BACKGROUND
recent advance in molecular biology have introduced new high-throughput tools for the analysis of differential gene expression in complex diseases, such as alzheimer , providing simultaneous overviews of the genes or proteins associated with multiple cellular pathways.
the most commonly used technology for the assessment of gene expression changes in postmortem brain is the dna microarray  <cit>  this approach has not only confirmed the involvement of genes implicated in ad by conventional methods, but also revealed changes in additional genes, not previously associated with ad  <cit> .
however, as this method requires a priori knowledge of gene sequences, it cannot be applied as a discovery tool for novel transcripts.
furthermore, the expression levels of low abundance genes cannot be readily assessed by dna microarray hybridization, since reliable results are usually obtained only for genes that are expressed in high or moderate levels.
this is a significant limitation since many transcripts expressed preferentially in brain  are present at very low levels  <cit> .
differential display and conventional subtractive hybridization approaches are capable of detecting expression changes in both known and novel genes.
differential display uses arbitrarily primed pcr to fingerprint differences  in gene expression between two samples, with the results being determined by the intensities of bands on a polyacrylamide gel  <cit> .
the major disadvantages of this method include its lack of sensitivity for the detection of rare rna species, the high number of false positives generated during pcr and cloning of the differentially expressed products from low resolution polyacrylamide gels, where an apparent single band may contain multiple cdna species.
consequently, differential display is labor intensive and unreliable for this application.
subtractive hybridization, on the other hand, permits the isolation of target sequences from one single-stranded dna population, referred to as "tester", from another dna population, referred to as "driver" by using an excess of sequences.
the two populations are mixed and put through iterative rounds of subtraction of cross-hybridized products.
earlier subtractive methods required physical removal of hybridized driver and tester sequences, which contributed to the loss of low abundance tester sequences.
suppression subtractive hybridization  is a newer method  <cit>  which couples hybridization-based de-selection of common cdnas to pcr amplification which enriches differentially expressed transcripts from two mrna sources.
in contrast to differential display, the primers for pcr amplification are clearly defined, thus avoiding problems associated with random primers.
the main disadvantage of this procedure is its higher detection threshold.
according to the kit manufacturer's recommendation , the difference in mrna levels needs to be at least  <dig> fold to allow reliable detection.
here, we have developed a novel approach to the identification of differentially expressed rare sequences through a combination of subtractive hybridization and rna amplification, termed a subtractive transcription-based amplification of mrna .
in our method, the expressed rnas from two source are used for the preparation of specialized cdna libraries, from which single stranded  sense tester rna and single stranded  sense driver dna are generated.
subtraction is accomplished by the hybridization of single-stranded driver dna to the complementary single-stranded tester rna, followed by rnase h digestion.
this process not only eliminates the necessity for physical removal of hybridized common sequence, but also eliminates the self-annealing step of the tester nucleic acids that is required by the ssh method for the amplification of target sequences.
the self-annealing step usually imposes kinetic limitations and requires lengthy hybridization in order to recover rare cdna sequences.
furthermore, in the star method, the tester rna is designed with a defined terminal sequence which allows the unhybridized tester rna to be amplified in a linear rna amplification process, rather than exponential pcr amplification, thereby minimizing biased sequence amplification  <cit>  since the tester rna remains unchanged in the process, the products of one round of star are used directly in subsequent rounds to provide further enrichment of the unique sequences.
in this study, we applied the star method to an investigation of changes in gene expression in port-mortem ad brain.
we show that, indeed, the star process significantly increases the levels of unique and rare sequences relative to abundant housekeeping genes and identified changes in the expression of genes not previously linked to the ad.
we also performed extensive literature mining to provide a basis for considering their likely involvement in neurodegenerative processes.
