Heart Transplant Rejection Profiling in Peripheral Blood
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Mario Deng
PROVIDER: E-GEOD-2445 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling.
Deng M C MC Eisen H J HJ Mehra M R MR Billingham M M Marboe C C CC Berry G G Kobashigawa J J Johnson F L FL Starling R C RC Murali S S Pauly D F DF Baron H H Wohlgemuth J G JG Woodward R N RN Klingler T M TM Walther D D Lal P G PG Rosenberg S S Hunt S S
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 20060101 1
Rejection diagnosis by endomyocardial biopsy (EMB) is invasive, expensive and variable. We investigated gene expression profiling of peripheral blood mononuclear cells (PBMC) to discriminate ISHLT grade 0 rejection (quiescence) from moderate/severe rejection (ISHLT > or = 3A). Patients were followed prospectively with blood sampling at post-transplant visits. Biopsies were graded by ISHLT criteria locally and by three independent pathologists blinded to clinical data. Known alloimmune pathways a ...[more]
Similar Datasets
Project description:TIME cells either expressing KSHV-RTA or KSHV-vGPCR alone, or TIME cells infected with KSHV and lytically reactivated with RTA for 6, 12, or 20 hours. Keywords = KSHV Keywords = host shutoff Keywords = vGPCR
2010-06-09 | E-GEOD-1406 | biostudies-arrayexpress
Project description:To obtain insight into the molecular basis of ductal carcinoma in situ (DCIS) and its progression by infiltrating surrounding tissue, we have performed cellular-based gene expression analysis of pure DCIS and DCIS with co-existing invasive ductal carcinoma (IDC) and compared the histological and molecular aspects between these morphologically identical lesions seeking to find key genes involved in DCIS progression. For that, 30 samples were evaluated, 4 non-neoplastic (N), 5 pure DCIS, 11 DCIS with co-existing IDC (DCIS-IDC) and 10 IDC. All samples were laser capture microdissected and RNAs were amplified using T7-based methodology. Microarray technology was performed using a customized cDNA platform containing 4,608 human genes. To classify the 4 sample groups according to molecular similarity we performed comparisons of their general expression pattern using ANOVA test (pFDR<0,01) followed by Tukey´s test (fold>l2l). Among the 4 sample groups, as expected, non-neoplastic cells reported the most distinct gene expression pattern. However, among the 3 groups of neoplastic cells, in contrast to morphological aspects, pure DCIS had the most distinct expression profile when compared to the other lesions: DCIS-IDC and IDC. Additionally, by comparison among pure DCIS, DCIS-IDC and N, we identified 147 genes potentially involved in DCIS progression. Unsupervised hierarchical cluster based on expression profile of this gene-set could discriminate DCIS-IDC from 60% of pure DCIS samples. Keywords: disease state analysis Fresh-frozen human breast samples were retrieved from the Tumor Tissue Biobank of the Medical and Research Center - Hospital A. C. Camargo, São Paulo. This research was approved by Ethic Committee of the Medical and Research Center - Hospital A. C. Camargo under number 587/04 and a written informed consent signed by all participants. All patients had presented at least 5 years of follow-up. Thirty samples were evaluated, 4 non-neoplastic breast samples (MN), 5 pure DCIS (stage 0; DCIS-0), 11 DCIS with co-existing IDC (DCIS) and 10 IDC. The non-neoplastic samples were obtained from perilesional mammary specimens from patients submitted to resection of benign lesions. All cells types were laser capture microdissected using PixCell II LCM system (Arcturus Engineering, Mountain View, CA). The total RNA was extracted by using the PicoPureä RNA Isolation kit (Arcturus Engineering # KT0204). A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP. HB4a normal luminal epithelial mammary cell line (O’Hare et al 1991) was amplified following the same protocol and used as reference for microarray hybridizations. Dye swap was performed for each sample analyzed and used as replicate samples. For the raw_data (lowess_data), see Web Link below.
2008-04-04 | E-GEOD-11042 | biostudies-arrayexpress
Project description:Previous studies have shown that normal and HPV immortalized keratinocytes are sensitive to TNF anti-proliferative effect. Conversely, HPV18-immortalized keratinocytes are resistant to the cytostatic effect mediated by this cytokine. In this study we have compared gene expression patterns in primary cultures of human foreskin epidermal keratinocytes (PHK or NHFK) and HPV16 (HF698) and HPV18(HF18Nco)-immortalized cell lines, and profile the transcriptional changes 3 and 60 hours after TNF treatment. Keywords: global expression profile, microarray, HPV, TNF In order to determine the effects of HPV infection and TNF treatment on global gene expression, were performed 2 independent experiment for each cell line, including the two periods of treatment with TNF. Furthermore, were performed 2 experiments for each control plate containing the non-treated cells.
