Functional Genomics of the Endocrine Pancreas

Scearce, L. Marie; Brestelli, John; McWeeney, Shannon K.; Lee, Catherine S.; Mazzarelli, Joan M.; Pinney, Deborah F.; Pizarro, Angel; Stoeckert, Christian J.; Clifton, Sandra W.; Permutt, M. A.; Brown, Juliana; Melton, Douglas A.; Kaestner, Klaus H.

doi:10.2337/diabetes.51.7.1997

Cited by 75 publications

(61 citation statements)

References 28 publications

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“…5, which is published as supporting information on the PNAS web site). This finding might be consistent with the hypothesis that because ␣ cells differentiate early in pancreatic development, this lineage may preserve multipotential characteristics of its less well differentiated or undifferentiated progenitors, as suggested also by the high percentage of TFR among early expressed molecules [peaking at embryonic day (E)14.5] in embryonic pancreatic cells (25).…”

Section: Resultssupporting

confidence: 76%

Contrasting patterns of expression of transcription factors in pancreatic α and β cells

Wang

Webb

Cao

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Pancreatic ␣ and ␤ cells are derived from the same progenitors but play opposing roles in the control of glucose homeostasis. Disturbances in their function are associated with diabetes mellitus. To identify many of the proteins that define their unique pathways of differentiation and functional features, we have analyzed patterns of gene expression in ␣TC1.6 vs. MIN6 cell lines by using oligonucleotide microarrays. Approximately 9 -10% of >11,000 transcripts examined showed significant differences between the two cell types. Of >700 known transcripts enriched in either cell type, transcription factors and their regulators (TFR) was one of the most significantly different categories. Ninety-six members of the basic zipper, basic helix-loop-helix, homeodomain, zinc finger, high mobility group, and other transcription factor families were enriched in ␣ cells; in contrast, homeodomain proteins accounted for 51% of a total of 45 TFRs enriched in ␤ cells. Our analysis thus highlights fundamental differences in expression of TFR subtypes within these functionally distinct islet cell types. Interestingly, the ␣ cells appear to express a large proportion of factors associated with progenitor or stem-type cells, perhaps reflecting their earlier appearance during pancreatic development. The implications of these findings for a better understanding of ␣ and ␤ cell dysfunction in diabetes mellitus are also considered. P ancreatic islets consist of four endocrine cell types, ␣, ␤, D, and pancreatic peptide (PP). These cell types produce and secrete the major islet hormones: glucagon, insulin, islet amyloid polypeptide (IAPP), somatostatin, and PP, respectively, which regulate fuel and energy homeostasis (1). The ␣ cells secrete glucagon, which stimulates gluconeogenesis and glycogenolysis to prevent hypoglycemia, whereas the ␤ cells increase insulin secretion in response to elevated blood glucose levels. Glucagon and insulin antagonistically regulate the balance of glucose storage, production, and consumption to maintain physiological plasma glucose concentrations. Therefore, the ␣ and ␤ cells together play a central role in glucose homeostasis.Excessive production and secretion of glucagon by the ␣ cells is a common accompaniment to the two main types of diabetes. Physiologically, glucagon secretion is suppressed by hyperglycemia. However, this normal homeostatic suppression is lost in diabetic states, which in turn perpetuates hyperglycemia by stimulating hepatic glucose output (2). Another major typical manifestation of diabetes is an absolute or relative deficiency of insulin from the ␤ cells, resulting in failure to adequately control the blood glucose level (3). Disturbances of ␣ and͞or ␤ cell function thus are central to the failure to maintain physiological glucose levels and related metabolic concomitants of diabetes mellitus.To understand the molecular basis for the development and specialized functions of ␣ and ␤ cells is an important goal for understanding and effectively treating diabetes. Although much effort h...

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Section: Resultssupporting

confidence: 76%

Contrasting patterns of expression of transcription factors in pancreatic α and β cells

Wang

Webb

Cao

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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“…shtml. Human and mouse pancreas, islet, and insulinoma libraries were constructed and over 170 000 ESTs submitted to the public databases [26]. These ESTs were derived from a mixture of developmental stages of pancreas, not exclusively islet transcripts, and for these reasons cannot be compared directly to the two islet SAGE libraries presented here.…”

