 3.44 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Adult hippocampal neurogenesis is not a single phenotype, but consists of a number of sub-processes, each of which is under complex genetic control. Interpretation of gene expression studies using existing resources often does not lead to results that address the interrelatedness of these processes. Formal structure, such as provided by ontologies, is essential in any field for comprehensive interpretation of existing knowledge but, until now, such a structure has been lacking for adult neurogenesis.
We have created a resource with three components 1. A structured ontology describing the key stages in the development of adult hippocampal neural stem cells into functional granule cell neurons. 2. A comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes) to the appropriate terms in our ontology. 3. An easy-to-use searchable interface to the resulting database made freely available online. The manuscript presents an overview of the database highlighting global trends such as the current bias towards research on early proliferative stages, and an example gene set enrichment analysis. A limitation of the resource is the current scope of the literature which, however, is growing by around 100 publications per year. With the ontology and database in place, new findings can be rapidly annotated and regular updates of the database will be made publicly available.
The resource we present allows relevant interpretation of gene expression screens in terms of defined stages of postnatal neuronal development. Annotation of genes by hand from the adult neurogenesis literature ensures the data are directly applicable to the system under study. We believe this approach could also serve as an example to other fields in a 'bottom-up' community effort complementing the already successful 'top-down' approach of the Gene Ontology.
PLoS ONE 11/2012; 7(11):e48527. DOI:10.1371/journal.pone.0048527 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In the search for ways to combat degenerative neurological disorders, neurogenesis-stimulating factors are proving to be a promising area of research. In this study, we show that the hormonal factor prolactin (PRL) can activate a pool of latent precursor cells in the adult mouse hippocampus. Using an in vitro neurosphere assay, we found that the addition of exogenous PRL to primary adult hippocampal cells resulted in an approximate 50% increase in neurosphere number. In addition, direct infusion of PRL into the adult dentate gyrus also resulted in a significant increase in neurosphere number. Together these data indicate that exogenous PRL can increase hippocampal precursor numbers both in vitro and in vivo. Conversely, PRL null mice showed a significant reduction (approximately 80%) in the number of hippocampal-derived neurospheres. Interestingly, no deficit in precursor proliferation was observed in vivo, indicating that in this situation other niche factors can compensate for a loss in PRL. The PRL loss resulted in learning and memory deficits in the PRL null mice, as indicated by significant deficits in the standard behavioral tests requiring input from the hippocampus. This behavioral deficit was rescued by direct infusion of recombinant PRL into the hippocampus, indicating that a lack of PRL in the adult mouse hippocampus can be correlated with impaired learning and memory.
PLoS ONE 09/2012; 7(9):e44371. DOI:10.1371/journal.pone.0044371 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Durable osseointegration of metallic bone implants requires that progenitor cells attach, proliferate and differentiate on the implant surface. Previously, we demonstrated superior biocompatibility of human mesenchymal stromal cells (MSCs) cultivated on ultrasmooth tantalum (Ta) as compared to titanium (Ti) surface. The aim of this study was to extend the previous investigation of biocompatibility by monitoring temporal gene expression of MSCs on topographically comparable smooth Ta and Ti surfaces using whole-genome gene expression analysis. Total RNA samples from telomerase-immortalized human MSCs cultivated on plain sputter-coated surfaces of Ta or Ti for 1, 2, 4, and 8 days were hybridized to n = 16 U133 Plus 2.0 arrays (Affymetrix®). Functional annotation, cluster and pathway analyses were performed. The vast majority of genes were differentially regulated after 4 days of cultivation and genes upregulated by MSCs exposed to Ta and Ti were predominantly related to the processes of differentiation and transcription, respectively. Functional annotation analysis of the 1,000 temporally most significantly regulated genes suggests earlier cellular differentiation on Ta compared to Ti surface. Key genes related to osteogenesis and cell adhesion were upregulated by MSCs exposed to Ta. We further identified differentially regulated candidate transcription factors, e.g., NRF2, EGR1, IRF-1, IRF-8, NF-Y, and p53 as well as relevant signaling pathways, e.g., p53 and mTOR, indicating e.g., differences in the Ta- and Ti-induced oxidative stress reactions at the cell/biomaterial interface. These findings suggest that Ta is a promising material for bone implants.
[Show abstract][Hide abstract] ABSTRACT: BESIDES THE MASSIVE PLASTICITY AT THE LEVEL OF SYNAPSES, WE FIND IN THE HIPPOCAMPUS OF ADULT MICE AND RATS TWO SYSTEMS WITH VERY STRONG MACROSCOPIC STRUCTURAL PLASTICITY: adult neurogenesis, that is the lifelong generation of new granule cells, and dynamic changes in the mossy fibers linking the dentate gyrus to area CA3. In particular the anatomy of the infrapyramidal mossy fiber tract (IMF) changes in response to a variety of extrinsic and intrinsic stimuli. Because mossy fibers are the axons of granule cells, the question arises whether these two types of plasticity are linked. Using immunohistochemistry for markers associated with axonal growth and pro-opiomelanocortin (POMC)-GFP mice to visualize the post-mitotic maturation phase of adult hippocampal neurogenesis, we found that newly generated mossy fibers preferentially but not exclusively contribute to the IMF. The neurogenic stimulus of an enriched environment increased the volume of the IMF. In addition, the IMF grew with a time course consistent with axonal outgrowth from the newborn neurons after the induction of neurogenic seizures using kainate. These results indicate that two aspects of plasticity in the adult hippocampus, mossy fiber size and neurogenesis, are related and may share underlying mechanisms. In a second part of this study, published separately (Krebs et al., 2011) we have addressed the question of whether there is a shared genetics underlying both traits.
