Identifying changes in gene expression in the nervous system: mRNA differential display

Caste-specific cytochrome P450 in the damp-wood termite Hodotermopsis sjostedti (Isoptera, Termopsidae)

Termites are eusocial insects with a well-defined caste system, which is an example of polyphenism. This polyphenism is based on hormonally controlled differential gene expression. In the damp-wood termite Hodotermopsis sjostedti, we induced differentiation into the soldier caste by using juvenile hormone analogue treatment. We then investigated specific gene expression, which appeared during the hormonal response and triggered caste differentiation, using fluorescent differential display. A candidate cDNA sequence with similarity to cytochromes P450, CYP6AM1, was characterized and its transcript shown to be repressed between 1 and 3 days after hormone treatment. CYP6AM1 was specifically expressed in the fat body of pseudergates and soldiers. The putative function of this P450 is discussed with respect to the caste differentiation system.

Differential expression of glutamate receptors in avian neural pathways for learned vocalization

Learned vocalization, the substrate for human language, is a rare trait. It is found in three distantly related groups of birds-parrots, hummingbirds, and songbirds. These three groups contain cerebral vocal nuclei for learned vocalization not found in their more closely related vocal nonlearning relatives. Here, we cloned 21 receptor subunits/subtypes of all four glutamate receptor families (AMPA, kainate, NMDA, and metabotropic) and examined their expression in vocal nuclei of songbirds. We also examined expression of a subset of these receptors in vocal nuclei of hummingbirds and parrots, as well as in the brains of dove species as examples of close vocal nonlearning relatives. Among the 21 subunits/subtypes, 19 showed higher and/or lower prominent differential expression in songbird vocal nuclei relative to the surrounding brain subdivisions in which the vocal nuclei are located. This included relatively lower levels of all four AMPA subunits in lMAN, strikingly higher levels of the kainite subunit GluR5 in the robust nucleus of the arcopallium (RA), higher and lower levels respectively of the NMDA subunits NR2A and NR2B in most vocal nuclei and lower levels of the metabotropic group I subtypes (mGluR1 and -5) in most vocal nuclei and the group II subtype (mGluR2), showing a unique expression pattern of very low levels in RA and very high levels in HVC. The splice variants of AMPA subunits showed further differential expression in vocal nuclei. Some of the receptor subunits/subtypes also showed differential expression in hummingbird and parrot vocal nuclei. The magnitude of differential expression in vocal nuclei of all three vocal learners was unique compared with the smaller magnitude of differences found for nonvocal areas of vocal learners and vocal nonlearners. Our results suggest that evolution of vocal learning was accompanied by differential expression of a conserved gene family for synaptic transmission and plasticity in vocal nuclei. They also suggest that neural activity and signal transduction in vocal nuclei of vocal learners will be different relative to the surrounding brain areas.

Intraocular delivery of BDNF following visual cortex lesion upregulates cytosolic branched chain aminotransferase (BCATc) in the rat dorsal lateral geniculate nucleus

Visual cortex ablation in newborn rats determines the almost complete degeneration of neurons in the dorsal lateral geniculate nucleus (dLGN), as a consequence of the axotomy of the geniculo-cortical fibres. Death of dLGN neurons is massive and rapid, and occurs by apoptosis. We recently showed that exogenous administration of the neurotrophin brain-derived neurotrophic factor (BDNF) in the eye prevents the degeneration of dLGN neurons occurring after visual cortex lesion in newborn rats. To elucidate the molecular mechanisms of BDNF-mediated neuroprotection, we sought to identify novel genes regulated by BDNF in the rat dLGN after visual cortex lesion. By using mRNA fingerprinting, we isolated a cDNA fragment upregulated in the dLGN of lesioned rats treated with BDNF. This cDNA fragment shared 100% homology with the rat cytosolic branched chain aminotransferase (BCATc), a key enzyme of glutamate metabolism. Quantitative reverse transcription-polymerase chain reaction and in situ hybridization confirmed that BCATc mRNA is markedly overexpressed by exogenous supply of BDNF to axotomized dLGNs. Immunohistochemical analysis showed that upregulation of BCATc in the dLGN of lesioned rats treated with BDNF takes place in astrocytes. These results suggest that modulation of glutamate metabolism by astrocytes might play an important role in BDNF-mediated survival of axotomized dLGN neurons.

