Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional response of Candida albicans to endothelial cells

ABSTRACT: Candida albicans is exposed to a different host environment during different site of infection. Thus, different virulence factors may be active during differenttypes of infection. However,little is known about the C. albicans genes that are required for the initiation and maintenance of candidiasis. To identify potential virulence factors relevant to hematogenously disseminated candidiasis, we determined the transcriptional response of C. albicans to human umbilical vein endothelial cells (HUVECs) in vitro. Keywords: cell interaction Two different Candida albicans strains, CAI4-URA and a clinical isolate 36082, were used to identify the transcriptional response of C. albicans to HUVECs. The strains were incubated with either the HUVECs or bare plastic for 45, 90, and 180 min. C. albicans RNA was extracted and the transcriptional profile of these organisms was analyzed using the C. albicans oligonucleotide microarray. The transcriptional response to HUVECs was compared to that to bare plastic as a control condition. Each time point contains six biological replicates, three of which are from each C. albicans strain.

ORGANISM(S): Candida albicans

SUBMITTER: Hyunsook Park

PROVIDER: E-GEOD-5344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional responses of candida albicans to epithelial and endothelial cells.

Park Hyunsook H Liu Yaoping Y Solis Norma N Spotkov Joshua J Hamaker Jessica J Blankenship Jill R JR Yeaman Michael R MR Mitchell Aaron P AP Liu Haoping H Filler Scott G SG

Eukaryotic cell 20090821 10

Candida albicans interacts with oral epithelial cells during oropharyngeal candidiasis and with vascular endothelial cells when it disseminates hematogenously. We set out to identify C. albicans genes that govern interactions with these host cells in vitro. The transcriptional response of C. albicans to the FaDu oral epithelial cell line and primary endothelial cells was determined by microarray analysis. Contact with epithelial cells caused a decrease in transcript levels of genes related to pr ...[more]

