scholarly journals Genes Regulated in Metastatic Osteosarcoma: Evaluation by Microarray Analysis in Four Human and Two Mouse Cell Line Systems

Sarcoma ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Roman Muff ◽  
Ram Mohan Ram Kumar ◽  
Sander M. Botter ◽  
Walter Born ◽  
Bruno Fuchs
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Cell Lines ◽  
Expression Profiles ◽  
Treatment Strategies ◽  
Metastatic Potential ◽  
New Drugs ◽  
Differentially Expressed ◽  
Osteoblastic Cell ◽  
Osteoblastic Cell Line

Osteosarcoma (OS) is a rare bone neoplasm that affects mainly adolescents. It is associated with poor prognosis in case of metastases formation. The search for metastasis predicting markers is therefore imperative to optimize treatment strategies for patients at risk and important for the search of new drugs for the treatment of this devastating disease. Here, we have analyzed by microarray the differential gene expression in four human and two mouse OS cell line systems consisting of parental cell lines with low metastatic potential and derivatives thereof with increased metastatic potential. Using two osteoblastic cell line systems, the most common OS phenotype, we have identified forty-eight common genes that are differentially expressed in metastatic cell lines compared to parental cells. The identified subset of metastasis relevant genes in osteoblastic OS overlapped only minimally with differentially expressed genes in the other four preosteoblast or nonosteoblastic cell line systems. The results imply an OS phenotype specific expression pattern of metastasis regulating proteins and form a basis for further investigation of gene expression profiles in patients’ samples combined with survival analysis with the aim to optimize treatment strategies to develop new drugs and to consequently improve the survival of patients with the most common form of osteoblastic OS.

24 GLOBAL TRANSCRIPT PROFILING OF CLONED BOVINE BLASTOCYSTS USING AFFYMETRIX GENECHIP TECHNOLOGY

2006 ◽  
Vol 18 (2) ◽  
pp. 120
Author(s):  
Z. Beyhan ◽  
P. Ross ◽  
A. Iager ◽  
A. Kocabas ◽  
K. Cunniff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Expression Profiles ◽  
Cell Structure ◽  
Donor Cell ◽  
Lipid Binding ◽  
Differentially Expressed ◽  
Gtp Binding ◽  
Cloned Bovine

Identification of genes implicated in the biological processes of somatic cell nuclear transfer will improve our understanding of reprogramming events, i.e. the transformation of a lineage-committed cell into a pluripotent one. In addition, the gene expression profile of cloned embryos can help explain the widely reported developmental failures in cloned animals. In this study, we investigated global gene expression profiles of bovine in vitro-fertilized and cloned embryos using Gene Chip Bovine Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA). For the generation of cloned bovine blastocysts from two adult fibroblast lines (C and D), we employed methods previously proven to generate live offspring and compared these offspring to in vitro-produced blastocysts. Total RNA isolated from groups of 10 blastocysts was amplified by a template-switching PCR. Amplified cDNAs were used to synthesize biotin-labeled antisense RNAs (aRNAs) during and in vitro transcription reaction. Labeled aRNAs were hybridized to microarrays as described by the manufacturer. Experiments were performed in four replicates. Expression data were analyzed using the Significance Analysis of Microarrays (SAM; Tusher et al. 2001 Proc. Natl. Acad. Sci. 98, 5116-5121) procedure and software. Overall, 48.4% and 46% of 23 000 bovine transcripts spotted on the arrays were present in cloned and in in vitro-produced control blastocysts, respectively. The SAM procedure identified 43 genes that changed at least 1.5-fold, with an estimated false discovery rate (FDR) of 20%. Comparison of gene expression between NT embryos produced from two different cell lines and IVF controls with the same criteria revealed 6 (clones from cell line C vs. IVF) and 46 (clones from cell line D vs. IVF) differentially expressed genes. The number of transcripts expressed differentially between the cloned embryos with different donor cell origin was 437. Of the 43 differentially expressed transcripts in cloned blastocysts, 13 have unknown functions and the rest of the genes related to cell structure (tuftelin, desmoplakin), cell cycle/mitosis (Kinesin like 4, katanin, stathmin, PCNA), energy metabolism (lactate dehydrogenase, ATPsynthase, lipid-binding protein, keto acid dehydrogenase E1, metallothionein), and cell signaling (GTP-binding protein1, GTP binding stimulatory protein). Our results indicate that expression profiles of cloned blastocysts could be affected by somatic donor cell.

Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e14544-e14544
Author(s):  
Eva Budinska ◽  
Jenny Wilding ◽  
Vlad Calin Popovici ◽  
Edoardo Missiaglia ◽  
Arnaud Roth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Clinical Significance ◽  
Cell Lines ◽  
Drug Response ◽  
Drug Sensitivity ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models for the poor prognosis subtypes Mesenchymal and CIMP-H like (characterized by EMT/stroma and immune-associated gene modules, respectively). Methods: We analyzed gene expression profiles of 35 publicly available cell lines with sensitivity data for 82 drug compounds, and our 94 cell lines with data on sensitivity for 7 compounds and colony morphology. As in vitro, stromal and immune-associated genes loose their relevance, we trained a new classifier based on genes expressed in both systems, which identifies the subtypes in both tissue and cell cultures. Cell line subtypes were validated by comparing their enrichment for molecular markers with that of our CRC subtypes. Drug sensitivity was assessed by linking original subtypes with 92 drug response signatures (MsigDB) via gene set enrichment analysis, and by screening drug sensitivity of cell line panels against our subtypes (Kruskal-Wallis test). Results: Of the cell lines 70% could be assigned to a subtype with a probability as high as 0.95. The cell line subtypes were significantly associated with their KRAS, BRAF and MSI status and corresponded to our CRC subtypes. Interestingly, the cell lines which in matrigel created a network of undifferentiated cells were assigned to the Mesenchymal subtype. Drug response studies revealed potential sensitivity of subtypes to multiple compounds, in addition to what could be predicted based on their mutational profile (e.g. sensitivity of the CIMP-H subtype to Dasatinib, p<0.01). Conclusions: Our data support the biological and potentially clinical significance of the CRC subtypes in their association with cell line models, including results of drug sensitivity analysis. Our subtypes might not only have prognostic value but might also be predictive for response to drugs. Subtyping cell lines further substantiates their significance as relevant model for functional studies.

scholarly journals Gene expression profiles of progressive pancreatic endocrine tumours and their liver metastases reveal potential novel markers and therapeutic targets

2006 ◽  
Vol 13 (2) ◽  
pp. 541-558 ◽  
Author(s):  
G Capurso ◽  
S Lattimore ◽  
T Crnogorac-Jurcevic ◽  
F Panzuto ◽  
M Milione ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Metastases ◽  
Cell Lines ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Therapeutic Targets ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Striking Similarity ◽  
Metastatic Lesions

The intrinsic nature of tumour behaviour (stable vs progressive) and the presence of liver metastases are key factors in determining the outcome of patients with a pancreatic endocrine tumour (PET). Previous expression profile analyses of PETs were limited to non-homogeneous groups or to primary lesions only. The aim of this study was to investigate the gene expression profiles of a more uniform series of sporadic, non-functioning (NF) PETs with progressive disease and, for the first time, their liver metastases, on the Affymetrix human genome U133A and B GeneChip set. Thirteen NF PET samples (eight primaries and five liver metastases) from ten patients with progressive, metastatic disease, three cell lines (BON, QGP and CM) and four purified islet samples were analysed. The same samples were employed for confirmation of candidate gene expression by means of quantitative RT-PCR, while a further 37 PET and 15 carcinoid samples were analysed by immunohistochemistry. Analysis of genes differentially expressed between islets and primaries and metastases revealed 667 up- and 223 down-regulated genes, most of which have not previously been observed in PETs, and whose gene ontology molecular function has been detailed. Overexpression of bridging integrator 1 (BIN1) and protein Z dependent protease inhibitor (SERPINA10) which may represent useful biomarkers, and of lymphocyte specific protein tyrosine kinase (LCK) and bone marrow stromal cell antigen (BST2) which could be used as therapeutic targets, has been validated. When primary tumours were compared with metastatic lesions, no significantly differentially expressed genes were found, in accord with cluster analysis which revealed a striking similarity between primary and metastatic lesions, with the cell lines clustering separately. We have provided a comprehensive list of differentially expressed genes in a uniform set of aggressive NF PETs. A number of dysregulated genes deserve further in-depth study as potentially promising candidates for new diagnostic and treatment strategies. The analysis of liver metastases revealed a previously unknown high level of similarity with the primary lesions.

scholarly journals MicroRNA-133a Inhibits Osteosarcoma Cells Proliferation and Invasion via Targeting IGF-1R

2016 ◽  
Vol 38 (2) ◽  
pp. 598-608 ◽  
Author(s):  
Guangnan Chen ◽  
Tingting Fang ◽  
Zhongming Huang ◽  
Yiying Qi ◽  
Shaohua Du ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Luciferase Reporter ◽  
Osteoblastic Cell ◽  
Osteosarcoma Cell ◽  
Osteosarcoma Cells ◽  
Invasion And Metastasis ◽  
Osteoblastic Cell Line ◽  
Human Osteosarcoma ◽  
Human Osteosarcoma Cell

