Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast-specific regulation of the insulin-like growth factor binding protein 4 gene

Estradiol (E2) is believed to modulate physiological functions relevant to osteoblast biology through the actions of estrogen receptors (ERs) that in turn regulate the expression of target genes. The molecular effects of estrogen action in bone remain to be fully elucidated. This study reports a genome-wide molecular and computational analysis of the interaction between ER and regulatory elements on the DNA of target genes in human primary osteoblasts. Of approximately 54,000 gene probes surveyed in this study, a total of 375 genes were up-regulated and 418 genes were down-regulated on exposure to E2, with only 46 of these being direct target genes after 24 h, as determined by concomitant cycloheximide treatment. Computational analysis discovered several pathways where E2 co-regulates multiple functionally linked components. Examination of the genomic sequence of IGF binding protein 4 located ER response elements within the first intron. Using by chromatin immunoprecipitation, we show a site- and cell-specific recruitment of transcription factors to this newly identified regulatory region. Transient transfection studies revealed that this intronic region acts as a functional promoter in human osteoblasts. Taken together, this analysis provides a comprehensive gene transcription profile and identifies several genes of potential physiological importance in controlling estrogen-mediated signaling in primary osteoblasts.

The introduction of verteporfin photodynamic therapy in the UK: PDT users group (PDTUG) surveillance programme report 1

AIMS

To report overall patient recruitment characteristics and visual acuity (VA) outcome related to baseline lesion characteristics for patients with choroidal neovascularisation (CNV) treated with verteporfin photodynamic therapy (PDT) during its introduction into routine National Health Service practice.

METHODS

Thirteen treatment centres prospectively submitted data on patients undergoing verteporfin PDT for CNV of mixed aetiology between November 1999 and May 2004 into the PDT Users Group (PDTUG) surveillance database. The primary outcome was the proportion of eyes losing <15 letters of VA at 12 and 24 months, follow-up compared with the baseline examination.

RESULTS

One thousand eight hundred and ninety-four eyes of 1755 patients were analysed. Lesion characteristics at baseline were: classic no occult 1152 (67.4%), predominantly classic with occult 531 (31.1%). Recruitment rate rose steadily from 13 in the first to 188 in the final quarter. Data were available at 12 months on 1010 (53.3%) and at 24 months on 310 (16.4%) eyes. The proportion of eyes losing <15 letters was 71% (716/1010) at 12 months and 70% (217/310) at 24 months. At 12 months 91% (917/1010) of patients lost <30 letters. The mean number of PDT treatments for the cohort was 2.4 in the first 12 months. An adverse reaction or event was reported in 8.1% (364/4515) of treatments. Non-visual adverse events were infrequent.

CONCLUSIONS

Efficacy and safety of verteporfin PDT in reducing vision loss in macular degeneration can be reproduced in routine clinical practice. Compared to the TAP study, the fewer treatments needed in the PDTUG cohort indicate the potential for better cost-effectiveness.

The heterogeneity of human mesenchymal stem cell preparations--evidence from simultaneous analysis of proteomes and transcriptomes

OBJECTIVE

Mesenchymal stem cells (MSC) raise high hopes in clinical applications. However, the lack of common standards and a precise definition of MSC preparations remains a major obstacle in research and application of MSC. Whereas surface antigen markers have failed to precisely define this population, a combination of proteomic data and microarray data provides a new dimension for the definition of MSC preparations.

METHODS

In our continuing effort to characterize MSC, we have analyzed the differential transcriptome and proteome expression profiles of MSC preparations isolated from human bone marrow under two different expansion media (BM-MSC-M1 and BM-MSC-M2).

RESULTS

In proteomics, 136 protein spots were unambiguously identified by MALDI-TOF-MS and corresponding cDNA spots were selected on our "Human Transcriptome cDNA Microarray." Combination of datasets revealed a correlation in differential gene expression and protein expression of BM-MSC-M1 vs BM-MSC-M2. Genes involved in metabolism were more highly expressed in BM-MSC-M1, whereas genes involved in development, morphogenesis, extracellular matrix, and differentiation were more highly expressed in BM-MSC-M2. Interchanging culture conditions for 8 days revealed that differential expression was retained in several genes whereas it was altered in others.

