The hippocampus consists of distinct anatomic regions that have been demonstrated to have different biological functions. To explore the molecular differences between hippocampal subregions, we performed transcriptional profiling analysis by using DNA microarray technology. The cRNA derived from the CA1, CA3, and dentate gyrus regions of the hippocampus and from spinal cord was hybridized to Affymetrix high-density oligo arrays. This systematic approach revealed sets of genes that were expressed specifically in subregions of the hippocampus corresponding to predefined cytoarchitectural boundaries, which could be confirmed by in situ hybridization and Real Time quantitative polymerase chain reaction. The relative enrichment and absence of genes in the hippocampal subregions support the conclusion that there is a molecular basis for the previously defined anatomic subregions of the hippocampus and also reveal genes that could be important in defining the unique functions of the hippocampal subfields.

Degeneration of neurons in Alzheimer's disease is mediated by ␤-amyloid peptide by diverse mechanisms, which include a putative apoptotic component stimulated by unidentified signaling events. This report describes a novel ␤-amyloid peptide-binding protein (denoted BBP) containing a G protein-coupling module. BBP is one member of a family of three proteins containing this conserved structure. The BBP subtype bound human ␤-amyloid peptide in vitro with high affinity and specificity. Expression of BBP in cell culture induced caspase-dependent vulnerability to ␤-amyloid peptide toxicity. Expression of a signaling-deficient dominant negative BBP mutant suppressed sensitivity of human Ntera-2 neurons to ␤-amyloid peptide mediated toxicity. These findings suggest that BBP is a target of neurotoxic ␤-amyloid peptide and provide new insight into the molecular pathophysiology of Alzheimer's disease.Genetic and biochemical data have coalesced to establish that ␤-amyloid peptide (A␤) 1 is a causative factor in neuron death and the consequent dimunition of cognitive abilities observed in Alzheimer's disease (1, 2). Plasma lipoproteins and their cell surface receptors influence sequestration and clearance of soluble A␤, contributing to the etiology of the disease (3-6). Inflammatory responses and oxidative damage also appear to contribute to the loss of neurons in Alzheimer's disease (7-10). Although the earliest cellular perturbations remain unclear, recent findings indicate that A␤ may act as an initiating factor in the death of neurons by inducing signaling pathways leading to apoptosis (11-17). However, the specific molecular target(s) transducing these A␤ effects has not been identified. The intracellular protein ERAB can bind A␤ in vitro, and neuroblastoma cells expressing recombinant ERAB undergo apoptosis when treated with exogenously added A␤ (18), but the mechanism by which ERAB may affect apoptotic signaling remains obscure. We identified a novel human ␤-amyloid peptide binding protein (BBP) utilizing yeast 2-hybrid technology. Analysis of the BBP amino acid sequence revealed the presence of a structural module related to that of the 7 transmembrane domain G protein-coupled receptor superfamily and known to be important in heterotrimeric G protein activation. Data suggest that BBP mediates cellular vulnerability to A␤ toxicity through a G protein-regulated program of cell death. Two related proteins (BLP1, BLP2; BBP-like proteins) were identified by sequence and structural similarities to BBP, but only the BBP subtype regulates a response to A␤. EXPERIMENTAL PROCEDURESYeast Two-hybrid Systems-Yeast 2-hybrid (Y2H) expression plasmids were constructed in the vectors pAS2 and pACT2 (19). Strain CY770 (20) served as host for Y2H assays. Sequences encoding A␤ 42 were amplified by PCR using primers incorporating restriction sites for subsequent ligation into pAS2, using a human APP (amyloid precursor protein) cDNA clone as template. A Y2H plasmid library consisting of cDNA fragments isolated from human fetal brain clone...

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Pluripotent stem cell lines can be induced to differentiate into a range of somatic cell types in response to various stimuli. Such cell-based systems provide powerful tools for the investigation of molecules that modulate cellular development. For instance, the formation of the nervous system is a highly regulated process, controlled by molecular pathways that determine the expression of specific proteins involved in cell differentiation. To begin to decipher this mechanism in humans, we used oligonucleotide microarrays to profile the complex patterns of gene expression during the differentiation of neurons from pluripotent human stem cells. Samples of mRNA were isolated from cultured NTERA2 human embryonal carcinoma stem cells and their retinoic-acid-induced derivatives and were prepared for hybridization on custom microarrays designed to detect the expression of genes primarily associated with the neural lineage. In response to retinoic acid, human NTERA2 cells coordinately regulate the expression of large numbers of neural transcripts simultaneously. Transcriptional profiles of many individual genes aligned closely with expression patterns previously recorded by developing neural cells in vitro and in vivo, demonstrating that cultured human pluripotent stem cells appear to form neurons in a conserved manner. These experiments have produced many new expression data concerning neuronal differentiation from human stem cells in vitro. Of particular interest was the regulated expression of Pax6 and Nkx6.1 mRNA and the absence of Pax7 transcription, indicating that neurons derived from NTERA2 pluripotent stem cells are characteristic of neuroectodermal cells of the ventral phenotype.

In an effort to understand the process of human neuronal differentiation, we have monitored gene expression in a cell culture model, NTERA2/D1 (NT2). This pluripotent human teratinocarcinoma cell line was induced to differentiate with retinoic acid (RA) over a 21-day period. We monitored gene expression at four time points using a custom-fabricated oligonucleotide GenechipÒ. A panel of human genes that were expected to participate in the process of neurogenesis or act as differentiation markers were chosen and FASTA analysis determined regions of unique sequence. Oligonucleotide selection, masking and fabrication of GenechipsÒ were performed at Affymetrix. Arrays contained 50 probe pairs per gene and 589 genes per chip, as well as controls (probe pairs for housekeeping genes and spiked samples). We analysed data using GenechipÒ software and performed pairwise comparison between untreated NT2 at 0 days and RA-treated NT2 at 3, 7, 14 and 21 days. Increased and decreased expression of select genes was seen throughout the time course. The largest differences observed were in the order of a 50-fold difference from control. As expected, expression of the intermediate filament neuroepithelial marker nestin increased rapidly following RAtreatment and decreased toward the end of the time course. This regulation likely reflects the appearance and differentiation of neuronal precursors in the cultures. These data suggest that the experimental design and analysis techniques were valid. Expression of Hox genes A1, A4, B2, B3, B5 and C5 were greatly altered throughout the time course, as were expression of helix-loop-helix domain-containing genes important to the process of neuronal specification. The ability to study the coordinate regulation of such genes with oligonucleotide arrays may enable signal transduction pathways associated with human neurogenesis and differentiation to be deciphered.