Serial Analysis Of Gene Expression Technique Research Articles

Application of serial analysis of gene expression to the study of human genetic disease

Sequence tag analysis using serial analysis of gene expression (SAGE) is a powerful strategy for the quantitative analysis of gene expression in human genetic disorders. SAGE facilitates the measurement of mRNA transcripts and generates a non-biased gene expression profile of normal and pathological disease tissue. In addition, the SAGE technique has the capacity of detecting the expression of novel transcripts allowing for the identification of previously uncharacterised genes, thus providing a unique advantage over the traditional microarray-based approach for expression profiling. The technique has been successful in providing pathological gene expression profiles in a number of common genetic disorders including diabetes, cardiovascular disease, Parkinson disease and Down syndrome. When combined with next generation sequencing platforms, SAGE has the potential to become a more powerful and sensitive technique making it more amenable for diagnostic use. This review will therefore discuss the application of SAGE to several common genetic disorders and will further evaluate its potential use in diagnosing human genetic disease.

Modified PCR methods for 3′ end amplification from serial analysis of gene expression (SAGE) tags

Serial analysis of gene expression (SAGE) is a powerful technique to study gene expression at the genome level. However, a disadvantage of the shortness of SAGE tags is that it prevents further study of SAGE library data, thus limiting extensive application of the SAGE method in gene expression studies. However, this problem can be solved by extension of the SAGE tags to 3' cDNAs. Therefore, several methods based on PCR have been developed to generate a 3' longer fragment cDNA corresponding to a SAGE tag. The list of modified methods is extensive, and includes rapid RT-PCR analysis of unknown SAGE tags (RAST-PCR), generation of longer cDNA fragments from SAGE tags for gene identification (GLGI), a high-throughput GLGI procedure, reverse SAGE (rSAGE), two-step analysis of unknown SAGE tags (TSAT-PCR), etc. These procedures are constantly being updated because they have characteristics and advantages that can be shared. Development of these methods has promoted the widespread use of the SAGE technique, and has accelerated the speed of studies of large-scale gene expression.

Identification of Genes with Prognostic and Therapeutic Relevance in Multiple Myeloma Using Serial Analysis of Gene Expression Technique.

Serial analysis of gene expression (SAGE) allows a comprehensive profiling of gene expression within a given tissue and also an assessment of transcript abundance.Objectives: We generated SAGE libraries from normal and neoplastic plasma cells with the aim of identifying genes differentially expressed in MM that could be useful as new potential diagnostic, prognostic markers or therapeutic targets.Material and methods: Normal plasma cells were obtained from palatine tonsils of 20 children who underwent tonsillectomy. MM SAGE library was obtained from bone marrow plasma cells of two IgGk newly diagnosed MM patients. Purified normal and neoplastic plasma cells were isolated after magnetic sorting of CD-138-positive cells.Results: We obtained 29,918 SAGE tags from normal and 10,340 tags from tumor libraries. Computer-generated genomic analysis identified 50 overexpressed genes in MM library. After comparison of unique tags expression levels, we selected 12 overexpressed (at least 10 times) genes in the MM library (ZFHX1B, XBP1, PIM2, LGALS1, RANBP2, P53CSV, DDX5, LSM5, JUND, MAPKAPK2, SP140 and NTN1) for further investigation. Expression of 10 out of 12 genes was validated by quantitative real-time PCR in purified plasma cells of 31 MM patients and three controls. XBP1, RANBP2, P53CSV, DDX5, MAPKAPK2 were overexpressed in at least 50% of MM cases. Comparative analyses of relative expression (2-D D CT) of the 10 genes in 31 MM cases and 3 controls showed statistically significant difference between cases and controls for all genes but PIM2 and ZHFX1B, confirming the SAGE data. Also, we could identify that RANBP2 and ZHFX1B have prognostic impact in MM OS (p = 0.040 and p = 0.0502, respectively). Multivariate analysis confirmed RANBP2 expression as a good independent prognostic marker.Conclusions: SAGE technique allowed the identification of genes differentially expressed in normal and neoplastic plasma cells. These genes may have important role in tumorigenesis or may be possible therapeutic targets for MM control, particularly P53CSV and MAPKAPK2, or prognostic impact, as RANBP2.