Section: Discussionmentioning

confidence: 99%

An expression profile of human pancreatic islet mRNAs by Serial Analysis of Gene Expression (SAGE)

et al. 2004

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Aims/hypothesis. The Human Genome Project seeks to identify all genes with the ultimate goal of evaluation of relative expression levels in physiology and in disease states. The purpose of the current study was the identification of the most abundant transcripts in human pancreatic islets and their relative expression levels using Serial Analysis of Gene Expression. Methods. By cutting cDNAs into small uniform fragments (tags) and concatemerizing them into larger clones, the identity and relative abundance of genes can be estimated for a cDNA library. Approximately 49 000 SAGE tags were obtained from three human libraries: (i) ficoll gradient-purified islets (ii) islets further individually isolated by hand-picking, and (iii) pancreatic exocrine tissue. Results. The relative abundance of each of the genes identified was approximated by the frequency of the tags. Gene ontology functions showed that all three libraries contained transcripts mostly encoding secreted factors. Comparison of the two islet libraries showed various degrees of contamination from the surrounding exocrine tissue (11 vs 25%). After removal of exocrine transcripts, the relative abundance of 2180 islet transcripts was determined. In addition to the most common genes (e.g. insulin, transthyretin, glucagon), a number of other abundant genes with ill-defined functions such as proSAAS or secretagogin, were also observed. Conclusion/interpretation. This information could serve as a resource for gene discovery, for comparison of transcript abundance between tissues, and for monitoring gene expression in the study of beta-cell dysfunction of diabetes. Since the chromosomal location of the identified genes is known, this SAGE expression data can be used in setting priorities for candidate genes that map to linkage peaks in families affected with diabetes. [Diabetologia (2004) 47:284-299]

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“…RNA was labeled with amino-allyl dUTP and d(T) 21 to prime reverse transcription. The fluorescent label was coupled to the cDNA and the cDNA was hybridized to PANCCHIP V. 5.0 (22,23). The median intensities of each spot were measured by an Agilent scanner with the GENEPIX software.…”

Section: Methodsmentioning

confidence: 99%

Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation

Friedman

Larris

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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CCAAT enhancer-binding protein ␤ (C͞EBP␤), a basic-leucine zipper transcription factor, is an important effector of signals in physiologic growth and cancer. The identification of direct C͞EBP␤ targets in vivo has been limited by functional compensation by other C͞EBP family proteins and the low stringency of the consensus sequence. Here we use the combined power of expression profiling and high-throughput chromatin immunoprecipitation to identify direct and biologically relevant targets of C͞EBP␤. We identified 25 potential C͞EBP␤ targets, of which 88% of those tested were confirmed as in vivo C͞EBP␤-binding sites. Six of these genes also displayed differential expression in C͞EBP␤ ؊/؊ livers. Computational analysis revealed that bona fide C͞EBP␤ target genes can be distinguished by the presence of binding motifs for specific additional transcription factors in the vicinity of the C͞EBP␤ site. This approach is generally applicable to the discovery of direct, biologically relevant targets of mammalian transcription factors.C CAAT enhancer-binding proteins (C͞EBPs) constitute a family of basic-leucine zipper (bZIP) transcription factors that are critical for the regulation of numerous biological processes, including differentiation, metabolic homeostasis, proliferation, tumorigenesis, inflammation, and apoptosis (1-9). C͞EBP proteins are regulated at multiple levels, including gene transcription, translation, and phosphorylation, in response to a variety of stimuli including hormonal, cytokine and growth factor-signaling pathways (1). C͞EBP proteins are able to form hetero-and homodimeric complexes with other C͞EBP family members, thereby creating additional diversity in target sequence recognition.C͞EBP␤ is an important effector of growth signals in experimental models of physiologic and neoplastic growth, the acutephase response, and metabolic homeostasis (1-11). Livers from C͞EBP␤ Ϫ/Ϫ mice exhibit a blunted regenerative response associated with prolonged hypoglycemia and altered expression of several cell-cycle-associated genes (10). In addition, a recent microarray analysis of human tumors has implicated C͞EBP␤ as a downstream mediator of cyclin D (12). Although these studies provide strong support for the role of C͞EBP␤ as a regulator of cell growth, at present, neither the mechanism by which C͞EBP␤ modulates the growth effects of cyclin D1 nor the targets of C͞EBP␤ in this pathway have been elucidated.A variety of approaches has been used to identify C͞EBP␤-binding sites, including cell culture systems, C͞EBP␤ Ϫ/Ϫ mice, and analyses of promoter sequences. However, several obstacles have limited the identification of direct C͞EBP␤-dependent transcriptional targets in vivo. All C͞EBP family members with the exception of C͞EBP possess identical in vitro DNA-binding affinity for C͞EBP consensus sequences, suggesting that other C͞EBP family members may be able to compensate for the loss of C͞EBP␤ (13). Second, the application of computational sequence analysis to identify C͞EBP promoter sequences has been impede...

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Functional Genomics of the Endocrine Pancreas

Cited by 75 publications

References 28 publications

Contrasting patterns of expression of transcription factors in pancreatic α and β cells

Contrasting patterns of expression of transcription factors in pancreatic α and β cells

An expression profile of human pancreatic islet mRNAs by Serial Analysis of Gene Expression (SAGE)

Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation

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