Novel functional view of the crocidolite asbestos-treated A549 human lung epithelial transcriptome reveals an intricate network of pathways with opposing functions

Our plain-English summary of Novel functional view of the crocidolite asbestos-treated A549 human lung epithelial transcriptome reveals an intricate network of pathways with opposing functions, by J.M. Hevel, L.C. Olson-Buelow, B. Ganesan, et al (BMC Genomics, 2008).

The study

• Authors: J.M. Hevel, L.C. Olson-Buelow, B. Ganesan, J.R. Stevens, J.P. Hardman, A.E. Aust
• Journal: BMC Genomics
• Published: 2008;9:376
• Cited by: 20 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: Although exposure to asbestos is now regulated, patients continue to be diagnosed with mesothelioma, asbestosis, fibrosis and lung carcinoma because of the long latent period between exposure and clinical disease. Asbestosis is observed in approximately 200,000 patients annually and asbestos-related deaths are estimated at 4,000 annually. Although advances have been made using single gene/gene product or pathway studies, the complexity of the response to asbestos and the many unanswered questions suggested the need for a systems biology approach. The objective of this study was to generate a comprehensive view of the transcriptional changes induced by crocidolite asbestos in A549 human lung epithelial cells.

Results: A statistically robust, comprehensive data set documenting the crocidolite-induced changes in the A549 transcriptome was collected. A systems biology approach involving global observations from gene ontological analyses coupled with functional network analyses was used to explore the effects of crocidolite in the context of known molecular interactions. The analyses uniquely document a transcriptome with function-based networks in cell death, cancer, cell cycle, cellular growth, proliferation, and gene expression. These functional modules show signs of a complex interplay between signaling pathways consisting of both novel and previously described asbestos-related genes/gene products. These networks allowed for the identification of novel, putative crocidolite-related genes, leading to several new hypotheses regarding genes that are important for the asbestos response. The global analysis revealed a transcriptome that bears signatures of both apoptosis/cell death and cell survival/proliferation.

Conclusion: Our analyses demonstrate the power of combining a statistically robust, comprehensive dataset and a functional network genomics approach to 1) identify and explore relationships between genes of known importance 2) identify novel candidate genes, and 3) observe the complex interplay between genes/gene products that function in seemingly different processes. This study represents the first function-based global approach toward understanding the response of human lung epithelial cells to the carcinogen crocidolite. Importantly, our investigation paints a much broader landscape for the crocidolite response than was previously appreciated and reveals novel paths to study. Our graphical representations of the function-based global network will be a valuable resource to model new research findings.

In plain English

This was a laboratory study of cells, not people. The authors exposed A549 cells, a human lung adenocarcinoma cell line, to crocidolite asbestos at 6 micrograms per square centimetre for 24 hours. They compared them with control cells in three replicates, using a genome-wide gene chip. At a false discovery rate of 0.05, 2,546 genes were statistically significant: 1808 probe sets went up, 738 down. The largest increase listed was for EGR1 (115.7-fold). A second method confirmed four gene increases; three also appeared in primary human small airway cells. Some changes matched those an earlier study saw with hydrogen peroxide, which the authors suggested may reflect oxidative stress. DNA repair gene groups were not highly represented overall, though specific groups related to DNA damage-induced phosphorylation, DNA methylation, alkylation and dealkylation were highlighted. Network software found 16 interconnected networks involving cell death, cancer, cell cycle, growth, proliferation and gene expression. The authors concluded the cells showed signs of both cell death and survival or proliferation, and proposed new candidate genes. They noted that a transformed cell line may not fully reflect normal lung cells.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory cell-culture experiment: whole-genome gene expression (microarray) comparison of crocidolite-treated versus control cells, with follow-up quantitative RT-PCR, gene ontology and network (pathway) analyses
• Who was studied: A549 human lung adenocarcinoma cell line (purchased from American Type Culture Collection), three biological replicates, each with a control plate and a crocidolite-treated plate, all at passage 9. Some follow-up RT-PCR was done in primary human small airway epithelial cells (SAEC).
• Exposure: Crocidolite asbestos (obtained from NIEHS/NTP; mean length 10 μm, 27% iron by weight) at 6 μg/cm2 for 24 hours, compared with fresh medium alone
• Main results:
  • Using a false discovery rate of 0.05, 2,546 genes were called statistically significant in crocidolite-treated A549 cells versus controls
  • Of the probe sets on the chip, 1808 were significantly up-regulated (492 of them two-fold or greater) and 738 were significantly down-regulated (27 of them two-fold or greater)
  • The largest listed increase was EGR1 (115.7-fold on the microarray; 281.7 plus or minus 3.8-fold by quantitative RT-PCR). By quantitative RT-PCR, increases in Egr-1, ATF3, c-Jun and JunB began by 6 hours and continued through 24 hours.
  • In primary human small airway epithelial cells treated with crocidolite, increased mRNA of ATF3, c-Jun and JunB was also seen by quantitative RT-PCR
  • Genes up-regulated by both crocidolite and hydrogen peroxide (compared with an earlier hydrogen peroxide study in A549 cells) were interpreted as possibly reflecting an oxidative stress response
  • Gene ontology analysis showed transcriptional corepressor and repressor activities were highly represented, while DNA repair terms were not highly represented
  • Although DNA repair/damage processes were not highly represented overall, the global test highlighted specific gene ontology groups related to DNA damage-induced phosphorylation, DNA dealkylation, DNA methylation and DNA alkylation
  • Ingenuity pathway analysis (genes changed two-fold or more, p 0.01 or less) produced 16 interconnected networks related to cell death, cancer, cell cycle, cellular growth and proliferation, and gene expression
  • The authors found p53 targets associated with both apoptosis and cell survival/proliferation, and suggested p53 may be a turning point in cell fate
• The authors' conclusion: The authors concluded that crocidolite-treated A549 cells showed a network of pathways associated with both apoptosis and proliferation/cell survival, and that the network identified novel, putative crocidolite-related genes, leading to new hypotheses
• Limitations the authors state:
  • The A549 cell line is a transformed (cancer-derived) cell line and may not be entirely applicable to normal human lung cells

Topics

The National Library of Medicine indexes this study under subjects our site covers: Crocidolite.

Medical terms in this study, explained in our Lexicon: Crocidolite, Mesothelioma, Fibrosis, Carcinoma, Apoptosis.

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