Suppression Subtractive Hybridization Approach Research Articles

Overexpression of Human Dickkopf-1, an Antagonist of wingless/WNT Signaling, in Human Hepatoblastomas and Wilms' Tumors

Hepatoblastomas (HBs) represent the most frequent malignant liver tumors of childhood; yet little is known about the molecular pathogenesis and the alterations in expression patterns of these tumors. We used a suppression subtractive hybridization approach to identify new candidate genes that may play a role in HB tumorigenesis. cDNA species derived from corresponding liver and fetal liver were subtracted from HB cDNAs, and a series of interesting candidates were isolated that were differentially expressed. One of the transcripts overexpressed in HB was derived from the human Dickkopf-1 (hDkk-1) gene, which encodes a secreted protein acting as a potent inhibitor of the wingless/WNT signaling pathway. We examined the hDkk-1 expression levels in 32 HB biopsy specimens and in the corresponding liver samples, in 4 HB cell lines, and in a panel of other tumors and normal tissues using a differential PCR approach and Northern blotting. Eighty-one percent of the HBs but none of the normal pediatric or fetal liver tissues showed hDkk-1 expression. hDkk-1 transcripts were also present in 5 of 6 Wilms' tumors but only weakly detectable in 2 of 20 hepatocellular carcinoma samples and in 1 of 5 medulloblastoma cell lines; transcripts were absent in malignant gliomas and breast cancer. The central effector molecule in the WNT developmental control pathway is the β-catenin protein. Interestingly, activating mutations of the β-catenin gene have previously been identified in 48% of HBs, and more than 85% of HBs show accumulation of β-catenin protein as the indicator for an activated pathway. The overexpression of the inhibitor Dkk-1 may therefore be related to uncontrolled wingless/WNT signaling and may represent a negative feedback mechanism. hDkk-1 expression represents a novel marker for HBs and Wilms' tumors.

Molecular characterization of genomic activities at the onset of zygotic transcription in mammals.

In rabbit embryos, zygotic transcripts are required for the development of the embryo only from the 8- to 16-cell stage onward, more than 44 h after fertilization (i.e., zygotic gene activation; ZGA). In order to characterize the first zygotic transcripts expressed in this species we used a suppression subtractive hybridization approach to isolate RNA that was present after the major transcriptional activation (morula stage), but absent at the 1-cell stage as maternal transcripts. One hundred fourteen differentially expressed inserts were selected and sequenced. A statistical analysis of expression patterns throughout the preimplantation period of development shows that genes transcribed from ZGA onward follow different patterns of expression. Considering their early post-ZGA behavior, we describe at least two main patterns: a gradual increase from ZGA onward, and a sharp increase in expression at ZGA followed by a marked decrease at the morula stage. Our data show that both ZGA and some early post-ZGA events are involved in the establishment of specific patterns of embryonic gene expression.

Differential regulation of the Fe-hydrogenase during anaerobic adaptation in the green alga Chlamydomonas reinhardtii.

Chlamydomonas reinhardtii, a unicellular green alga, contains a hydrogenase enzyme, which is induced by anaerobic adaptation of the cells. Using the suppression subtractive hybridization (SSH) approach, the differential expression of genes under anaerobiosis was analyzed. A PCR fragment with similarity to the genes of bacterial Fe-hydrogenases was isolated and used to screen an anaerobic cDNA expression library of C. reinhardtii. The cDNA sequence of hydA contains a 1494-bp ORF encoding a protein with an apparent molecular mass of 53.1 kDa. The transcription of the hydrogenase gene is very rapidly induced during anaerobic adaptation of the cells. The deduced amino-acid sequence corresponds to two polypeptide sequences determined by sequence analysis of the isolated native protein. The Fe-hydrogenase contains a short transit peptide of 56 amino acids, which routes the hydrogenase to the chloroplast stroma. The isolated protein belongs to a new class of Fe-hydrogenases. All four cysteine residues and 12 other amino acids, which are strictly conserved in the active site (H-cluster) of Fe-hydrogenases, have been identified. The N-terminus of the C. reinhardtii protein is markedly truncated compared to other non-algal Fe-hydrogenases. Further conserved cysteines that coordinate additional Fe-S-cluster in other Fe-hydrogenases are missing. Ferredoxin PetF, the natural electron donor, links the hydrogenase from C. reinhardtii to the photosynthetic electron transport chain. The hydrogenase enables the survival of the green algae under anaerobic conditions by transferring the electrons from reducing equivalents to the enzyme.

Use of suppression subtractive hybridization for differential gene expression in stroke: discovery of CD44 gene expression and localization in permanent focal stroke in rats.

