Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray

Haiyong Han, David J. Bearss, L. Walden Browne, Robert Calaluce, Raymond B Nagle, Daniel D. Von Hoff

Research output: Contribution to journalArticle

326 Citations (Scopus)

Abstract

To identify new diagnostic markers and drug targets for pancreatic cancer, we compared the gene expression patterns of pancreatic cancer cell lines growing in tissue culture with those of normal pancreas using cDNA microarray analysis. Fluorescently (cyanine 5) labeled cDNA probes, made individually from mRNA samples of nine pancreatic cell lines, were each combined with fluorescently (cyanine 3) labeled universal reference mRNA. The mixed probes of each sample were then hybridized with 5760 cDNA arrays (5289 unique cDNA sequences) printed on individual microscope slides. Fluorescently (cyanine 5) labeled normal pancreas mRNA was also compared with the same universal reference mRNA reference pool. The expression ratios of neoplastic versus normal pancreas cells were then calculated by multiplying the ratio of cancer versus the universal reference mRNA and the ratio of the universal reference mRNA cell versus normal pancreas. For 5289 different genes interrogated by the arrays, 30 of them showed an expression ratio 2 SD from the mean in at least three of the nine pancreatic cell lines studied. To confirm the expression profiles of these genes, quantitative reverse transcription-PCR and Northern blot were carried out for 25 of the overexpressed genes. To verify the overexpression in patient samples, two of the overexpressed genes, c-Myc and Rad5l, were selected to undergo analysis by reverse transcription-PCR in frozen tumor tissues and by immunostaining in paraffin-embedded tissue section microarrays. The results of these experiments are in agreement with the microarray data. Potential up-regulated targets of note from this study include urokinase-type plasminogen activator receptor, serine/threonine kinase 15, thioredoxin reductase, and CDC28 protein kinase 2, as well as several others.

Original languageEnglish (US)
Pages (from-to)2890-2896
Number of pages7
JournalCancer Research
Volume62
Issue number10
StatePublished - May 15 2002

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Oligonucleotide Array Sequence Analysis
Pancreatic Neoplasms
Messenger RNA
Pancreas
Genes
Cell Line
Reverse Transcription
Complementary DNA
Urokinase Plasminogen Activator Receptors
Thioredoxin-Disulfide Reductase
Polymerase Chain Reaction
myc Genes
Neoplasm Genes
Protein-Serine-Threonine Kinases
Microarray Analysis
Transcriptome
Northern Blotting
Paraffin
Protein Kinases
Neoplasms

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Han, H., Bearss, D. J., Browne, L. W., Calaluce, R., Nagle, R. B., & Von Hoff, D. D. (2002). Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Research, 62(10), 2890-2896.

Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. / Han, Haiyong; Bearss, David J.; Browne, L. Walden; Calaluce, Robert; Nagle, Raymond B; Von Hoff, Daniel D.

In: Cancer Research, Vol. 62, No. 10, 15.05.2002, p. 2890-2896.

Research output: Contribution to journalArticle

Han, H, Bearss, DJ, Browne, LW, Calaluce, R, Nagle, RB & Von Hoff, DD 2002, 'Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray', Cancer Research, vol. 62, no. 10, pp. 2890-2896.
Han H, Bearss DJ, Browne LW, Calaluce R, Nagle RB, Von Hoff DD. Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Research. 2002 May 15;62(10):2890-2896.
Han, Haiyong ; Bearss, David J. ; Browne, L. Walden ; Calaluce, Robert ; Nagle, Raymond B ; Von Hoff, Daniel D. / Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. In: Cancer Research. 2002 ; Vol. 62, No. 10. pp. 2890-2896.
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