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Gene Profiling (gene + profiling)
Selected AbstractsGene profiling and pathway analysis of neuroendocrine transdifferentiated prostate cancer cellsTHE PROSTATE, Issue 1 2009Ryutaro Mori Abstract BACKGROUND Neuroendocrine (NE) cells are present in both normal prostate and prostate cancer. In addition, NE differentiation can be induced by various factors, such as IL-6, in vitro and in vivo. However, the mechanism of this differentiation and the role of NE cells in prostate cancer are not well understood. In this study, we evaluated the gene expression and analyzed the pathways in prostate cancer cells exposed to various NE differentiation inducing factors in vitro. METHODS Gene expression signatures between control LNCaP cells and each treatment induced NE cell line were compared using Affymetrix GeneChip with network and pathway analysis. RESULTS All treatments were able to transdifferentiate LNCaP cells into NE phenotype as shown by morphology changes and NE marker measurements. Of the 54,675 oligonucleotide-based probe sets in microarray, 44,975 were mapped into the Ingenuity Pathway Analysis database and were filtered according to the t -test P value. At P,<,0.002, the number of genes that were differentially expressed included 302 of the IL-6 treated cells, 201 of genistein, 233 of epinephrine, and 191 of the charcoal stripped serum ones. A pooled data approach also showed 346 differentially expressed genes at the same P value. Gene ontology analysis showed that cancer-related function had the highest significance. CONCLUSIONS Despite some overlap, each NE transdifferentiation inducing treatment was associated with a changed expression of a unique set of genes, and such gene profiling may help to elucidate the molecular mechanisms involved in NE transdifferentiation of prostate cancer cells. Prostate 69: 12,23, 2009. © 2008 Wiley,Liss, Inc. [source] Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell researchDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 1 2010Tetsutaro Hayashi To achieve an integrated understanding of the stem cell system of planarians at both the cellular and molecular levels, we developed a new method by combining "fluorescent activated cell sorting (FACS) index sorting" analysis and single-cell reverse transcription,polymerase chain reaction (RT,PCR) to detect the gene expression and cell cycle state of stem cells simultaneously. Single cells were collected using FACS, and cDNAs of each cell were used for semi-quantitative RT,PCR. The results were plotted on the FACS sorting profile using the "index sorting" function, which enabled us to analyze the gene expression in combination with cell biological data (such as cell cycle phase) for each cell. Here we investigated the adult stem cells of planarians using this method and obtained findings suggesting that the stem cells might undergo commitment during S to G2/M phase. This method could be a powerful and straightforward tool for examining the stem cell biology of not only planarians but also other organisms, including vertebrates. [source] Superantigen gene profile diversity among clinical group A streptococcal isolatesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 2 2008Linda Maripuu Abstract This study examines the diversity of superantigen gene profiles between and within emm -genotypes of 92 clinical group A streptococcal isolates (30 STSS, 24 sepsis, 25 erysipelas, and 12 tonsillitis) collected in Sweden between 1986 and 2001. The emm- genotype and the distribution of smeZ, speG, speJ, speA, speC, speH, speI, speK/L, speL/M, speM, and ssa genes, and the smeZ allelic variant were determined using PCR and DNA sequencing. Forty-five emm1 isolates revealed 10 superantigen gene profiles. One profile dominated and was identified in 22 isolates collected over 14 years. The results indicate that a selective advantage maintained this genotype in circulation. The superantigen content among the emm1 isolates ranged from three to seven, with smeZ-1, speG, and speA present in all but one profile. The 47 isolates of 27 other emm -genotypes exhibited 29 superantigen gene profiles. Thus, the distribution of superantigen genes was highly variable within isolates regardless of emm -genotype. Two novel emm1 subtypes and 14 novel smeZ allelic variants were identified. The 22 smeZ alleles were generally linked to the emm -genotype. The results of the investigation show that superantigen gene profiling is useful for tracking spread of clones in the community. [source] From gene profiling to diagnostic markers: IL-18 and FGF-2 complement CA125 as serum-based markers in epithelial ovarian cancerINTERNATIONAL JOURNAL OF CANCER, Issue 7 2006Cécile Le Page Abstract We used an oligonucleotide-based DNA microarray to identify potential markers in 39 primary cultures of ovarian cancer specimens compared with 11 primary cultures of normal ovarian epithelia. Differential gene expression of IL-18 and FGF-2 was validated