Transcriptomes of the major human pancreatic cell types.

AIMS/HYPOTHESIS: We sought to determine the mRNA transcriptome of all major human pancreatic endocrine and exocrine cell subtypes, including human alpha, beta, duct and acinar cells. In addition, we identified the cell type-specific distribution of transcription factors, signalling ligands and their receptors. METHODS: Islet samples from healthy human donors were enzymatically dispersed to single cells and labelled with cell type-specific surface-reactive antibodies. Live endocrine and exocrine cell subpopulations were isolated by FACS and gene expression analyses were performed using microarray analysis and quantitative RT-PCR. Computational tools were used to evaluate receptor-ligand representation in these populations. RESULTS: Analysis of the transcriptomes of alpha, beta, large duct, small duct and acinar cells revealed previously unrecognised gene expression patterns in these cell types, including transcriptional regulators HOPX and HDAC9 in the human beta cell population. The abundance of some regulatory proteins was different from that reported in mouse tissue. For example, v-maf musculoaponeurotic fibrosarcoma oncogene homologue B (avian) (MAFB) was detected at equal levels in adult human alpha and beta cells, but is absent from adult mouse beta cells. Analysis of ligand-receptor interactions suggested that EPH receptor-ephrin communication between exocrine and endocrine cells contributes to pancreatic function. CONCLUSIONS/INTERPRETATION: This is the first comprehensive analysis of the transcriptomes of human exocrine and endocrine pancreatic cell types-including beta cells-and provides a useful resource for diabetes research. In addition, paracrine signalling pathways within the pancreas are shown. These results will help guide efforts to specify human beta cell fate by embryonic stem cell or induced pluripotent stem cell differentiation or genetic reprogramming.

Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks.

Stem cells represent not only a potential source of treatment for degenerative diseases but can also shed light on developmental biology and cancer. It is believed that stem cells differentiation and fate is triggered by a common genetic program that endows those cells with the ability to differentiate into specialized progenitors and fully differentiated cells. To extract the stemness signature of several cells types at the transcription level, we integrated heterogeneous datasets (microarray experiments) performed in different adult and embryonic tissues (liver, blood, bone, prostate and stomach in Homo sapiens and Mus musculus). Data were integrated by generalization of the hematopoietic stem cell hierarchy and by homology between mouse and human. The variation-filtered and integrated gene expression dataset was fed to a single-layered neural network to create a classifier to (i) extract the stemness signature and (ii) characterize unknown stem cell tissue samples by attribution of a stem cell differentiation stage. We were able to characterize mouse stomach progenitor and human prostate progenitor samples and isolate gene signatures playing a fundamental role for every level of the generalized stem cell hierarchy.

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

MOTIVATION: Gene expression array technology has become increasingly widespread among researchers who recognize its numerous promises. At the same time, bench biologists and bioinformaticians have come to appreciate increasingly the importance of establishing a collaborative dialog from the onset of a study and of collecting and exchanging detailed information on the many experimental and computational procedures using a structured mechanism. This is crucial for adequate analyses of this kind of data. RESULTS: The RNA Abundance Database (RAD; http://www.cbil.upenn.edu/RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc. are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). RAD is part of a more general Genomics Unified Schema (http://www.gusdb.org), which includes a richly annotated gene index (http://www.allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.

Maintaining data integrity in microarray data management.

Gene expression microarrays are a relatively new technology, dating back just a few years, yet they have already become a very widely used tool in biology, and have evolved to a wide range of applications well beyond their original design intent. However, while the use of microarrays has expanded, and the issues of performance optimization have been intensively studied, the fundamental issue of data integrity management has largely been ignored. Now that performance has improved so greatly, the shortcomings of data integrity control methods constitute a greater percent of the stumbling blocks for investigators. Microarray data are cumbersome, and the rule up to this point has mostly been one of hands-on transformations, leading to human errors which often have dramatic consequences. We show in this review that the time lost on such mistakes is enormous and dramatically affects results; therefore, mistakes should be mitigated in any way possible. We outline the scope of the data integrity issue, to survey some of the most common and dangerous data transformations, and their shortcomings. To illustrate, we review some case studies. We then look at the work done by the research community on this issue (which admittedly is meager up to this point). Some data integrity issues are always going to be difficult, while others will become easier-one of our goals is to expedite the use of integrity control methods. Finally, we present some preliminary guidelines and some specific approaches that we believe should be the focus of future research.