CONCLUSION

Our results have provided evidence that homogeneous BM-MSC preparations can reproducibly be isolated under standardized conditions, whereas culture conditions exert a prominent impact on transcriptome, proteome, and cellular organization of BM-MSC.

Reliability and validity of the CMT neuropathy score as a measure of disability

OBJECTIVE

To determine the validity and reliability of the Charcot-Marie-Tooth disease (CMT) neuropathy score (CMTNS) in patients with inherited neuropathy.

BACKGROUND

Natural history studies and potential treatment trials for patients with various forms of CMT are limited by the lack of quantitative methodologies to monitor disease progression. Most cases of CMT can be considered length-dependent axonal neuropathies because disability for even the demyelinating forms correlates with length-dependent axonal degeneration. The total neuropathy score (TNS) is a validated composite measure of disability in length-dependent axonal neuropathies but is weighted toward predominantly sensory neuropathies. Thus, the authors have devised a CMTNS, modified from the TNS, to provide a single measure to quantify CMT disability.

METHODS

The authors measured inter- and intrainvestigator reliability of the CMTNS and performed a validation of the score with the Neuropathy Impairment Score (NIS), patient self-assessment scores, an ambulation index, and other measures of disability.

RESULTS

Inter- and intrainvestigator reliability was more than 95% in the 60 patients evaluated. Patients could be divided into mild (CMTNS, < or =10), moderate (CMTNS, 11 to 20), and severe (CMTNS, > or =21) categories and demonstrated excellent correlations among all measures of disability.

CONCLUSION

The Charcot-Marie-Tooth disease (CMT) neuropathy score is a validated measure of length-dependent axonal and demyelinating CMT disability and can be investigated as an end point for longitudinal studies and clinical trials of CMT.

Comparative characteristics of mesenchymal stem cells from human bone marrow, adipose tissue, and umbilical cord blood

OBJECTIVE

Various preparative protocols have been proposed for the acquisition and cultivation of mesenchymal stem cells (MSC). Whereas surface antigen markers have failed to precisely define this population, microarray analysis might provide a better tool for characterization of MSC.

METHODS

In this study, we have analyzed global gene expression profiles of human MSC isolated from adipose tissue (AT), from umbilical cord blood (CB), and from bone marrow (BM) under two growth conditions and have compared them to terminally differentiated human fibroblasts (HS68). Profiles were compared using our Human Genome Microarray representing 51.144 different cDNA clones.

RESULTS

Cultured with the appropriate conditions, osteogenic and adipogenic differentiation could be confirmed in all MSC preparations but not in fibroblasts. No phenotypic differences were observed by flow cytometry using a panel of 22 surface antigen markers. Whereas MSC derived from different donors using the same culture procedure yielded a consistent and reproducible gene expression profile, many genes were differentially expressed in MSC from different ontogenetic sources or from different culture conditions. Twenty-five genes were overlapping and upregulated in all MSC preparations from AT, CB, and BM as compared to HS68 fibroblasts. These genes included fibronectin, ECM2, glypican-4, ID1, NF1B, HOXA5, and HOXB6. Many genes upregulated in MSC are involved in extracellular matrix, morphogenesis, and development, whereas several inhibitors of the Wnt pathway (DKK1, DKK3, SFRP1) were highly expressed in fibroblasts.

CONCLUSION

Our results have provided a foundation for a more reproducible and reliable quality control using genotypic analysis for defining MSC.

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression

With the production of whole genome microarray chips the ability arises to investigate whether the regulation of particular groups of genes may be influenced by their chromosomal localization. Chromosome Co-Localization probability calculator (ChroCoLoc) is a publicly available web-based tool for the analysis of co-localization of co-expressed genes identified by microarray experiments.

