cDNA-RDA of genes expressed in fetal and adult lungs identifies factors important in development and function

Using Representational Difference Analysis to detect changes in transcript expression of Aiptasia genes after laboratory exposure to lindane

Molecular stress responses to pesticide exposures represent an understudied area of cnidarian transcriptome investigations. The organochlorine pesticide lindane is known to disrupt normal neuron function. Cnidarians with simple nervous systems are recognized as sensitive indicators of water quality, yet nothing is known about cnidarian responses to lindane. Sea anemones (Aiptasia pallida) were exposed for 4h to lindane (20 μg/l). Because anemones have neurons and lindane is known to target neurons, it is anticipated that cnidarian stress responses will include changes in transcription of genes associated with neurons. Representational Difference Analysis (RDA) was utilized to isolate differentially transcribed genes in the anemones exposed to the pesticide. After two rounds of RDA hybridizations, 148 amplified fragments ranging in size from 150 to 800 bp were cloned. Sequencing and bioinformatic analyses of 106 clones revealed 56 different gene fragments. Virtual Northern dot blots were used as a preliminary screening tool to identify the most responsive RDA products. To further characterize the specificity of response, additional anemones were exposed to a series of lindane concentrations (0, 0.2, 2.0, 10, and 20 μg/l). Northern dot blots were subsequently used to develop expression profiles for selected RDA products over the range of pesticide concentrations. The seven most responsive RDA products represent genes with products associated with neuron development, immune responses, and Ca(2+) binding/transport. The resulting expression profiles illustrate that these RDA products exhibit various degrees of concentration specificity with some RDA products being significantly up-regulated at 20 μg/l while other RDA products are most responsive at concentrations <20 μg/l. Results also demonstrate how RDA can be used to identify potentially important biomarkers of organochlorine exposure while generating new hypotheses about important phenomena such as endocrine disruption in cnidarians.

Inorganic arsenic as a developmental toxicant: in utero exposure and alterations in the developing rat lungs

In the present study, we characterize the toxic effects of in utero arsenic exposure on the developing lung. We hypothesize that in utero exposure to inorganic arsenic through maternal drinking water causes altered gene and protein expression in the developing lung, indicative of downstream molecular and functional changes. From conception to embryonic day 18, we exposed pregnant Sprague-Dawley rats to 500 ppb arsenic (as arsenite) via the drinking water. Subtracted cDNA libraries comparing control to arsenic exposed embryonic lungs were generated. In addition, a broad Western blot analysis was performed to identify altered protein expression. A total of 59 genes and 34 proteins were identified as being altered. Pathway mapping and analysis showed that cell motility was the process most affected. The most likely affected pathway was alteration in integrin signaling through the beta-catenin pathway, altering c-myc. The present study shows that arsenic induces alterations in the developing lung. These data may be useful in the elucidation of molecular targets and biomarkers of arsenic exposure during lung development and may aid in understanding the etiology of arsenic induced adult respiratory disease and lung cancers.

Differential expression of a V-type ATPase C subunit gene, Atp6v1c2, during culture of rat lung type II pneumocytes

The lung alveolar epithelium consists of type I and type II pneumocytes. In vivo, the type II cell is the progenitor cell from which the type I cell originates. When freshly-isolated type II cells are cultured under conventional conditions they rapidly lose their phenotypic properties and attain characteristics of type I cells. Taking advantage of this transdifferentiation, we sought to identify genes that are differentially expressed during culture of rat type II cells. Using suppression subtractive hybridization (SSH), a vacuolar-type H+-ATPase (V-ATPase) C2 subunit gene (Atp6v1c2) was found to be enriched in freshly isolated rat type II cells compared to those cultured for 4 days. Northern blotting and reverse-transcription polymerase chain reaction (RT-PCR) confirmed the differential expression of Atp6v1c2 during in vitro culture of isolated type II cells. Expression ofAtp6v1c2 was significantly reduced early during in vitro culture: almost 90% reduction was observed after 24 h of incubation as determined by real-time PCR. In situ hybridization showed that Atp6v1c2 is expressed in both bronchiolar and alveolar lung epithelial cells, an expression pattern similar to that of surfactant protein B (SP-B). Multi-tissue Northern blotting revealed a unique tissue distribution with Atp6v1c2 expression limited to lung, kidney and testis. The presence and expression of Atp6v1c2 gene transcript isoforms, resulting from alternative splicing, were also investigated. Elucidation of differential expression of Atp6v1c2 in type II cells and further studies of its regulation may provide information useful in understanding the molecular mechanism underlying phenotypic and functional changes during transdifferentiation of alveolar epithelial cells.