RESULTS
characterization of the subtracted ad cdna libraries
two subtracted cdna libraries, using either the 3' cdna of the control sample  or the 3' cdna of the ad sample  as tester, were prepared using the star method .
it was expected that they would contain genes that were down regulated  and up regulated  in ad brain, respectively.
to isolate these genes, three rounds of star subtraction were performed, and the remaining 3' biased cdna tester fragments were linearly amplified, ligated into a puc-modified vector and transformed into e. coli dh10b cells.
approximately  <dig> colonies were obtained for each star library.
subsequently, pcr and dna sequencing were performed on amplified cdna inserts from  <dig> individual colonies for each subtracted library.
data analysis indicated that this number of colonies was sufficient to represent the entire subtracted library since many genes, including some of low abundance, appeared to be represented by more than one colony.
the results summarizing the genes found in the c-ad and ad-c libraries are listed in tables  <dig> and  <dig>  respectively.
of the  <dig> colonies analyzed from each library, over  <dig> contained inserts and produced readable sequences after pcr.
sequence annotation grouped the genes into three categories:  known genes,  ests and  novel genes, whose sequences either only match a fragment of genomic dna or the database search did not hit any existing known sequence.
the known genes were represented by multiple colonies  far more often than the novel genes , indicating that known genes are relatively more abundant than the novel genes, explaining why they are more easily identified by traditional approaches.
sequence annotation also revealed that genes involved in maintenance of neuronal cell structure and function, the ubiquitin pathway and energy metabolism were predominant in the c-ad library, indicating that they were down regulated in ad brains.
whereas in the ad-c library, genes involved in inflammation, protein translation, cytoskeleton/cell adhesion and apoptosis/neurodegeneration were up-regulated in ad.
over 55% of the sequenced fragments in each subtracted library represented unknown genes, of which one half were not previously described as cdna sequences.
representative data from these libraries is shown below.
validation of changes from the subtracted libraries
more than  <dig> genes from the c-ad library were randomly selected for analysis by qrt-pcr using the pools of control and ad mrnas as input.
the results confirmed down-regulation of over 80% of them, consistent with the results of the subtracted library .
the data also confirmed that a majority of these genes  were less abundant than β-actin.
furthermore, all novel transcripts were expressed at extremely low levels, some of them at only  <dig> –2% of the abundance of β-actin .
taken together these results indicated that the star method permitted the isolation of differentially expressed genes, including very rare ones.
this approach also revealed the existence of large number of previously unidentified genes expressed in the human brain which appear to have a disease association.
nearly  <dig> randomly selected genes from the ad-c library were also analyzed by qrt-pcr in order to further validate the library data.
in this case, less than 50% of the selected transcripts were found to be up regulated, with a lower percentage of novel genes .
this might be indicative of a higher content of false positive in this library, pointing out to the necessity of independent validation prior to gene selection for down stream functional studies.
one possibility for the relatively low confirmation rate of the data from the ad-c library is that the increases in the expression of unconfirmed transcripts were small and, therefore, might also be difficult to validate by qrt-pcr, although this wasn't evident in the qrt-pcr validation of down regulated genes from the c-ad library.
despite this, the technique clearly identifies novel sequences that are up regulated in ad brain.
supporting evidence for gene association with ad
an additional approach to increase confidence in the identified genes as likely disease candidates was to mine knowledge pertaining to gene function in ad in the existing literature using a custom built literature mining tool, litminer.
using this approach, we generated short lists of genes whose association with ad could be further rationalized .
the data mining analysis identified  <dig> genes , whose down-regulation in ad has been previously reported, in agreement with our results as these genes were present in the c-ad subtractive library.
furthermore, down-regulation of synuclein alpha was also confirmed by qrt-pcr analysis .
the remaining genes on this list  have never been formally linked to ad, but their possible involvement could be either inferred from the literature or from the results of the present study.
for example, mutations in a2m, bri <dig>  eef1a <dig>  eif2s <dig>  mapt and ubb  have been linked to various other neurodegenerative diseases  <cit>   have been shown to be down-regulated in some brain disorders  <cit>  the down-regulation of  <dig> genes from the c-ad library  was validated by qrt-pcr  and a similar literature analysis further supports the potential involvement of reln, prkce and syt <dig>   <cit>  therefore, it is likely that the down-regulation and the loss of these gene functions could play a role in ad.
possible associations between the  <dig> down-regulated  and  <dig> up-regulated  genes from the subtracted libraries were mapped by additional literature mining.
we imported the unigene names of each group of genes into litminer and used "alzheimer" and "neurodegeneration" as knowledge terms.
all articles containing a gene name, or alias and the knowledge terms, in either title, mesh terms or abstract were reported in a graphic format.