AVAILABILITY

http://www.ebi.ac.uk/expressionprofiler/

Hematopoietic Progenitor Cells and Cellular Microenvironment: Behavioral and Molecular Changes upon Interaction

Cell-cell contact between stem cells and cellular determinants of the microenvironment plays an essential role in controlling cell division. Using human hematopoietic progenitor cells (CD34+/CD38-) and a stroma cell line (AFT024) as a model, we have studied the initial behavioral and molecular sequel of this interaction. Time-lapse microscopy showed that CD34+/CD38- cells actively migrated toward and sought contact with stroma cells and 30% of them adhered firmly to AFT024 stroma through the uropod. CD44 and CD34 are colocalized at the site of contact. Gene expression profiles of CD34+/CD38- cells upon cultivation with or without stroma for 16, 20, 48, or 72 hours were analyzed using our human genome cDNA microarray. Chk1, egr1, and cxcl2 were among the first genes upregulated within 16 hours. Genes with the highest upregulation throughout the time course included tubulin genes, ezrin, c1qr1, fos, pcna, mcm6, ung, and dnmt1, genes that play an essential role in reorganization of the cytoskeleton system, stabilization of DNA, and methylation patterns. Our results demonstrate directed migration of CD34+/CD38- cells toward AFT024 and adhesion through the uropod and that upon interaction with supportive stroma, reorganization of the cytoskeleton system, regulation of cell division, and maintenance of genetic stability represent the most essential steps.

Retroviral Integration Sites Correlate with Expressed Genes in Hematopoietic Stem Cells

In this study, we analyzed whether retroviral integration sites in repopulating hematopoietic cells correlate with genes expressed in fractions enriched in hematopoietic stem cells (HSCs). We have previously described microarray studies of two populations enriched in HSCs: CD34+/CD38- and the slow dividing fraction of CD34+/CD38- cells (SDF). Furthermore, we demonstrated that oncoretroviral integrations in severe combined immunodeficient repopulating cells are preferentially located near the transcription start. Here, we have identified 117 corresponding cDNA clones on our micro-array representing genes with retroviral integration sites. These genes revealed a higher mean signal intensity in comparison with either all genes on the array or a subset of control genes with retroviral integrations in HeLa cells. Furthermore, these genes demonstrated a higher expression in CD34+/CD38- cells and SDF. The association of gene expression and retrovirally targeted genes observed here will help to elucidate the molecular characteristics of primitive repopulating hematopoietic cells.

Bloader--a batch loader application for MIAMExpress

BLoader is a client server application for annotating and loading large amounts of Microarray data into a local installation of the MIAMExpress database. A set of nested spreadsheets is used to collect the required MIAME annotation. Controlled vocabularies are downloaded from MIAMExpress and ArrayExpress databases to guarantee MIAME compliance.

AVAILABILITY

The application is available from the author at http://www.ansorge-group.embl.de/bloader

CONTACT

schwager@embl.de

SUPPLEMENTARY INFORMATION

For more details on BLoader visit the above web page.

Embryonic Stem Cell-Like Features of Testicular Carcinoma Revealed by Genome-Wide Gene Expression Profiling

Carcinoma in situ (CIS) is the common precursor of histologically heterogeneous testicular germ cell tumors (TGCTs), which in recent decades have markedly increased and now are the most common malignancy of young men. Using genome-wide gene expression profiling, we identified &gt;200 genes highly expressed in testicular CIS, including many never reported in testicular neoplasms. Expression was further verified by semiquantitative reverse transcription-PCR and in situ hybridization. Among the highest expressed genes were NANOG and POU5F1, and reverse transcription-PCR revealed possible changes in their stoichiometry on progression into embryonic carcinoma. We compared the CIS expression profile with patterns reported in embryonic stem cells (ESCs), which revealed a substantial overlap that may be as high as 50%. We also demonstrated an over-representation of expressed genes in regions of 17q and 12, reported as unstable in cultured ESCs. The close similarity between CIS and ESCs explains the pluripotency of CIS. Moreover, the findings are consistent with an early prenatal origin of TGCTs and thus suggest that etiologic factors operating in utero are of primary importance for the incidence trends of TGCTs. Finally, some of the highly expressed genes identified in this study are promising candidates for new diagnostic markers for CIS and/or TGCTs.