Overexpression of FABP7 in Down syndrome fetal brains is associated with PKNOX1 gene-dosage imbalance

Suppression subtractive hybridization performed on Down syndrome (DS) fetal brains revealed a differentially expressed gene, FABP7, mapped to 6q22-23. FABP7 overexpression in DS brains was verified by real-time PCR (1.63-fold). To elucidate the molecular basis of FABP7 overexpression and establish the relationship with chromosome 21 trisomy, the FABP7 promoter was cloned by genomic inverse PCR. Comparison to the mouse ortholog revealed conservation of reported regulatory elements, among them a Pbx/POU binding site, known to be the target of PBX heteromeric complexes. PBX partners include homeobox-containing proteins, such as PKNOX1 (PREP1), a transcription factor mapping at 21q22.3. We report here: (i) overexpression of PKNOX1 in DS fetal brains; (ii) in vitro specific binding of PKNOX1 to the Pbx/POU site of the FABP7 promoter; (iii) in vivo FABP7 promoter trans-activation in cultured neuroblastoma cells caused by PKNOX1 overexpression. To our knowledge this is the first report of a direct relation between dosage imbalance of a chromosome 21 gene and altered expression of a downstream gene mapping on another chromosome. Given the role of FABP7 in the establishment, development and maintenance of the CNS, we suggest that the overexpression of FABP7 could contribute to DS-associated neurological disorders.

Identification of regeneration-associated genes after central and peripheral nerve injury in the adult rat

BACKGROUND

It is well known that neurons of the peripheral nervous system have the capacity to regenerate a severed axon leading to functional recovery, whereas neurons of the central nervous system do not regenerate successfully after injury. The underlying molecular programs initiated by axotomized peripheral and central nervous system neurons are not yet fully understood.

RESULTS

To gain insight into the molecular mechanisms underlying the process of regeneration in the nervous system, differential display polymerase chain reaction has been used to identify differentially expressed genes following axotomy of peripheral and central nerve fibers. For this purpose, axotomy induced changes of regenerating facial nucleus neurons, and non-regenerating red nucleus and Clarke's nucleus neurons have been analyzed in an intra-animal side-to-side comparison. One hundred and thirty five gene fragments have been isolated, of which 69 correspond to known genes encoding for a number of different functional classes of proteins such as transcription factors, signaling molecules, homeobox-genes, receptors and proteins involved in metabolism. Sixty gene fragments correspond to genomic mouse sequences without known function. In situ-hybridization has been used to confirm differential expression and to analyze the cellular localization of these gene fragments. Twenty one genes (approximately 15%) have been demonstrated to be differentially expressed.

CONCLUSIONS

The detailed analysis of differentially expressed genes in different lesion paradigms provides new insights into the molecular mechanisms underlying the process of regeneration and may lead to the identification of genes which play key roles in functional repair of central nervous tissues.

Ero1-L, an ischemia-inducible gene from rat brain with homology to global ischemia-induced gene 11 (Giig11), is localized to neuronal dendrites by a dispersed identifier (ID) element-dependent mechanism

Many changes in neuronal gene expression occur in response to ischemia, and these may play a role in determining the fate of ischemic neurons. To identify genes induced in the rat brain following cerebral ischemia, a strategy was used that combines subtractive hybridization and differential screening. Among the genes identified was one referred to as global ischemia-inducible gene 11(Giig11). Sequence analysis indicated that Giig11 exhibited 97% and 91% identity to the known Ero1-L (S. cereviseae ero1-like oxidoreductase) of mouse and human origin, which is involved in oxidative endoplasmic reticulum protein folding. Rat Ero1-L/Giig11 also contains a l07-bp sequence that is nearly identical (> 95%) to the known dispersed repetitive identifier (ID), but which is lacking in mouse and human Ero1-L. Northern blotting showed that expression of the ID element and Ero1-L/Giig11 mRNA increased after global cerebral ischemia. In situ hybridization demonstrated increased expression of Ero1-L/Giig11 in the brain following ischemic injury, with the highest levels in the vulnerable hippocampal CA1 pyramidal neurons. Transfection of cultured primary hippocampal neurons with a plasmid containing green fluorescent protein (gfp) and Ero1-L/Giig11 cDNA (with and without the ID element) produced a gfp-Ero1-L/Giig11 fusion protein, and more fusion protein was localized into dendrites in the presence of the ID element, suggesting that the ID element promotes Ero1-L/Giig11 protein localization to dendrites. Therefore, Ero-1L/Giig11 may have a role in ischemia-induced neuronal repair or survival mechanisms directed at counteracting abnormalities in protein folding, maturation and distribution.