any two given genes or a gene and one of the knowledge terms appearing in the same article were considered to constitute an association.
the frequencies of these associations are represented by the number adjacent to the connecting lines.
within litminer, we could rapidly retrieve and manually scan articles to eliminate false association due to the misuse of gene aliases in the database.
the graphs in figs  <dig> and  <dig> contain genes that exhibited actual association to the knowledge terms or to other genes.
some genes summarized in table  <dig> and  <dig> are not included in figs  <dig> and  <dig> because the current software finds only associations identified in the title, abstract or mesh terms.
nevertheless, the litminer output gives a high level overview of the relationships of these differentially expressed genes that is not obtainable from a simple gene list.
discussion
with the advent of high throughput genomics and proteomics technologies, the involvement of new genes in ad continues to emerge, indicating clearly that the full extent of molecular and functional aberrations responsible for the etiology of ad is not yet understood.
the current high throughput methods are mainly designed to identify changes in relatively abundant genes, whereas weakly expressed genes or proteins are still overlooked.
for example, cdna microarrays, although widely used, are limited to known mrna sequences or ests, thus it is not suitable for the identification and isolation of novel rare transcripts.
complementary to microarray technology, subtractive hybridization is capable of detecting changes of both known and novel genes.
the existing ssh method enriches the differentially expressed genes by selectively suppressing the amplification of non-differentially expressed transcripts in the pcr reaction, resulting in the enrichment of differentially expressed transcripts.
an annealing step is necessary for pcr amplification and subsequent cloning and since rare sequences re-anneal more slowly, this process reduces their chances of discovery.
the star technology uses single strand rna/dna hybridization to remove non-differentially expressed genes.
rare sequences are enriched by slower hybridization and the non-hybridized rna is recovered and amplified by a linear rna amplification procedure, which minimizes the biased exponential amplification of subsets of genes in a mixture.
these features make the star method attractive for examining changes of gene expression in normal and diseased brain tissues, where many mrnas are present in low abundance.
in the present study, we used the star method to identify genes that are not only novel in human brains, but also differentially expressed in ad.
our subtracted cdna libraries constructed by the star technology contained genes whose relative differences in expression levels ranged from 25% to 100%, illustrating the fidelity of this method.
although there has been little, and in some cases, no overlap in identified genes between different microarray studies of ad samples, due to experimental variability, different sources of microarray bearing different sets of genes and different areas of brain tissues used, star has identified a number of known, moderately abundant genes, whose alternation in ad was in agreement with previous microarray analyses.
of these app and snca were found down regulated  <cit> , agt  <cit> , clu  <cit> , ftl  <cit> , map <dig> and stxbp <dig>  <cit>  were reported up-regulated.
more than 55% of clones in each subtracted library contain cdna of unknown function and more then 25% are novel sequences only matching genomic dna in database searches.
these novel genes can now be vigorously pursued to identify their function and precise role in ad pathology.
similar to other high throughput approaches, the changes in gene expression identified by the star method need to be validated by qrt-pcr.
this is especially true for the rare and novel sequences, for which there is no information available in the literature.
combinations of pcr-selected cdna subtraction and cdna microarray analysis of the subtracted clones, or using probes generated by pcr-selected subtraction to screen affymetrix genechips have been attempted  <cit> .
the clones produced by star can be printed on microarray slides for hybridization with labeled cdnas from individual brains samples, however, the rare rna species must be enriched by amplification in order to give reliable hybridization signals.
this method, currently under development, could be a high throughput approach to eliminate false positives before qrt-pcr validation on individual genes.
we have measured changes in nearly  <dig> genes from each subtracted cdna library by qrt-pcr.
however, there was a difference in the confirmation rate between the two subtracted libraries.
besides the fact that there seemed to be more down- than up- regulated genes in the ad brains where neurodegeneration was already evident  <cit> ., we cannot offer an definite explanation why some genes, such as, syntaxin binding protein  <dig> and kinesin  <dig> found up-regulated by star procedure, consistent with the results obtained by others  <cit> , yet not confirmed by qrt-pcr.
further investigations with different fine-tuned qrt-pcr primers and conditions and by using individual brain samples may offer insight on this issue.
while identification of novel genes functions in neurodegeneration remains to be our ongoing objective, the current study was focused on the association of some of the known genes with ad.
