Gene expression profiling and gene copy-number changes in malignant mesothelioma cell lines

Our plain-English summary of Gene expression profiling and gene copy-number changes in malignant mesothelioma cell lines, by C. Zanazzi, R. Hersmus, I.M. Veltman, et al (Genes, Chromosomes & Cancer, 2007).

The study

• Authors: C. Zanazzi, R. Hersmus, I.M. Veltman, A.J. Gillis, E. van Drunen, H.B. Beverloo, J.P. Hegmans, M. Verweij, B.N. Lambrecht, J.W. Oosterhuis, L.H. Looijenga
• Journal: Genes, Chromosomes & Cancer
• Published: 2007;46(10):895-908
• Cited by: 15 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Malignant mesothelioma (MM) is an asbestos-induced tumor that acquires aneuploid DNA content during the tumorigenic process. We used instable MM cell lines as an in vitro model to study the impact of DNA copy-number changes on gene expression profiling, in the course of their chromosomal redistribution process. Two MM cell lines, PMR-MM2 (early passages of in vitro culture) and PMR-MM7 (both early and late passages of in vitro culture), were cytogenetically characterized. Genomic gains and losses were precisely defined using microarray-based comparative genomic hybridization (array-CGH), and minimal overlapping analysis led to the identification of the common unbalanced genomic regions. Using the U133Plus 2.0 Affymetrix gene chip array, we analyzed PMR-MM7 early and late passages for genome-wide gene expression, and correlated the differentially expressed genes with copy-number changes. The presence of a high number of genetic imbalances occurring from early to late culture steps reflected the tendency of MM cells toward genomic instability. The selection of specific chromosomal abnormalities observed during subsequent cultures demonstrated the spontaneous evolution of the cancer cells in an in vitro environment. MM cell lines were characterized by copy-number changes associated with the TP53 apoptotic pathway already present at the first steps of in vitro culture. Prolonged culture led to acquisition of additional chromosomal copy-number changes associated with dysregulation of genes involved in cell adhesion, regulation of mitotic cell cycle, signal transduction, carbohydrate metabolism, motor activity, glycosaminoglycan biosynthesis, protein binding activity, lipid transport, ATP synthesis, and methyltransferase activity.

Copyright (c) 2007 Wiley-Liss, Inc.

In plain English

This was a laboratory study of two malignant mesothelioma cell lines, PMR-MM2 and PMR-MM7. The authors grew them from pleural effusions of two men aged 63 and 79, both with a history of occupational asbestos exposure. They mapped chromosome gains and losses. For PMR-MM7 only, they compared gene activity at an early culture passage (DP18) and a late one (DP112). Across both lines they found 27 gained and 14 lost chromosome regions. In PMR-MM7, triploid cells made up 60% at DP18 and 80% at DP112. In a colony-forming test, counts were 21 at DP18, 283 at DP112, and 154 for PMR-MM2. Of 1,091 highly active genes, 24 differed at least two-fold between passages, but the size of the expression changes did not track the copy-number changes. PMR-MM7 carried a TP53 polymorphism and a TP53 mutation on the same gene copy, alongside unaltered copies, while PMR-MM2 had an unmutated (wild-type) TP53 sequence. Highly active genes lay mainly in gained chromosome regions, but the authors found no clear-cut correlation between copy-number changes and expression levels. They noted that they had no normal control cell line.

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 (in vitro) study of two human malignant mesothelioma cell lines: cytogenetics, array-CGH, gene expression profiling and TP53 analysis across culture passages
• Who was studied: Two cell lines (PMR-MM2, PMR-MM7) established at Erasmus MC, Rotterdam, The Netherlands, from pleural effusions of two male patients aged 63 and 79. PMR-MM7 was studied at early (DP18) and late (DP112) culture passages; PMR-MM2 at DP18.
• Exposure: Both patients had a history of occupational asbestos exposure; fiber type and dose were not reported. The study itself compared early and late in vitro culture passages, not asbestos exposure.
• Main results:
  • Colonies formed in semi-solid medium: 154 for PMR-MM2, 21 for PMR-MM7 DP18 and 283 for PMR-MM7 DP112
  • In PMR-MM7, the percentage of triploid cells was 60% at DP18 and 80% at DP112
  • Array-CGH analysis of both cell lines found more gains than losses: 27 over-represented and 14 under-represented regions
  • In PMR-MM7, highly expressed genes in the minimal overlapping regions correlated with over-represented (gained) chromosomal regions
  • In PMR-MM7, 1,091 genes were selected as highly expressed (at least twice the median)
  • Of these, 24 genes differed at least two-fold between DP18 and DP112. All 24 lay in regions with copy-number changes differing between the passages, but fold differences in expression and copy number did not correlate.
  • Pathway analysis of all highly expressed genes in the minimal overlapping regions gave 'cell death' as the first significant pathway
  • The SET gene, in a region with normal copy number, had the highest expression value (reported as 90 times the median)
  • PMR-MM2 had wild-type TP53 sequence
  • PMR-MM7 (both DP18 and DP112) had a nonsynonymous SNP at codon 72 and a mutation at codon 230 on the same allele; wild-type alleles were also present
  • TP53 protein was highest in PMR-MM7 DP18 and lowest in PMR-MM2. The authors described the level in PMR-MM7 DP112 as significantly lower.
• The authors' conclusion: The authors concluded the following. Chromosomal abnormalities selected during culture were associated with dysregulation of genes in several cell functions. Highly expressed genes in aberrant regions were associated with the TP53 apoptotic pathway. Expression was not regulated linearly by ploidy, and no unequivocal correlation was found between copy-number changes and expression levels.
• Limitations the authors state:
  • Without a normal control cell line, the authors could not distinguish genes that are always highly expressed from genes that were up-regulated
  • The coexisting diploid and triploid populations in PMR-MM7 could have influenced the expression analysis
  • Genes with low expression were not considered because of possible background contamination

Topics

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

Medical terms in this study, explained in our Lexicon: Malignant Mesothelioma.

Related studies

• DNA copy number changes in familial malignant mesothelioma — V. Ascoli, Y. Aalto, et al. (2001)
• Identification of specific gene copy number changes in asbestos-related lung cancer — P. Nymark, H. Wikman, et al. (2006)
• Gene expression and copy number profiling suggests the importance of allelic imbalance in 19p in asbestos-associated lung cancer — H. Wikman, S. Ruosaari, et al. (2007)
• Elevated PDGFRB gene copy number gain is prognostic for improved survival outcomes in resected malignant pleural mesothelioma — A.S. Tsao, N. Harun, et al. (2014)
• Comparison of DNA copy number changes in malignant mesothelioma, adenocarcinoma and large-cell anaplastic carcinoma of the lung — A.M. Björkqvist, L. Tammilehto, et al. (1998)
• Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines — P. Nymark, P.M. Lindholm, et al. (2007)

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