Synergizing Genomic Analysis with Biological Knowledge to Identify and Validate Novel Genes in Pancreatic Development
| Autor: | Jason D. Dinella, Suparna A. Sarkar, Hannah R. Tipney, Lawrence Hunter, Anis Karimpour-Fard, Catherine E. Lee, John C. Hutton, Kirstine Juhl, Jay A. Walters |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Endocrinology
Diabetes and Metabolism Morphogenesis Cystathionine beta-Synthase Enteroendocrine cell Gestational Age Biology Real-Time Polymerase Chain Reaction Article Transcriptome Paracrine signalling Mice Endocrinology Databases Genetic Internal Medicine medicine Animals RNA Messenger Progenitor cell Myeloid Ecotropic Viral Integration Site 1 Protein Pancreas In Situ Hybridization Oligonucleotide Array Sequence Analysis Genetics Homeodomain Proteins Hepatology Gene Expression Profiling Computational Biology Gene Expression Regulation Developmental Reproducibility of Results Genomics Aldehyde Dehydrogenase Immunohistochemistry Cell biology Neoplasm Proteins Gene expression profiling DNA-Binding Proteins medicine.anatomical_structure PDX1 Female Transcription Factors |
| Popis: | The molecular mechanism of pancreatic morphogenesis and differentiation is a fundamental enigma during pancreas development. Early pancreatic organogenesis shares a common pool of pancreatic progenitor cells that originate from the foregut endoderm1, 2. The dynamic signaling interactions between surrounding mesoderm, in an autocrine and paracrine manner leads to the branching morphogenesis of the pancreatic epithelium3. The key transcription factors like Pdx1, Hlxb9, Ptf1a, Nkx6-1, and Nkx2-2, Nkx6-2, Sox 9 and many more unidentified such factors mark the pancreatic progenitor cells in the undifferentiated epithelium. These known and unknown entities allow an orchestrated series of complex differentiation and proliferation steps leading to the parallel differentiation of endocrine and exocrine (acinar and ductal) compartments4. The critical events governing the differentiation of endocrine cells occur when Neurog3 is transiently expressed in a subset of cells derived from the pancreatic epithelium from E9.5 to E18.55, 6. These Neurog3 expressing cells are identifiable by lineage tracing as endocrine progenitor cells7, 8. We have previously shown that endocrine differentiation in the human fetal pancreas also takes place in the islands of epithelial tissue but within a much larger volume of mesenchymal tissue9. In humans, endocrine progenitor marker, NGN3-positive cells also persist from 9–23 weeks of gestation9, 10. In mice, unlike humans where secondary transition has not been documented9, the differentiation of the acinar compartment is synchronized with that of endocrine differentiation during the secondary transition11 and is governed by the shift and segregation in expression of Ptf1a from the central to the expanding tips of the pancreatic epithelium3. Unfortunately, the data regarding ductal development is relatively sparse12–14. Tremendous progress has been made in understanding the molecular dynamics of some of these known factors mentioned above and the identification and validation of novel entities that drive the differentiation process may further enhance our ability to generate therapeutic beta cells from ES and or iPS cells15–17. To document the transcriptome of the developing pancreas in the mouse and highlight the qualitative and quantitative features of global gene expression that contributes to the specification, growth and differentiation of the major endocrine and exocrine (acinar and ductal) cell types, we performed microarray analysis at E12.5, E13.5, E15.5 and E18.5 on murine embryonic pancreas. In order to expedite the discovery of novel factors that govern pancreatic differentiation, we have synergized the differential analysis of significant genes with an advanced computational approach called the Hanalyzer18, 19. The Hanalyzer extracts information from external resources, either by parsing structured data or by using biomedical language processing to glean information from unstructured data, and tracks knowledge provenance about genes. The use of the tool was critical in the identification of four novel genes whose roles have not been extensively characterized in the murine pancreatic developmental context; Cystathionine beta synthase (Cbs), Growth Factor Independent 1 (Gfi1), Meis homeobox 1 (Meis 1) and Aldehyde dehydrogenase 18 family member a1 (Aldh18a1). In the current study, we validated the temporal expression of Cbs, Gfi1, Meis1 and Aldh18a1 and further documented the localization of Cbs in embryonic and adult pancreas. We identified Cbs as one of the previously unknown cellular markers expressed in early pancreatic epithelium that may contribute to the acinar differentiation in the murine pancreas. |
| Databáze: | OpenAIRE |
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