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Identification of transcripts with enriched expression in the developing and adult pancreas.

Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJ, Marra MA, Helgason CD - Genome Biol. (2008)

Bottom Line: Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development.Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development.Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada. bhoffman@bccrc.ca

ABSTRACT

Background: Despite recent advances, the transcriptional hierarchy driving pancreas organogenesis remains largely unknown, in part due to the paucity of comprehensive analyses. To address this deficit we generated ten SAGE libraries from the developing murine pancreas spanning Theiler stages 17-26, making use of available Pdx1 enhanced green fluorescent protein (EGFP) and Neurog3 EGFP reporter strains, as well as tissue from adult islets and ducts.

Results: We used a specificity metric to identify 2,536 tags with pancreas-enriched expression compared to 195 other mouse SAGE libraries. We subsequently grouped co-expressed transcripts with differential expression during pancreas development using K-means clustering. We validated the clusters first using quantitative real time PCR and then by analyzing the Theiler stage 22 pancreas in situ hybridization staining patterns of over 600 of the identified genes using the GenePaint database. These were then categorized into one of the five expression domains within the developing pancreas. Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development.

Conclusion: Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development. Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.

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Related in: MedlinePlus

Representative in situ staining patterns for genes expressed in each of the identified expression profiles. Representative genes for each of the identified spatial expression profiles, including genes with known and previously un-described, or novel, staining profiles in pancreas development, are shown. For this, images of in situ hybridization staining patterns for whole embryo sagittal sections were obtained from the GenePaint website and magnified to show the pancreas (outlined in red). Relevant GenePaint probe IDs can be found in Additional data file 4.
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Figure 5: Representative in situ staining patterns for genes expressed in each of the identified expression profiles. Representative genes for each of the identified spatial expression profiles, including genes with known and previously un-described, or novel, staining profiles in pancreas development, are shown. For this, images of in situ hybridization staining patterns for whole embryo sagittal sections were obtained from the GenePaint website and magnified to show the pancreas (outlined in red). Relevant GenePaint probe IDs can be found in Additional data file 4.

Mentions: Taken together, the data suggested that the generated clusters represent transcript sets with distinct roles in pancreas development. To further confirm this, we assessed whether the transcripts identified in each of the SAGE tag clusters had spatial expression profiles consistent with these roles using the GenePaint database [27,28]. For each of the 923 genes present in our clusters and in the GenePaint database, we analyzed the in situ hybridization staining pattern in the pancreas from TS22 whole embryo sections. In sum, 601 of the genes showed informative staining, and these were categorized based on their staining patterns into one of five expression domains found in the pancreas [40] (Figure 5). For the remaining 316 genes, either the probes did not show stain in any sections or sections with pancreas were not present in the database. Regardless, we identified 88 genes expressed in the tips of epithelial branches that at E14.5 primarily contain exocrine progenitor cell types. A further 81 genes were identified as expressed in the trunk of the epithelial branches that contains endocrine and ductal progenitor cells; 221 genes were identified as expressed throughout the epithelium; and a further 51 were found only in the mesenchyme, and 42 in the vasculature. For a full categorization of the genes see Additional data file 4. There were 124 (13%) genes identified in our SAGE data that were not detected in the pancreas at the time point assessed. The average tag count for these genes was only 6.8 while for detected genes it was 24, suggesting this is, in part, due to the low expression levels of these genes. Moreover, the number of genes not detected was highest in clusters 1, 2 and 13, which include genes that show low relative expression at TS22.


Identification of transcripts with enriched expression in the developing and adult pancreas.

Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJ, Marra MA, Helgason CD - Genome Biol. (2008)

Representative in situ staining patterns for genes expressed in each of the identified expression profiles. Representative genes for each of the identified spatial expression profiles, including genes with known and previously un-described, or novel, staining profiles in pancreas development, are shown. For this, images of in situ hybridization staining patterns for whole embryo sagittal sections were obtained from the GenePaint website and magnified to show the pancreas (outlined in red). Relevant GenePaint probe IDs can be found in Additional data file 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2481431&req=5

Figure 5: Representative in situ staining patterns for genes expressed in each of the identified expression profiles. Representative genes for each of the identified spatial expression profiles, including genes with known and previously un-described, or novel, staining profiles in pancreas development, are shown. For this, images of in situ hybridization staining patterns for whole embryo sagittal sections were obtained from the GenePaint website and magnified to show the pancreas (outlined in red). Relevant GenePaint probe IDs can be found in Additional data file 4.
Mentions: Taken together, the data suggested that the generated clusters represent transcript sets with distinct roles in pancreas development. To further confirm this, we assessed whether the transcripts identified in each of the SAGE tag clusters had spatial expression profiles consistent with these roles using the GenePaint database [27,28]. For each of the 923 genes present in our clusters and in the GenePaint database, we analyzed the in situ hybridization staining pattern in the pancreas from TS22 whole embryo sections. In sum, 601 of the genes showed informative staining, and these were categorized based on their staining patterns into one of five expression domains found in the pancreas [40] (Figure 5). For the remaining 316 genes, either the probes did not show stain in any sections or sections with pancreas were not present in the database. Regardless, we identified 88 genes expressed in the tips of epithelial branches that at E14.5 primarily contain exocrine progenitor cell types. A further 81 genes were identified as expressed in the trunk of the epithelial branches that contains endocrine and ductal progenitor cells; 221 genes were identified as expressed throughout the epithelium; and a further 51 were found only in the mesenchyme, and 42 in the vasculature. For a full categorization of the genes see Additional data file 4. There were 124 (13%) genes identified in our SAGE data that were not detected in the pancreas at the time point assessed. The average tag count for these genes was only 6.8 while for detected genes it was 24, suggesting this is, in part, due to the low expression levels of these genes. Moreover, the number of genes not detected was highest in clusters 1, 2 and 13, which include genes that show low relative expression at TS22.

Bottom Line: Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development.Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development.Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada. bhoffman@bccrc.ca

ABSTRACT

Background: Despite recent advances, the transcriptional hierarchy driving pancreas organogenesis remains largely unknown, in part due to the paucity of comprehensive analyses. To address this deficit we generated ten SAGE libraries from the developing murine pancreas spanning Theiler stages 17-26, making use of available Pdx1 enhanced green fluorescent protein (EGFP) and Neurog3 EGFP reporter strains, as well as tissue from adult islets and ducts.

Results: We used a specificity metric to identify 2,536 tags with pancreas-enriched expression compared to 195 other mouse SAGE libraries. We subsequently grouped co-expressed transcripts with differential expression during pancreas development using K-means clustering. We validated the clusters first using quantitative real time PCR and then by analyzing the Theiler stage 22 pancreas in situ hybridization staining patterns of over 600 of the identified genes using the GenePaint database. These were then categorized into one of the five expression domains within the developing pancreas. Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development.

Conclusion: Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development. Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.

Show MeSH
Related in: MedlinePlus