Frontiers in Neuroscience 09/2011; 5:107. DOI:10.3389/fnins.2011.00107 · 3.70 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The hippocampus of adult rodents harbors two systems exhibiting structural plasticity beyond the level of synapses and dendrites. First, the persistent generation of granule cells (adult neurogenesis); second, dynamic changes in the mossy fibers (MF), in particular in the infrapyramidal mossy fiber (IMF) tract. Because MFs are the axons of granule cells, the question arises whether these two types of plasticity are linked. In the first part of this study (Römer et al., 2011) we have asked how both traits are regulated in relation to each other. In the present part, we asked whether, besides activity-dependent co-regulation, there would also be signs of genetic co-regulation and co-variance. For this purpose we used the BXD panel of recombinant inbred strains of mice, a unique genetic reference population that allows genetic association studies. In 31 BXD strains we did not find correlations between the traits describing the volume of the MF subfields and measures of adult neurogenesis. When we carried out quantitative trait locus mapping for these traits, we found that the map for IMF volume showed little overlap with the maps for the other parts of the projection or for adult neurogenesis, suggesting that to a large degree the IMF is regulated independently. The highest overlapping peak in the genome-wide association maps for IMF volume and the number of new neurons was on distal chromosome 5 (118.3-199.2 Mb) with an LRS score of 5.5 for IMF and 6.0 for new neurons. Within this interval we identified Nos1 (neuronal nitric oxide synthase) as a cis-acting (i.e., presumably autoregulatory) candidate gene. The expression of Nos1 is has been previously linked with both IMF and adult neurogenesis, supporting our findings. Despite explaining on its own very little of the variance in the highly multigenic traits studied, our results suggest Nos1 may play a part in the complex genetic control of adult neurogenesis and IMF morphology.
Frontiers in Neuroscience 09/2011; 5:106. DOI:10.3389/fnins.2011.00106 · 3.70 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Strong epidemiological and experimental evidence links folate deficiency and resultant hyperhomocysteinemia with cognitive decline and neurodegeneration. Here, we tested the hypothesis that uracil misincorporation contributes to mitochondrial pathology in aged brain following folate deprivation. In a 2 × 2 design, 14-month-old mice lacking uracil DNA glycosylase (Ung-/-) versus wild-type controls were subjected to a folate-deficient versus a regular diet for six weeks. Folate-deficient feeding significantly enhanced mtDNA content and overall abundance of the D-1 mtDNA deletion in brain of Ung-/-, but not of wild-type mice. Independent of folate status, the frequency of the D-1 mtDNA deletion in mtDNA was significantly increased in Ung-/- mice. The rate of mitochondrial biogenesis as assessed at six weeks of the experimental diet by mRNA expression levels of transcriptional coactivator peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and of mitochondrial transcription factor A (Tfam) was not affected by either Ung-/- genotype or short-term folate deficiency. Similarly, citrate synthase (CS) activity in the brain did not differ across experimental groups. By contrast, independent of genotype, lactate dehydrogenase (LDH) activity was significantly reduced in folate-deficient animals. Our results suggest that impaired uracil excision repair causes an increase in mitochondrial mutagenesis in aged brain along with a compensatory increase in mtDNA content in response to low folate status. Folate deficiency may contribute to neurodegeneration via mtDNA damage.
[Show abstract][Hide abstract] ABSTRACT: The study of expression quantitative trait loci (eQTL) is a powerful way of detecting transcriptional regulators at a genomic scale and for elucidating how natural genetic variation impacts gene expression. Power and genetic resolution are heavily affected by the study population: whereas recombinant inbred (RI) strains yield greater statistical power with low genetic resolution, using diverse inbred or outbred strains improves genetic resolution at the cost of lower power. In order to overcome the limitations of both individual approaches, we combine data from RI strains with genetically more diverse strains and analyze hippocampus eQTL data obtained from mouse RI strains (BXD) and from a panel of diverse inbred strains (Mouse Diversity Panel, MDP). We perform a systematic analysis of the consistency of eQTL independently obtained from these two populations and demonstrate that a significant fraction of eQTL can be replicated. Based on existing knowledge from pathway databases we assess different approaches for using the high-resolution MDP data for fine mapping BXD eQTL. Finally, we apply this framework to an eQTL hotspot on chromosome 1 (Qrr1), which has been implicated in a range of neurological traits. Here we present the first systematic examination of the consistency between eQTL obtained independently from the BXD and MDP populations. Our analysis of fine-mapping approaches is based on 'real life' data as opposed to simulated data and it allows us to propose a strategy for using MDP data to fine map BXD eQTL. Application of this framework to Qrr1 reveals that this eQTL hotspot is not caused by just one (or few) 'master regulators', but actually by a set of polymorphic genes specific to the central nervous system.