on a subset of samples by quantitative PCR and by IHC, using an independent tissue array of 90 cores of 20 normal ovarian surface epithelia and 70 EOCs representing different grades and pathologies of ovarian disease. We further compared, by ELISA, these two markers with CA125 in sera from 25 cancer-free and 47 ovarian cancer patients. IL-18 and FGF-2 proteins were significantly elevated in tumor tissues (p<0.04) and sera (p<0.05) from patients with ovarian cancer. In combination, the three markers (IL-18, FGF-2, and CA125) showed similar sensitivity in scoring for ovarian cancer (35/45 patients) compared to that of CA125 alone (37/45) and significantly improved the specificity of detection (20/25 patients) compared to each marker individually (15/25 for CA125; 18/25 FGF-2; 16/25 for IL-18). In conclusion we show that a combination of the three serum markers (IL-18, FGF-2 and CA125) is associated with EOC, with higher specificity than CA125 alone. Prospective studies with a large cohort of susceptible ovarian cancer patients will be required to expand these findings. © 2005 Wiley-Liss, Inc. [source] Gene expression profiling of porokeratosisJOURNAL OF CUTANEOUS PATHOLOGY, Issue 11 2008Zheng-Hua Zhang Background:, Porokeratosis (PK) represents a heterogeneous group of disorders of keratinization and has a wide variety of clinical manifestations. PK may exhibit similarities with psoriasis at both clinical and molecular levels. The genetic basis and pathogenesis for PK remain elusive. Methods:, We studied the transcriptional profiles of three pairwise lesional and uninvolved skin biopsies from patients with different subtypes of PK using the Illumina® BeadArrayÔ platform. Results:, A total of 37 upregulated genes were identified in our study, including wound-induced keratins, S100 calcium-binding protein genes involved in epidermal differentiation, as well as genes involved in mediating intercellular communication and the immune response. To our knowledge, this is the first study that characterizes the immune profile of PK lesions. Conclusions:, Here, we report that keratinocytes (KCs)-harboring lesions have activated and overexpressed wound-induced keratin genes, which appear to be coregulated with other genes involved in mediating epidermal differentiation, intercellular communication and immunity. This study, from the perspective of gene profiling, supports that gene misregulation in PK mimics that of psoriasis. Our data indicate that the genes implicated in the T-cell-mediated immune response pathway and activation of KCs play a key role in the pathogenesis of PK. [source] Differential gene expression in LPS/IFN, activated microglia and macrophages: in vitro versus in vivoJOURNAL OF NEUROCHEMISTRY, Issue 2009Christoph D. Schmid Abstract Two different macrophage populations contribute to CNS neuroinflammation: CNS-resident microglia and CNS-infiltrating peripheral macrophages. Markers distinguishing these two populations in tissue sections have not been identified. Therefore, we compared gene expression between LPS (lipopolysaccharide)/interferon (IFN),-treated microglia from neonatal mixed glial cultures and similarly treated peritoneal macrophages. Fifteen molecules were identified by quantative PCR (qPCR) as being enriched from 2-fold to 250-fold in cultured neonatal microglia when compared with peritoneal macrophages. Only three of these molecules (C1qA, Trem2, and CXCL14) were found by qPCR to be also enriched in adult microglia isolated from LPS/IFN,-injected CNS when compared with infiltrating peripheral macrophages from the same CNS. The discrepancy between the in vitro and in vivo qPCR data sets was primarily because of induced expression of the ,microglial' molecules (such as the tolerance associated transcript, Tmem176b) in CNS-infiltrating macrophages. Bioinformatic analysis of the ,19000 mRNAs detected by TOGA gene profiling confirmed that LPS/IFN,-activated microglia isolated from adult CNS displayed greater similarity in total gene expression to CNS-infiltrating macrophages than to microglia isolated from unmanipulated healthy adult CNS. In situ hybridization analysis revealed that nearly all microglia expressed high levels of C1qA, while subsets of microglia expressed Trem2 and CXCL14. Expression of C1qA and Trem2 was limited to microglia, while large numbers of GABA+ neurons expressed CXCL14. These data suggest that (i) CNS-resident microglia are heterogeneous and thus a universal microglia-specific marker may not exist; (ii) the CNS micro-environment plays significant roles in determining the phenotypes of both CNS-resident microglia and CNS-infiltrating macrophages; (iii) the CNS microenvironment may contribute to immune privilege by inducing macrophage expression of anti-inflammatory molecules. [source] Global gene profiling reveals a downregulation of BMP gene expression in experimental atrophic nonunions compared to standard healing fracturesJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 7 2006Takahiro