Differentially expressed genes in sporadic amyotrophic lateral sclerosis spinal cords--screening by molecular indexing and subsequent cDNA microarray analysis

To analyze the genes related to the pathophysiology of sporadic amyotrophic lateral sclerosis (SALS) we performed gene profiling of SALS spinal cords using molecular indexing combined with cDNA microarray. Eighty-four fragments were cloned in the first screening procedure with molecular indexing. Subsequent quantitative microarray screening revealed 11 genes which were differentially expressed in SALS. Real-time RT-PCR verified that the expression level of the following six genes was altered in SALS: dorfin, metallothionein-3, 30 kDa TATA-binding protein-associated factor, neugrin, ubiquitin-like protein 5 and macrophage-inhibiting factor-related protein-8. These results indicated that genes associated with the ubiquitin-proteasome system, oxidative toxicity, transcription, neuronal differentiation and inflammation might be involved in the pathogenesis of SALS.

Molecular genetic approaches to investigate individual variations in behavioral and neuroendocrine stress responses

A large response range can be observed in both behavioral and neuroendocrine responses to environmental challenges. This variation can arise from central mechanisms such as those involved in the shaping of general response tendencies (temperaments) or involves only one or the other output system (behavioral vs. endocrine response). The participation of genetic factors in this variability is demonstrated by family and twin studies in humans, the comparison of inbred strains and selection experiments in animals. Those inbred strains diverging for specific traits of stress reactivity are invaluable tools for the study of the molecular bases of this genetic variability. Until recently, it was only possible to study biological differences between contrasting strains, such as neurotransmitter pathways in the brain or hormone receptor properties, in order to suggest structural differences in candidate genes. The increase of the power of molecular biology tools allows the systematic screening of significant genes for the search of molecular variants. More recently, it was possible to search for genes without any preliminary functional hypothesis (mRNA differential expression, nucleic acid arrays, QTL search). The approach known as quantitative trait loci (QTL) analysis is based on the association between polymorphic anonymous markers and the phenotypical value of the trait under study in a segregating population (such as F2 or backcross). It allows the location of chromosomal regions involved in trait variability and ultimately the identification of the mutated gene(s). Therefore, in a first step, those studies skip the 'black box' of intermediate mechanisms, but the knowledge of the gene(s) responsible for trait variability will point out to the pathway responsible for the phenotypical differences. Since variations in stress-related responses may be related to numerous pathological conditions such as behavioral and mood disorders, drug abuse, cardiovascular diseases or obesity, and production traits in farm animals, these studies can be expected to bring significant knowledge for new therapeutic approaches in humans and improved efficiency of selection in farm animals.

Change of gene expression profiles in the retina following optic nerve injury

The purpose of the present study was to search for changes in gene expression patterns in the retina following optic nerve injury. We conducted a subtractive hybridization for comparison of the mRNAs in those retinas receiving optic nerve crush injury and those receiving sham operation. Both forward and reverse subtractions were carried out for 8-h and 24-h time points postoperatively. Resultant subtractive cDNA for each group was re-amplified and cloned to a plasmid. After DNA sequencing, the identity of subtractive cDNA was analyzed by blasting sequences to the Nonredundant gene database, Unigene database, and dbest database at NCBI. Thirty-four known genes and 32 EST were found in the forward subtractions. Forty-two known genes and 46 EST were found in reverse subtractions. Identities of the rest could not been found in the databases. To verify the subtractive results, RT-PCR was performed to test expression patterns of eight known genes found in the above analysis. Among these eight genes, seven demonstrated a statistically significant difference between the crushed eyes and the control eyes by quantitative image analysis. Together, our data show that expression of fatso, ephrin B2, NonO, Zfx, vitronectin, and XLRS increased after optic nerve injury, and expression of stathmin exhibited reduction after injury.

Gene expression profiling in the post-mortem human brain--no cause for dismay

Global expression profiling techniques such as microarray technology promise to revolutionize biology. Soon it will be possible to investigate alterations at the transcript level of the entire human genome. There is great hope that these techniques will at last shed light on the pathological processes involved in complex neuropsychiatric disorders such as schizophrenia. These scientific advances in turn have re-kindled a great interest and demand for post-mortem brain tissue. Good quality post-mortem tissue undoubtedly is the fundamental prerequisite to investigate complex brain disorders with molecular profiling techniques. In this review we show that post-mortem brain tissue can yield good quality mRNA and intact protein antigens which allow the successful application of traditional molecular biology methods as well as novel profiling techniques. We also consider the use of laser-capture microdissection on post-mortem tissue. This recently developed technique allows the experimenter to explore the molecular basis of cellular function at the single cell level. The combination of laser-capture microdissection with high throughput profiling techniques offers opportunities to obtain precise genetic fingerprints of individual neurons allowing comparisons of normal and pathological states.

