Xenopus cDNA microarray identification of genes with endodermal organ expression

Abstract

The endoderm is classically defined as the innermost layer of three Metazoan germ layers. During organogenesis, the endoderm gives rise to the digestive and respiratory tracts as well as associated organs such as the liver, pancreas, and lung. At present, however, how the endoderm forms the variety of cell types of digestive and respiratory tracts as well as the budding organs is not well understood. In order to investigate the molecular basis and mechanism of organogenesis and to identify the endodermal organ-related marker genes, we carried out microarray analysis using Xenopus cDNA chips. To achieve this goal, we isolated the Xenopus gut endoderm from three different stages of Xenopus organogenesis, and separated each stage of gut endoderm into anterior and posterior regions. Competitive hybridization of cDNA between the anterior and posterior endoderm regions, to screen genes that specifically expressed in the major organs, revealed 915 candidates. We then selected 104 clones for in situ hybridization analysis. Here, we report the identification and expression patterns of the 104 Xenopus endodermal genes, which would serve as useful markers for studying endodermal organ development.

Identification of embryonic pancreatic genes using Xenopus DNA microarrays

“…Similarly in Group L, we found genes associated with liver development, which are A2M, ALB, AMBP, BF, FGG, HHEX, KNG1, TBX2 and TF (Zorn and Mason, 2001, Park et al, 2007). Group S included ATP4B, CTSE, SOX2, and STARD10, which are expressed in the stomach (Park et al, 2007). XBP1 is expressed in both the liver and pancreas (Park et al, 2007) and belongs to Group PL.…”

“…Group P genes included AMY2A, CEL, CLDN6, CPA1, DNASE1, ELA1, ELA2A, HLXB9, INS, PDIA2, and PRSS2, which are known to be expressed in the pancreas (Afelik et al, 2004; Sogame et al, 2003, Horb and Slack, 2002; Kelly and Melton, 2000; Chen et al, 2004; Park et al, 2007). Similarly in Group L, we found genes associated with liver development, which are A2M, ALB, AMBP, BF, FGG, HHEX, KNG1, TBX2 and TF (Zorn and Mason, 2001, Park et al, 2007). Group S included ATP4B, CTSE, SOX2, and STARD10, which are expressed in the stomach (Park et al, 2007).…”

“…Group S included ATP4B, CTSE, SOX2, and STARD10, which are expressed in the stomach (Park et al, 2007). XBP1 is expressed in both the liver and pancreas (Park et al, 2007) and belongs to Group PL. PAX6 is expressed in both the pancreas and intestine of stage 45 embryos (Kelly and Melton, 2000) and is assigned to Group PS.…”

“…Using DNA microarrays, novel regulators of β cell development and signature marker genes representing specific pancreatic cells were identified in mice (Gu et al, 2004; Chiang and Melton, 2003). In Xenopus, we have previously reported on the isolation and characterization of various organ specific endodermal markers using our homemade Xenopus neurula stage (stage 15) and tailbud stage (stage 25) cDNA microarrays (Shin et al, 2005; Park et al, 2007). In this current study, we instead utilized Xenopus Affymetrix GeneChip arrays representing over 14,400 transcripts and compared the gene expression profiles of the developing pancreas, liver, and stomach of tadpole stage (stage 42) embryos.…”

Xenopus as a Model for GI/Pancreas Disease

“…Fate map studies provide the necessary information to enable targeted manipulation of specific regions and organs in the developing endoderm [8, 9]. Xenopus embryos and tadpoles represent an excellent source for endoderm-derived organs, and precursor tissues for molecular analysis [10–13]. Aided by an expansive collection of expression data (e.g.…”