Digital Differential Display Research Articles

Cloning and functional verification of a porcine adipose tissue-specific promoter

BackgroundFat deposition is an important economic trait in pigs. In the past decades, many genes regulating porcine fat deposition were identified by Omics technology and verified by cell biology studies. Using genetically modified pigs to investigate the function of these genes in vivo is necessary before applying in breeding. However, lack of tissue-specific promoters of pigs hinders the generation of adipose tissue-specific genetically modified pigs.ResultsIn order to identify a porcine adipose tissue-specific promoter, we used the software Digital Differential Display (DDD) to screen 99 genes highly expressed in porcine adipose tissue. GO and KEGG enrichment analysis indicated that the 99 genes were mainly related to lipid metabolism. Q-PCR proved that LGALS12 was an adipose tissue-specific gene. Five truncated fragments of the LGALS12 promoter were cloned and the 4 kb fragment (L-4 kb) exhibited a high level of promoter activity in adipocytes and no promoter activity in non-adipocytes. Following co-transfection with adipogenic transcription factors, the promoter activity of L-4 kb was enhanced by PPARγ, C/EBPβ, and KLF15, whereas it was suppressed by KLF4. Finally, we demonstrated that L-4 kb can drive APOR gene expression to exert its function in adipocytes.ConclusionsThis study demonstrates that porcine LGALS12 is an adipose tissue-specific gene, and identified the 4 kb fragment of LGALS12 promoter that exhibited adipocyte-specific promoter activity. These results provide new evidence for understanding porcine fat deposition and a promoter element for adipose tissue-specific genetic modification in pigs.HighlightsIdentified porcine LGALS12 as an adipose tissue-specific gene.Truncated LGALS12 promoter (L-4 kb) showed adipose tissue-specific promoter activity.Identified transcription factors involved in the regulation of L-4 kb promoter activity.

Utilization of digital differential display to identify differentially expressed genes related to rumen development.

This study aimed to identify the genes associated with the development of the rumen epithelium by screening for candidate genes by digital differential display (DDD) in silico. Using DDD in NCBI's UniGene database, expressed sequence tag (EST)-based gene expression profiles were analyzed in rumen, reticulum, omasum, abomasum and other tissues in cattle. One hundred and ten candidate genes with high expression in the rumen were derived from a library of all tissues. The expression levels of 11 genes in all candidate genes were analyzed in the rumen, reticulum, omasum and abomasum of nine Japanese Black male calves (5-week-old pre-weaning: n = 3; 15-week-old weaned calves: n = 6). Among the 11 genes, only 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), aldo-keto reductase family 1, member C1-like (AKR1C1), and fatty acid binding protein 3 (FABP3) showed significant changes in the levels of gene expression in the rumen between the pre- and post-weaning of calves. These results indicate that DDD analysis in silico can be useful for screening candidate genes related to rumen development, and that the changes in expression levels of three genes in the rumen may have been caused by weaning, aging or both.

AB181. In vitro study on shRNA decreasing the expression of human testis-specific gene TDRG1 and affecting the proliferation, invasion and apoptosis of NTERA-2 Cell

ObjectiveWe have screened and cloned a novel human testis-specific gene, named Testis developmental related gene 1 (TDRG1 GenBank DQ168992), using Digital Differential Display. In our previous work, we hypothesized that this gene might be involved in the occurrence and development of testiculoma. To investigate this possibility, we have successfully established a stabilized RNA interference system to decrease the expression of TDRG1 in NTERA-2 cell line. In this study, to explore the function of TDRG1 in testiculoma further, we successfully transfected the TDRG1-shRNA486 and TDRG1-shRNA/control expression vectors described in our previous work (PubMed PMID: 23117448) into NTERA-2 cells in vitro and tested the biological behaviors of NTERA-2 cells.MethodsFirstly, we checked the expression of TDRG1 in NTERA-2 cell line. Then we used fluorescence microscope to ensure the successful transfection. The expression of TDRG1 mRNA and protein was verified by fluorescence quantitative PCR and indirect cell immunofluorescence, respectively. Furthermore, we used such methods as MTT assay, transwell assay and flow cytometry to detect the biological behaviors of NTERA-2 cells.ResultsWe determined that the TDRG1 mRNA and protein levels were significantly reduced by TDRG1-shRNA486expression vector. Moreover, the ability to proliferate and invade in vitro was suppressed in cells where the expression of TDRG1 was down-regulated, and a corresponding increase in the apoptotic potential was observed.ConclusionsFirstly, these results indicate that the TDRG1-shRNA486 expression vector constructed previously can interfere the TDRG1 expression effectively and stably. We construct a good cell line model in which TDRG1 expression was inhibited. Secondly, the ability of proliferation and invasion of NTERA-2 cells in vitro can be positively regulated by TDRG1, while the potential of apoptosis can be negatively regulated. This gene has some characters resembling oncogene.

Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data.

Soybean is one of the most economically important crops in the world. Soybean seeds have abundant protein and lipid content and very high economic value. In this study, a total of 184 seed-specific genes were obtained using online microarray databases, DDD, and RNA-seq data. The reported seed-specific genes in soybean and the 184 seed-specific genes analyzed in this paper were compared. Of the screened genes, 26 were common to both previous reports and the current screening. Meanwhile, 90 of the 184 genes have homologous counterparts in Arabidopsis, among which 24 have seed-specific expression, as indicated by microarray data for Arabidopsis. Furthermore, promoter analysis showed that almost all seed-specific genes contain at least one seed specific-related element. Seed-specific element Skn-1 motif exists in most, if not all, of the seed-specific genes screened. Five genes were randomly selected from 184 soybean seed specific gene pool and their expressions were quantified using quantitative real time polymerase chain reaction (qRT-PCR) to further confirm the specificity of the screened genes. The results indicated that all five genes showed seed-specific expression. Moreover, the identification of genes with seed-specific expression screened in this study provides information valuable to the in-depth study of soybean.

5.5 Successful insilico discovery of novel hypoxia regulated genes in pre-eclampsia

IntroductionPre-eclampsia is a pregnancy specific disorder with still unknown aetiology. Placental hypoxia is one of the mechanisms suggested in the pathogenesis of pre-eclampsia. Here, we have used insilico techniques to...

Oestrogen receptor‐mediated expression of Olfactomedin 4 regulates the progression of endometrial adenocarcinoma

Endometrial adenocarcinoma is the most common tumour of the female genital tract in developed countries, and oestrogen receptor (ER) signalling plays a pivotal role in its pathogenesis. When we used bioinformatics tools to search for the genes contributing to gynecological cancers, the expression of Olfactomedin 4 (OLFM4) was found by digital differential display to be associated with differentiation of endometrial adenocarcinoma. Aberrant expression of OLFM4 has been primarily reported in tumours of the digestive system. The mechanism of OLFM4 in tumuorigenesis is elusive. We investigated OLFM4 expression in endometrium, analysed the association of OLFM4 with ER signalling in endometrial adenocarcinoma, and examined the roles of OLFM4 in endometrial adenocarcinoma. Expression of OLFM4 was increased during endometrial carcinogenesis, linked to the differentiation of endometrioid adenocarcinoma, and positively related to the expression of oestrogen receptor-α (ERα) and progesterone receptor. Moreover, ERα-mediated signalling regulated expression of OLFM4, and knockdown of OLFM4 enhanced proliferation, migration and invasion of endometrial carcinoma cells. Down-regulation of OLFM4 was associated with decreased cumulative survival rate of patients with endometrioid adenocarcinoma. Our data suggested that impairment of ERα signal-mediated OLFM4 expression promoted the malignant progression of endometrioid adenocarcinoma, which may have significance for the therapy of this carcinoma.

Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue

Adipose tissue plays important roles in whole body energy homeostasis and is now known to be a very important and active endocrine organ. The transcriptional regulatory network of adipose tissue metabolism is complex and much yet to be known. To identify transcriptional profile in adipose tissue, expressed sequence tag (EST) analysis using Digital Differential Display (DDD) was employed. The results of EST analysis were re-evaluated by microarray data using COXPRESdb (an available expression data repository). To uncover transcriptional regulatory mechanisms which play key roles in the adipose tissue metabolism, transcriptional regulatory network analysis was applied, using the promoter analysis and interaction network toolset. Sixty-five transcripts were found to be more frequent in adipose tissue in comparison to the other tissues. COXPRESdb result showed that 62 % of the identified over-expressed genes in adipose tissue by DDD had expression level greater than 1 (in base 2 logarithm). Based on coincidence of regulatory sites, candidate TFs were identified including TFs that previously known to be involved in adipose tissue metabolism (SP1, KROX, STAT1, LRF, VDR, LXR, SRF and HIF1) and TFs, such as CKROX, ZF5, ETF, AP-2, AP-2alpha, PAX-5, SPZ1, RBPJ and CACD, that had not been recognized previously. This work yielded several TF candidates activating in adipose tissue metabolism. These findings open a new avenue for future research on promoter occupancy and TF perturbation.

