Mechanisms of neuronal plasticity as analyzed at the single cell level

cDNA library construction from single cells

Analysis of gene expression or comparing gene expression patterns between cells and/or tissues facilitates the identification of molecules activated by a cellular program or by a particular physiological or pharmacological treatment. This unit presents a protocol for studying these molecules at the level of a single cell.

Expression profile analysis of neurodegenerative disease: advances in specificity and resolution

Microarray technology has become a common tool for developing expression profiles. Initially used in the analysis of cells lines and homogeneous tissues, this platform has been applied to more diverse tissues, such as the brain. Several neural disorders have already been profiled by microarrays using relatively large amounts of tissue. This data has unveiled many genes with differential expression between normal and diseased tissue that could potentially be used as gene markers for these afflictions. Because of the heterogeneity of the CNS, it is likely that small differences between gene expression in these studies would be enhanced by the sampling of a subset of cells based on these newly characterized gene markers. Subtraction of normal, unaffected cells from the sample may also result in a more accurate profile of a diseased cell. Expression profile studies from several neuropathological states are presented, with emphasis placed on those studies using small samples of cellular material and those using specialized methods of cell isolation and RNA amplification.

Transcriptional analysis in the brain: trophin-induced hippocampal synaptic plasticity

Gene profiling in the central nervous system presents unique challenges due to the unprecedented heterogeneity of cells, systems and functions in time and space. We have employed a multidisciplinary approach using whole cell patch clamp recording and transcriptional analysis to define the genomic basis of trophin-induced hippocampal synaptic plasticity. Transcriptional analysis of single cells by linear amplification of antisense RNA has added a new dimension of sensitivity and selectivity to the study of the complex and heterogeneous population of neurons. We describe different gene expression profiling techniques that offer novel approaches to monitoring thousands of genes in parallel, fostering identification of circuits involved in learning and memory.

Expression profile of 30,000 genes in rat hippocampus using SAGE

Using the serial analysis of gene expression (SAGE) method, we generated a gene expression profile of the rat hippocampus. A total of 76,790 SAGE tags was analyzed, allowing identification of 28,748 different tag species, each representing a unique mRNA transcript. The tags were divided into different abundancy classes, ranging from tags that were detected over 500 times to tags encountered only once in the 76,790 tags analyzed. The mRNA species detected more than 50 times represented 0.3% of the total number of unique tags while accounting for 22% of the total hippocampal mRNA mass. The majority of tags were encountered 5 times or less. The genes expressed at the highest levels were of mitochondrial origin, consistent with a high requirement for energy in neuronal tissue. At a lower level of expression, several neuron-specific transcripts were encountered, encoding various neurotransmitter receptors, transporters, and enzymes involved in neurotransmitter synthesis and turnover, ion channels and pumps, and synaptic components. Comparison of relative expression levels demonstrated that glutamate receptors are the most frequent neurotransmitter receptors expressed in the hippocampus, consistent with the important role of glutamatergic neurotransmission in the hippocampus, while GABA receptors were present at approximately 10-fold lower levels. Several kinases were present including CaMKII, which was expressed at high levels, consistent with its being the most abundant protein in the spines of hippocampal pyramidal cells. This is the first extensive inventory of gene expression in the hippocampus and serves as a reference for future studies aimed at elucidating hippocampal transcriptional responses under various conditions.

Regulation of cyclin-dependent kinase 5 and casein kinase 1 by metabotropic glutamate receptors

Cyclin-dependent kinase 5 (Cdk5) is a multifunctional neuronal protein kinase that is required for neurite outgrowth and cortical lamination and that plays an important role in dopaminergic signaling in the neostriatum through phosphorylation of Thr-75 of DARPP-32 (dopamine and cAMP-regulated phosphoprotein, molecular mass 32 kDa). Casein kinase 1 (CK1) has been implicated in a variety of cellular functions such as DNA repair, circadian rhythm, and intracellular trafficking. In the neostriatum, CK1 has been found to phosphorylate Ser-137 of DARPP-32. However, first messengers for the regulation of Cdk5 or CK1 have remained unknown. Here we report that both Cdk5 and CK1 are regulated by metabotropic glutamate receptors (mGluRs) in neostriatal neurons. (S)-3,5-dihydroxyphenylglycine (DHPG), an agonist for group I mGluRs, increased Cdk5 and CK1 activities in neostriatal slices, leading to the enhanced phosphorylation of Thr-75 and Ser-137 of DARPP-32, respectively. The effect of DHPG on Thr-75, but not on Ser-137, was blocked by a Cdk5-specific inhibitor, butyrolactone. In contrast, the effects of DHPG on both Thr-75 and Ser-137 were blocked by CK1-7 and IC261, specific inhibitors of CK1, suggesting that activation of Cdk5 by mGluRs requires CK1 activity. In support of this possibility, the DHPG-induced increase in Cdk5 activity, measured in extracts of neostriatal slices, was abolished by CK1-7 and IC261. Treatment of acutely dissociated neurons with DHPG enhanced voltage-dependent Ca(2+) currents. This enhancement was eliminated by either butyrolactone or CK1-7 and was absent in DARPP-32 knockout mice. Together these results indicate that a CK1-Cdk5-DARPP-32 cascade may be involved in the regulation by mGluR agonists of Ca(2+) channels.

