Expression data for participants in iWITH study at screening visit
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE118587 | GEO | 2018/11/13
REPOSITORIES: GEO
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Project description:A longitudinal study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial. Microarrays were used to understand the gene expression profile differences between IS withdrawal outcomes (Tolerant and Non-tolerant)
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Project description:Complications due to long-term administration of immunosuppressive therapy increase the morbidity and mortality of liver transplant recipients. Discontinuation of immunosuppressive drugs in recipients spontaneously developing operational tolerance could substantially lessen this burden. However, this strategy results in the development of rejection in a high proportion of recipients who require lifelong immunosuppression. Thus, there is a need to identify predictive factors of successful drug withdrawal and to define the clinical and histological outcomes of operationally tolerant liver recipients. Methods. We enrolled 102 stable liver transplant recipients in an immunosuppression withdrawal trial in which drugs were gradually discontinued over a 6-9 month period. Patients with stable graft function and no signs of rejection in a liver biopsy conducted 12 months after cessation of immunosuppressive therapy were considered operationally tolerant. Results. Out of the 98 recipients who completed the study, immunosuppression discontinuation was successful in 41 recipients and rejection occurred in 57. Rejection episodes were mild and were resolved in all cases. Development of tolerance was independently associated with time elapsed since transplantation, recipient age, and male gender. No histological damage was apparent in protocol biopsies performed after successful drug withdrawal.
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Project description:Liver biopsy samples were obtained as part of the LITMUS trial (ClinicalTrials.gov NCT02541916). All samples were obtained from liver transplant recipients prior to immunosuppression withdrawal. Percutaneous liver biopsies were performed under local anaesthesia using an 18-gauge Jamshidi needle. A 0.5cm portion of the biopsy to be used for gene expression was stored in RNAlater (Qiagen) for 24 hours at 4 °C and then transferred to -80 °C. Specimens were thawed and transferred to a clean, RNase free microcentrifuge tube. Tissue samples were incubated in 600 ul of lysis buffer (Ambion) with 6 ul of 2-mercaptoethanol for 10 minutes. Tissue samples were then homogenized using a nuclease-free disposable pellet pestle (Kimble Kontes) and processed using the PureLink RNA Mini Kit (Ambion). RNA quality was evaluated using an Bioanalyzer 2100 (Agilent) and samples with RIN > 7 were submitted for sequencing and analysis at The Center for Applied Genomics (Toronto, Canada).
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Project description:In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection. We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA). Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms. Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%.This set contains the data for samples hybridized to Affymetrix arrays. Disease State: Acute Rejection (AR#sampleid) or Stable (S#sampleid) samples. This dataset is part of the TransQST collection.
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Project description:In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection. This SuperSeries is composed of the SubSeries listed below. We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA). Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms. Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%.This set contains the data for samples hybridized to Affymetrix arrays. Refer to individual Series
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Project description:Interventions: Down-Up-Crossing Group:enteroscopy
Primary outcome(s): tissue biopsy
Study Design: Cross-sectional
| 2676909 | ecrin-mdr-crc