Gene expression profile in Alzheimer's brain screened by molecular indexing

Gene expression in the Alzheimer brain and normal brain was compared by molecular indexing, an advanced version of differential display. Using this technique, each gene was represented by a 3'-end cDNA fragment generated by class IIS restriction enzymes. The fragments were divided into 384 groups, and each group was separated by denaturing polyacrylamide gel electrophoresis. Comparison of gel patterns revealed 70 genes exhibiting marked differences in gene expression between AD and normal brain. A similarity search revealed 22 genes already reported, including those considered to be related to the pathogenesis such as G protein, G protein-related, and mitochondrial components. Detailed analysis of one from those only matched to EST sequences revealed a novel protein with leucine-zipper and SH3-binding motifs. Its expression was suppressed in a subpopulation of cortical pyramidal neurons in the AD brain, suggesting a possible relation to the pathogenesis. Thus, genome-scale analysis of gene expression of neurodegeneration is a potentially powerful approach to listing genes related to the pathogenesis.

Identifying pain genes: Bottom-up and top-down approaches

A major goal of pain research at the present time is the identification of pain genes. Such genes have been informally defined in a number of ways, including the deletion or transcriptional inhibition of which produces alterations in behavioral responses on nociceptive assays; those the transcription of which is selective to pain-relevant anatomic loci (eg, small-diameter cells of the dorsal root ganglion); those the transcription of which is enhanced in animals experiencing tonic nociception or hypersensitivity states; and, finally, those existing in polymorphic forms relevant to interindividual variability. The purpose of this review is to compare the utility of various bottom-up and top-down approaches in defining, identifying, and studying pain genes. We will focus on 4 major techniques: transgenic knockouts, antisense knockdowns, gene expression assays (including DNA microarray-based expression profiling), and linkage mapping.

Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.

Identification and characterization of differentially expressed genes in denervated muscle

Denervation results in a series of changes in skeletal muscle. To elucidate the molecular basis underlying these changes, it is important to identify the profile of altered gene expression in skeletal muscle following nerve injury. In the present study, we have examined the differentially expressed genes in denervated gastrocnemius muscle using RNA fingerprinting by arbitrarily primed PCR. Eight differentially expressed mRNA transcripts have been identified. A bilateral regulatory profile can be observed for the up-regulated genes in both denervated and contralateral control muscle following unilateral sciatic nerve injury. The temporal expression profiles of the denervation-regulated genes in muscle during development, together with their dependency on nerve activity, suggest potential functional roles following nerve injury in vivo. In particular, the identification of two apoptosis-related genes in denervated muscle provides molecular evidence that the apoptotic process is likely to be involved in the intricate changes that lead to muscle atrophy. Our findings not only allow the identification of novel genes, but also suggest possible functions for some known genes in muscle following nerve injury. Taken together, these findings provide important insights into our understanding of the molecular events in denervated muscle and suggest that the differentially expressed genes may play potential roles during muscle denervation and regeneration.

Parallel gene expression monitoring using oligonucleotide probe arrays of multiple transcripts with an animal model of focal ischemia

High density oligonucleotide arrays offer tremendous potential to study gene changes occurring in disease states. The authors described the first case of using a custom designed high density oligonucleotide probe array containing 750 genes to monitor the changes in mRNA transcript levels occurring after focal ischemia for a period of 3 hours. Permanent middle cerebral artery occlusion in the rat resulted in neuronal degeneration in the dorsolateral cortex and striatum over a time course of 24 hours. Comparing the changes in hybridization levels in the frontal and parietal cortices and the striatum, between the ipsilateral and contralateral sides of the brain using the probe arrays resulted in the up-regulation of 24 genes, which showed greater than a twofold change. Very few genes were found to be downregulated after the ischemic insult. Many of the immediate early genes (IEGs) such as c-fos, NGFI-A, NGFI-C, and Krox-20 were found to be robustly upregulated in the three different regions studied. Other genes that were up-regulated in perifocal regions included Arc, Inhibin-beta-A, and the phosphatases MKP-1 and MKP-3. The hybridization signal intensity from the probe arrays enabled quantification of many genes relative to one another, and robust changes in expression were obtained with very little interanimal variability. Furthermore, the authors were able to validate the increased expression of NGFI-C and Arc using in situ hybridization. This represented the first example of using high density oligonucleotide probe arrays in studying the expression of many genes in parallel and in discrete brain regions after focal ischemia.

Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.

Upregulation of cytosolic branched chain aminotransferase in substantia nigra following developmental striatal target injury

We have previously shown that apoptotic cell death can be induced in substantia nigra (SN) by developmental striatal target lesion. In this model, only a portion of nigral neurons dies, so it provides a paradigm to examine not only the molecular basis of cell death, but also the cellular responses of adjacent neurons which survive. Using a differential display approach, we have found that cytosolic branched chain aminotransferase (BCATc) mRNA is upregulated in SN in this model. This upregulation is associated with an increased number of BCATc-positive neuronal profiles, demonstrated by immunostaining. BCATc-positive neurons show normal morphology and rarely contain apoptotic chromatin. We conclude that BCATc is upregulated in neurons, which are likely to survive, and plays a role in either maintenance of viability or restoration of normal function.

High throughput analysis of gene expression in the human brain

The human brain is thought to have the greatest complexity of gene expression of any region of the body, reflecting the diverse functions of neurons and glia. Studies of gene expression in the human brain may yield fundamental information about the phenotype of brain cells in different stages of development, in different brain regions, and in different physiological and pathological states. As the human genome project nears completion, several technological advances allow the analysis of thousands of expressed genes in a small brain sample. This review describes available sources of human brain material, and several high throughput techniques used to measure the expression of thousands of genes. These techniques include expressed sequence tag (EST) sequencing of cDNA libraries; differential display; subtractive hybridization; serial analysis of gene expression (SAGE); and the emerging technology of high density DNA microarrays. Measurement of gene expression with microarrays and other technologies has potential applications in the study of human brain diseases, including cognitive disorders for which animal models are typically not available. Gene expression measurements may be used to identify genes that are abnormally regulated as a secondary consequence of a disease state, or to identify the response of brain cells to pharmacological treatments.

Soldier caste-specific gene expression in the mandibular glands of Hodotermopsis japonica (Isoptera: termopsidae)

Although "polymorphic castes" in social insects are well known as one of the most important phenomena of polyphenism, few studies of caste-specific gene expressions have been performed in social insects. To identify genes specifically expressed in the soldier caste of the Japanese damp-wood termite Hodotermopsis japonica, we employed the differential-display method using oligo(dT) and arbitrary primers, compared mRNA from the heads of mature soldiers and pseudergates (worker caste), and identified a clone (PCR product) 329 bp in length termed SOL1. Northern blot analysis showed that the SOL1 mRNA is about 1.0 kb in length and is expressed specifically in mature soldiers, but not in pseudergates, even in the presoldier induction by juvenile hormone analogue, suggesting that the product is specific for terminally differentiated soldiers. By using the method of 5'- and 3'-rapid amplification of cDNA ends, we isolated the full length of SOL1 cDNA, which contained an ORF with a putative signal peptide at the N terminus. The sequence showed no significant homology with any other known protein sequences. In situ hybridization analysis showed that SOL1 is expressed specifically in the mandibular glands. These results strongly suggest that the SOL1 gene encodes a secretory protein specifically synthesized in the mandibular glands of the soldiers. Histological observations revealed that the gland actually develops during the differentiation into the soldier caste.

Modulation of gene expression following long-term synaptic depression in the striatum

A number of behavioural and cellular studies have suggested that activity-dependent synaptic plasticity associated with learning and memory may lead to the expression of various genes whose protein products can play a critical role in memory acquisition and consolidation. Long-term potentiation (LTP) and long-term depression (LTD) represent two forms of synaptic plasticity which have been widely studied by electrophysiological techniques. However, the molecular mechanisms at target gene involved in the generation of long term depression remain to be determined. To elucidate the molecular mechanism underlying activity dependent synaptic remodeling in striatal long term depression, we used the mRNA differential display technology to isolate genes that are induced or modulated by high frequency stimulation of the corticostriatal pathway in a rat brain slice preparation. We have differentially displayed, by means of reverse transcriptase-polymerase chain reaction, mRNA species isolated from striatal slices in which long term depression was induced by tetanic stimuli as well as from slices stimulated at low frequency. We then compared radio-labeled RT-PCR banding patterns to isolate cDNAs that are differentially expressed. Three independent cDNAs were isolated and identified whose mRNA level were enhanced by tetanic stimulation inducing long term depression. We provide evidence that two of these genes encode proteins involved in synaptic vesicle trafficking (dynamin I and amphiphysin II). Moreover, expression of tissue plasminogen activator (t-PA) gene was also increased following striatal long term depression. Our data suggest that a complex pattern of genes acting at presynaptic level and extracellularly may be involved in LTD-associated synaptic remodeling.