High-resolution BAC-based map of the central portion of mouse chromosome 5.

The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation for assembling contiguous segments of sequence. We have established a bacterial artificial chromosome (BAC)-based map of a 5-Mb region on mouse Chromosome 5, encompassing three gene families: receptor tyrosine kinases (PdgfraKit-Kdr), nonreceptor protein-tyrosine type kinases (Tec-Txk), and type-A receptors for the neurotransmitter GABA (Gabra2, Gabrb1, Gabrg1, and Gabra4). The construction of a BAC contig was initiated by hybridization screening the C57BL/6J (RPCI-23) BAC library, using known genes and sequence tagged sites (STSs). Additional overlapping clones were identified by searching the database of available restriction fingerprints for the RPCI-23 and RPCI-24 libraries. This effort resulted in the selection of >600 BAC clones, 251 kb of BAC-end sequences, and the placement of 40 known and/or predicted genes within this 5-Mb region. We use this high-resolution map to illustrate the integration of the BAC fingerprint map with a radiation-hybrid map via assembled expressed sequence tags (ESTs). From annotation of three representative BAC clones we demonstrate that up to 98% of the draft sequence for each contig could be ordered and oriented using known genes, BAC ends, consensus sequences for transcript assemblies, and comparisons with orthologous human sequence. For functional studies, annotation of sequence fragments as they are assembled into 50-200-kb stretches will be remarkably valuable.

Generation of patterns from gene expression data by assigning confidence to differentially expressed genes.

MOTIVATION: A protocol is described to attach expression patterns to genes represented in a collection of hybridization array experiments. Discrete values are used to provide an easily interpretable description of differential expression. Binning cutoffs for each sample type are chosen automatically, depending on the desired false-positive rate for the predictions of differential expression. Confidence levels are derived for the statement that changes in observed levels represent true changes in expression. We have a novel method for calculating this confidence, which gives better results than the standard methods. Our method reflects the broader change of focus in the field from studying a few genes with many replicates to studying many (possibly thousands) of genes simultaneously, but with relatively few replicates. Our approach differs from standard methods in that it exploits the fact that there are many genes on the arrays. These are used to estimate for each sample type an appropriate distribution that is employed to control the false-positive rate of the predictions made. Satisfactory results can be obtained using this method with as few as two replicates. RESULTS: The method is illustrated through applications to macroarray and microarray datasets. The first is an erythroid development dataset that we have generated using nylon filter arrays. Clones for genes whose expression is known in these cells were assigned expression patterns which are in accordance with what was expected and which are not picked up by the standards methods. Moreover, genes differentially expressed between normal and leukemic cells were identified. These included genes whose expression was altered upon induction of the leukemic cells to differentiate. The second application is to the microarray data by Alizadeh et al. (2000). Our results are in accordance with their major findings and offer confidence measures for the predictions made. They also provide new insights for further analysis.

Maturation and developmental stage-related changes in fetal globin gene expression are reproduced in transiently transfected primary adult human erythroblasts.

A novel system is described, which uses transfection of primary human erythroblasts for the study of gene regulation in differentiating human red cells. This system includes a protocol for liquid culture of erythroid progenitors, which reproduces developmental differences in globin gene expression found between adult and cord blood as well as the maturation-related changes in fetal globin levels observed in adult cells. Reporter constructs driven by globin gene promoters were electroporated into adult and cord blood-derived erythroblasts at different time points during culture. Both the developmental stage and maturation-related differences in endogenous fetal and adult globin gene expression could be reproduced by the transiently transfected reporter constructs. Transfection of primary human erythroblasts during differentiation provides a previously unavailable opportunity to study dynamic aspects of erythropoiesis.

EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis.

EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence analysis aimed at understanding gene regulation during erythropoiesis. New protocols have been developed for data integration and updating entries. Using a BLAST-based algorithm, we have grouped GenBank entries representing the same gene together. This sequence similarity protocol was also used to identify new entries to be included in EpoDB. We have recently implemented our database in Sybase (relational tables) in addition to SICStus Prolog to provide us with greater flexibility in asking complex queries that utilize information from multiple sources. New additions to the public web site (http://www.cbil.upenn.edu/epodb) for accessing EpoDB are the ability to retrieve groups of entries representing different variants of the same gene and to retrieve gene expression data. The BLAST query has been enhanced by incorporating BLASTView, an interactive and graphical display of BLAST results. We have also enhanced the queries for retrieving sequence from specified genes by the addition of MEME, a motif discovery tool, to the integrated analysis tools which include CLUSTALW and TESS.

EpoDB: a database of genes expressed during vertebrate erythropoiesis.

EpoDB is a database designed for the study of gene regulation during differentiation and development of vertebrate red blood cells. In building EpoDB, we have taken the in advance approach to the data integration problem: we have extracted data relevant to red blood cells from GenBank, SWISS-PROT, TRRD (transcriptional regulation data) and GERD (expression levels data) to create a single integrated, highly curated view. Tools have been developed to automate data extraction from online resources, cleanse data of errors, enter information manually from the primary literature, generate a uniform, canonical representation of information and maintain data currency. The database is organized around biological features, e.g., genes, rather than sequences, which are supported by a controlled and consistent vocabulary for gene names and gene family names. Beyond the standard database queries, the functionality of EpoDB includes the ability to extract features and subsequences, display sequences and features graphically using bioWidget viewers and integrated analysis tools. EpoDB may be accessed at: http://cbil.humgen.upenn.edu/epodb/

Prevention of islet allograft rejection with engineered myoblasts expressing FasL in mice.

Allogeneic transplantation of islets of Langerhans was facilitated by the cotransplantation of syngeneic myoblasts genetically engineered to express the Fas ligand (FasL). Composite grafting of allogeneic islets with syngeneic myoblasts expressing FasL protected the islet graft from immune rejection and maintained normoglycemia for more than 80 days in mice with streptozotocin-induced diabetes. Graft survival was not prolonged with composite grafts of unmodified myoblasts or Fas-expressing myoblasts. Islet allografts transplanted separately from FasL-expressing myoblasts into the contralateral kidney were rejected, as were similarly transplanted third-party thyroid allografts. Thus, the FasL signal provided site- and immune-specific protection of islet allografts.

Partial repression of human gamma-globin genes by LCR element HS3 when linked to beta-globin genes and LCR element HS2 in MEL cells.

Clues for overcoming fetal (gamma-) globin gene repression in adult human erythroid cells may come from understanding why repression of isolated gamma-globin genes has not previously been achieved in the adult erythroid environment of mouse erythroleukemia cells (MEL). Repression of human gamma-globin genes has been demonstrated in MEL cells when transferred as part of the entire beta-globin gene cluster packaged in chromatin. Major differences in these approaches are prior packaging into chromatin and the presence of additional sequences, notably from the locus control region (LCR). In this report we focus on the contribution to gamma-globin gene repression that multiple elements of the LCR may have. We first show preferential activation of beta-globin genes over gamma-globin genes in MEL cells when linked to each other and to LCR sequences containing the core elements of DNase I hypersensitive sites 4, 3, and 2. Removal of the HS4 element had no effect, however, removal of the 225 bp HS3 core element resulted in a five-fold increase in gamma-globin gene expression. The enhancer 3' to the A gamma-globin gene also had no apparent effect on gamma-globin gene expression. These results provide first evidence of gamma-globin gene repression involving the core region of HS3 in the presence of the core region of HS2 and a beta-globin gene. A mechanism for repression involving sequestration of the gamma-promoter away from the strong enhancer activity of HS2 is proposed.

Erythroid progenitors in the peripheral blood of children with sickle cell disease.