PMID: 19700637

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Project description:Metabolic processes and sexual maturation closely interact during the long-distance reproductive migration of many fish species to their spawning grounds. In the present study, we have for the first time used exercise experimentally to investigate the effects on sexual maturation in rainbow trout. Pubertal autumn-spawning seawater-raised female rainbow trout Oncorhynchus mykiss (n=26; 50-cm, 1.5-kg) were rested or swum at a near optimal speed of 0.75 body-lengths per second in a 6,000 L swim-flume under natural reproductive conditions (16 Â°C fresh-water, starvation, 8h-light:16h-dark photoperiod). Fish were sampled after arrival and subsequently after 10 days (resting or swimming 307 km) and 20 days (resting or swimming 636 km). Ovarian development was significantly reduced in the swimmers. Analysis of the expression of key factors in the reproductive axis included pituitary kiss1-receptor, lh and fsh and ovarian lh-receptor, fsh-receptor, aromatase and vitellogenin-receptor (vtgr). Swimmers had lower pituitary lh and ovarian vtgr expression than resters. Furthermore, the number of late vitellogenic oocytes was lower in swimmers than in resters, probably resulting from the lower vtgr expression, and vitellogenin plasma levels were higher. Therefore, swimming exercise suppresses oocyte development possibly by inhibiting vitellogenin uptake. Transcriptomic changes that occurred in the ovary of exercised fish were investigated using a salmonid cDNA microarray platform. Protein biosynthesis and energy provision were among the sixteen functional categories that were all down-regulated in the ovary. Down-regulation of the transcriptomic response in the ovary illustrates the priority of energy reallocation and will save energy to fuel exercise. A swimming-induced ovarian developmental suppression at the start of vitellogenesis during long-term reproductive migration may be a strategy to avoid precocious muscle atrophy. In order to simulate the natural reproductive conditions of anadromous salmonids, experiments were performed with sea water-raised rainbow trout, Oncorhynchus mykiss. Resters and swimmers were starved during the experiment, seawater was replaced by fresh water and photoperiod was changed. These changes were expected to affect reproductive parameters but as âbackgroundâ effect because both resters as swimmers were experiencing these conditions at the same time in the same set-up. Any additional effects in swimming fish would thus be caused by swimming only. Pubertal autumn spawning rainbow trout (n=26; ~50 cm, ~1.5 kg) were purchased from a Danish exporter (Frederiksvaerk Aleexport) where they had been raised for 2 years in freshwater followed by 4 months in sea water cages at 10 â°. They were transferred by truck within 16 h to Spakenburg (Spakenburg Paling, The Netherlands) and subsequently in the same water in a similar holding tank to the swim-flume at Leiden University (The Netherlands). The next day, 5 randomly chosen fish were sampled as âstartâ-group while others were randomly divided into a ârestâ-group (n=10) and a âswimâ-group (n=11). During the following 4 days, the brackish 10 â° water was stepwise replaced by freshwater at 16 Â°C and photoperiod was changed from 16L:8D to 8L:16D. Fish were then acclimatized for two days to their new conditions. Subsequently, swimmers were first swum at a speed of 0.33 body-lengths per second (BL/s) which was increased the next day to the final, near optimal speed of 0.75 BL/s (0.34 m/s or 29.4 km/day). Fish were sampled after 10 days (5 resters and 5 swimmers) and 20 days (5 resters and 6 swimmers). At sampling, fish were anesthetized using oil of cloves that was commercially purchased from a drugstore (diluted 1:10 in ethanol and used at a dosage of 1.5 ml/l). Fish were euthanized by decapitation and dissected for the ovary which was flash frozen in liquid nitrogen. RNA was isolated from pituitary and ovary samples according to the TRIZOL reagent protocol by Invitrogen (Baro, Spain). Isolated RNA was DNAse treated using RQ1 DNAse Promega (Madison, USA) and reverse transcribed using Superscript IIITM (Baro, Spain) according to the manufacturerâs protocol. Microarray analyses were performed on ovarian tissue for 20-days-swimmers vs. 20-days-resters. A rainbow trout cDNA microarray platform was used that was previously validated and described by Koskinen et al., 2004ab, Krasnov et al., 2005, MacKenzie et al., 2006ab, 2008 and Djordjevic et al., 2009, and deposited in GEO under accession number GPL1212, the original cDNA microarray (SFA2.0 chip), and GPL6154; the updated 1.8 K platform. This platform compromises 1818 genes representing 366 functional categories. Total RNA was extracted from flash frozen samples from experimental fish of the 20-days-swim group (n=5) and 20-days-rest group (n=5) like described before. Total RNA corresponding to pooled samples from the swim or rest groups was labeled with Cye3 and Cye5-dCTP (GE Healthcare, Barcelona, Spain) using SuperScript III reverse transcriptase (Invitrogen, Baro, Spain) and oligo(dT) primer. In our experience, reverse labeling combined with multiple replication of spots provide robust normalization and high statistical power of analyses. cDNA was purified with MicroconYM30 (Millipore). The slides were pretreated with 1% BSA(fraction V), 20 Ã SSC, 10% SDS (30 min at 50Â°C) and washed with 2 Ã SSC (3 min) and 0.2 Ã SSC (3 min) and hybridized overnight in cocktail containing 50 Ã Denhardt's, 20 Ã SSC, 10% SDS, 10Î¼g/Î¼l polyadenylate and 10 Î¼g/Î¼l yeast tRNA. All chemicals were from Sigma-Aldrich. Scanning was performed with ScanArray 5000 and images were processed with QuantArray (GSI Luminomics). The measurements in spots were filtered by criteria I/B â¥ 3 and (I-B)/(SI + SB) â¥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalization was performed. To assess differential expression of genes, the normalized log intensity ratios (expression ratio) were analyzed with Student's t-test (P <0.05). Validation of the microarray was performed by Q-PCR of 6 differentially expressed genes (DEGs) as described above. The used primers were either published (Alpha-globin I-1: Donate Jimeno, 2008) or designed, again by using the Genamics software.