Background/Aims: MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression by repressing translation or cleaving RNA transcripts in a sequence-specific manner. Downregulated microRNAs and their roles in cancer development have attracted much attention. A growing body of evidence showed that microRNA-133a (miR-133a) has inhibitory effects on cell proliferation, migration, invasion, and metastasis of osteosarcoma. Methods: MiR-133a expression in human osteosarcoma cell lines and human normal osteoblastic cell line hFOB was investigated by real-time PCR (RT-PCR). The role of miR-133a in human osteosarcoma growth and invasion was assessed in cell lines in vitro and in vivo. Then, luciferase reporter assay validated IGF-1R as a downstream and functional target of miR-133a, and functional studies revealed that the anti-tumor effect of miR-133a was probably due to targeting and repressing of IGF-1R expression. Results: MiR-133a was lower expressed in human osteosarcoma cell lines than human normal osteoblastic cell line hFOB and its effect on inhibiting proliferation, invasion and metastasis is mediated by its direct interaction with the IGF-1R. Furthermore, the tumour-suppressive function of miR-133a probably contributed to inhibiting the activation AKT and ERK signaling pathway. Conclusion: MiR-133a suppresses osteosarcoma progression and metastasis by targeting IGF-1R in human osteosarcoma cells, providing a novel candidate prognostic factor and a potential anti-metastasis therapeutic target in osteosarcoma.

Subcloning of three osteoblastic cell lines with distinct differentiation phenotypes from the mouse osteoblastic cell line KS-4

Bone ◽  
1996 ◽  
Vol 19 (5) ◽  
pp. 429-436 ◽  
Author(s):  
T. Yamashita ◽  
H. Ishii ◽  
K. Shimoda ◽  
T.K. Sampath ◽  
T. Katagiri ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Osteoblastic Cell ◽  
Osteoblastic Cell Line

scholarly journals Defining the landscape of metabolic dysregulations in cancer metastasis

2021 ◽  
Author(s):  
Sara Abdul Kader ◽  
Shaima Dib ◽  
Iman W. Achkar ◽  
Gaurav Thareja ◽  
Karsten Suhre ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Metabolism ◽  
Treatment Strategies ◽  
Metastatic Potential ◽  
Breast Cancer Cell Lines ◽  
Growth Media ◽  
High Metastatic Potential ◽  
Tnbc Cell

AbstractMetastasis is the primary cause of cancer related deaths due to the limited number of efficient druggable targets. Signatures of dysregulated cancer metabolism could serve as a roadmap for the determination of new treatment strategies. However, the metabolic signatures of metastatic cells remain vastly elusive. Our aim was to determine metabolic dysregulations associated with high metastatic potential in breast cancer cell lines. We have selected 5 triple negative breast cancer (TNBC) cell lines including three with high metastatic potential (HMP) (MDA-MB-231, MDA-MB-436, MDA-MB-468) and two with low metastatic potential (LMP) (BT549, HCC1143). The normal epithelial breast cell line (hTERT-HME1) was also investigated. The untargeted metabolic profiling of cells and growth media was conducted and total of 479 metabolites were quantified. First we characterized metabolic features differentiating TNBC cell lines from normal cells as well as identified cell line specific metabolic fingerprints. Next, we determined 92 metabolites in cells and 22 in growth medium that display significant differences between LMP and HMP. The HMP cell lines had elevated level of molecules involved in glycolysis, TCA cycle and lipid metabolism. We identified metabolic advantages of cell lines with HMP beyond enhanced glycolysis by pinpointing the role of branched chain amino acids (BCAA) catabolism as well as molecules supporting coagulation and platelet activation as important contributors to the metastatic cascade. The landscape of metabolic dysregulations, characterized in our study, could serve as a roadmap for the identification of treatment strategies targeting cancer cells with enhanced metastatic potential.

