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UC San Diego_Friedmann_Kang_Human fibroblast knockdown

ABSTRACT: To characterize mechanisms responsible for the CNS dopamine deficiency and the resulting neuropathology caused by deficiency of the housekeeping purine salvage function hypoxanthine guanine phospho- ribosyltransferase (HPRT) in the Lesch Nyhan Disease (LND), we have used microarray-based methods of global gene expression together with quantitative PCR and Western blot analysis to identify dysregulation of genes and aberrant cellular processes in human fibroblasts and in SH-SY5Y neuroblastoma cells made HPRT-deficient by transduction with a retrovirus stably expressing an shRNA targeted against HPRT. Analysis of the microarray expression data by Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) as well as by GeneSpring GX10 and Panther Classification System reveal that HPRT deficiency is accompanied by aberrations in a variety of pathways known to regulate neurogenesis or to be implicated in neurodegenerative disease, including the canonical Wnt/β-catenin and the Alzheimer’s disease/presenilin signaling pathways. Dysregulation of the Wnt/β-catenin pathway is confirmed by Western blot demonstration of cytosolic sequestration of β-catenin during in vitro differentiation of the SH-SY5Y cells toward the neuronal phenotype. We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration, we found that expression of presenilin-1 shows a severely disturbed expression in HPRT-deficient cells, reflected by marked instability of the 23kDa C-terminal fragment of presenilin-1 in knockdown cells. Western blot analysis of primary cultures of two LND patients with 2.5% and 0% residual HPRT activity also shows dysregulated b-catenin and presenilin-1 expression, including elevated levels of cytosolic phospho-catenin and, in one of the two patient cells, failure of nuclear transport. Similarly, the presenilin-1 processing defect was most clearly demonstrated by markedly increased levels of both the N-terminal and C-terminal presenilin-1 fragments in the human cell line with no detectable residual enzyme activity but less marked over-expression in the cell with 2.5% residual enzyme activity. These demonstrations of dysregulated Wnt and presenilin-1 signaling and impaired expression of transcription factors necessary for dopaminergic development reveal broad pleitropic neuro-regulatory defects played by HPRT and suggest new directions for investigating mechanisms of aberrant neurogenesis and neuropathology in LND and potential new targets for restoration of effective signaling in this neuro-developmental defect.

ORGANISM(S): Homo sapiens

PROVIDER: GSE24345 | GEO | 2010/09/25

SECONDARY ACCESSION(S): PRJNA132909

REPOSITORIES: GEO

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Project description:To characterize mechanisms responsible for the CNS dopamine deficiency and the resulting neuropathology caused by deficiency of the housekeeping purine salvage function hypoxanthine guanine phospho- ribosyltransferase (HPRT) in the Lesch Nyhan Disease (LND), we have used microarray-based methods of global gene expression together with quantitative PCR and Western blot analysis to identify dysregulation of genes and aberrant cellular processes in human fibroblasts and in SH-SY5Y neuroblastoma cells made HPRT-deficient by transduction with a retrovirus stably expressing an shRNA targeted against HPRT. Analysis of the microarray expression data by Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) as well as by GeneSpring GX10 and Panther Classification System reveal that HPRT deficiency is accompanied by aberrations in a variety of pathways known to regulate neurogenesis or to be implicated in neurodegenerative disease, including the canonical Wnt/β-catenin and the Alzheimer’s disease/presenilin signaling pathways. Dysregulation of the Wnt/β-catenin pathway is confirmed by Western blot demonstration of cytosolic sequestration of β-catenin during in vitro differentiation of the SH-SY5Y cells toward the neuronal phenotype. We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration, we found that expression of presenilin-1 shows a severely disturbed expression in HPRT-deficient cells, reflected by marked instability of the 23kDa C-terminal fragment of presenilin-1 in knockdown cells. Western blot analysis of primary cultures of two LND patients with 2.5% and 0% residual HPRT activity also shows dysregulated b-catenin and presenilin-1 expression, including elevated levels of cytosolic phospho-catenin and, in one of the two patient cells, failure of nuclear transport. Similarly, the presenilin-1 processing defect was most clearly demonstrated by markedly increased levels of both the N-terminal and C-terminal presenilin-1 fragments in the human cell line with no detectable residual enzyme activity but less marked over-expression in the cell with 2.5% residual enzyme activity. These demonstrations of dysregulated Wnt and presenilin-1 signaling and impaired expression of transcription factors necessary for dopaminergic development reveal broad pleitropic neuro-regulatory defects played by HPRT and suggest new directions for investigating mechanisms of aberrant neurogenesis and neuropathology in LND and potential new targets for restoration of effective signaling in this neuro-developmental defect. For microarray analysis, RNAs from triplicate independent cultures of vector-infected HPRT knockdown and control fibroblasts were prepared separately, pooled and used to prepare cRNA and finally subjected to microarray transcriptional analysis in triplicate. The integrity of total RNA from HPRT knockdown and control cells was confirmed by bioanalyzer (Agilent Technologies, Santa Clara, CA). The quality of total RNA samples from HPRT knockdown and control cells was assessed by 2100 bioanalyzer before application to microarray analysis. We determined that the RNA integrity number (RIN), (maximal degradation = 1; maximal molecular integrity = 10) was 10 for both the normal and knockdown cells (data not shown), indicating that isolated RNA samples were of sufficiently high quality to permit subsequent preparation of cDNA for microarray analysis. Microarray transcriptional analysis was performed in triplicate using the HumanWG-6 v3.0 Expression BeadChip system (Illumina, San Diego, CA). All reagents were obtained from HumanWG-6 v.3 Expression BeadChip Kit (Illumina) and all experimental processes were carried out according to manufacturer’s instruction (Illumina). After scanning of hybridized BeadChip, quantitation of slide images were performed using Illumina’s BeadArray software and the raw data were normalized by Loess normalization method, and then the normalized raw data in BeadStudio was exported to GeneSpring GX 10.0.2 (Agilent, Santa Clara, CA). For identification of genes significantly altered in knockdown cell compared with the control normal gene set, total detected entities were filtered by signal intensity value (upper cut-off 100th and lower cut-off 20th percentile) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, t-test unpaired (p < 0.05) was applied and all significant changes above 2-fold were selected. Signals were selected if they were above microarray background (detection p-value < 0.05) in either all six experiments or in at least three knockdown or control experiments. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 10.0.2 (Agilent) and the PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using GeneSpring GX 10.0.2 (Agilent), a total of 140 cellular pathways were identified. For GSEA analysis, we used the false discovery rate (FDR) of <0.4 and p ≤ 0.1.