Applying the SAGE technique to study the effects of electromagnetic field on biological systems

Identification of genes alternatively expressed in electromagnetic field (EMF)-exposed cells could provide direct evidence for biological effects of EMF. As there are a few indications so far for certain genes to be influenced by EMF, genome-wide scans of the transcriptome appear to be necessary. Among the several technologies used for genome-wide gene expression analysis, serial analysis of gene expression (SAGE) is one promising method, which seems particularly applicable for EMF research. This review provides a brief description of the features of gene expression, illustrates the basic principle of SAGE, and discusses the advantages and limitations of SAGE as well as examples of application. This information should help investigators determine if the SAGE technique is an optimal method for evaluating the biological effects of EMF.

Serial Analysis of Gene Expression in Mouse Uterus at the Implantation Site

Although oligonucleotide chips, cDNA microarrays, differential display reverse transcription-PCR, and other approaches have been used to screen implantation-related molecules, the mechanism by which embryo implantation occurs is still unknown. The aim of this study was to profile the differential gene expression between interimplantation site and implantation site in mouse uterus on day 5 of pregnancy by serial analysis of gene expression (SAGE). In our two SAGE libraries of 11-bp tags, the total numbers of tags sequenced were 48,121 for the interimplantation site and 50,227 for the implantation site. There were 1,039 tags specifically expressed at interimplantation site, and 1,252 tags specifically expressed at the implantation site. Based on the p value, there were 195 tags significantly up-regulated at the interimplantation site and 261 tags significantly up-regulated at the implantation site, of which 100 genes were single matched at the interimplantation site and 127 genes were single matched at the implantation site, respectively. By reverse transcription-PCR, the tag ratio between the implantation site and interimplantation site was verified on 14 significantly changed genes. Using in situ hybridization, 1810014L12Rik, Psmb5, Cd63, Npm1, Fads3, and Tagln2 were shown to be highly expressed at the implantation site compared with the interimplantation site. Compared with the interimplantation site, Ddx39 was strongly expressed in the subluminal stromal cells at the implantation site on day 5 of pregnancy. Ddx39 expression at the implantation site was specifically induced by active blastocysts. Additionally, Ddx39 expression was significantly up-regulated by estrogen in the ovariectomized mice. In our SAGE data, many implantation-related genes were identified in mouse uterus. Our data could be a valuable source for future study on embryo implantation.

A SAGE approach to identifying novel trans-acting factors involved in the X inactivation process

X chromosome inactivation ensures the dosage compensation of X-linked genes in XX females compared to their XY male counterpart. It is characterised by the specific recruitment of an inhibitory ribonucleoprotein complex involving the non-coding Xist RNA to the presumptive inactive X chromosome and associated chromatin modifications, which result in the transcriptional silencing of the X chromosome. As an approach to the identification of some of the potential molecular players in this process we have performed comparative transcriptional profiling of mouse 6.5-dpc (days post-coitum) female and male embryos using a modified SAGE (Serial analysis of gene expression) technique which allows the analysis of small quantities of biological material. At 6.5 dpc, a moment when random X inactivation of embryonic tissues has just been achieved, some two hundred transcripts that were significantly enriched in the female gastrula compared to its male counterpart could be identified. The validation of an association with the X inactivation process of a subset of these transcripts has been studied, ex vivo, in differentiating female and male ES cells and in female ES cells in which the establishment of X inactivation is interrupted through the post-transcriptional inhibition of Xist synthesis.

Serial Analysis of Gene Expression Revealed Consistent Downregulation of More Than 100 Genes in Hodgkin Lymphoma.

