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Differential gene expression in normal esophagus and Barrett’s esophagus

Journal of Gastroenterology volume 44, pages 897–911 (2009)Cite this article

Abstract

Purpose

As the premalignant lesion of human esophageal adenocarcinoma (EAC), Barrett’s esophagus (BE) is characterized by intestinal metaplasia in the normal esophagus (NE). Gene expression profiling with microarray and serial analysis of gene expression (SAGE) may help us understand the potential molecular mechanism of human BE.

Methods

We analyzed three microarray datasets (two cDNA arrays and one oligonucleotide array) and one SAGE dataset with statistical tools, significance analysis of microarrays (SAM) and SAGE(Poisson), to identify individual genes differentially expressed in BE. Gene set enrichment analysis (GSEA) was used to identify a priori defined sets of genes that were differentially expressed. These gene sets were grouped according to either certain signaling pathways (GSEA curated), or the presence of consensus binding sequences of known transcription factors (GSEA motif). Immunohistochemical staining (IHC) was used to validate differential gene expression.

Results

Both SAM and SAGE(Poisson) identified 68 differentially expressed genes (55 BE genes and 13 NE genes) with an arbitrary cutoff ratio (≥4-fold). With IHC on matched pairs of NE and BE tissues from 6 patients, these genes were grouped into 6 categories: category I (25 genes only expressed in BE), category II (5 genes only expressed in NE), category III (8 genes expressed more in BE than in NE), and category IV (2 genes expressed more in NE than in BE). Differential expression of the remaining genes was not confirmed by IHC either due to false discovery (category V), or lack of proper antibodies (category VI). Besides individual genes, the TGFβ pathway and several transcription factors (CDX2, HNF1, and HNF4) were identified by GSEA as enriched pathways and motifs in BE. Apart from 9 target genes known to be up-regulated in BE, IHC staining confirmed up-regulation of 19 additional CDX1 and CDX2 target genes in BE.

Conclusion

Our data suggested an important role of CDX1 and CDX2 in the development of BE. The IHC-confirmed gene list will lead to future studies on the molecular mechanism of BE.

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Abbreviations

BE:

Barrett’s esophagus

EAC:

Esophageal adenocarcinoma

FDR:

False discovery rate

GenMapp:

Gene Map Annotator and Pathway Profiler

GO:

Gene ontology

GSEA:

Gene set enrichment analysis

IHC:

Immunohistochemical staining

IM:

Intestinal metaplasia

NE:

Normal esophagus

SAGE:

Serial analysis of gene expression

SAM:

Significance analysis of microarrays

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Acknowledgments

We thank Dr. Li Cai, Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, in helping in SAGE(Poisson) analysis; Dr. Vasilis Vasiliou, Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, Denver, CO, for providing the anti-ALDH3A1 used in this study; Drs. Danielle M. Greenawalt and Wayne A. Phillips, Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, Victoria, Australia, for providing original data and information regarding pathology; Dr. Jerzy Ostrowski, Department of Gastroenterology, Medical Center for Postgraduate Education, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland, for providing original data and information regarding pathology; Dr. William R. Otto, Histopathology Unit, London Research Institute, Cancer Research UK, London, UK, for staining our tissue sections for GDDR. This study was supported by NIH grants U56 CA092077 and P20 MD000175.

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Affiliations

  1. Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC, 27707, USA

    Jacob Wang, Rong Qin, Yan Ma & Xiaoxin Chen

  2. Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA

    Jacob Wang, Nicholas J. Shaheen & Xiaoxin Chen

  3. Department of Biostatistics, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center/Biostatistics Shared Resource, Nashville, TN, 37232-2158, USA

    Huiyun Wu

  4. Institute of Human Genetics, International Centre for Life, University of Newcastle upon Tyne, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK

    Heiko Peters

  5. Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA

    Matthew Tyska

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  1. Jacob Wang
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  2. Rong Qin
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  3. Yan Ma
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  4. Huiyun Wu
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  7. Nicholas J. Shaheen
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  8. Xiaoxin Chen
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Correspondence to Xiaoxin Chen.

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Wang, J., Qin, R., Ma, Y. et al. Differential gene expression in normal esophagus and Barrett’s esophagus. J Gastroenterol 44, 897–911 (2009). https://doi.org/10.1007/s00535-009-0082-2

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Keywords

  • Barrett’s esophagus
  • Intestinal metaplasia
  • Expression profile
  • SAM
  • GSEA