Adult and neonatal astrocytes exhibit diverse gene expression profiles in response to beta amyloid &lt;i&gt;ex vivo&lt;/i&gt;

Novel treatment strategies are of paramount importance to improve clinical outcomes in pediatric AML. Since chemotherapy is likely to remain the cornerstone of curative treatment of AML, insights in the molecular mechanisms that determine its cytotoxic effects could aid further treatment optimization. To assess which genes and pathways are implicated in tumor drug resistance, we correlated ex vivo drug response data to genome-wide gene expression profiles of 73 primary pediatric AML samples obtained at initial diagnosis. Ex vivo response of primary AML blasts towards cytarabine (Ara C), daunorubicin (DNR), etoposide (VP16), and cladribine (2-CdA) was associated with the expression of 101, 345, 206, and 599 genes, respectively (p < 0.001, FDR 0.004–0.416). Microarray based expression of multiple genes was technically validated using qRT-PCR for a selection of genes. Moreover, expression levels of BRE, HIF1A, and CLEC7A were confirmed to be significantly (p < 0.05) associated with ex vivo drug response in an independent set of 48 primary pediatric AML patients. We present unique data that addresses transcriptomic analyses of the mechanisms underlying ex vivo drug response of primary tumor samples. Our data suggest that distinct gene expression profiles are associated with ex vivo drug response, and may confer a priori drug resistance in leukemic cells. The described associations represent a fundament for the development of interventions to overcome drug resistance in AML, and maximize the benefits of current chemotherapy for sensitive patients.

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Identification of Tissue-Restricted Transcripts in Human Islets

Endocrinology ◽

10.1210/en.2004-0691 ◽

2004 ◽

Vol 145 (10) ◽

pp. 4513-4521 ◽

Cited By ~ 58

Author(s):

Antonella Maffei ◽

Zhuoru Liu ◽

Piotr Witkowski ◽

Federica Moschella ◽

Giovanna Del Pozzo ◽

...

Keyword(s):

Gene Expression ◽

Islet Cell ◽

Ex Vivo ◽

Expression Profiles ◽

Kidney Tissue ◽

Gene Expression Profiles ◽

Human Islets ◽

Gene Products ◽

Associated Proteins

Abstract The purpose of our study was to identify transcripts specific for tissue-restricted, membrane-associated proteins in human islets that, in turn, might serve as markers of healthy or diseased islet cell masses. Using oligonucleotide chips, we obtained gene expression profiles of human islets for comparison with the profiles of exocrine pancreas, liver, and kidney tissue. As periislet presence of type 1 interferon is associated with the development of type 1 diabetes, the expression profile of human islets treated ex vivo with interferon-α2β (IFNα2β) was also determined. A set of genes encoding transmembrane- or membrane-associated proteins with novel islet-restricted expression was resolved by determining the intersection of the islet set with the complement of datasets obtained from other tissues. Under the influence of IFNα2β, the expression levels of transcripts for several of the identified gene products were up- or down-regulated. One of the islet-restricted gene products identified in this study, vesicular monoamine transporter type 2, was shown to bind [3H]dihydrotetrabenazine, a ligand with derivatives suitable for positron emission tomography imaging. We report here the first comparison of gene expression profiles of human islets with other tissues and the identification of a target molecule with possible use in determining islet cell masses.

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Effect ofEx VivoCulture Conditions on Immunosuppression by Human Mesenchymal Stem Cells

BioMed Research International ◽

10.1155/2013/154919 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Myoung Woo Lee ◽

Dae Seong Kim ◽

Somi Ryu ◽

In Keun Jang ◽

Hye Jin Kim ◽

...