Niikura Abstract Nonunion is a challenging problem that may occur following certain bone fractures. However, there has been little investigation of the molecular basis of nonunions. Bone morphogenetic proteins (BMPs) play a significant role in osteogenesis. However, little is known about the expression patterns of BMPs in abnormal bone healing that results in nonunion formation. These facts prompted us to investigate and compare the gene expression patterns of BMPs and their antagonists in standard healing fractures and nonunions using rat experimental models. Standard closed healing fractures and experimental atrophic nonunions produced by periosteal cauterization at the fracture site were created in rat femurs. At postfracture days 3, 7, 10, 14, 21, and 28, total RNA was extracted from the callus of standard healing fracture and fibrous tissue of nonunion (n,=,4 per each time point and each group). Gene expression of BMPs, BMP antagonists, and other regulatory molecules were studied by methods including Genechip® microarray and real-time quantitative RT-PCR. Gene expression of BMP-2, 3, 3B, 4, 6, 7, GDF-5, 7, and BMP antagonists noggin, drm, screlostin, and BAMBI were significantly lower in nonunions compared to standard healing fractures at several time points. Downregulation in expression of osteogenic BMPs may account for the nonunions of fracture. The balance between BMPs and their endogenous antagonists is critical for optimal fracture healing. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:1463,1471, 2006 [source] Molecular characterization of tumour heterogeneity and malignant mesothelioma cell differentiation by gene profilingTHE JOURNAL OF PATHOLOGY, Issue 1 2005Xiaojuan Sun Abstract Malignant mesothelioma is an aggressive tumour, characterized by a variable differentiation pattern and poor prognosis. At present, the clinical outcome in patients with malignant mesothelioma is mainly predicted by the morphological phenotype of the tumour. However, this conventional clinicopathological parameter is of limited value, partly because of the biological heterogeneity of this tumour and poor understanding of the regulatory mechanisms underlying the various patterns of growth. To elucidate the intrinsic molecular programmes that determine tumour differentiation, oligonucleotide arrays were used in an in vitro model of mesothelioma differentiation. The analysis of 2059 genes detected 102 genes that were significantly deregulated. Clustering of these genes into functional categories showed distinctive patterns for the two phenotypes, namely epithelioid and sarcomatoid. The molecular fingerprint of the sarcomatoid tumour component indicates overrepresentation of growth factor receptors and growth factor binding proteins, whereas epithelioid mesothelioma cells express other tumour-promoting factors involved in differentiation, metabolism, and regulation of apoptosis. These differences in the molecular phenotype may give a better basis for diagnosis and for designing novel therapies. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Gene profiling and pathway analysis of neuroendocrine transdifferentiated prostate cancer cellsTHE PROSTATE, Issue 1 2009Ryutaro Mori Abstract BACKGROUND Neuroendocrine (NE) cells are present in both normal prostate and prostate cancer. In addition, NE differentiation can be induced by various factors, such as IL-6, in vitro and in vivo. However, the mechanism of this differentiation and the role of NE cells in prostate cancer are not well understood. In this study, we evaluated the gene expression and analyzed the pathways in prostate cancer cells exposed to various NE differentiation inducing factors in vitro. METHODS Gene expression signatures between control LNCaP cells and each treatment induced NE cell line were compared using Affymetrix GeneChip with network and pathway analysis. RESULTS All treatments were able to transdifferentiate LNCaP cells into NE phenotype as shown by morphology changes and NE marker measurements. Of the 54,675 oligonucleotide-based probe sets in microarray, 44,975 were mapped into the Ingenuity Pathway Analysis database and were filtered according to the t -test P value. At P,<,0.002, the number of genes that were differentially expressed included 302 of the IL-6 treated cells, 201 of genistein, 233 of epinephrine, and 191 of the charcoal stripped serum ones. A pooled data approach also showed 346 differentially expressed genes at the same P value. Gene ontology analysis showed that cancer-related function had the highest significance. CONCLUSIONS Despite some overlap, each NE transdifferentiation inducing treatment was associated with a changed expression of a unique set of genes, and such gene profiling may help to elucidate the molecular mechanisms involved in NE transdifferentiation of prostate cancer cells. Prostate 69: 12,23, 2009. © 2008 Wiley,Liss, Inc. [source] Emergence of fluoroquinolone-resistant clonal group A: clonal analysis of Norwegian and Russian E. coli