among the down regulated genes in table  <dig>  those belonging to two major functional categories are noteworthy.
the first group contains genes involved in maintenance of neuronal cell function, including cast, pfrk, serpine <dig>  snca, sv2a and syt <dig>  <cit>  their roles in normal brain are to promote neurite outgrowth and to regulate synaptic vesicle transport or trafficking at the synapse.
their down regulation is consistent with the compromised synaptic transmission observed in ad brain.
this undoubtedly contributes to the impairment of memory and cognitive function.
our findings support the current view that ad is a disease of synaptic failure  <cit> .
the second group of genes consists of members of the ubiquitin pathway involved in protein degradation.
although only ubb, ube2b and uchl <dig> passed our current screening criteria, several other ubiquitin pathway-related genes also appeared in the c-ad library.
a straightforward interpretation of this result would be that the decreased ability of protein degradation caused by the down regulation of ubiquitin pathway genes, resulted in the accumulation of unwanted proteins in the senile plaques and neurofibrillary tangles.
however, studies of individual ubiquitin pathway genes, such as uchl <dig>  suggest other mechanisms.
for example, uchl <dig> is sensitive to redox changes and is oxidized in ad brain  <cit> .
indicating that its function under stressed conditions is more than "house keeping"  <cit> .
elevated expression of other ubiquitin pathway proteins in response to oxidative stress has also been documented.
<cit>  however, a better understanding of the role of individual ubiquitin pathway genes in ad pathology requires comprehensive study.
extensive evidence suggests that inflammation plays a major role in ad  <cit> .
it is therefore not surprising to find genes, such as mbp, nptx <dig> and scarb <dig> involved in neuroinflammation  <cit> , to be up regulated in ad brains .
we also found several genes related to the cellular distribution of iron , transport of copper  and metal-binding  that were up-regulated in ad .
<cit>  these data strongly suggest a disruption of metal homeostasis and a potential metal neurotoxicity component in ad.
the increase of these proteins may indicate an acute phase-type reaction and/or a compensatory response to stress conditions.
we did not find any typical cytoskeletal proteins, such as members of the actin or tubulin families, to be significantly up-regulated in ad brain.
however, we did identify three clusters of genes related to cytoskeletal organization .
the first group contains organelle membrane skeletal proteins such as safa, lmna and sptbn <dig>  <cit>  the second group encodes skeletal binding proteins, including fkbp <dig>  interacting with erythrocyte membrane cytoskeletal protein  <cit> , kns <dig> and map <dig>  all associated with microtubules  <cit>  the third group contains gtpase activating proteins, arhgap <dig>  centg <dig> , srgap <dig>  which regulate membrane trafficking and actin remodeling  <cit>  sept <dig> can also be categorized into this group since it is a polymerizing gtpase required for cytokinesis and cortical organization  <cit> .
it is intriguing that so many cytoskeleton related genes are up regulated in the degenerating brains.
it is currently unclear whether these changes were the causes or the consequences of neurodegeneration.
one possibility is that these genes might be up regulated in activated microglia or astrocytes, which triggered signals that mediate cytoskeletal reorganization and vesicular trafficking during glial cell migration.
CONCLUSIONS
we have used a proprietary subtractive hybridization technology  to identify differentially expressed genes in ad brains, extending existing gene profiling and subtraction methods, such as dna or protein microarray analyses to identify rare sequences.
55% of the identified differentially expressed genes have no known function, of which, 25% had no matching ests in the databases.
these sequences represented novel and newly discovered transcripts in the brain and were also differentially expressed in ad brains.
using literature mining tools we have established  many new gene associations, not yet reported to be involved in ad.
this information will facilitate future efforts aimed at establishing alterations in molecular pathways involved ad pathology.