Identification of Sec14‐like 3 as a novel lipid‐packing sensor in the lung

Pulmonary surfactant, a complex composed primarily of lipids and associated proteins, is synthesized in alveolar type II (ATII) cells and secreted into alveoli to prevent collapse during respiration. Although numerous studies have clarified the fundamental roles of pulmonary surfactant, the molecular mechanisms of transport and secretion of pulmonary surfactant remain totally unknown. Thus, we screened candidate genes by comparing genes with the expressed sequence tag (EST) libraries of embryonic and adult lungs by using the digital differential display method in the National Center for Biotechnology Information (NCBI) database. We identified Sec14-like 3 (Sec14L3) as a new class of lipid-associated proteins highly expressed in ATII cells. We found that Sec14L3 expression is >100-fold increased during the perinatal period in the lung. Furthermore, Sec14L3 bound to small-sized liposomes (30 nm in diameter), but not to large-sized liposomes (100 nm diameter), through its Sec14 domain. Because of the increased curvature, lipid-packing defects are more likely to occur in small-sized liposomes than in large-sized liposomes. Based on these results, we conclude that Sec14L3 is a new class of lipid-packing sensor. Sec14L3 may play important roles in the lung, such as intracellular lipid transport, surfactant maturation, and endo/exocytosis.

Functional analysis of human cancer-associated genes and their association with the testes and epididymis

Human cancer-associated UniGene sets (NCBI GeneBank) provide a platform for identifying differentially-expressed genes in human cancers. The present study identified and characterized a set of human cancer-associated genes using the Digital Differential Display (DDD) and functional analysis tools. A total of 1,904 genes were differentially expressed in 15 cancer types, including genes that had been previously shown to be specific in certain human cancers. A total of 274 genes were uniquely expressed in certain cancer types, including 37 genes that were highly expressed in the human testes and epididymis. These genes mainly functioned as ribosomal proteins, enzymes, receptors, secretory proteins and cell adhesion molecules. The most common domains that were encoded by the cancer-associated genes were those of cytochrome P450 CYP2D6, serpin and apolipoprotein A-I. A further gene ontology (GO) enrichment analysis revealed seven major functional clusters, which corresponded to the enriched pathways involved in cancer. The present study provides a source of cancer-associated genes and their functions. The results provide new insights into cancer biology and the involvement of highly-expressed epididymal genes in cancer biomarkers.

Lung Cancer Signature Biomarkers: tissue specific semantic similarity based clustering of Digital Differential Display (DDD) data

BackgroundThe tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used ‘Gene Ontology semantic similarity score’ to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability.ResultsSubsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1–4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4).ConclusionsExpression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated. All down regulated genes in this panel were highly up regulated in most other types of cancers. These panels of proteins may represent signature biomarkers for lung cancer and will aid in lung cancer diagnosis and disease monitoring as well as in the prediction of responses to therapeutics.

Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach

Rainbow trout, Oncorhynchus mykiss, is an important aquaculture species worldwide and, in addition to being of commercial interest, it is also a research model organism of considerable scientific importance. Because of the lack of a whole genome sequence in that species, transcriptomic analyses of this species have often been hindered. Using next-generation sequencing (NGS) technologies, we sought to fill these informational gaps. Here, using Roche 454-Titanium technology, we provide new tissue-specific cDNA repertoires from several rainbow trout tissues. Non-normalized cDNA libraries were constructed from testis, ovary, brain and gill rainbow trout tissue samples, and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall, we produced a total of 3million quality sequences with an average size of 328bp, representing more than 1Gb of expressed sequence information. These sequences have been combined with all publicly available rainbow trout sequences, resulting in a total of 242,187 clusters of putative transcript groups and 22,373 singletons. To identify the predominantly expressed genes in different tissues of interest, we developed a Digital Differential Display (DDD) approach. This approach allowed us to characterize the genes that are predominantly expressed within each tissue of interest. Of these genes, some were already known to be tissue-specific, thereby validating our approach. Many others, however, were novel candidates, demonstrating the usefulness of our strategy and of such tissue-specific resources. This new sequence information, acquired using NGS 454-Titanium technology, deeply enriched our current knowledge of the expressed genes in rainbow trout through the identification of an increased number of tissue-specific sequences. This identification allowed a precise cDNA tissue repertoire to be characterized in several important rainbow trout tissues. The rainbow trout contig browser can be accessed at the following publicly available web site (http://www.sigenae.org/).