Hodgkin Lymphoma (HL) is unique in its cellular composition, consisting of a minority of tumor cells in an inflammatory background. The tumor cells (Reed-Sternberg cells, RS cells) are thought to be derived from germinal center B cells (centroblasts, CB) that have escaped apoptosis during antigen selection. Global gene expression studies in HL have been hampered by the fact that RS cells only represent less than 1% of the cells in the tumor tissue. Only a few large-scale gene expression studies are available, mostly using cell lines derived from patients with classical HL. To get more insight into the gene expression profile of RS cells we applied the Serial Analysis of Gene Expression Technique (SAGE) on several HL cell lines. SAGE was performed on the cell lines L428 and L1236 (classical cell lines, cHL), DEV (Nodular Lymphocyte Predominant cell line, NLP) and on CB as normal counterparts.In total, about 100.000 tags were sequenced (Table 1). After normalization and exclusion of tags present only once, 3.635 genes were retained and used for further analyses. A five-fold difference in tag frequency between the HL cell lines and CB was used to select for up- or downregulated genes. Although many genes were upregulated in every individual HL cell line compared to CB, only few genes were consistently upregulated. In contrast, comparison of the downregulated genes revealed that 125 were downregulated in all three HL cell lines compared to CB (Table 2). Tags corresponding to Fascin, TARC/CCL17 and BIC, known to be highly expressed in HL indeed were observed in the SAGE libraries. Among the genes downregulated in L428 a loss of B lineage-specific genes was observed confirming the previous findings in L1236. Interestingly our SAGE results suggest that the NLP cell line DEV has an intermediate loss of B-lineage specific genes compared to CB. To gain more insight in the biology, differentially expressed genes were grouped according to gene ontology's (based on biological process or molecular function) and pathways. We have now selected more than 70 genes that will be subjected to quantitative RT-PCR analysis to confirm our SAGE results and to study their expression in tumor cell enriched HL samples.In conclusion: Downregulation of gene expression seems to be important in the pathogenesis of HL since we observed a consistent downregulation of more than 100 genes in HL compared to CB.Table 1. Overview of Hodgkin lymphoma SAGE librariesTable 2. Number of up- and downregulated genes in Hodgkin lymphoma compared to centroblastsLibraryDEVL428L1236CBHL typeNLPcHLcHLCentroblastsTags16316209903062329787Genes470356021056111095L428L1236cHLDEVcHL & NLP HLUpregulated396116143307Downregulated329169141309125L428 and L1236 are derived from classical Hodgkin lyphoma (cHL) cases, DEV is derived from a case of Nodular Predominant Hodgkin lymhoma (NLP HL)

Overexpression of Bax inhibitor suppresses the fungal elicitor-induced cell death in rice (Oryza sativa L) cells.

Treatment of suspension-cultured cells of rice (Oryza sativa L.) with cell wall extract of rice blast fungus (Magnaporthe grisea) elicits a rapid generation of H2O2, alkalinization of culture medium, and eventual cell death. To elucidate genes involved in these processes, we exploited SAGE (Serial Analysis of Gene Expression) technique for the molecular analysis of cell death in suspension-cultured cells treated with the elicitor. Among the downregulated genes in the elicitor-treated cells, a BI-1 gene coding for Bax inhibitor was identified. Transgenic rice cells overexpressing Arabidopsis BI-1 gene showed sustainable cell survival when challenged with M. grisea elicitor. Thus, the plant Bax inhibitor plays a functional role in regulating cell death in the rice cell culture system.

Gene expression profiling of human diseases by serial analysis of gene expression.

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.

Transcriptome analysis of saccharomyces cerevisiae using serial analysis of gene expression

Publisher Summary This chapter describes the technique and application of serial analysis of gene expression (SAGE), an approach that allows the rapid, detailed, systematic, and quantitative analysis of thousands of transcripts. SAGE can be used to determine global or differential gene expression under a set of defined conditions. Unlike other methods, SAGE provides an absolute level of gene expression for all transcribed genes in a defined population of cells and does not depend on prior availability of sequence information. SAGE also does not require specialized equipment beyond access to a sequencing apparatus and a PCR (polymerase chain reaction) machine. SAGE is used to define the transcriptome of Saccharomyces cerevisiae during normal growth and cell cycle arrest in S or G2/M phases of the cell cycle. This organism was chosen because it is used widely to define the biochemical and physiologic parameters underlying eukaryotic cellular functions and its genome is completely sequenced. SAGE studies done with S. cerevisiae cells grown in oleate-containing media have led to the identification of about 100 differentially regulated genes. In mammalian cells, SAGE analysis has provided valuable information about the global gene expression level and also to determine if the transcription of a given gene is specific to a particular tissue, developmental or cell cycle stage, or pathological condition. The chapter discusses an important application of the SAGE technique—namely, the identification of previously unidentified transcripts from NORFs.