 recent advance in molecular biology have introduced new high-throughput tools for the analysis of differential gene expression in complex diseases, such as alzheimer, providing simultaneous overviews of the genes or proteins associated with multiple cellular pathways. the most commonly used technology for the assessment of gene expression changes in postmortem brain is the dna microarray this approach has not only confirmed the involvement of genes implicated in ad by conventional methods, but also revealed changes in additional genes, not previously associated with ad. however, as this method requires a priori knowledge of gene sequences, it cannot be applied as a discovery tool for novel transcripts. furthermore, the expression levels of low abundance genes cannot be readily assessed by dna microarray hybridization, since reliable results are usually obtained only for genes that are expressed in high or moderate levels. this is a significant limitation since many transcripts expressed preferentially in brain are present at very low levels. differential display and conventional subtractive hybridization approaches are capable of detecting expression changes in both known and novel genes. differential display uses arbitrarily primed pcr to fingerprint differences in gene expression between two samples, with the results being determined by the intensities of bands on a polyacrylamide gel. the major disadvantages of this method include its lack of sensitivity for the detection of rare rna species, the high number of false positives generated during pcr and cloning of the differentially expressed products from low resolution polyacrylamide gels, where an apparent single band may contain multiple cdna species. consequently, differential display is labor intensive and unreliable for this application. subtractive hybridization, on the other hand, permits the isolation of target sequences from one single-stranded dna population, referred to as "tester", from another dna population, referred to as "driver" by using an excess of sequences. the two populations are mixed and put through iterative rounds of subtraction of cross-hybridized products. earlier subtractive methods required physical removal of hybridized driver and tester sequences, which contributed to the loss of low abundance tester sequences. suppression subtractive hybridization is a newer method which couples hybridization-based de-selection of common cdnas to pcr amplification which enriches differentially expressed transcripts from two mrna sources. in contrast to differential display, the primers for pcr amplification are clearly defined, thus avoiding problems associated with random primers. the main disadvantage of this procedure is its higher detection threshold. according to the kit manufacturer's recommendation, the difference in mrna levels needs to be at least fold to allow reliable detection. here, we have developed a novel approach to the identification of differentially expressed rare sequences through a combination of subtractive hybridization and rna amplification, termed a subtractive transcription-based amplification of mrna. in our method, the expressed rnas from two source are used for the preparation of specialized cdna libraries, from which single stranded sense tester rna and single stranded sense driver dna are generated. subtraction is accomplished by the hybridization of single-stranded driver dna to the complementary single-stranded tester rna, followed by rnase h digestion. this process not only eliminates the necessity for physical removal of hybridized common sequence, but also eliminates the self-annealing step of the tester nucleic acids that is required by the ssh method for the amplification of target sequences. the self-annealing step usually imposes kinetic limitations and requires lengthy hybridization in order to recover rare cdna sequences. furthermore, in the star method, the tester rna is designed with a defined terminal sequence which allows the unhybridized tester rna to be amplified in a linear rna amplification process, rather than exponential pcr amplification, thereby minimizing biased sequence amplification since the tester rna remains unchanged in the process, the products of one round of star are used directly in subsequent rounds to provide further enrichment of the unique sequences. in this study, we applied the star method to an investigation of changes in gene expression in port-mortem ad brain. we show that, indeed, the star process significantly increases the levels of unique and rare sequences relative to abundant housekeeping genes and identified changes in the expression of genes not previously linked to the ad. we also performed extensive literature mining to provide a basis for considering their likely involvement in neurodegenerative processes.  characterization of the subtracted ad cdna libraries two subtracted cdna libraries, using either the 3' cdna of the control sample or the 3' cdna of the ad sample as tester, were prepared using the star method. it was expected that they would contain genes that were down regulated and up regulated in ad brain, respectively. to isolate these genes, three rounds of star subtraction were performed, and the remaining 3' biased cdna tester fragments were linearly amplified, ligated into a puc-modified vector and transformed into e. coli dh10b cells. approximately colonies were obtained for each star library. subsequently, pcr and dna sequencing were performed on amplified cdna inserts from individual colonies for each subtracted library. data analysis indicated that this number of colonies was sufficient to represent the entire subtracted library since many genes, including some of low abundance, appeared to be represented by more than one colony. the results summarizing the genes