PLoS ONE 11/2010; 5(11):e13920. DOI:10.1371/journal.pone.0013920 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The subgranular zone of the dentate gyrus of sexually mature mice contains a highly variable number of pluripotent stem cells that produce a stream of intermediate progenitors which give rise to neurons and glial cells. Genetic factors, age, and the environment control variation in the fate and rate of neurogenesis. Discovery of stem cells in the adult CNS has catalyzed wide-ranging research into the molecular control of regeneration and repair. In recent work we have explored the genetic basis of variation in adult neurogenesis in C57BL/6J (B), DBA/2J (D) and the BXD family of inbred mice . Here we exploit expression quantitative trait locus (eQTL) mapping and advanced graph theoretical algorithms to extract and analyze small sets of genes-so-called cliques and paracliques-that have tightly coupled expression with brain-derived neurotrophic factor (BDNF). Isoforms of BDNF are key modulators of neuronal proliferation, dendritic plasticity, and also influence disease susceptibility. Two independent BDNF cliques that are associated with all Bdnf transcripts or dendritic transcripts were studied using gene ontology analysis, direct literature analysis, and eQTL mapping methods. We show that these two Bdnf cliques are modulated by gene variants located on distal Chr 1 (the Fmn2/Qrr1 region) and proximal Chr 19 near Prune2. Prune2, which controls the clique primarily associated with total Bdnf expression, is a novel adult neurogenesis candidate gene with proapoptotic function that has recently been linked to Alzheimer's disease.
Biomedical Sciences and Engineering Conference (BSEC), 2010; 06/2010
[Show abstract][Hide abstract] ABSTRACT: Differences in gene expression in the CNS influence behavior and disease susceptibility. To systematically explore the role of normal variation in expression on hippocampal structure and function, we generated an online microarray database for a diverse panel of strains of mice, including most common inbred strains and numerous recombinant inbred lines (www.genenetwork.org). Using this resource, coexpression networks for families of genes can be generated rapidly to test causal models related to function. The data set is optimized for quantitative trait locus (QTL) mapping and was used to identify over 5500 QTLs that modulate mRNA levels. We describe a wide variety of analyses and novel synthetic approaches that take advantage of this resource, and demonstrate how both the data and associated tools can be applied to the study of gene regulation in the hippocampus and relations to structure and function.
Frontiers in Neuroscience 11/2009; 3:55. DOI:10.3389/neuro.15.003.2009 · 3.70 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Author Summary
Neural stem cells divide and generate new neurons throughout life in the mammalian hippocampus. After a distinct maturation process, newborn neurons become functionally integrated into the preexisting circuitry and appear to participate in hippocampal function, which is critically involved in certain forms of learning and memory. However, the molecular mechanisms by which new neurons find their position and project to their appropriate target area remain largely unknown. We here show that cell-type–specific reduction of cyclin-dependent kinase 5 (cdk5) activity in newborn neurons results in impaired neuronal migration and leads to the extension of incorrectly targeted neuronal processes. Strikingly, ectopic processes extending from newborn cells synaptically integrate, suggesting a dissociation between accurate targeting of processes extending from newborn neurons and subsequent synapse formation, which might have important implications for the restorative use of neural stem cells in neurological disease.
[Show abstract][Hide abstract] ABSTRACT: In aging mice, activity maintains hippocampal plasticity and adult hippocampal neurogenesis at a level corresponding to a younger age. Here we studied whether physical exercise and environmental enrichment would also affect brain plasticity in a mouse model of Alzheimer's disease (AD).
Amyloid precursor protein (APP)-23 mice were housed under standard or enriched conditions or in cages equipped with a running wheel. We assessed beta-amyloid plaque load, adult hippocampal neurogenesis, spatial learning, and mRNA levels of trophic factors in the brain.
Despite stable beta-amyloid plaque load, enriched-living mice showed improved water maze performance, an up-regulation of hippocampal neurotrophin (NT-3) and brain-derived neurotrophic factor (BDNF) and increased hippocampal neurogenesis. In contrast, despite increased bodily fitness, wheel-running APP23 mice showed no change in spatial learning and no change in adult hippocampal neurogenesis but a down-regulation of hippocampal and cortical growth factors.
We conclude that structural and molecular prerequisites for activity-dependent plasticity are preserved in mutant mice with an AD-like pathology. Our study might help explain benefits of activity for the aging brain but also demonstrates differences between physical and more cognitive activity. It also suggests a possible cellular correlate for the dissociation between structural and functional pathology often found in AD.