Identification of genes regulated by muscarinic acetylcholine receptors: application of an improved and statistically comprehensive mRNA differential display technique

In order to identify genes that are regulated by muscarinic acetylcholine receptors, we developed an mRNA differential display technique (DD) approach. By increasing redundancy and by evaluating optimised reagents and conditions for reverse transcription of total RNA, PCR and separation of PCR products, we generated a DD protocol that yields highly consistent results. A set of 64 distinct random primers was specifically designed in order to approach a statistically comprehensive analysis of all mRNA species in a defined cell population. This modified DD protocol was applied to total RNA of HEK293 cells stably expressing muscarinic m1 acetylcholine receptors and cells stimulated with the receptor agonist carbachol were compared to identical but non-stimulated cells. In 81 of 192 possible PCR experiments, 38 differential bands were identified. Sequence analysis followed by northern blot analyses confirmed differentially expressed genes in 19 of 23 bands analysed. These represented 10 distinct immediate-early genes that were up-regulated by m1AChR activation: Egr-1, Egr-2, Egr-3, NGFi-B, ETR101, c- jun, jun -D, Gos-3 and hcyr61, as well as the unknown gene Gig-2. These data show that this improved DD protocol can be readily applied to reliably identify differentially expressed genes.

Temporal and cell-specific gene expression by human endometrium after coculture with trophoblast

OBJECTIVE

Our purpose was to identify temporal and stage-specific expression of endometrial genes during coculture with trophoblast cells.

STUDY DESIGN

Endometrial stromal cells were cultured to confluence in the presence of estradiol and progesterone. During these culture conditions the gene expression of 1 tissue specimen that secreted abundant prolactin (415 ng/mL culture medium at 21 days) was compared with a second specimen that did not. These 2 tissues were coincubated with trophoblast tissue in a specialized coculture flask. After 4 and 24 hours of culture messenger ribonucleic acid was extracted and reverse transcribed, and the complementary deoxyribonucleic acid products were amplified by polymerase chain reactions. The reverse transcriptase-polymerase chain reaction products were separated by electrophoresis, and potentially important complementary deoxyribonucleic acid fragments were reamplified, inserted into a plasmid vector, and sequenced after recovery. Sequences were submitted for Basic Local Alignment Search Tool searches of GenBank.

RESULTS

We observed up-regulation of 6 gene fragments in decidualized endometrium after 4 hours of coculture with choriocarcinoma-derived trophoblast BeWo cells, but only 1 gene fragment was up-regulated after 24 hours of exposure. Conversely, 2 fragments were down-regulated in decidualized stroma that was exposed to BeWo for 4 hours and 2 fragments were underexpressed after the 24-hour exposure. In the parallel experiment stromal cells that failed to secrete prolactin did not elicit the same regulation of expression. The nondecidualized endometrium overexpressed 1 gene fragment after 4 hours of BeWo exposure and overexpressed 4 gene fragments after exposure to BeWo for 24 hours. Underexpression of gene products also occurred with the nondecidualized endometrium, and we observed 2 fragments and 1 fragment to be underexpressed after 4 and 24 hours of BeWo exposure, respectively. To date, 3 of the candidate differential display fragments from these experiments have been cloned and sequenced. An up-regulated fragment (C6225J4EB-1) was 99% identical (167/168 sequences) to a reported nonredundant expressed sequence tags isolated from muscle, brain, ovary, testis, liver, and pregnant uterus tissues. A second up-regulated fragment (C4375J4EB-1) matched 100% identity (117/117) with a reported gene fragment in the expressed sequence tags database of GenBank that was derived from fetal heart and pregnant uterus. Additional characterization of these expressed sequence tags has not been reported. The third up-regulated fragment (C4250J24EB-2) was 100% identical (265/265) to human reduced nicotinamide adenine dinucleotide dehydrogenase III in the nonredundant gene database of GenBank.