Project description:Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB. Experiment Overall Design: Human neuroblastomas, SK-N-SH (HTB-11) and SH-SY5Y-A cells (CRL-2266) were obtained from the American Type Culture Collection (ATCC). We also obtained SH-SY5Y-E cells (EC94030304) from the European Collection of Cell Cultures (ECACC). Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week. For the RA-inducible experiment, random culture cells from two clone subtypes of SH-SY5Y and SK-N-SH were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences, Billerica, MA, USA) for 1 day and then transferred to a medium containing 10 μM of RA in the presence or the absence of LY294002 (10μM) for five days. For BDNF-induced sequential differentiation of the SH-SY5Y-E strain, cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.

Project description:Purpose: The present study was carried out to investigate the global m6A modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid. Method: 14 normal skin and 14 keloid tissue were firstly collected on clinic. Then 3 samples from each group were randomly selected to be verified with the Western Blot to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP-sequencing and RNA-sequencing. With the software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change > 2 and p -value < 0.05. The top 10 pathways of m6A modified genes in each group and the differentially-expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined with the Western Blot and immunofluorescence staining. Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. 21,020 unique m6A peaks with 6573 unique m6A-associated genetic transcripts appeared in the keloid samples. In the normal tissue, 4028 unique m6A peaks with 779-associated modified genes appeared in the keloid. In the RNA-sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A modified Wnt / β-catenin pathway in keloid was verified with western blotting. From immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid and the Wnt/β-catenin signaling pathway was mainly activated in the fibroblasts. Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A methylated condition, and the hyper-m6A modified highly-expressed Wnt / β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.

Project description:Purpose: We aimed to investigate the effect of several anti-leukemia drugs in combination with decitabine (DAC) on the proliferation of myeloid leukemia cells in vitro and in vivo, to select the most efficient combination group and explore associated mechanisms of these combination therapies. Experimental Design: After comparing with five anti-leukemia drugs in several different kinds of cell lines, the combination effect of idarubicin (IDA) with DAC was best. In vivo, by using microPET, TUNEL, and transmission electron microscopy, the inhibitory effects obtained by sequentially combining DAC with IDA, evidenced by evaluating tumor cell proliferation and cell apoptosis. Molecular studies were conducted using gene chip, which was used to explore associated pathways, and real-time quantitative reverse transcription-PCR, western blot and immunohistochemistry (IHC), used to assess regulation of Wnt/β-catenin pathway. Results: The sequential combination of DAC and IDA showed synergistic induction of cell death in U937, HEL, SKM-1 and cells isolated from AML patients. Importantly, the inhibition of tumor growth in the sequential combination group was found to be significantly higher than that of single drug group or control group in vivo. Moreover, sequential treatment with DAC and IDA induced apoptosis and depression of the Wnt/β-catenin pathway in both culture and animal studies. Conclusions: Our findings showed that sequentially combining decitabine with idarubicin had a synergistic anti-leukemia effect. These findings were attributed to demethylation of Wnt pathway inhibitors and downregulation of Wnt pathway nuclear targets observed in vitro and in vivo. After comparing with five anti-leukemia drugs in several different kinds of cell lines, the combination effect of idarubicin (IDA) with DAC was best. In vivo, by using microPET, TUNEL, and transmission electron microscopy, the inhibitory effects obtained by sequentially combining DAC with IDA, evidenced by evaluating tumor cell proliferation and cell apoptosis. Molecular studies were conducted using gene chip, which was used to explore associated pathways, and real-time quantitative reverse transcription-PCR, western blot and immunohistochemistry (IHC), used to assess regulation of Wnt/β-catenin pathway.

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UC San Diego_Friedmann_Kang_Human fibroblast knockdown

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