Molecular evidence for stem cell function of the slow-dividing fraction among human hematopoietic progenitor cells by genome-wide analysis

The molecular mechanisms that regulate asymmetric divisions of hematopoietic progenitor cells (HPCs) are not yet understood. The slow-dividing fraction (SDF) of HPCs is associated with primitive function and self-renewal, whereas the fast-dividing fraction (FDF) predominantly proceeds to differentiation. CD34+/CD38- cells of human umbilical cord blood were separated into the SDF and FDF. Genomewide gene expression analysis of these populations was determined using the newly developed Human Transcriptome Microarray containing 51 145 cDNA clones of the Unigene Set-RZPD3. In addition, gene expression profiles of CD34+/CD38- cells were compared with those of CD34+/CD38+ cells. Among the genes showing the highest expression levels in the SDF were the following: CD133, ERG, cyclin G2, MDR1, osteopontin, CLQR1, IFI16, JAK3, FZD6, and HOXA9, a pattern compatible with their primitive function and self-renewal capacity. Furthermore, morphologic differences between the SDF and FDF were determined. Cells in the SDF have more membrane protrusions and CD133 is located on these lamellipodia. The majority of cells in the SDF are rhodamine-123dull. These results provide molecular evidence that the SDF is associated with primitive function and serves as basis for a detailed understanding of asymmetric division of stem cells.

Aberrant PAX3 and PAX7 expression. A link to the metastatic potential of embryonal rhabdomyosarcoma and cutaneous malignant melanoma?

Transcription factors encoded by PAX3 and PAX7 are amongst the first expressed in the embryo, being principal regulators of neurogenic and myogenic progenitor cell specification and embryonic segmentation. The basis for this review lies in the supposition that genetic programs for cell migration, thought regulated by PAX3 and PAX7 during embryonic development, become tools used by the metastatic cell. In highly metastatic neoplasms arising from cells of neurogenic and myogenic lineages such as embryonal rhabdomyosarcoma and cutaneous malignant melanoma, markedly high expression levels of PAX3 and PAX7 support this supposition. As PAX3 and PAX7 are known to play a role in the regulation of migratory events in embryogenesis, it is possible that the metastatic potential of these tumours is directly linked to migratory properties conferred them through PAX expression. Here we provide a novel perspective by correlating metastasis with expression of PAX3, PAX7 and ephrin/Eph receptors as well as NCAMs, cell surface markers normally involved in migration and adhesion during development, and propose a role for PAX genes in the increased metastatic potential of these tumours.

Six novel connexin32 (GJB1) mutations in X-linked Charcot-Marie-Tooth disease

X-linked Charcot-Marie-Tooth disease (CMTX) is a clinically heterogeneous hereditary motor and sensory neuropathy with X-linked transmission. Common clinical manifestations of CMTX, as in other forms of Charcot-Marie-Tooth disease (CMT), are distal muscle wasting and weakness, hyporeflexia, distal sensory disturbance, and foot deformities. Motor nerve conduction velocity is reduced. In male patients it is often less than 38 m/s in the median nerve (a value often used to distinguish between "demyelinating" and "axonal" forms of CMT), but in female patients conduction velocity may be faster than this or normal. Mutations in the connexin32 (gap junction protein beta 1 (GJB1)) gene are responsible for the majority of CMTX cases. This report describes six British CMTX families with six novel mutations (four missense, one nonsense, and one frame shift) of the GJB1 gene. Affected members in these six families had typical signs of CMT but in some affected members of three families there was additional central nervous system involvement or deafness in the absence of any other explanation other than CMT.

Mineral and heavy metal status as related to a mortality event and poor recruitment in a moose population in Alaska

Moose (Alces alces) found dead (FD) and hunter-killed (HK) in 1995 on the north slope of Alaska (USA) in the Colville River Drainage were evaluated for heavy metal and mineral status. Compared to previous reports for moose and domestic cattle, and data presented here from Alaska moose outside the Colville River area, levels of Cu were determined to be low in hoof, hair, liver, kidney, rumen contents, and muscle for these north slope moose. Iron (Fe) was low in muscle as well. These findings, in conjunction with evidence of poor calf survival and adult mortality prompted investigation of a mineral deficiency in moose (serum, blood, and hair) captured in the spring of 1996 and 1997. Captured males had higher Ca, Zn and Cu levels in hair than captured females. Female moose hair samples were determined to be low (deficient) in Cu, Ca, Fe, and Se with mean levels (ppm) of 2.77, 599.7, 37.4, and 0.30, respectively. Serum Cu level was low, and to a lesser degree Zn was deficient as well. Whole blood (1997 only) was marginally deficient in Se and all animals were deficient in Cu. Based on whole blood, sera and hair, Cu levels were considered low for moose captured in spring 1996 and 1997 in the Colville River area as compared to published data and other populations evaluated in this study. Low levels of ceruloplasmin activity support this Cu deficiency theory. Evidence indicates that these moose are deficient in Cu and other minerals; however, the remote location precluded sufficient examination of animals to associate this apparent deficiency with direct effects or lesions. Renal levels of Cd increased with age at expected levels.