Growth and migration markers of rat C6 glioma cells identified by serial analysis of gene expression

Tumors derived from rat C6 cell implants into rat brain exhibit similar morphological characteristics and degree of vascularization to human glioblastomas. To establish a molecular basis for C6 gliosarcoma malignancy, we have constructed a molecular profile of the most abundantly expressed genes, using serial analysis of gene expression (SAGE). Sequence tags (1168) representing 738 individual transcripts were collected and tag-to-gene mapping was carried out using the UniGene data set for rat. Differentially expressed C6 transcripts were identified by comparison of tags collected for C6 cells with a similar number (1002) of tags from a rat primary astrocyte library. Genes found to be expressed at increased levels in C6 cells are associated with cell surface interactions, migration, or metastasis formation and proliferation. These include the receptor for hyaluronan-mediated motility (RHAMM), S-100 related protein 42A, galectin I, preproenkephalin, osteopontin, autocrine motility factor, α-tubulin, ad1 antigen, and cofilin. In addition, a tag with no database match probably representing a previously uncharacterized transcript was differentially expressed in C6 cells. Transcripts showing reduced expression in C6 cells relative to astrocytes included the extracellular matrix glycoprotein osteonectin/SPARC (secreted protein, acidic, rich in cysteine), actin-binding proteins thymosins β-4 and β-10, the cysteine protease inhibitor cystatin C, the actin-gelling protein SM22/transgelin, and ferritin-H. SAGE results were confirmed by Northern blot for all transcripts tested, reaffirming the value of the SAGE technique for expression profiling in cancer biology. GLIA 32:146–154, 2000. © 2000 Wiley-Liss, Inc.

Serial analysis of gene expression as a tool to assess the human thyroid expression profile and to identify novel thyroidal genes.

The assessment of the expression profile of normal human thyroid tissue using serial analysis of gene expression (SAGE) generated a collection of 10,994 sequence transcripts (tags). Each tag represented a messenger RNA transcript, and, in total, 6099 different tags could be distinguished. The presence and abundance of thyroid-specific transcripts showed the overall expression profile to be from a normal thyroid cell. The expression level of several transcripts was confirmed on Northern blot. Seventy percent of tags could not be attributed to a known human gene and, therefore, possibly correspond to novel genes putatively involved in thyroid function. The tag sequence generated by the SAGE technique can be used to further characterize these novel genes. In this way, application of the SAGE technique to thyroid tissue gives insight in the expression profile of a normal thyroid gland and provides the information to characterize novel genes involved in thyroid pathology, such as congenital hypothyroidism and thyroid neoplasia.

Patterns of gene expression associated with BMP-2-induced osteoblast and adipocyte differentiation of mesenchymal progenitor cell 3T3-F442A.

The pluripotent mesenchymal stem cells give rise to osteoblasts, adipocytes, chondrocytes, and myoblasts. The differentiation of these stem cells into each of the mature functional cells may be controlled by a distinctive master gene(s) and is associated with temporal and spatial expression of diverse genes. Identification of genes that are expressed during the differentiation of the mesenchymal cells to osteoblasts is, therefore, important to obtain insights into the molecular mechanisms of osteogenesis. The murine undifferentiated mesenchymal cell 3T3-F442A, when treated with the bone morphogenetic protein 2 (BMP-2), a well-characterized inducer of mesenchymal cell differentiation, exhibited both osteoblastic and adipocytic differentiation. Using the SAGE (serial analysis of gene expression) technique, which has been shown to enable quantitative analysis of large numbers of genes in a simple and quick manner, we obtained 1600 sequence tags representing 2107 individual nucleotide sequences from control and BMP-2-treated 3T3-F442A cells, respectively. By comparing the frequency of tag occurrence, we found profiles of up- or downregulated genes associated with osteoblast or adipocyte phenotype such as type I collagen, osteonectin and OSF-2, or C/EBPbeta, aP2, fatty acid synthase, and lipoprotein lipase, respectively, in BMP-2-treated 3T3-F442A cells. Our data show that BMP-2 induces not only osteoblastic but also adipocytic differentiation in the 3T3-F442A cells. They also show that the 3T3-F442A cells have bipotentials of differentiating toward osteoblasts and adipocytes. The results, therefore, might explain the inverse correlation between trabecular bone volume and fat volume in the bone marrow cavity. The results also suggest that the SAGE may be a useful technique that allows us a fast and efficient way to generate global and local views of gene expression associated with cellular differentiation of the mesenchymal stem cells.

Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification.

We have developed a technique called the generation of longer cDNA fragments from serial analysis of gene expression (SAGE) tags for gene identification (GLGI), to convert SAGE tags of 10 bases into their corresponding 3' cDNA fragments covering hundred bases. A primer containing the 10-base SAGE tag is used as the sense primer, and a single base anchored oligo(dT) primer is used as an antisense primer in PCR, together with Pfu DNA polymerase. By using this approach, a cDNA fragment extending from the SAGE tag toward the 3' end of the corresponding sequence can be generated. Application of the GLGI technique can solve two critical issues in applying the SAGE technique: one is that a longer fragment corresponding to a SAGE tag, which has no match in databases, can be generated for further studies; the other is that the specific fragment corresponding to a SAGE tag can be identified from multiple sequences that match the same SAGE tag. The development of the GLGI method provides several potential applications. First, it provides a strategy for even wider application of the SAGE technique for quantitative analysis of global gene expression. Second, a combined application of SAGE/GLGI can be used to complete the catalogue of the expressed genes in human and in other eukaryotic species. Third, it can be used to identify the 3' cDNA sequence from any exon within a gene. It can also be used to confirm the reality of exons predicted by bioinformatic tools in genomic sequences. Fourth, a combined application of SAGE/GLGI can be applied to define the 3' boundary of expressed genes in the genomic sequences in human and in other eukaryotic genomes.

Growth and migration markers of rat C6 glioma cells identified by serial analysis of gene expression

Tumors derived from rat C6 cell implants into rat brain exhibit similar morphological characteristics and degree of vascularization to human glioblastomas. To establish a molecular basis for C6 gliosarcoma malignancy, we have constructed a molecular profile of the most abundantly expressed genes, using serial analysis of gene expression (SAGE). Sequence tags (1168) representing 738 individual transcripts were collected and tag-to-gene mapping was carried out using the UniGene data set for rat. Differentially expressed C6 transcripts were identified by comparison of tags collected for C6 cells with a similar number (1002) of tags from a rat primary astrocyte library. Genes found to be expressed at increased levels in C6 cells are associated with cell surface interactions, migration, or metastasis formation and proliferation. These include the receptor for hyaluronan-mediated motility (RHAMM), S-100 related protein 42A, galectin I, preproenkephalin, osteopontin, autocrine motility factor, alpha-tubulin, ad1 antigen, and cofilin. In addition, a tag with no database match probably representing a previously uncharacterized transcript was differentially expressed in C6 cells. Transcripts showing reduced expression in C6 cells relative to astrocytes included the extracellular matrix glycoprotein osteonectin/SPARC (secreted protein, acidic, rich in cysteine), actin-binding proteins thymosins beta-4 and beta-10, the cysteine protease inhibitor cystatin C, the actin-gelling protein SM22/transgelin, and ferritin-H. SAGE results were confirmed by Northern blot for all transcripts tested, reaffirming the value of the SAGE technique for expression profiling in cancer biology.

Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE)

Serial analysis of gene expression (SAGE) was applied for profiling expressed genes in rice seedlings. In the SAGE method, a 9-11 bp fragment (tag) represents each transcript, and frequency of a tag in the sample directly reflects the abundance of the respective mRNA. We studied 10 122 tags derived from 5921 expressed genes in rice (Oryza sativa L.) seedlings, among which only 1367 genes (23.1%) matched the rice cDNA or EST sequences in the DNA database. SAGE showed that most of the highly expressed genes in rice seedlings belong to the category of housekeeping genes (genes encoding ribosomal proteins or proteins responsible for metabolism and cell structure). Unexpectedly, the most highly expressed gene in rice seedlings was a metallothionein (MT) gene, and together with three other messages for MT, it accounts for 2.7% of total gene expression. To our knowledge, this is the first quantitative study of global gene expression in a higher plant. We further applied the SAGE technique to identify differentially expressed genes between anaerobically treated and untreated rice seedlings. Additionally, we show that a longer cDNA fragment can be easily recovered by PCR using the SAGE tag sequence as a primer, thereby facilitating the analysis of unknown genes identified by tag sequence in SAGE. In combination with micro-array analysis, SAGE should serve as a highly efficient tool for the identification and isolation of differentially expressed genes in plants.