CONCLUSION

This report demonstrates the potential usefulness that endometrial-trophoblast coculture and differential display can offer for the molecular analysis of implantation phenomena. We have recognized both overexpression and underexpression of interesting gene fragments during the early phases of endometrial responses to paracrine regulators derived from BeWo trophoblast cells. These responses appear to be specific to the degree of endometrial transformation (decidualization) before challenge by the trophoblast and to the duration of the BeWo exposure. Sequence data identified 1 gene with an unidentified function, another gene with a known function, and a fragment not previously recognized. We submit that our model of endometrial-trophoblast coculture offers a novel tool to test cellular responses during implantation, and differential display represents a sensitive technique that can identify many of the important elements of genomic signaling during nidation.

Differential display cloning of genes induced in regenerating neurons

Mammalian adult motor and sensory neurons are thought to reexpress a complement of genes that are originally expressed during development when they regenerate following injury. Therefore, one strategy for identifying key genes involved in development of the peripheral nervous system is to identify those genes reexpressed in the regenerating system. To test this hypothesis, we used the single-base anchor method of mRNA differential display to study changes in gene expression in regenerating adult mammalian sensory neurons. From an initial sample of 36 different primer combinations [3 oligo(dT)M primers x 12 arbitrary 13-mers], 6 candidate upregulated and 6 candidate downregulated genes were identified. Candidate genes were screened by the reverse Northern blot method to eliminate obvious false positives and the three remaining candidates cloned and sequenced. In addition to comparing isolated sequences with the public databases, sequences were also compared with assembled clusters of expressed sequence tag sequences, enabling extension of the sequence data by more than a kilobase from the isolated 3' cDNA fragments. Ultimate confirmation of differential expression was carried out by in situ hybridization using 45-base oligonucleotides complementary to the predicted 5'-3' orientation of the corresponding mRNAs of all three cDNAs. Two, LA12.2 and LC12, were definitively confirmed as induced in regenerating neurons. The sequence of LC12 is identical to that of the secreted protein Reg-2 and a detailed study of the functions of this secreted protein in neural development and regeneration has been published (F. J. Livesey, J. A. O'Brien, M. Li, A. G. Smith, L. J. Murphy, and S. P. Hunt, 1997, Nature 390, 614-618). The LA12.2 gene is currently being characterized, the available sequence of this cDNA being novel.

Apoptosis in Degenerative Diseases of the Basal Ganglia

Degenerative disorders of the basal ganglia are characterized by disturbances of motor control. Prototypic examples are Parkinson's disease, which is caused by degeneration of dopamine neurons of the substantia nigra, and Huntington's disease, which is caused by degeneration of neurons of the striatum. In recent years, it has been postulated that some of these disorders may be caused by programmed cell death or apoptosis, a genetically regulated form of cell death. There is clear evidence that apoptosis occurs in neurons of the basal ganglia during normal development, that it can be regulated, and that it can be induced in some animal models of these disorders. Although there is some suggestive direct evidence that apoptosis may occur in the human brain in these disorders, the evidence to date is partial and not yet compelling. Nevertheless, programmed cell death is an important new hypothesis for the pathogenesis of these disorders and warrants vigorous further investigation, particularly with molecular markers in addition to classic morphological markers. The concept of programmed cell death is relevant not only to the pathogenesis of these diseases but also to therapeutic issues, such as transplantation approaches.

Cell-specific dendritic localization of glycine receptor alpha subunit messenger RNAs

The regional and subcellular localizations of glycine receptor complex messenger RNAs were determined in the adult rat central nervous system using non-radioactive in situ hybridization. The present investigation focused on glycine receptors alpha1 and alpha2 subunit messenger RNAs. Within the central nervous system we observed that the glycine receptor alpha1 and alpha2 subunit messenger RNAs are widely expressed. At the subcellular level, these messenger RNAs are present either in neuronal somata and dendrites or somata only. Furthermore, among different regions as well as within the same region the subcellular localizations of both alpha subunit messenger RNAs are cell type-dependent. In contrast, the regional distributions of beta subunit and gephyrin messenger RNAs are essentially as previously described [Fujita M. (1991) Brain Res. 560, 23-37; Malosio M.-L. et al. (1991) Eur. molec. Biol. Org. J. 9, 2401-2409; Kirsch J. et al. (1993) Eur. J. Neurosci. 5, 1109-1117] and their messenger RNAs are confined predominantly within the somata of neurons [Kirsch J. et al. (1993); Racca et al. (1997) J. Neurosci. 17, 1691-1700]. These results demonstrate that the glycine receptor complex messenger RNAs are broadly expressed in the central nervous system and that the glycine receptor alpha1 and alpha2 subunit messenger RNAs differ in their subcellular localization depending on the neuronal population. The latter finding suggests that different mechanisms for the localization of glycine receptor alpha1 and alpha2 subunit messenger RNAs are used by distinct populations of neurons.