Keyword(s):

Gene Expression ◽

Ex Vivo ◽

Expression Profiles ◽

Human Mesenchymal Stem Cells ◽

Gene Expression Profiles ◽

Culture Conditions ◽

Seeding Density ◽

Initial Seeding ◽

Density Treatment

A microarray analysis was performed to investigate whetherex vivoculture conditions affect the characteristics of MSCs. Gene expression profiles were mainly influenced by the level of cell confluence rather than initial seeding density. The analysis showed that 276 genes were upregulated and 230 genes downregulated in MSCs harvested at~90% versus~50% confluence (P<0.05,FC>2). The genes that were highly expressed in MSCs largely corresponded to chemotaxis, inflammation, and immune responses, indicating direct or indirect involvement in immunomodulatory functions. Specifically, PTGES and ULBP1 were up-regulated in MSCs harvested at high density. Treatment of MSCs withPTGESorULBP1siRNA reversed their inhibition of T-cell proliferationin vitro. The culture conditions such as cell confluence at harvest seem to be important for gene expression profile of MSCs; therefore, the results of this study may provide useful guidelines for the harvest of MSCs that can appropriately suppress the immune response.

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Gene expression in mouse ovarian follicle development in vivo versus an ex vivo alginate culture system

Reproduction ◽

10.1530/rep-10-0481 ◽

2011 ◽

Vol 142 (2) ◽

pp. 309-318 ◽

Cited By ~ 26

Author(s):

Elizabeth M Parrish ◽

Anaar Siletz ◽

Min Xu ◽

Teresa K Woodruff ◽

Lonnie D Shea

Keyword(s):

Gene Expression ◽

Transforming Growth Factor ◽

Ex Vivo ◽

Expression Profiles ◽

Ovarian Follicle ◽

Gene Expression Profiles ◽

Follicle Development ◽

Α Subunit

Ovarian follicle maturation results from a complex interplay of endocrine, paracrine, and direct cell–cell interactions. This study compared the dynamic expression of key developmental genes during folliculogenesis in vivo and during in vitro culture in a 3D alginate hydrogel system. Candidate gene expression profiles were measured within mouse two-layered secondary follicles, multi-layered secondary follicles, and cumulus–oocyte complexes (COCs). The expression of 20 genes involved in endocrine communication, growth signaling, and oocyte development was investigated by real-time PCR. Gene product levels were compared between i) follicles of similar stage and ii) COCs derived either in vivo or by in vitro culture. For follicles cultured for 4 days, the expression pattern and the expression level of 12 genes were the same in vivo and in vitro. Some endocrine (cytochrome P450, family 19, subfamily A, polypeptide 1 (Cyp19a1) and inhibin βA subunit (Inhba)) and growth-related genes (bone morphogenetic protein 15 (Bmp15), kit ligand (Kitl), and transforming growth factor β receptor 2 (Tgfbr2)) were downregulated relative to in vivo follicles. For COCs obtained from cultured follicles, endocrine-related genes (inhibin α-subunit (Inha) and Inhba) had increased expression relative to in vivo counterparts, whereas growth-related genes (Bmp15, growth differentiation factor 9, and kit oncogene (Kit)) and zona pellucida genes were decreased. However, most of the oocyte-specific genes (e.g. factor in the germline α (Figla), jagged 1 (Jag1), and Nlrp5 (Mater)) were expressed in vitro at the same level and with the same pattern as in vivo-derived follicles. These studies establish the similarities and differences between in vivo and in vitro cultured follicles, guiding the creation of environments that maximize follicle development and oocyte quality.

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R123: Gene Expression Profiles in Ex Vivo Model of Nasal Polyp

Otolaryngology ◽

10.1016/j.otohns.2006.06.877 ◽

2006 ◽

Vol 135 (2_suppl) ◽

pp. P147-P147

Author(s):

Kyung-Wook Heo ◽

Seong-Kook Park

Keyword(s):

Gene Expression ◽

Nasal Polyp ◽

Ex Vivo ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ex Vivo Model

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Shifting Gene Expression Profiles During Ex Vivo Culture of Renal Tumor Cells: Implications for Cancer Immunotherapy

Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics ◽

10.3727/000000003771013080 ◽

2003 ◽

Vol 14 (3) ◽

pp. 133-145 ◽

Cited By ~ 5

Author(s):

Federica Moschella ◽

Richard P. Catanzaro ◽

Brygida Bisikirska ◽

Ihor S. Sawczuk ◽

Kyriakos P. Papadapoulos ◽

...

Keyword(s):

Gene Expression ◽

Cancer Immunotherapy ◽

Tumor Cells ◽

Renal Tumor ◽

Ex Vivo ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ex Vivo Culture

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Differential Gene Expression Profiles of Cord Blood Lineage-Negative Cells Prior to and Following Selective Amplification.