Melphalan Resistance in Multiple Myeloma Can Be Overcome by Proteasome Inhibition or Histone Deacetylation: Lack of Syngergism of the Combination.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3393-3393
Author(s):  
Pieter Sonneveld ◽  
Eric Kamst ◽  
Yvonne de Knegt ◽  
Naomi Klarenbeek ◽  
Martijn Schoester
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Line ◽  
Cell Lines ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Proteasome Inhibition ◽  
Histone Deacetylation ◽  
Interaction Factor ◽  
Resistant Cells

Abstract Multiple Myeloma (MM) is a disease of monoclonal plasma cells in the bone marrow which has a transient response to classic chemotherapy. At diagnosis, induction chemotherapy followed by high-dose melphalan (HDM) with stem cell support is used in most patients to achieve a clinical response. Because all patients will ultimately relapse, the treatment of melphalan-refractory disease represents a major clinical challenge and new agents are needed to overcome melphalan resistance. We have investigated the anti-myeloma efficacy of two new classes of targeted agents, i.e. proteasome inhibition and histone deacetylation inhibition alone or in combination in the melphalan sensitive MM1S and the Melphalan refractory MM1MEL2000 cell lines. The IC50 values of Bortezomib (B), Melphalan (M) and LAQ824 (L) in MM1S were 2.1 nM, 1.9 uM and 1.7 nM, respectively and in MM1MEL2000 3.9 nM, 50 uM and 4.0 nM. Using isobologram analysis a synergysm between B and L was observed in the sensitive, however not in the melphalan refractory cell line. These data indicate that B proteasome inhibition and histone deacetylation inhibition may be effective ways to overcome melphalan resistance. However, the previously reported synergism between these drugs does not seem to occur in melphalan resistant cells. The gene expression profiles of these cell lines were analysed using the Affymetrix U133plus 2.0 gene chip before and after treatment with melfaphalan or the proteasome inhibitor B or the histone deacetylation inhibitor L or the combination of B and L. Genes that were highly expressed in the melphalan refractory derivate cell line MM1MEL2000 as compared with wild-type MM1S included GP M6B, ADAM23 and HTPAP. Following melphalan exposure, TMF1, a CEBp glucocorticoid interaction factor, WHSC1L1, a MMSET homologue with EGF like domain and several transcription factors had highly increased expression as compared to MM1S. With exposure to B combined with L, increased expression in MM1MEL2000 over MM1S was observed for GTP exchange factor TIAM1 which interacts with RAS and JNK, and the lymphoid enhancer factor, a notch transcription factor. It is concluded that Bortezomib and the histone deacetylase inhibitor LAQ824 are effective agents to overcome melphalan resistance in multiple myeloma. However, the combination fails to show the synergism observed in melphalan sensitive cells. Gene analysis sofar does not provide a clear explanation for this lack of synergism. A comprehensive summary of the observed shifts of gene expression profiles in melphalan resistant cells following exposure to these agents, will be presented.

Metabolic evaluation of sporadic papillary kidney cancer.

2012 ◽  
Vol 30 (5_suppl) ◽  
pp. 377-377
Author(s):  
Brian Shuch ◽  
Christopher Ricketts ◽  
Carole Sourbier ◽  
Shinji Tsutsumi ◽  
Xiu-ying Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Membrane Potential ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Kidney Cancer ◽  
Expression Profiles ◽  
Fumarate Hydratase ◽  
Gene Expression Profiles ◽  
Cancer Cell Lines

377 Background: Papillary kidney cancer, which occurs in 15% of patients with kidney cancer, can be aggressive and there is currently no effective form of therapy for this disease. To evaluate the metabolic characteristics of sporadic papillary kidney cancer, we have evaluated metabolic parameters of several papillary kidney cancer cell lines and available gene expression profiles. Methods: Established cell lines derived from patients with sporadic papillary kidney cancer (LABAZ, MDACC-55, HRC-86T2) and from a hereditary form of fumarate hydratase-deficient kidney cancer (UOK262) were evaluated. All sporadic lines were initially sequenced for fumarate hydratase (FH). All cell lines were metabolically profiled using the Seahorse Extracellular Flux Analyzer and further evaluated for reactive oxygen species (ROS), mitochondrial membrane potential, and glucose dependence. Finally gene expression profiles of publically available datasets of papillary and HLRCC tumors were downloaded, normalized, and analyzed. Results: Sporadic lines had no alterations in FH and metabolic analysis demonstrated normal oxygen consumption and minimal lactate production, in contrast to highly glycolytic UOK262. Also unlike UOK262, the sporadic papillary kidney cancer lines were not sensitive to glucose withdrawal, had low levels of ROS, and had normal mitochondria membrane potential. Principal component analysis (PCA) demonstrated that HLRCC tumor specimens are very different from sporadic papillary tumors at the molecular level. Conclusions: Our study of established sporadic papillary RCC and fumarate hydratase-deficient HLRCC cell line together with analysis of available gene expression profiles demonstrates that these sporadic papillary kidney cancer cell lines appear to have a distinct metabolic profile from those in the fumarate hydratase deficient kidney cancer cell line. Understanding the metabolic basis of papillary kidney cancer could provide the foundation for the development of targeted approaches to therapy for patients with this disease.

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