CD44 is a transmembrane glycoprotein involved in endothelial cell recognition, lymphocyte trafficking, and regulation of cytokine gene expression in inflammatory diseases. The present report describes the discovery of upregulated CD44 gene expression and its spatial and temporal distribution in the brain after focal stroke. Rats were subjected to permanent occlusion of the middle cerebral artery (MCAO). Suppression subtractive hybridization (SSH) strategy was used to identify differentially expressed genes. Northern blotting and real-time polymerase chain reaction were used to evaluate the expression of CD44 and hyaluronan synthase 2 (HAS-2) mRNA. Western blotting and immunohistochemistry were used to examine CD44 expression and cellular distribution. CD44 upregulation after focal stroke was discovered by the SSH approach and confirmed by DNA sequencing. Northern blot using a pooled poly(A)+ RNA revealed 3 splice variants of CD44 mRNA, and their inducible expression started at 6 hours (5.3-fold increase over sham operation), peaked at 24 hours (28.6-fold increase), and persisted up to 72 hours (17.8-fold increase) after MCAO. A parallel induction profile of HAS-2 mRNA was observed in the ischemic brain tissue. The levels of CD44 were markedly elevated at 6 hours (1.8-fold increase over sham; n=3), 24 hours (2.9-fold, peak induction; P<0.01), and 72 hours (2.4-fold increase; P<0.05) after MCAO by means of Western analysis. Immunohistochemical and confocal microscopy confirmed that constitutive expression of CD44 is limited to microvessels in normal brain but is strongly induced after ischemia, where the immunoreactive signal mainly resided in endothelial cells and monocytes. Double-labeling immunohistochemistry demonstrated that a marked induction of CD44 in the ischemic lesion is dominantly located in microglia and a subset of macrophages. The discovery of concomitant induction of CD44 and HAS-2 mRNA expression and the localization of CD44 in the microglia, macrophages, and microvessels of the ischemic brain tissue suggest that an active interaction between CD44 and hyaluronan may occur and play a role in the known inflammatory response and tissue remodeling after stroke.

Use of suppression subtractive hybridization strategy for discovery of increased tissue inhibitor of matrix metalloproteinase-1 gene expression in brain ischemic tolerance.

Brief occlusion of the middle cerebral artery (i.e., ischemic preconditioning; PC) induces significant brain protection to subsequent severe ischemic events. In an effort to discover genes responsible for ischemic tolerance, we have applied a new technique, suppression subtractive hybridization (SSH), to identify genes that are upregulated by PC. Using this SSH approach, a cDNA that encodes tissue inhibitor of matrix metalloproteinase- (TIMP-1) was identified. Time course studies using Northern analysis revealed that TIMP-1 mRNA was significantly elevated at 24 hours (3.3-fold over controls, P < 0.05, n = 5) and 2 days (4.3-fold increase, P < 0.01) after PC, corresponding to the onset of significant ischemic tolerance. Our data not only demonstrate the utility of this new polymerase chain reaction-based SSH strategy for discovery of genes differentially expressed in PC, but also suggest a potential role of TIMP-1 in PC-induced ischemic tolerance.

Increased expression of the novel molecule OX-2 is involved in prolongation of murine renal allograft survival.

Portal venous (p.v.) peritransplant immunization with dendritic cells from bone marrow cultures, along with cyclosporine (10 mg/kg), produces antigen-specific increased renal allograft survival compared with recipients receiving intravenous (i.v.) immunization. Increased survival is associated with altered cytokine production from recipient T cells restimulated with donor antigen. We used a suppressive subtractive hybridization approach to explore a role in the regulation of transplant rejection for other genes differentially expressed after p.v. immunization. Subtractive hybridization was performed using tissue from p.v. and i.v. immunized mice and a novel polymerase chain reaction-based approach. A gene-bank search was used to identify the source of the differentially expressed cDNAs. One product, the mouse homologue of rat OX-2, was further analyzed using Western gels and FACS analysis of dendritic cells (NLDC145+) isolated from p.v.-immunized mice. Eighty cDNA clones were obtained by suppressive subtractive hybridization. Differential expression was confirmed in Northern RNA blots. One clone showed sequence homology to a gene encoding a molecule on rat dendritic cells (MRC OX-2), with homology to genes encoding the costimulatory molecules CD80 (B7-1) and CD86 (B7-2). In p.v.-immunized mice, a monoclonal antibody to the rat OX-2 molecule identified, by Western blot analysis, increased expression of a molecule with molecular weight (43 kDa) analogous to rat MRC-OX-2; labels (by FACS analysis) indentified increased numbers of a population of cells staining with NLDC145; and blocks indentified increased graft survival. Our data suggest that OX-2 is functionally important in the increased graft survival seen in p.v.-immunized mice receiving renal allografts.