Identification of calcium- and nitric oxide-regulated genes by differential analysis of library expression (DAzLE)

Using a method of expression profiling called differential analysis of cDNA library expression (DAzLE), we report the expression profile of late response genes in a model of activity-dependent neuronal survival and neurite outgrowth. Using DAzLE, we isolated differentially expressed genes from cultured rat embryonic cortical neurons after KCl (50 mM)-mediated membrane depolarization. We identified 469 activity-dependent regulated genes, of which 174 are genes of unknown function. The regulation of 63 genes was found to be nitric oxide (NO)-dependent. Identifiable genes fell into several major categories, including signal transduction pathways, neuronal development, DNA replication, gene transcription, protein metabolism, energy regulatory proteins, and antiapoptotic proteins. These genes may be important in activity-dependent neuron survival and development. Furthermore, these late response genes provide the tools to begin to investigate downstream events in activity-dependent neuronal survival and development. The major advantage of DAzLE is that it provides a nearly complete and relatively comprehensive differential screening profile that has the potential to be a powerful and useful tool in other fields of study.

Monitoring of the subtraction process in solid-phase representational difference analysis: characterization of a candidate drug

In this study, we have applied and evaluated a modified cDNA representational difference analysis (RDA) protocol based on magnetic bead technology to study the molecular effects of a candidate drug (N,N'-diacetyl-L-cystine, DiNAC) in a model for atherosclerosis. Alterations in a gene expression profile induced by DiNAC were investigated in a human monocytic cell line (THP-1) differentiated into macrophage-like cells by lipopolysaccharide and further exposed to DiNAC. Three rounds of subtraction have been performed and the difference products from the second and third rounds have been characterized in detail by analysis of over 1000 gene sequences. Two protocols for analysis of the subtraction products have been evaluated, a shotgun approach and size selection of both distinct fragments and band-patterned smear. We demonstrate that in order to obtain a representative view of the most abundant gene fragments, the shotgun procedure is preferred. The obtained sequences were analyzed against the UniGene and Expressed Gene Anatomy Database (EGAD) databases and the results were visualized and analyzed with the ExProView software enabling rapid pair-wise comparison and identification of individual genes or functional groups of genes with altered expression levels. The identified differentially expressed gene sequences were comprised of both genes with known involvement in atherosclerosis or cholesterol biosynthesis and genes previously not implicated in these processes. The applicability of a solid-phase shotgun RDA protocol, combined with virtual chip monitoring, results in new starting points for characterization of novel candidate drugs.

Identification of genes induced by inflammatory cytokines in airway epithelium

Epithelial cells lining the airways are thought to play a prominent role in respiratory diseases. We utilized cDNA representational difference analysis to identify the genes in which expression is induced by the proinflammatory cytokines tumor necrosis factor-alpha and interleukin-1beta in primary human bronchial epithelial cells and hence are relevant to airway inflammation. Hybridization of the subtraction product to arrayed cDNAs indicated that known tumor necrosis factor-alpha- and interleukin-1beta-inducible genes such as B94, Zfp36, and regulated on activation normal T cell expressed and secreted were represented, confirming the success of the subtraction experiment. A 1,152-clone library potentially representing genes with higher transcript levels in cytokine-treated human bronchial epithelial cells was generated and sequenced. Sequence similarity searches indicated that these clones represented 57 genes of known function, 1 gene of unknown function, 6 expressed sequence tags, and 2 novel sequences. The expression of 19 of these clones was studied by a combination of Northern blotting and RT-PCR analyses and confirmation of differential expression for 10 known genes, 2 expressed sequence tags, and a novel sequence not represented in any of the public databases was obtained. Thus cDNA representational difference analysis was utilized to isolate known and novel differentially expressed genes, which putatively play a role in airway inflammation.

Chondrocyte expressed protein-68 (CEP-68), a novel human marker gene for cultured chondrocytes

In the search for new marker genes suitable to distinguish chondrocytes from osteoblasts and mesenchymal stem cells in culture, we have identified and characterized a novel gene called chondrocyte expressed protein-68 (CEP-68), harbouring an N-terminal leader peptide and an epidermal growth factor-like calcium-binding domain. CEP-68 defines a new family of proteins and complements collagen type II as a new marker for stem-cell-based chondrogenic tissue engineering.