An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish

BackgroundThe striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome.ResultsSequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs.ConclusionsThis first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).

LYL1, Class II Basic Helix-Loop-Helix Transcription Factor, Induces the Differentiation of Common Marmoset Embryonic Stem Cells to Hematopoietic Stem Cells

Abstract 2348Since the successful establishment of human embryonic stem cells (ESCs) in 1998, transplantation of functional cells differentiated from ESCs to the specific impaired organ has been expected to cure its defective function [Thomson JA et al., Science 282:1145–47, 1998]. For the establishment of the regenerative medicine using ESCs, the preclinical studies utilizing animal model systems including non-human primates are essential. We have demonstrated that non-human primate of common marmoset (CM) is a suitable experimental animal for the preclinical studies of hematopoietic stem cells (HSCs) therapy [Hibino H et al., Blood 93:2839–48, 1999]. Since then we have continuously investigated the in vitro and in vivo differentiation of CM ESCs to hematopoietic cells by the exogenous hematopoietic gene transfer. In earlier study, we showed that the induction of CD34+ cells having a blood colony forming capacity from CM ESCs is promoted by lentiviral transduction of TAL1 cDNA [Kurita R et al., Stem Cells 24:2014-22,2006]. However those CD34+ cells did not have a bone marrow reconstituting ability in irradiated NOG (NOD/Shi-scid/IL-2Rγnull) mice, suggesting that transduction of TAL1 gene is not enough to induce functional HSCs which have self-renewal capability and multipotency. Thus we tried to find other hematopoietic genes being able to promote hematopoietic differetiation more efficiently than TAL1. We selected 6 genes (LYL1, HOXB4, BMI1, GATA2, c-MYB and LMO2) as candidates for factors that induce the differentiation from ESCs to HSCs, based on the comparison of gene expression level between human ESCs and HSCs by Digital Differential Display from the Uni-Gene database at the NCBI web site (http://www.ncbi.nlm.nih.gov/UniGene/). Then, we transduced the respective candidate gene in CM ESCs (Cj11), and performed embryoid body (EB) formation assay to induce their differentiation to HSCs for 9 days. We found that lentiviral transduction of LYL1, a basic helix-loop-helix transcription factor, in EBs derived from Cj11, one of CM ESC lines, markedly increased the number of cells positive for CD34, a marker for hematopoietic stem/progenitors.The lymphoblastic leukemia 1 (LYL1) was originally identified as the factor of a chromosomal translocation, resulting in T cell acute lymphoblastic leukemia [Mellentin JD et al., Cell 58:77-83.1989]. These class II bHLH transcription factors regulate gene expression by binding to target gene sequences as heterodimers with E-proteins, in association with Gata1 and Gata2 [Goldfarb AN et al., Blood 85:465-71.1995][Hofmann T et al., Oncogene 13:617-24.1996][Hsu HL et al., Proc Natl Acad Sci USA 91:5947-51.1994]. The Lyl1-deficient mice display the reduction of B cells and impaired long-term hematopoietic reconstitution capacity [Capron C et al., Blood 107:4678-4686. 2006]. And, overexpression of Lyl1 in mouse bone marrow cells induced the increase of HSCs, HPCs and lymphocytes in vitro and in vivo [Lukov GL et al., Leuk Res 35:405-12. 2011]. These information indicate that LYL1 plays important roles in hematopoietic differentiation in primate animals including human and common marmoset.To examine whether overexpression of LYL1 in EBs can promote hematopoietic differentiation in vitro we performed colony-forming unit (CFU) assay, and found that LYL1-overexpressing EBs showed the formation of multi-lineage blood cells consisting of erythroid cells, granulocytes and macrophages. Next, we analyzed gene expression level by RT-PCR, and found that the transduction of LYL1 induced the expression of various hematopoietic genes. These results suggested that the overexpression of LYL1 can promote the differentiation of CM ESCs to HSCs in vitro. Furthermore we found that the combined overexpression of TAL1 and LYL1 could enhance the differentiation of CD34+ cells from CM ESCs than the respective overexrpession of TAL1 or LYL1.Collectively, our novel technology to differentiate hematopoietic cells from ESCs by the transduction of specific transcription factors is novel, and might be applicable to expand human hematopoietic stem/progenitor cells in vitro for future regenerative medicine to cure human hematopoietic cell dyscrasias. Disclosures:No relevant conflicts of interest to declare.

Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

BackgroundWheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed maturation. The goal of this study was to screen and identify genes specifically expressed in the developing seed of wheat with an integrative utilization of digital differential display (DDD) and available online microarray databases.ResultsA total of 201 unigenes were identified as the results of DDD screening and microarray database searching. The expressions of 6 of these were shown to be seed-specific by qRT-PCR analysis. Further GO enrichment analysis indicated that seed-specific genes were mainly associated with defense response, response to stress, multi-organism process, pathogenesis, extracellular region, nutrient reservoir activity, enzyme inhibitor activity, antioxidant activity and oxidoreductase activity. A comparison of this set of genes with the rice (Oryza sativa) genome was also performed and approximately three-fifths of them have rice counterparts. Between the counterparts, around 63% showed similar expression patterns according to the microarray data.ConclusionsIn conclusion, the DDD screening combined with microarray data analysis is an effective strategy for the identification of seed-specific expressed genes in wheat. These seed-specific genes screened during this study will provide valuable information for further studies about the functions of these genes in wheat.

Characterization of a Novel Human Testis-Specific Gene: Testis Developmental Related Gene 1 (TDRG1)

Spermatogenesis is a highly coordinated physiological process that requires the correct expression and functions of thousands of developmentally regulated genes. The regulation of spermatogenesis is not well defined, since majority of the related genes have neither been identified nor fully characterized. Hence, it is meaningful to identify and characterize these genes to reveal the mechanism underlying spermatogenesis. In this study, using digital differential display, we identified a novel human testis-specific gene, testis developmental related gene 1 (TDRG1, GenBank DQ168992), via electronic subtraction of human testis UniGene databases from those of non-reproductive tissues. The transcript of the TDRG1 gene has an open-reading frame that encodes 100 amino acids. We next prepared the anti-TDRG1 monoclonal antibody 10B6 and confirmed that it specifically recognizes an 11-kDa protein in the tissue extracts from an adult human testicular sample (age 31 years) by Western blot analysis. RT-PCR coupled with immunohistochemistry of human tissues demonstrated that TDRG1 is exclusively expressed in the testis but not in any other non-reproductive tissues. TDRG1 is mainly located in spermatogenic cells in seminiferous tubules of adult testis. Furthermore, TDRG1 shows the highest expression level in human post-puberty testis, with the expression levels decreasing afterwards with aging. Importantly, TDRG1 mRNA is undetectable in the fetal testis, as judged by RT-PCR. In conclusion, TDRG1 is a developmentally regulated testicular-specific gene. We suggest that TDRG1, a newly identified testis-specific gene, may play important roles in human spermatogenesis.

Expression of the Wnt antagonist DKK3 is frequently suppressed in sporadic epithelial ovarian cancer

The Wnt pathway plays an important role in embryonic development, and defects in this pathway have been implicated in the tumorigenesis. The Dickkopf 3 (DKK3) is a putative Wnt signaling inhibitor that is frequently inactivated in human cancers. However, the expression of DKK3 in ovarian cancer remains unknown. We investigated the expression of DKK3 in silico using the Digital Differential Display. DKK3 mRNA expression was also analyzed by real-time RT-PCR in ovarian carcinomas and normal ovarian tissues. DKK3 protein expression was determined by immunohistochemistry in the same ovarian carcinomas and normal ovarian tissues. A significantly reduced expression of DKK3 (P < 0.05) was found after comparison of normal ovary- and tumor-derived libraries in the Cancer Genome Anatomy Project (CGAP). DKK3 mRNA expression was reduced in 63% (35 of 56) of tumors compared with normal ovarian samples (P < 0.02). Analysis of 13 matched pairs of ovarian carcinomas and adjacent normal tissues showed significant transcriptional downregulation of DKK3 (>twofold) in 9 paired carcinomas (69%). Loss or weak membranous expression of DKK3 protein was observed in 66% of ovarian cancers (37 of 56) including all tumors with low transcriptional level of DKK3 gene analyzed by real-time PCR. To our best knowledge, this is the first time to demonstrate altered expression of DKK3 in ovarian cancer. The latter could be a relevant mechanism for the activation of the Wnt pathway in the carcinogenesis of ovarian cancer but additional studies are required to elucidate the function of DKK3 silencing in ovarian carcinogenesis.