Application of mRNA differential display to investigate gene expression in thermotolerant cells of Saccharomyces cerevisiae

We have described the use of differential display of PCR-amplified reverse transcribed mRNA (DDRT-PCR) to survey changes in gene expression profiles induced by heat shock and carbon catabolite derepression in Saccharomyces cerevisiae. It is well established that either of these states elicits thermotolerant phenotypes. An initial analysis conducted on cells of an inherently thermosensitive strain (Ysen) indicated that approximately 10% of the total number of cDNAs detected were either up or down regulated following heat shock at 37 degrees C (30 min) in comparison to control cells (25 degrees C). In addition, whereas 7% of all PCR products were preferentially expressed during derepressive growth, approximately 2% were found to be common to both heat-shocked and derepressed cells. A repeat analysis, performed on all three cell types of Ysen as well as cells of a relatively thermoresistant strain (Yres) yielded 30 differentially displayed cDNA fragments common to heat-shocked and derepressed cells of both strains. Eighteen of these generated signals on Northern blots, of which three were confirmed as regulated. Five amplicons, including one not detected by Northern analysis and another from the derepressed state, were cloned and sequenced. Three of these exhibited homology to S. cerevisiae genes with well-characterized protein products: HSP 90, HXK1 and STA1. The remaining two applicons showed nucleotide identity to YTIS11, a homolog of the mammalian TIS11 and putative transcriptional activator, and an orphan gene encoding a hypothetical transmembrane protein belonging to the multi-drug resistance translocase family. Our novel application of DDRT-PCR has identified new and known genes that may be further evaluated as factors involved in stress regulation and has demonstrated the potential of the technique to systematically analyse gene expression in yeast.

Molecular characterization of fetal alcohol syndrome using mRNA differential display

The molecular pathogenesis of fetal alcohol syndrome (FAS) has not been well elucidated. The technique of mRNA differential display was used to characterize the etiology and to identify potential markers for FAS. Out of approximately 1,080 mRNA transcripts in mouse embryos that were analyzed, the levels of three mRNAs were altered by ethanol. Two of these mRNAs (one novel and one encoding heat shock protein 47) were also modulated by another teratogen, 3-methylcholanthrene. The third mRNA, encoding alpha-tropomyosin, was specifically up-regulated by ethanol. Consistent with the Northern blot data, immunoblot analysis demonstrated that the level of alpha-tropomyosin protein (31 kDa, most likely a brain specific isoform) was elevated in the embryos exposed to ethanol.

Cloning differentially expressed mRNAs

Differential gene expression occurs in the process of development, maintenance, injury, and death of unicellular as well as complex organisms. Differentially expressed genes are usually identified by comparing steady-state mRNA concentrations. Electronic subtraction (ES), subtractive hybridization (SH), and differential display (DD) are methods commonly used for this purpose. A rigorous examination has been lacking and therefore quantitative aspects of these methods remain speculative. We compare these methods by identifying a total of 58 unique differentially expressed mRNAs within the same experimental system (HeLa cells treated with interferon-gamma). ES yields digital, reusable data that quantitated steady-state mRNA concentrations but only identified abundant mRNAs (seven were identified), which represent a small fraction of the total number of differentially expressed mRNAs. SH and DD identified abundant and rare mRNAs (33 and 23 unique mRNAs respectively) with redundancy. The redundancy is mRNA abundance-dependent for SH and primer-dependent for DD. We conclude that DD is the method of choice because it identifies mRNAs independent of prevalence, uses small amounts of RNA, identifies increases and decreases of mRNA steady-state levels simultaneously, and has rapid output.

Schizophrenia, the heteromodal association neocortex and development: potential for a neurogenetic approach

The heteromodal association neocortex is believed to be a major site of involvement in schizophrenia. This system includes the prefrontal cortex and portions of the superior temporal and inferior parietal cortices, which are linked in cognitive networks observing complex executive functions. The heteromodal cortex is highly elaborated in humans and is believed to continue to develop past birth. The neuropathology of schizophrenia is likely to be heterogeneous and appears to involve developmental abnormalities, with a prominent genetic component. However, the genes involved in the development of the neocortex, and particularly the heteromodal cortex, are not well understood. A candidate-gene approach to schizophrenia using techniques of differential expression might now be feasible and could illuminate the basic neurobiology of the heteromodal cortical network.