PURPOSE: The goals of this study were (a) to determine the number of peripheral blood burst forming units-erythroid (BFU-E); (b) to define the relationship between circulating BFU-E number and fetal hemoglobin (HbF) level; and (c) to define the relationship between BFU-E number and age in pediatric sickle cell disease (SCD) patients. PATIENTS AND METHODS: Fetal hemoglobin (HbF) level and peripheral blood BFU-E number were determined in children < 18 years of age with SCD in a steady state of their disease. These data were compared with those of normal children. RESULTS: An increased number of BFU-E was observed in the peripheral blood of children with SCD compared with normals (30.7 vs. 15.7 per 10(5) mononuclear cells, respectively; p = 0.009). Overall there was the suggestion of a direct relationship between HbF level and peripheral blood BFU-E number (regression coefficient = 0.445; p = 0.06). Additionally, a strong inverse relationship between BFU-E number and age (regression coefficient = -0.671; p < 0.0001) was observed. CONCLUSIONS: In children with SCD (a) there are an increased number of peripheral blood BFU-E compared with normal children; (b) the inverse relationship between HbF level and BFU-E number observed in adult SCD patients is not seen in children; and (c) there is a strong inverse relationship between age and BFU-E number. This information may help to further clarify the relationship between peripheral blood BFU-E and erythropoietic stress.

Erythropoietin and hydroxyurea can act on early erythroid progenitors from adult human peripheral blood to modulate fetal globin mRNA levels.

Fetal hemoglobin production in adult human erythroid progenitors can be influenced by exogenous factors. In this report, we examine the effects of erythropoietin (Epo) and hydroxyurea (HU) in serum-free media on fetal (gamma-) globin mRNA levels when present during the first week of peripheral blood burst-forming unit-erythroid (BFU-E) culture. Fetal calf serum (FCS) is known to elevate gamma-globin mRNA levels in BFU-E culture and has been shown to do so even when added after the first week of culture. Removal of FCS from the first week of our BFU-E cultures did not significantly reduce gamma-globin mRNA levels, in agreement with these earlier findings. Addition of Epo to BFU-E cultures 4 days before addition of FCS led to a significant drop in gamma-globin mRNA levels; Epo addition also led to a significant increase in the number of erythroid bursts. Culture conditions, including Epo in serum-free liquid medium for 1 week followed by plating in semisolid medium containing FCS and Epo, resulted in low gamma-globin mRNA levels, similar to levels found in vivo, and high burst numbers. These conditions were used to demonstrate significant elevation of gamma-globin mRNA levels by HU present during the first week of BFU-E culture. Our findings suggest that gamma-globin mRNA levels can be influenced early in erythropoiesis by Epo and HU.

Desmin/vimentin intermediate filaments are dispensable for many aspects of myogenesis.

An expression vector was prepared containing a cDNA coding for a truncated version of the intermediate filament (IF) protein desmin. The encoded truncated desmin protein lacks a portion of the highly conserved alpha-helical rod region as well as the entire nonhelical carboxy-terminal domain. When transiently expressed in primary fibroblasts, or in differentiating postmitotic myoblasts and multinucleated myotubes, the truncated protein induces the complete dismantling of the preexisting vimentin or desmin/vimentin IF networks, respectively. Instead, in both cell types vimentin and desmin are packaged into hybrid spheroid bodies scattered throughout the cytoplasm. Despite the complete lack of intact IFs, myoblasts and myotubes expressing truncated desmin assemble and laterally align normal striated myofibrils and contract spontaneously in a manner indistinguishable from that of control myogenic cells. In older cultures the spheroid bodies shift from a longitudinal to a predominantly transverse orientation and loosely align along the I-Z-I-regions of striated myofibrils (Bennett, G.S., S. Fellini, Y. Toyama, and H. Holtzer. 1979. J. Cell Biol. 82:577-584), analogous to the translocation of intact desmin/vimentin IFs in control muscle. These results suggest the need for a critical reexamination of currently held concepts regarding the functions of desmin IFs during myogenesis.

Retroviral transfer of a human fetal globin gene carrying the -202 G gamma beta (+)-HPFH mutation into the human erythroleukemia line, KMOE.

The presence of point mutations at position -202 relative to the mRNA Cap site of both human fetal gamma-globin genes is linked with elevated fetal globin levels in adults. The question addressed in this study is whether the -202 mutation affects gamma-globin gene expression in the same manner as the -117 hereditary persistence of fetal hemoglobin (HPFH) A gamma-globin mutation. The -117 mutation was found to cause over-expression and confer inducibility of a retrovirally transferred gamma-globin gene in cytosine arabinoside (araC)-treated KMOE cells in an earlier study. In this study, fetal globin genes driven by either the normal G gamma or -202 HPFH G gamma-globin promoter were retrovirally transferred into human erythroid KMOE cells. The -202 HPFH mutation did not cause over-expression or confer inducibility of the transferred gamma-globin gene in araC-treated KMOE cells. Thus, the -202 HPFH mutation affects gamma-globin gene expression by a different mechanism than the -117 HPFH mutation. Furthermore, this study provides evidence against a general increasing of gamma-globin gene expression as might be expected from the -202 mutation altering binding of a ubiquitous factor such as Sp1.