Functional annotation of a full-length mouse cDNA collection

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Diffusion of paramagnetically labeled proteins in cartilage: enhancement of the 1-D NMR imaging technique

Quantifying the diffusive transport of large molecules in avascular cartilage tissue is important both for planning potential pharamacological treatments and for gaining insight into the molecular-scale structure of cartilage. In this work, the diffusion coefficients of gadolinium-DTPA and Gd-labeled versions of four proteins-lysozyme, trypsinogen, ovalbumin, and bovine serum albumin (BSA) with molecular weights of 14,300, 24,000, 45,000, and 67,000, respectively-have been measured in healthy and degraded calf cartilage. The experimental technique relies on the effect of the paramagnetic on the relaxation properties of the surrounding water, combined with the time course of a 1-dimensional spatial profile of the water signal in the cartilage sample. The enhanced technique presented here does not require a prior measurement of the relaxivity of the paramagnetic compound in the sample of interest. The data are expressed as the ratio of the diffusion coefficient of a compound in cartilage to its diffusion coefficient in water. For healthy cartilage, this ratio was 0.34 +/- 0.07 for Gd-DTPA, the smallest compound, and fell to 0.3 +/- 0.1 for Gd-lysozyme, 0.08 +/- 0.04 for Gd-trypsinogen, and 0.07 +/- 0.04 for Gd-ovalbumin. Gd-BSA did not appear to enter healthy cartilage tissue beyond a surface layer. After the cartilage had been degraded by 24-h trypsinization, these ratios were 0.60 +/- 0.03 for Gd-DTPA, 0.40 +/- 0.08 for Gd-lysozyme, 0.42 +/- 0.09 for Gd-trypsinogen, 0.16 +/- 0.14 for Gd-ovalbumin, and 0.11 +/- 0.05 for Gd-BSA. Thus, degradation of the cartilage led to increases in the diffusion coefficient of up to fivefold for the Gd-labeled proteins. These basic transport parameters yield insights on the nature of pore sizes and chemical-matrix interactions in the cartilage tissue and may prove diagnostically useful for identifying the degree and nature of damage to cartilage.

Social costs of untreated opioid dependence

Using cost-of-illness methodology applied to a comprehensive survey of 114 daily opiate users not currently in or seeking treatment for their addiction, we estimated the 1996 social costs of untreated opioid dependence in Toronto (Ontario, Canada). The survey collected data on social and demographic characteristics, drug use history, physical and mental health status, the use of health care and substance treatment services, drug use modality and sex-related risks of infectious diseases, sources of income, as well as criminality and involvement with the law enforcement system. The annual social cost generated by this sample, calculated at Canadian $5.086 million, is explained mostly by crime victimization (44.6%) and law enforcement (42.4%), followed by productivity losses (7.0%) and the utilization of health care (6.1%). Applying the $13,100 cost to the estimated 8,000 to 13,000 users and 2.456 million residents living in Toronto yields a range of social cost between $43 and $69 per capita.

The influence of experience and specialisation on the reliability of a common clinical sign

OBJECTIVES

To explore the influence of experience and specialisation on clinical judgement by comparing accuracy in diagnosing anaemia between a consultant general surgeon, a consultant ophthalmologist and their registrars.

PATIENTS AND METHODS

Conjunctival inspection of 101 patients, subsequent correlation with haemoglobin concentration.

MAIN OUTCOME MEASURES

Number of correct and incorrect diagnoses of anaemia.

RESULTS

54 patients were anaemic and 47 were not. Overall accuracy in diagnosing anaemia ranged from 0.61-0.69, sensitivity 0.52-0.65 and specificity 0.62-0.83. Agreements between pairs of examiners were 0.68-0.81, with kappa values of 0.36-0.60 when adjusted for chance agreement.

CONCLUSIONS

Neither experience nor specialisation significantly influenced our ability to diagnose anaemia, based on conjunctival inspection. Without critical analysis of clinical signs, we are unaware of their diagnostic limitations.