2007-08-25 | E-GEOD-4524 | biostudies-arrayexpress
Project description:Chronic constant hypoxia (CCH), such as in pulmonary diseases or high altitude, and chronic intermittent hypoxia (CIH), such as in sleep apnea, can lead to major changes in the heart. The molecular mechanisms underlying these cardiac alterations are not well understood. We hypothesized that analysis on the changes in gene expression could help to delineate such mechanisms. In addition, the differences that can be anticipated between CCH and CIH could be potentially dissected. Current study used CCH and CIH mouse models combined with cDNA microarrays to determine the changes of gene expression in CCH or CIH mice heart. Keywords = heart Keywords = hypoxia Keywords = mouse Keywords = microarray Keywords: time-course
2010-06-10 | E-GEOD-2271 | biostudies-arrayexpress
Project description:Time-course microarray data set of mdx and wild type mice ranging from 1-20 weeks of age Keywords: time-course
2010-05-27 | E-GEOD-1574 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE5075: Aerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions. GSE5076: Anaerobic transcriptional responses of Escherichia coli to NO under defined chemostat conditions. GSE5084: Anaerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses GSE5137: Aerobic NO-exposed Chemostat Comparison of Wt & norR mutant Responses GSE5139: Aerobic NO-exposed Chemostat Comparison of Wt & hmp mutant Responses Keywords: SuperSeries Refer to individual Series
2006-08-31 | E-GEOD-5098 | biostudies-arrayexpress
Project description:In normal skin, interactions between melanocytes and keratinocytes, and between melanocytes and the basal membrane are functionally relevant for maintenance of homeostasis and epidermal melanin unit whose deregulation may trigger a continuous proliferation of the melanocytes. In order to further elucidate the molecular events related to cell-cell and cell-ECM interactions in relation to the biology of melanomas, we analyzed the expression profile of 64 human melanomas, 21 primary samples and 43 independent metastasis. Tissue samples melanomas were obtained at Hospital A. C. Camargo. All patients signed an informed consent and the study was approved by our internal ethics committee. Tissue samples obtained by surgery were snap-frozen in liquid nitrogen and biopsy samples were collected in RNAlaterTM (Ambion, Austin, TX). Non-tumor areas were removed by handy dissection and only samples represented by at least 70% of tumors cells within their natural stroma were selected for RNA extraction. Total RNA was extracted using RNeasy Midi-Kit® and amplified by a T7-based protocol. An indirect cDNA-labeling was performed as described by Cox et al. (2004). We used dual-label system in which two RNA samples (test and reference) were separately reverse-transcribed, labeled, mixed, and hybridized together to each array. Each sample was hybridized in duplicate, with dye swap between sample and reference. As reference RNA we used a pool of equal amounts of total RNA from 5 human cutaneous melanoma cell lines (SK-MEL 05; 17; 28; 37 and 188, kindly provided by Dr. Alan Houghton, MSKCC, New York, NY, USA). We used glass arrays containing 4.800 cDNA sequences (Brentani et al. 2003) were prepared in our lab with the aid of the Flexys robot17 (Genomic Solutions, Cambridgeshire, United Kingdom). The list of immobilized genes can be obtained at GEO, accession number GPL1930. Pre-hybridization, hybridization and washing were performed as previously described (Gomes et al. 2003; 2005), and slides were scanned on a laser scanner (ScanArray Express, PerkinElmer Life Sciences, Boston, MA). Data were extracted with ScanArray Express software (PerkinElmer Life Sciences, Boston, MA) using the histogram method.
