Profiling of growth and differentiation factor 15 regulated genes in hepatoma cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Wei Yang
PROVIDER: E-GEOD-25397 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To systematically profile the GDF15-regulated genes in hepatoma cells and to elucidate the possible role of GDF15 on biological processes, high-density oligonucleotide microarrays were hybridized with samples prepared from GDF15- or PBS-treated Huh7.5.1 cells. We found that a total of 894 genes were differentially expressed in response to GDF15 treatment based on the 2-fold cut-off range, and a majority (828 genes, about 92.6%) of the genes is up-regulated. According to the descriptions outlined by the Gene Ontology Biological Process, the differentially expressed genes were found to belong to a variety of functional categories.
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Project description:This study uses microarray analyses to examine gene expression profiles for Mycobacterium tuberculosis (Mtb) induced by exposure in vitro to bovine lung surfactant preparations that vary in apoprotein content: (i) whole lung surfactant (WLS) containing the complete mix of endogenous lipids and surfactant proteins (SP)-A, -B, -C, and -D; (ii) extracted lung surfactant (CLSE) containing lipids plus SP-B and -C; (iii) column-purified surfactant lipids (PPL) containing no apoproteins, and (iv) purified human SP-A. Exposure to WLS evoked a multitude of transcriptional responses in Mtb, with 52 genes up-regulated and 23 genes down-regulated at 30 min exposure, plus 146 genes up-regulated and 27 genes down-regulated at 2 h. Notably, WLS rapidly induced several membrane-associated lipases that presumptively act on surfactant lipids as substrates, and a large number of genes involved in the synthesis of phthiocerol dimycocerosate (PDIM), a cell wall component known to be important in macrophage interactions and Mtb virulence. Exposure of Mtb to CLSE, PPL, or purified SP-A caused a substantially weaker transcriptional response (⤠20 genes were induced) suggesting that interactions among multiple lipid-protein components of WLS may contribute to its effects on Mtb transcription. Whole lung surfactant (WLS) was obtained by centrifugation of lavage fluid (0.15M NaCl) from the intact lungs of freshly killed calves (ONY, Inc, Amherst, NY). Centrifugation was done at 12,000 x g at room temperature to pellet the active large aggregate surfactant fraction. CLSE was prepared by extraction of WLS into chloroform-methanol by the method of Bligh and Dyer (1959), as described in our prior work (Notter et al. 2002). CLSE is conceptually identical to the substance of the clinical surfactant Infasurf®. The composition of CLSE by weight was approximately 94% phospholipid, 4.5% cholesterol, and 1.5% protein (a mixture of SP-B and SP-C) as defined previously (Notter et al. 2002). Mixed lung surfactant phospholipids (PPL) were isolated from CLSE by column chromatography with an elution solvent of 1:1 (v/v) chloroform-methanol plus 5% 0.1 N HCl. Two passes through a Sephadex LH-20 column (Pharmacia-LKB Biotechnology, Piscataway, NJ) separated phospholipids away from hydrophobic surfactant apoproteins and neutral lipids. Acid remaining in PPL fractions was removed by a second chloroform-methanol extraction. Final PPL had a protein content below the limits of detection of both the Folin-phenol assay of Lowry et al. (1951) and the amido black assay of Kaplin and Pedersen (1989) modified by the addition of 15% sodium dodecyl sulfate (SDS) to allow accurate quantitation in the presence of lipid. Human SP-A was a gift from Dr. J. R. Wright at Duke University, and was isolated from bronchoalveolar lavage from patients with alveolar proteinosis as described previously (Wright et al. 1987). For exposure studies with Mtb, amounts of WLS, CLSE, and PPL used per experiment were 3.3 mg in a total volume of 4 ml. In preliminary studies, this concentration was shown to induce a transcriptional response in Mtb without affecting viability after a 2 h treatment as determined by serial dilutions compared to untreated Mtb. SP-A was studied at a level of 0.165 mg based on its putative concentration of approximately 5% in endogenous surfactant. To determine the effects of lung surfactant on the transcriptional response of Mtb, preparations of WLS, CLSE, or PPL (in 650 µl PBS) were initially coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. A minimum of two independent biological replicates were studied for each surfactant preparation. Purified human SP-A was also examined for its effects on Mtb transcription, and phosphate buffered saline (PBS) was used as a âno treatmentâ control. In experiments with SP-A (in 650 µl PBS), the pure apoprotein was either pre-coated on the flask as done with the surfactant preparations, or was directly added and incubated with Mtb during study. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant/SP-A or PBS control for 30 min or 2h at 37oC, followed by RNA isolation as detailed by Rohde et al. (2008). GTC lysis/stabilization buffer was added, and pelleted Mtb were washed and then digested with lysozyme. TRIzol (Invitrogen) was added, and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK). After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto RNeasy mini columns (Qiagen, Valencia, CA). Subsequent steps were then performed according to the manufacturerâs instructions. Following elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA), and stored at -70oC until analysis. The MessageAmpTMII-Bacteria system (Applied Biosystems) was used to amplify mycobacterial RNA for all samples [16]. Total RNA was reverse transcribed to yield double-stranded amino-allyl modified aRNA, which was labeled with Alexa Fluor 555 and Alexa Fluor 647 (Invitrogen). Excess reactive dyes were removed with a Mega Clear purification kit (Applied Biosystems). Next, Alexa-labeled aRNA from paired samples was dried using a Speedvac, and re-suspended in hybridization buffer (5x SSC, 25% formamide, 0.15% SDS, and 25 μg salmon sperm DNA). 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