Project description:Candida albicans is the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections which are often life threatening. Hematogenously disseminated candidiasis (HDC) has a 47% mortality rate despite current antifungal therapy. An increase in prevalence, as well as an increasing resistance to most of the clinically important antifungal therapies, provides a strong impetus to understand the molecular mechanisms of pathogenesis and the acquisition of drug resistance. This information holds promise to identify novel therapeutic targets. A complete and accurate characterization of how the transcriptome of C. albicans responds to its interaction with cells from the host is an absolute necessity to accomplish this goal. RNA-seq (deep-sequencing of cDNA) provides an unbiased method to define comprehensively and systematically the transcriptome of an organism. We propose a comprehensive characterization of the C. albicans transcriptome in two different human tissue culture models, using RNA-seq. Such a characterization will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion. We performed a comprehensive characterization of the C. albicans transcriptome in two different murine models of candidiasis (HDC and oropharyngeal candidiasis (OPC)), and two different human tissue culture models, using RNA-seq. Because the two murine models accurately recapitulate the pathology that is observed in clinical cases of candidiasis, we are confident that gene expression levels will provide an accurate representation of what occurs during the course of an infection in humans. Such a characterization of the in vivo transcriptome will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion. PRJNA86065 Two different strains of C. albicans (SC5314 or WO-1) were used to infect two different types of human tissue culture monolayers (HUVECs or OKF6-TERT2). RNA from the infection mixtures were harvested at 90 minutes, 5 hours and 8 hours post infection. Experiments were performed in biological duplicate.

Project description:Samples were purchased from Clontech as mRNA. Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end. shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3' shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3' 1.5 g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C. The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick). The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification. Multiple polymerase chain reactions were run using 0.15 g of double stranded DNA and standard reaction conditions. Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase) DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3' T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3' followed by Qiaquick purification. Further amplification was achieved using in vitro transcription reactions with X0.5 g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II). The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray. Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, http://genomebiology.com/2003/4/10/R66 , Roberts CJ et al., Science 2000, 287:873-880, and Schadt, Edwards, et al., unpublished. Normalization of single channel data is described in Ying, et al., "Identification of Chromosomal Regions Containing Transcribed Sequences Using Microarrays and Computational Methods" , 2003 Proceedings of the American Statistical Association, Biopharmaceutical Section [CD-ROM], Alexandria, VA: American Statistical Association, 2003. Briefly, an invariant set of probes was selected based on their intensity ranks. Then, a LOESS regression model was fit for Cy5 vs. Cy3 intensities for all probes in the invariant set. Finally, for all probes on the array the Cy5 intensities were normalized to the corresponding Cy3 intensities using prediction values from the regression model. Note that the normalized intensity values given here were used for all analyses reported in the accompanying paper. The ratio values reported here were not used for the analysis described in the manuscript and are not calculated from the normalized intensity values given below.

Project description:Candida albicans is the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections which are often life threatening. Hematogenously disseminated candidiasis (HDC) has a 47% mortality rate despite current antifungal therapy. An increase in prevalence, as well as an increasing resistance to most of the clinically important antifungal therapies, provides a strong impetus to understand the molecular mechanisms of pathogenesis and the acquisition of drug resistance. This information holds promise to identify novel therapeutic targets. A complete and accurate characterization of how the transcriptome of C. albicans responds to its interaction with cells from the host is an absolute necessity to accomplish this goal. RNA-seq (deep-sequencing of cDNA) provides an unbiased method to define comprehensively and systematically the transcriptome of an organism. We propose a comprehensive characterization of the C. albicans transcriptome in two different human tissue culture models, using RNA-seq. Such a characterization will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion. We performed a comprehensive characterization of the C. albicans transcriptome in two different murine models of candidiasis (HDC and oropharyngeal candidiasis (OPC)), and two different human tissue culture models, using RNA-seq. Because the two murine models accurately recapitulate the pathology that is observed in clinical cases of candidiasis, we are confident that gene expression levels will provide an accurate representation of what occurs during the course of an infection in humans. Such a characterization of the in vivo transcriptome will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion. PRJNA211732 C. albicans strain SC5314 was used to infect mice in a murine model of systemic candidiasis as well as a murine model of oropharyngeal candidiasis. For the disseminated model, kidneys were harvested at 6 hours, 12 hours, 24 hours and 48 hours after infection. For the oropharyngeal model, tongues were harvest at 1 day, 2 days, 3 days, and 5 days after infection. Total RNA was extracted from all harvested tissues and subject to RNA-seq. We also tested 3 C. albicans mutants in the disseminated model. For the infections with the mutant strains, only 1 timepoint (24 hours post-infection) was analyzed.

Dataset Information

Transcriptional response of Candida albicans to endothelial cells

Publications

Transcriptional responses of candida albicans to epithelial and endothelial cells.

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