Retroviral transfer of genes into erythroid progenitors derived from human peripheral blood.

Human erythroblasts are a logical target for studies of expression of transferred globin genes because high-level expression is a prerequisite for gene therapy of hemoglobinopathies. Early erythroid progenitors (erythroid burst-forming units, BFU-E) are readily available from human peripheral blood and can be cultured to produce erythroblasts. However, conditions for efficient transfer into these normal progenitors have not been previously described. Here we demonstrate efficient transfer of the neomycin resistance gene into human peripheral blood BFU-E using the retrovirus vector, N2. We show that liquid culture of mononuclear cells from peripheral blood for 18-24 h prior to retroviral infection leads to increased transfer efficiency of N2 as determined by G418 resistance, and we are able to detect viral DNA by polymerase chain reaction (PCR) analysis. In addition, a second retrovirus, beta(gamma)-SVX, prepared with a human beta-globin gene containing a gamma-globin second exon to facilitate transcript detection and the 3'-enhancer sequence, was also used to determine whether similar results could be obtained when more than one gene is transferred. Using the beta(gamma)-SVX virus, increased transfer efficiency into BFU-E was similarly found after liquid culture for up to 4 days. Expression of the transferred globin gene was also detected by PCR analysis of cDNA made from erythroblast RNA. The human peripheral blood BFU-E system described should allow determination of sequences required for high-level expression of transferred globin and other erythroid genes.

A simple, efficient method for the separate isolation of RNA and DNA from the same cells.

A method for the isolation of total cytoplasmic RNA and high molecular weight DNA from the same cells is described. Cells are gently lysed with NP40 in the presence of vanadyl ribonucleoside complex and the nuclei pelleted by centrifugation. RNA is purified by phenol/CHCl3 extraction of the lysate supernatant followed by ethanol precipitation. Protein is removed from high molecular weight DNA by salt-precipitation after nuclei are digested with proteinase K in the presence of sodium dodecyl sulfate. High yields of clean, intact RNA and DNA are obtained. A major advantage of the method is that it can be scaled down to quantitatively extract RNA and DNA from as little as 1000 cells.

Cytosine arabinoside plus hemin treatment of a human erythroid cell line, KMOE, strongly induces embryonic, fetal, and adult beta-like globin genes.

A variety of regimens were utilized on KMOE cells to maximally raise globin mRNA levels for the purpose of improving the usefullness of this line for globin gene studies. Steady-state mRNA levels of embryonic (epsilon), fetal (gamma) and adult (beta) globin genes were assayed by the S1-nuclease protection method before and after exposure to inducing compounds. Exposure of KMOE cells to cytosine arabinoside and hemin leads to over 20-fold increases in beta- and gamma-globin mRNA steady-state levels, and an over 60-fold increase in epsilon-globin mRNA level. Exposure to cytosine arabinoside alone induced beta- and epsilon-globin but not gamma-globin gene expression. The alpha-like globin genes (zeta and alpha) were also monitored but found to be poorly expressed and not significantly inducible. The presence of epsilon-globin mRNA and the lack of alpha-globin mRNA distinguishes this line, KMOE-EL, from the KMOE sublines previously described.

Expression of the affected A gamma globin gene associated with Greek nondeletion hereditary persistence of fetal hemoglobin.

The overexpressed A gamma globin gene in the Greek type of nondeletion hereditary persistence of fetal hemoglobin has a unique single-base substitution located at position -117 relative to the site of transcription initiation. This gene and its normal counterpart were transferred into cultured cell lines by using a retroviral vector. The only difference in expression between the transferred normal and mutant gamma genes was observed in the human erythroleukemia cell line KMOE after exposure of the cells to cytosine arabinoside, a condition that resulted in an adult pattern of endogenous globin gene expression by the cells and was associated with increased expression of the mutant gene.