Elevated expression levels of testis-specific genesTEX101andSPATA19in basal cell carcinoma and their correlation with clinical and pathological features

Basal cell carcinoma (BCC) is characterized by a low rate of metastasis, slow growth and strong stroma dependency, with significant morbidity and public health burden. Cancer-testis (CT) genes are specifically expressed in normal testis, fetal ovary and different types of cancers. Testis immune privileged status makes CT genes promising candidates as cancer markers, vaccines and immunotherapy. To find new CT genes as cancer markers and candidate genes for immunotherapy and to correlate pathological and clinical features with their expression in patients with BCC. By means of digital differential display, seven testis-specific genes were selected. Their expression patterns were analysed in 78 BCC and 15 normal skin samples using semiquantitative reverse transcription-polymerase chain reaction. Pathological and clinical characteristics were determined using appropriate methods. SPATA19, TEX101, ODF1, ODF2 and ODF3 were expressed in 56.6%, 38.2%, 2.6%, 17.4% and 2.6% of BCCs but not in normal skin samples. ODF4 and PASD1 were not expressed in any BCC samples. TEX101 and SPATA19 expression in high-risk BCCs was higher than in low-risk tumours (P < 0.001). SPATA19 expression was correlated with a history of cancer radiotherapy (P < 0.001). Significant associations were found between expression of TEX101 with nodular subtype, ODF2 with infiltrating subtype, and ODF1 with tumours located on the neck. Among gene expressors, 42.1% co-expressed two genes and 5.3% co-expressed three genes. We report five new CT antigens, of which SPATA19 and TEX101 may be possible targets for cancer immunotherapy and novel markers for early detection of BCC.

Identification of a novel human cancer/testis gene MAEL that is regulated by DNA methylation

The mouse maelstrom (MAEL) gene has been found to be expressed in male germ cells and to play a role in spermatogenesis. Here, we cloned the human MAEL gene by digital differential display and found that, among human tissues, MAEL is only expressed in the testis, but it is also expressed in various cancer cell lines. The transcription start site of the MAEL gene is 74-bp upstream of the start codon. The region from -216 to +150 is the basal promoter of the MAEL gene, and a CpG island (-295 to +148) is located in this region. Treatment with the demethylating agent 5'-Aza-2-Deoxycytidine significantly upregulated MAEL expression. These results suggest that MAEL is a novel cancer/testis-associated gene and is regulated by DNA methylation.

Znrg, a novel gene expressed mainly in the developing notochord of zebrafish

The notochord, a defining characteristic of the chordate embryo is a critical midline structure required for axial skeletal formation in vertebrates, and acts as a signaling center throughout embryonic development. We utilized the digital differential display program of the National Center for Biotechnology Information, and identified a contig of expressed sequence tags (no. Dr. 83747) from the zebrafish ovary library in Genbank. Full-length cDNA of the identified gene was cloned by 5'- and 3'- RACE, and the resulting sequence was confirmed by polymerase chain reaction and sequencing. The cDNA clone contains 2,505 base pairs and encodes a novel protein of 707 amino acids that shares no significant homology with any known proteins. This gene was expressed in mature oocytes and at the one-cell stage, and persisted until the 5th day of development, as determined by RT-PCR. Transcripts were detected by whole-mount RNA in situ hybridization from the two-cell stage to 72 h of embryonic development. This gene was uniformly distributed from the cleavage stage up to the blastula stage. During early gastrulation, it was present in the dorsal region, and became restricted to the notochord and pectoral fin at 48 and 72 h of embryonic development. Based on its abundance in the notochord, we hypothesized that the novel gene may play an important role in notochord development in zebrafish; we named this gene, zebrafish notochord-related gene, or znrg.

Discovery, characterization and expression of a novel zebrafish gene, znfr, important for notochord formation

Genes specifically expressed in the notochord may be crucial for proper notochord development. Using the digital differential display program offered by the National Center for Biotechnology Information, we identified a novel EST sequence from a zebrafish ovary library (No. XM_701450). The full-length cDNA of this transcript was cloned by performing 3' and 5'-RACE and was further confirmed by PCR and sequencing. The resulting 614 bp gene was found to encode a novel 94 amino acid protein that did not share significant homology with any other known protein. Characterization of the genomic sequence revealed that the gene spanned 4.9 kb and was composed of four exons and three introns. RT-PCR gene expression analysis revealed that our gene of interest was expressed in ovary, kidney, brain, mature oocytes and during the early stages of embryogenesis. During embryonic development, znfr mRNA was found to be expressed in the embryonic shield, chordamesoderm and the vacuolated notochord cells by in situ hybridization. Based on this information, we hypothesize that this novel gene is an important maternal factor required for zebrafish notochord formation during early embryonic development. We have thus named this gene znfr (zebrafish notochord formation related).