isolatesAPMIS, Issue 8 2010LINDA STRAND Strand L, Jenkins A, Grude N, Allum A-G, Mykland H-C, Nowrouzian FL, Kristiansen B-E. Emergence of fluoroquinolone-resistant clonal group A: clonal analysis of Norwegian and Russian E. coli isolates. APMIS 2010; 118: 571,77. We describe a study of urinary tract and intestinal isolates of Escherichia coli from Norway and Russia using automated ribotyping, single nucleotide polymorphism analysis for clonal group A (CgA) supplemented with phylogrouping, virulence gene profiling and resistance profiling. CgA comprised 19% of the Norwegian UTI isolates from 2001. Two highly multiresistant fluoroquinolone-resistant CgA isolates were found. Ribotypes clustered into four major and six minor groups (ribogroups). Fluoroquinolone-resistant isolates and phylogroups A and B1 were associated with ribogroup RA. Ribogroup RB predominated among Russian UTI isolates and was predominantly phylogroup A and depleted in P-fimbriae. Ribogroup RC predominated among Norwegian UTI isolates and was rich in virulence factors (S-fimbriae, haemagglutinin and haemolysin) and predominantly phylogroup B2 and D. Ribogroup RG was associated with CgA and predominantly phylogroup D. Ribogroups RD, RE and RF had too few members for statistical analysis. The correlation between ribotype and phylogenetic group was not as strong as reported in other studies. [source] Nephritogenic Anti-DNA antibodies regulate gene expression in MRL/lpr mouse glomerular mesangial cellsARTHRITIS & RHEUMATISM, Issue 7 2006Xiaoping Qing Objective Lupus-associated IgG anti,double-stranded DNA antibodies are thought to be pathogenic in the kidney due to cross-reaction with glomerular antigens, leading subsequently to immune complex formation in situ and complement activation. We undertook this study to determine if pathogenic anti-DNA antibodies may also contribute to renal damage by directly influencing mesangial gene expression. Methods Complementary DNA microarray gene profiling was performed in primary mesangial cells (derived from lupus-prone MRL/lpr mice) treated with pathogenic, noncomplexed anti-DNA antibodies. Significant gene up-regulation induced by anti-DNA antibodies as determined by microarray analysis was further investigated by real-time polymerase chain reaction and methods to detect the relevant proteins. Induction of proinflammatory genes by pathogenic antibodies was confirmed by comparing gene expression in glomeruli of old versus young MRL/lpr mice, and by antibody injection in vivo. Results Pathogenic, but not nonpathogenic, antibodies significantly induced a number of transcripts, including CXCL1/KC, LCN2, iNOS, CX3CL1/fractalkine, SERPINA3G, and I,B, ("marker genes"). Blocking of Fc, receptors or using Fc, chain,knockout mesangial cells had no effect on the gene regulation effect of the pathogenic antibody R4A, indicating a non,Fc-dependent mechanism. The glomerular expression of these marker genes increased over time with the development of glomerular antibody deposition and active nephritis in MRL/lpr mice. Moreover, injection of R4A into SCID mice in vivo significantly up-regulated glomerular marker gene expression. Conclusion These findings indicate that the renal pathogenicity of anti-DNA antibodies may be attributed in part to their ability to directly modulate gene expression in kidney mesangial cells through both Fc-dependent and non,Fc-dependent mechanisms. [source] New multiplex PCR method for the detection of Clostridium difficile toxin A (tcdA) and toxin B (tcdB) and the binary toxin (cdtA/cdtB) genes applied to a Danish strain collectionCLINICAL MICROBIOLOGY AND INFECTION, Issue 11 2008S. Persson Abstract Isolates of Clostridium difficile from 159 hospitalized Danish patients (2005) were analysed by a new 5-plex PCR method targeting the toxin genes tcdA, tcdB, cdtA and cdtB, and 16S rDNA as an internal positive control. Additionally, the toxin-regulating gene tcdC was partially sequenced by a new sequencing-based method that revealed genetic changes that may render the gene product inactive. Finally tcdA was analysed using a previously published method for the detection of internal deletions. The 5-plex PCR revealed four different toxin gene profiles: 36 tcdA+, tcdB+, cdtA+/cdtB+; one tcdA+, tcdB,, cdtA+/cdtB+; 98 tcdA+, tcdB+, cdtA,/cdtB,; and 24 non-toxigenic tcdA,, tcdB,, cdtA,/cdtB,. Deletion studies revealed that 26 strains contained a c. 700-bp deletion in tcdA, and 39 strains contained at least one possible inactivation feature in tcdC. The prevalence of the binary toxin genes was 23%. All strains with the tcdA+, tcdB+, cdtA+/cdtB+ profile were investigated by PCR ribotyping, and this revealed eight different ribotypes, none of which were 027. The 5-plex PCR method offers a one-step, rapid and specific screening method for C. difficile toxin genes. This toxin gene profiling, together with deletion studies in tcdA and tcdC, may allow an evaluation of the pathogenic potential of C. difficile. [source] | |||||||||||||