2011-10-31 | E-GEOD-17275 | biostudies-arrayexpress
Project description:Wilms tumor (WT), the commonest renal tumor of the childhood, is originated from pluripotent metanephric blastemal cells resulting in tumors with triphasic histology, composed by blastemal, epithelial, and stromal cells. Histological subtype and tumor stage have long been recognized as important prognostic factors and used for the current therapeutic approach with blastema considered as the component with the highest clinical impact. Current clinical and molecular research is directed toward identifying prognostic factors for both purposes, definition of the minimal or intense required therapy for successful treatment of children with low or high risk of relapse, respectively. In this study, to identify molecular prognostic markers predictive of tumor relapse, samples from 26 advanced (Stage III or IV) blastemal WT, whose patients presented (13 samples) or did not present (13 samples) relapse, were interrogated by 4,608 human genes immobilized in a customized cDNA platform. This analysis revealed a set of 69 differentially expressed genes, where the nine top genes were evaluated by qRT-PCR in the initial WT samples. TSPAN3, NCOA6, CDO1, MPP2 and MCM2 were technically confirmed showing down-regulation in relapse WT. TSPAN3 and NCOA6 were validated in an independent sample group. Gene trios containing these two genes combined with one of the remaining three reported a reasonable capability of discriminating relapse and no-relapse WT. Negative protein expression of MCM2 and NCOA6 was observed in around 62% and 72% of 34 independent stage III and IV WT patients, respectively without association with relapse. However, a significant association between MCM2 negative staining and chemotherapy as first treatment was observed suggesting that MCM2 protein expression is implicated anyhow with chemotherapy treatment in WT. Twenty-six blastemal-enriched advanced stage (III or IV) WT samples from sporadic and favorable histology WT were received from Children Oncology Group (COG) and used were used for microarray experiments, from which 13 samples were from patients without relapse in 5 years of follow up. Tumors were taken from primary nephrectomy at the time of initial diagnosis. Blastemal histological component was isolated following protocol described in Maschietto et al. (2008). Only samples with >80% of blastemal cells were used. Total RNA was isolated using TRIzol (Sigma) according to manufacturer´s instructions. RNA quantity and integrity was assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Agilent 2100 Bioanalyzer, Agilent), respectively, selecting only RNA samples with OD around 2.0 and RIN>5.0. A two-round RNA amplification procedure (Gomes et al. 2003) was carried out for all samples. Labeled cDNA was generated in a reverse transcriptase reaction using 4 ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, Carlsbad, CA), Alexa-3 or 5-labeled dCTP (Amersham, Biosciences) and IMPROM (PROMEGA) using oligo-dT7(24), following manufacture recommendations. Five µg of test and reference cDNA reverse color Alexa-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes. Dye-swap was performed for each sample as control for dye bias and used as replicate. Pre-hybridization and hybridization were performed as described (Maschietto et al. 2008). A pool of RNAs obtained from 15 distinct human cell lines as was used as reference. Signal intensities capture and analysis were performed as described in Maschietto et al (2008).
2011-06-01 | E-GEOD-22696 | biostudies-arrayexpress
Project description:Set of experiments done on yeast deletion strains of various non-essential mRNA processing factors. Keywords = splicing
2010-05-27 | E-GEOD-35 | biostudies-arrayexpress
Project description:Hypoxia-induced cell injury has been related to multiple pathological conditions. In order to render hypoxia-sensitive cells and tissues resistant to low O2 environment, in this current study, we used Drosophila melanogaster as a model to dissect the mechanisms underlying hypoxia-tolerance. A D. melanogaster strain that lives perpetually in an extremely low-oxygen environment (4% O2, an oxygen level that is equivalent to that over about 4,000 m above Mt. Everest) was generated through laboratory selection pressure using a continuing reduction of O2 over many generations. This phenotype is genetically stable since selected flies, after several generations in room air, survive at this low O2 level. Gene expression profiling showed striking differences between tolerant and naïve flies, in larvae and adults, both quantitatively and qualitatively. Up-regulated genes in the tolerant flies included signal transduction pathways (e.g., Notch and Toll/Imd pathways), but metabolic genes were remarkably down-regulated in the larvae. Furthermore, a different allelic frequency and enzymatic activity of the triose phosphate isomerase (TPI) was present in the tolerant versus naïve flies. The transcriptional suppressor, hairy, was up-regulated in the microarrays and its binding elements were present in the regulatory region of the specifically down-regulated metabolic genes but not others, and mutations in hairy significantly reduced hypoxia tolerance. We conclude that, the hypoxia-selected flies: (a) altered their gene expression and genetic code, and (b) coordinated their metabolic suppression, especially during development, with hairy acting as a metabolic switch, thus playing a crucial role in hypoxia-tolerance. Keywords: genetic bases of hypoxia adaptation 27 isogenic D. melanogaster Lines were pooled and following long-term selection over generations with decreased oxygen level in the culture environment. The differences in gene expression were compared between adapted flies and generation matched naive controls by microarray. Pooled RNA samples from 3rd instar larvae of 27 parental lines were used as common reference.
2010-06-25 | E-GEOD-8803 | biostudies-arrayexpress