Rab3A is required for brain-derived neurotrophic factor-induced synaptic plasticity: transcriptional analysis at the population and single-cell levels

Brain-derived neurotrophic factor (BDNF) modulates synaptic strength in hippocampal neurons, in addition to promoting survival and differentiation. To identify genes involved in trophic regulation of synaptic plasticity, we have used a multidisciplinary approach of differential display and family-specific slot blots in combination with whole-cell patch-clamp recordings of dissociated hippocampal neurons. Three hour exposure to BDNF elicited a 2.6-fold increase in synaptic charge and a concomitant induction of 11 genes as revealed by differential display, including the small GTP-binding vesicular trafficking protein Rab3A and the enzyme guanylate cyclase (GC). Slot blot analysis on a population of neurons confirmed an average of 3.1-fold induction of these clones. In contrast, individual pyramidal-like neurons that were first characterized electrophysiologically in the presence of BDNF and subjected to transcriptional analysis displayed more robust increases (4.8-fold), emphasizing the neuronal heterogeneity. Transcriptional changes of Rab3A and GC were accompanied by translational regulation, shown by Western blot analysis. Furthermore, a number of GC-associated and Rab3A effector molecules were induced by BDNF at either the gene or protein levels. The functional role of Rab3A in BDNF-induced synaptic plasticity was assessed using cells derived from Rab3A knock-out mice. These neurons failed to show an increase in synaptic charge in response to BDNF at 10 min; however a late response to BDNF was detected at 20 min. This late response was similar in time course to that induced by postsynaptic activation of glutamate receptors. Our results demonstrate a requirement for Rab3A and may reveal a temporal distinction between presynaptic and postsynaptic mechanisms of BDNF-induced synaptic plasticity associated with learning and memory.

Molecular and functional characteristics of MAP-2a: ability of MAP-2a versus MAP-2b to induce stable microtubules in COS cells

Microtubule-associated protein-2 (MAP-2) is a prominent cytoskeletal protein in the mammalian nervous system. Two high-molecular-weight (HMW) MAP-2 isoforms, MAP-2a and MAP-2b, are developmentally regulated. MAP-2b is expressed through the life of the neuron, while MAP-2a expression coincides with the time of synaptic formation. MAP-2a and MAP-2b differ in size by approximately 10 kD. Attempts to differentiate MAP-2a from MAP-2b led to the identification of additional exons; exons 7A, 8, 13, and 16. The focus of the present study was to define the complete molecular composition of MAP-2a that was prerequisite for investigating the functional characteristic of the MAP-2a protein. Detailed examination of rat brain mRNA by Northern blot analysis and RT-PCR showed that MAP-2a contains only exon 8 in addition to the exons found in the MAP-2b transcript. Exons 7A, 13, and 16 are not present in the MAP-2a transcript. Antibody generated to exon 8 expressed protein, immunoprecipitated a HMW protein from adult rat brain that co-migrated with MAP-2a and was immunopositive with other MAP-2 antibodies. Comparative transfections of full-length MAP-2a and MAP-2b cDNA into COS-7 cells demonstrated that MAP-2a influenced the microtubule network differently than MAP-2b by inducing rapid and stable microtubule bundle formation even in the presence of nocodazole.

A spatial approach to transcriptional profiling: mechanotransduction and the focal origin of atherosclerosis

The initiation and progression of focal atherosclerotic lesions has long been known to be associated with regions of disturbed blood flow. Improved precision in experimental models of spatially defined flow has recently been combined with regional and single-cell gene-expression profiling to investigate the relationships linking haemodynamics to vessel-wall pathobiology.