Transporter and ion channel gene expression after Caco-2 cell diferentiation using 2 different microarray technologies

Christopher P. Landowski, Pascale Anderle, Duxin Sun, Wolfgang Sadee, Gordon L. Amidon

Research output: Contribution to journalArticleScientificpeer-review

22 Citations (Scopus)

Abstract

mRNA, expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r = 0.75, P < 0.01, n = 25) and poorly for genes expressed at low levels (r = 0.08, P > 0.05, n = 25). Overall correlation across the 2 platforms was r = 0.45 (P < 0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.

Original languageEnglish
Article number21
JournalAAPS Journal
Volume6
Issue number3
DOIs
Publication statusPublished - 7 Sep 2004
MoE publication typeA1 Journal article-refereed

Fingerprint

Caco-2 Cells
Ion Channels
Technology
Gene Expression
Genes
Oligonucleotide Array Sequence Analysis
Messenger RNA
Transcriptome
Cell Differentiation
Down-Regulation
Clone Cells
Carcinoma

Keywords

  • Caco-2 cells
  • Ion channel
  • Microarrays
  • Platform comparison
  • Transporter

Cite this

@article{d90c6e26ca54463ebf24b90d4e2c81ea,
title = "Transporter and ion channel gene expression after Caco-2 cell diferentiation using 2 different microarray technologies",
abstract = "mRNA, expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r = 0.75, P < 0.01, n = 25) and poorly for genes expressed at low levels (r = 0.08, P > 0.05, n = 25). Overall correlation across the 2 platforms was r = 0.45 (P < 0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.",
keywords = "Caco-2 cells, Ion channel, Microarrays, Platform comparison, Transporter",
author = "Landowski, {Christopher P.} and Pascale Anderle and Duxin Sun and Wolfgang Sadee and Amidon, {Gordon L.}",
year = "2004",
month = "9",
day = "7",
doi = "10.1208/aapsj060321",
language = "English",
volume = "6",
journal = "AAPS Journal",
issn = "1550-7416",
publisher = "Springer",
number = "3",

}

Transporter and ion channel gene expression after Caco-2 cell diferentiation using 2 different microarray technologies. / Landowski, Christopher P.; Anderle, Pascale; Sun, Duxin; Sadee, Wolfgang; Amidon, Gordon L.

In: AAPS Journal, Vol. 6, No. 3, 21, 07.09.2004.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Transporter and ion channel gene expression after Caco-2 cell diferentiation using 2 different microarray technologies

AU - Landowski, Christopher P.

AU - Anderle, Pascale

AU - Sun, Duxin

AU - Sadee, Wolfgang

AU - Amidon, Gordon L.

PY - 2004/9/7

Y1 - 2004/9/7

N2 - mRNA, expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r = 0.75, P < 0.01, n = 25) and poorly for genes expressed at low levels (r = 0.08, P > 0.05, n = 25). Overall correlation across the 2 platforms was r = 0.45 (P < 0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.

AB - mRNA, expression profiles had previously been measured in Caco-2 cells (human colonic carcinoma cells) using either custom-designed spotted oligonucleotide arrays or Affymetrix GeneChip oligonucleotide arrays. The Caco-2 cells used were from different clones and were examined under slightly different culture conditions commonly encountered when Caco-2 cells are used as a model tissue for studying intestinal transport and metabolism in different laboratories. In this study, we compared gene expression profiles of Caco-2 cells generated with different arrays to assess the validity of conclusions derived from the 2 independent studies, with a focus on changes in transporter and ion channel mRNA expression levels on Caco-2 cell differentiation. Significant changes in expression levels upon differentiation were observed with 78 genes, with probes common to both arrays. Of these, 18 genes were upregulated and 36 genes were downregulated. The 2 arrays yielded discrepant results for 24 genes, showing significant changes upon differentiation. The results from the 2 arrays correlated well for genes expressed above average levels (r = 0.75, P < 0.01, n = 25) and poorly for genes expressed at low levels (r = 0.08, P > 0.05, n = 25). Overall correlation across the 2 platforms was r = 0.45 (P < 0.01) for the 78 genes, with similar results from both arrays. Despite differences in experimental conditions and array technology, similar results were obtained for most genes.

KW - Caco-2 cells

KW - Ion channel

KW - Microarrays

KW - Platform comparison

KW - Transporter

UR - http://www.scopus.com/inward/record.url?scp=33646646022&partnerID=8YFLogxK

U2 - 10.1208/aapsj060321

DO - 10.1208/aapsj060321

M3 - Article

C2 - 15760106

AN - SCOPUS:33646646022

VL - 6

JO - AAPS Journal

JF - AAPS Journal

SN - 1550-7416

IS - 3

M1 - 21

ER -