Blood ◽

10.1182/blood.v104.11.4141.4141 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4141-4141

Author(s):

Meng-jiao Shi ◽

Jason Hermann ◽

Joseph Laning ◽

Henry Hoppe ◽

Morey Kraus ◽

...

Keyword(s):

Gene Expression ◽

Cord Blood ◽

Ex Vivo ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Ex Vivo Expansion ◽

Hematopoietic Stem ◽

Selective Amplification ◽

Cyclin E1

Abstract Using a selective-amplification system, we have ex vivo expanded umbilical cord blood (UCB) derived lineage-negative− (Lin−: CD2−, CD3−, CD14−, CD16−, CD19−, CD24−, CD56−, CD66b−, and Glycophorin A−) cells. To assess at the molecular level the effect of the ex vivo expansion on properties of UCB Lin−-cells, we compared gene expression profiles between cells at day 0 and cells cultured in serum-free medium supplemented with rhFlt-3L, rhSCF and rhTPO (100ng/ml each) for 14 days with a reselection using the same lineage depletion antibody cocktail at the 7th day of culture. In this study, we utilized a human stem cell gene cDNA array (SuperArray Bioscience Corp.), which include genes encoding surface markers, growth factor/cytokines, extracellular matrix molecules and cell cycle regulators for embryonic, neural, mesodermal and hematopoietic stem/progenitor cells. Of the 266 total genes in the array, we detected 85 genes expressed above background in either of the two populations. Among these expressed genes, 19 were found only in the day_0 (pre-culture) population and 11 were found only in the day_14 cultured cells. Ex vivo expansion under these conditions had no significant effect on the majority of the genes, which include highly expressed homing-related (CXCR4, CD44) and cell adhesion (CD31) molecules. Further analysis revealed that, compared to the levels in the original day_0 Lin− population, 7 genes showed more than 3-fold increases and 13 genes showed more than 3-fold decreases in their levels of expression in the cultured day_14 cell population. The up-regulated genes included those involved in cell cycling, proliferation and migration or anti-apoptosis (cyclin E1, IGFR-2, alpha(4)beta(1)-integrin, Mdm2, Cystatin C, ALK-5). The down-regulated genes included those involved in embryological or neural development (GCMb, FGF11), a subset of integrin molecules (integrin alpha E, beta 3 and 5) and an inhibitor of BMP signaling (CER1). In conclusion, our results indicate that selective ex vivo expansion conditions promote expression of genes related to the growth and expansion of targeted hematopoietic precursor cells while retaining expression of homing-related genes. Further studies are slated to link, where possible, these transcriptional expression patterns with expression and functions of these genes at the protein and cellular levels. Figure Figure

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PP 102 Gene expression profiles obtained from mouse hair, xenograft tumor and ex vivo human scalp hair to determine the effects of drug response following treatment with an EGFR inhibitor

European Journal of Cancer ◽

10.1016/s0959-8049(11)72696-x ◽

2011 ◽

Vol 47 ◽

pp. S28-S29

Author(s):

B. Reed ◽

E. Grimes ◽

T. Mefo ◽

E. Harrison ◽

L. Meyer-Turkson ◽

...

Keyword(s):

Gene Expression ◽

Drug Response ◽

Scalp Hair ◽

Ex Vivo ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Egfr Inhibitor ◽

Xenograft Tumor ◽

Human Scalp Hair

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Harnessing Gene Expression Profiles for the Identification of Drug Resistance Genes in Pediatric AML

Blood ◽

10.1182/blood.v120.21.283.283 ◽

2012 ◽

Vol 120 (21) ◽

pp. 283-283

Author(s):

Costa Bachas ◽

Gerrit Jan Schuurhuis ◽

C. Michel Zwaan ◽

Marry M. van den Heuvel-Eibrink ◽

Monique L. Den Boer ◽

...