found in the c-ad and ad-c libraries are listed in tables and respectively. of the colonies analyzed from each library, over contained inserts and produced readable sequences after pcr. sequence annotation grouped the genes into three categories: known genes, ests and novel genes, whose sequences either only match a fragment of genomic dna or the database search did not hit any existing known sequence. the known genes were represented by multiple colonies far more often than the novel genes, indicating that known genes are relatively more abundant than the novel genes, explaining why they are more easily identified by traditional approaches. sequence annotation also revealed that genes involved in maintenance of neuronal cell structure and function, the ubiquitin pathway and energy metabolism were predominant in the c-ad library, indicating that they were down regulated in ad brains. whereas in the ad-c library, genes involved in inflammation, protein translation, cytoskeleton/cell adhesion and apoptosis/neurodegeneration were up-regulated in ad. over 55% of the sequenced fragments in each subtracted library represented unknown genes, of which one half were not previously described as cdna sequences. representative data from these libraries is shown below. validation of changes from the subtracted libraries more than genes from the c-ad library were randomly selected for analysis by qrt-pcr using the pools of control and ad mrnas as input. the results confirmed down-regulation of over 80% of them, consistent with the results of the subtracted library. the data also confirmed that a majority of these genes were less abundant than β-actin. furthermore, all novel transcripts were expressed at extremely low levels, some of them at only –2% of the abundance of β-actin. taken together these results indicated that the star method permitted the isolation of differentially expressed genes, including very rare ones. this approach also revealed the existence of large number of previously unidentified genes expressed in the human brain which appear to have a disease association. nearly randomly selected genes from the ad-c library were also analyzed by qrt-pcr in order to further validate the library data. in this case, less than 50% of the selected transcripts were found to be up regulated, with a lower percentage of novel genes. this might be indicative of a higher content of false positive in this library, pointing out to the necessity of independent validation prior to gene selection for down stream functional studies. one possibility for the relatively low confirmation rate of the data from the ad-c library is that the increases in the expression of unconfirmed transcripts were small and, therefore, might also be difficult to validate by qrt-pcr, although this wasn't evident in the qrt-pcr validation of down regulated genes from the c-ad library. despite this, the technique clearly identifies novel sequences that are up regulated in ad brain. supporting evidence for gene association with ad an additional approach to increase confidence in the identified genes as likely disease candidates was to mine knowledge pertaining to gene function in ad in the existing literature using a custom built literature mining tool, litminer. using this approach, we generated short lists of genes whose association with ad could be further rationalized. the data mining analysis identified genes, whose down-regulation in ad has been previously reported, in agreement with our results as these genes were present in the c-ad subtractive library. furthermore, down-regulation of synuclein alpha was also confirmed by qrt-pcr analysis. the remaining genes on this list have never been formally linked to ad, but their possible involvement could be either inferred from the literature or from the results of the present study. for example, mutations in a2m, bri eef1a eif2s mapt and ubb have been linked to various other neurodegenerative diseases have been shown to be down-regulated in some brain disorders the down-regulation of genes from the c-ad library was validated by qrt-pcr and a similar literature analysis further supports the potential involvement of reln, prkce and syt therefore, it is likely that the down-regulation and the loss of these gene functions could play a role in ad. possible associations between the down-regulated and up-regulated genes from the subtracted libraries were mapped by additional literature mining. we imported the unigene names of each group of genes into litminer and used "alzheimer" and "neurodegeneration" as knowledge terms. all articles containing a gene name, or alias and the knowledge terms, in either title, mesh terms or abstract were reported in a graphic format. any two given genes or a gene and one of the knowledge terms appearing in the same article were considered to constitute an association. the frequencies of these associations are represented by the number adjacent to the connecting lines. within litminer, we could rapidly retrieve and manually scan articles to eliminate false association due to the misuse of gene aliases in the database. the graphs in figs and contain genes that exhibited actual association to the knowledge terms or to other genes. some genes summarized in table and are not included in figs and because the current software finds only associations identified in the title, abstract or mesh terms. nevertheless, the litminer output gives a high level overview of the relationships of these differentially expressed genes that is not obtainable from a simple gene list. discussion with the advent of high throughput genomics and proteomics technologies, the involvement of new genes in ad continues to emerge, indicating clearly that the full extent of molecular and functional aberrations responsible for the etiology of ad is not yet understood. the current high throughput methods are mainly designed to identify changes in relatively abundant genes, whereas weakly expressed genes or proteins are still overlooked. for example, cdna microarrays, although widely used, are limited to known mrna sequences or ests, thus it is not suitable for the identification and isolation of novel rare transcripts. complementary to microarray technology, subtractive hybridization is capable of detecting changes of both known and novel genes. the existing ssh method enriches the differentially expressed genes by selectively suppressing the amplification of non-differentially expressed transcripts in the pcr reaction, resulting in the enrichment of differentially expressed transcripts. an annealing step is necessary for pcr amplification and subsequent cloning and since rare sequences re-anneal more slowly, this process reduces their chances of discovery. the star technology uses single strand rna/dna hybridization to remove non-differentially expressed genes. rare sequences are enriched by slower hybridization and the non-hybridized rna is recovered and amplified by a linear rna amplification procedure, which minimizes the biased exponential amplification of subsets of genes in a mixture. these features make the star method attractive for examining changes of gene expression in normal and diseased brain tissues, where many mrnas are present in low abundance. in the present study, we used the star method to identify genes that are not only novel in human brains, but also differentially expressed in ad. our subtracted cdna libraries constructed by the star technology contained genes whose relative differences in expression levels ranged from 25% to 100%, illustrating the fidelity of this method. although there has been little, and in some cases, no overlap in identified genes between different microarray studies of ad samples, due to experimental variability, different sources of microarray bearing different sets of genes and different areas of brain tissues used, star has identified a number of known, moderately abundant genes, whose alternation in ad was in agreement with previous microarray analyses. of these app and snca were found down regulated, agt, clu, ftl, map and stxbp were reported up-regulated. more than 55% of clones in each subtracted library contain cdna of unknown function and more then 25% are novel sequences only matching genomic dna in database searches. these novel genes can now be vigorously pursued to identify their function and precise role in ad pathology. similar to other high throughput approaches, the changes in gene expression identified by the star method need to be validated by qrt-pcr. this is especially true for the rare and novel sequences, for which there is no information available in the literature. combinations of pcr-selected cdna subtraction and cdna microarray analysis of the subtracted clones, or using probes generated by pcr-selected subtraction to screen affymetrix genechips have been attempted. the clones produced by star can be printed on microarray slides for hybridization with labeled cdnas from individual brains samples, however, the rare rna species must be enriched by amplification in order to give reliable hybridization signals. this method, currently under development, could be a high throughput approach to eliminate false positives before qrt-pcr validation on individual genes. we have measured changes in nearly genes from each subtracted cdna library by qrt-pcr. however, there was a difference in the confirmation rate between the two subtracted libraries. besides the fact that there seemed to be more down- than up- regulated genes in the ad brains where neurodegeneration was already evident., we cannot offer an definite explanation why some genes, such as, syntaxin binding protein and kinesin found up-regulated by star procedure, consistent with the results obtained by others, yet not confirmed by qrt-pcr. further investigations with different fine-tuned qrt-pcr primers and conditions and by using individual brain samples may offer insight on this issue. while identification of novel genes functions in neurodegeneration remains to be our ongoing objective, the current study was focused on the association of some of the known genes with ad. among the down regulated genes in table those belonging to two major functional categories are noteworthy. the first group contains genes involved in maintenance of neuronal cell function, including cast, pfrk, serpine snca, sv2a and syt their roles in normal brain are to promote neurite outgrowth and to regulate synaptic vesicle transport or trafficking at the synapse. their down regulation is consistent with the compromised synaptic transmission observed in ad brain. this undoubtedly contributes to the impairment of memory and cognitive function. our findings support the current view that ad is a disease of synaptic failure. the second group of genes consists of members of the ubiquitin pathway involved in protein degradation. although only ubb, ube2b and uchl passed our current screening criteria, several other ubiquitin pathway-related genes also appeared in the c-ad library. a straightforward interpretation of this result would be that the decreased ability of protein degradation caused by the down regulation of ubiquitin pathway genes, resulted in the accumulation of unwanted proteins in the senile plaques and neurofibrillary tangles. however, studies of individual ubiquitin pathway genes, such as uchl suggest other mechanisms. for example, uchl is sensitive to redox changes and is oxidized in ad brain. indicating that its function under stressed conditions is more than "house keeping". elevated expression of other ubiquitin pathway proteins in response to oxidative stress has also