Keyword(s):

Gene Expression ◽

Drug Resistance ◽

Ex Vivo ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Drug Resistant ◽

Genome Wide ◽

Pediatric Aml ◽

Upstream Regulators ◽

Gene Expression Levels

Abstract Abstract 283 The vast majority of pediatric AML patients (>90%) achieve complete remission, however 30–40% relapse and face a dismal prognosis. Current therapy is insufficient as drug resistant cells survive chemotherapy; novel strategies are needed to overcome chemoresistance and improve outcome. The molecular basis underlying drug resistance in AML cells remains largely unknown. Based on the hypothesis that drug resistance in AML patients is largely due to intrinsic properties of leukemic blasts, we here correlated ex-vivo drug resistance data of primary patient samples to genome wide microarray gene expression profiles of AML blasts from diagnosis samples. Peripheral blood or bone marrow samples of 73 pediatric AML patients were enriched for leukemic blasts (median 89% blasts). Ex-vivo drug resistance towards cytarabine (ara-C, N=73), daunorubicin (DNR, N=69), etoposide (VP16, N=39) and cladribine (CDA, N=59) was assayed using the 4 days colorimetric MTT assay; median LC50 values are shown in Table 1. Genome wide expression profiling on the enriched samples was performed using the Affymetrix HGU 133 plus 2 platform (Balgobind et al, Hematologica, 2011). Spearman's rank correlation analyses were used to correlate gene expression levels to the LC50 values, nominal p-values < 0.001 were considered significant. The number of significant probe sets for each drug is shown in Table 1. The strongest correlation of ex-vivo drug resistance and gene expression was found for VP16 (r2 ranged from −0.78 to 0.69 with p values ranging from 1×10−4 to 2×10−7 for the above mentioned 656 probes). The figure illustrates the correlation of ex-vivo DNR resistance with gene expression levels. We performed Gene Ontology (GO) enrichment analysis and Ingenuity Pathway Analysis (IPA) using expression values of the probe sets that were associated with ex-vivo resistance for each drug to gain insight in the possible cellular pathways involved. Chromatin remodeling, epigenetic regulation of gene expression and methyltransferase activity were among the top GO categories for ara-C resistance. For example, a high expression of MLL2, MLL4, ASXL1, and CARM1 was associated with high ara-C LC50 values. For DNR, GO and IPA indicated a role for response to growth factor stimuli and mitochondrial response to oxidative stress; examples of individual genes are shown in the Figure below. For VP16, a low expression of genes that are implicated in cell cycle, DNA replication and DNA damage response was associated with increased resistance. This included DNA polymerases, genes in BRCA1 signaling as well as the target of VP16, topoisomerase 2α. Upstream regulators that contribute to the gene expression profiles that were associated with ex-vivo drug resistance according to IPA are shown in Table 2. Interestingly, for DNR, VP16 and CDA the expression profiles in part explained by regulation via CD40L, a gene that has been associated with drug resistance in lymphatic leukemias. Targeted therapeutics are being developed to interfere in the CD40L mediated anti-apoptotic signaling and thus may offer alternative treatment options in drug resistant AML. Hence, we present novel data in which diagnosis samples of a relatively large group of pediatric AML patients were used to identify gene expression profiles that are associated with cellular drug resistance. These data may pave the way to the identification of genes that contribute to drug resistance, e.g. CD40L. Moreover, our findings may enhance the development of personalized treatment strategies by sensitizing patients to conventional chemotherapeutic drugs. Table 1. Summary of ex-vivo drug resistance of primary AML blasts and its correlation with genome wide gene expression data Drug LC50 significant probe sets Ara-C .360 (.182-.616) 113 DNR .172 (.093-.250) 465 VP16 2.65 (1.84-6.70) 656 CDA .020 (.004-.027) 269 LC50 = lethal concentration needed to kill 50% of the cells depicted as median ug/mL(p25-p75). Table 2. Summary of pathway analysis of gene expression that correlated with ex-vivo drug sensitivity Drug top 3 upstream regulators p range upstream regulators Ara-C IL5 2.40×10−02 DNR CD40L, IRF8, OSCAR 7.4×10−4 to 4.4×10−5 VP16 CD40L, BRCA1, ACAT1 3.2×10−2 to 9.6×10−3 CDA CD40L, ASB2,IL10RB 1.15×10−2 to 8.3×10−4 Upstream regulators are ranked according to p-value. Disclosures: No relevant conflicts of interest to declare.

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