been documented. however, a better understanding of the role of individual ubiquitin pathway genes in ad pathology requires comprehensive study. extensive evidence suggests that inflammation plays a major role in ad. it is therefore not surprising to find genes, such as mbp, nptx and scarb involved in neuroinflammation, to be up regulated in ad brains. we also found several genes related to the cellular distribution of iron, transport of copper and metal-binding that were up-regulated in ad. these data strongly suggest a disruption of metal homeostasis and a potential metal neurotoxicity component in ad. the increase of these proteins may indicate an acute phase-type reaction and/or a compensatory response to stress conditions. we did not find any typical cytoskeletal proteins, such as members of the actin or tubulin families, to be significantly up-regulated in ad brain. however, we did identify three clusters of genes related to cytoskeletal organization. the first group contains organelle membrane skeletal proteins such as safa, lmna and sptbn the second group encodes skeletal binding proteins, including fkbp interacting with erythrocyte membrane cytoskeletal protein, kns and map all associated with microtubules the third group contains gtpase activating proteins, arhgap centg, srgap which regulate membrane trafficking and actin remodeling sept can also be categorized into this group since it is a polymerizing gtpase required for cytokinesis and cortical organization. it is intriguing that so many cytoskeleton related genes are up regulated in the degenerating brains. it is currently unclear whether these changes were the causes or the consequences of neurodegeneration. one possibility is that these genes might be up regulated in activated microglia or astrocytes, which triggered signals that mediate cytoskeletal reorganization and vesicular trafficking during glial cell migration.  we have used a proprietary subtractive hybridization technology to identify differentially expressed genes in ad brains, extending existing gene profiling and subtraction methods, such as dna or protein microarray analyses to identify rare sequences. 55% of the identified differentially expressed genes have no known function, of which, 25% had no matching ests in the databases. these sequences represented novel and newly discovered transcripts in the brain and were also differentially expressed in ad brains. using literature mining tools we have established many new gene associations, not yet reported to be involved in ad. this information will facilitate future efforts aimed at establishing alterations in molecular pathways involved ad pathology. 
many genes implicated in these processes may be present in low abundance in the human brain. over 55% of the sequences represent genes of unknown function and roughly half of them were novel and rare discoveries in the human brain. the expression changes of nearly unique genes were further confirmed by qrt-pcr and the association of additional genes with ad and/or neurodegeneration was established using an in-house literature mining tool. our method, termed subtractive transcription-based amplification of mrna, is a combination of subtractive rna/dna hybridization and rna amplification, which allows the removal of non-differentially expressed transcripts and the linear amplification of the differentially expressed genes. dna microarray analysis identifies changed genes that are expressed at high or moderate levels. the star process significantly amplifies unique and rare sequences relative to abundant housekeeping genes and, as a consequence, identifies genes not previously linked to ad. using the star technology we have identified over differentially expressed sequences in ad brains, both up- and down- regulated, compared to age-matched controls. complementary to this approach, we described here a novel technology designed specifically to isolate rare and novel genes previously undetectable by other methods. this method also offers new opportunities to study the subtle changes in gene expression that potentially contribute to the development and/or progression of ad.
 alzheimer's disease is a complex disorder that involves multiple biological processes. many genes implicated in these processes may be present in low abundance in the human brain. dna microarray analysis identifies changed genes that are expressed at high or moderate levels. complementary to this approach, we described here a novel technology designed specifically to isolate rare and novel genes previously undetectable by other methods. we have used this method to identify differentially expressed genes in brains affected by ad. our method, termed subtractive transcription-based amplification of mrna, is a combination of subtractive rna/dna hybridization and rna amplification, which allows the removal of non-differentially expressed transcripts and the linear amplification of the differentially expressed genes.  using the star technology we have identified over differentially expressed sequences in ad brains, both up- and down- regulated, compared to age-matched controls. over 55% of the sequences represent genes of unknown function and roughly half of them were novel and rare discoveries in the human brain. the expression changes of nearly unique genes were further confirmed by qrt-pcr and the association of additional genes with ad and/or neurodegeneration was established using an in-house literature mining tool.  the star process significantly amplifies unique and rare sequences relative to abundant housekeeping genes and, as a consequence, identifies genes not previously linked to ad. this method also offers new opportunities to study the subtle changes in gene expression that potentially contribute to the development and/or progression of ad. 