GEO DataSets

(Submitter supplied) The development of reliable biomarkers of transplant tolerance would enhance the safety and feasibility of clinical trials and potentially also facilitate management of patients on standard immunosuppressive therapies. To this end, we examined peripheral blood samples of spontaneously tolerant renal transplant recipients, as well as patients enrolled in two interventional tolerance trials, using multiparameter flow cytometry and gene expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL19858

158 Samples

Download data: TXT

(Submitter supplied) In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable allograft function while on immunosuppression and healthy non transplated, controls. Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4266

Platform:

GPL570

58 Samples

Download data: CEL

Analysis of whole blood from tolerant renal transplant recipients (i.e., with stable graft function and receiving no immunosuppressive drugs for >1 year) and from recipients stable on immunosuppressive drugs. Results provide insight into molecular mechanisms underlying renal transplant tolerance.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 individual sets

Platform:

GPL570

Series:

GSE22229

58 Samples

Download data: CEL

(Submitter supplied) mmunosuppressive drugs can be completely withdrawn in up to 20% of liver transplant recipients, commonly referred to as ‘operationally’ tolerant. Immune characterization of these patients, however, has not been performed in detail, and we lack tests capable of identifying tolerant patients among recipients receiving maintenance immunosuppression. In the current study we have analyzed a variety of biological traits in peripheral blood of operationally tolerant liver recipients in an attempt to define a multiparameter ‘fingerprint’ of tolerance. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3282

Platform:

GPL570

17 Samples

Download data: CEL

Analysis of peripheral blood mononuclear cells from operationally tolerant liver transplant patients. Operationally tolerant patients are fully immunocompetent but accept grafts without chronic immunosuppression. Results identify a molecular signature for operational tolerance.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 specimen sets

Platform:

GPL570

Series:

GSE11881

17 Samples

Download data: CEL

(Submitter supplied) miR-142-3p is highly expressed in peripheral blood mononuclear cells (PBMCs) and has been described as a hematopoietic-restricted lineage, suggesting immune functions (Chen, Li et al. 2004; Landgraf, Rusu et al. 2007; Merkerova, Belickova et al. 2008). In order to determine the roles of miR-142-3p in B lymphocytes, we over-expressed this miRNA in the Raji B-cell line using a synthetic mimic of miR-142-3p and analyzed gene expression 24 hours after the transfection.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

8 Samples

Download data: TXT

(Submitter supplied) Long-term allograft survival generally requires lifelong immunosuppression. Rarely, recipients display spontaneous operational tolerance with stable graft function in the absence of immunosuppression. The lack of biological markers of this phenomenon precludes identification of potentially tolerant patients in which immunosuppression could be tapered and hinders the development of new tolerance inducing strategies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6271

67 Samples

Download data: TXT

(Submitter supplied) Genomic Analysis of more than 400 patients from multi-center transplant programs and clinical trials provides a non-invasive QPCR based gene expression test for operational renal allograft tolerance

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6848 GPL6480

31 Samples

Download data: TXT

(Submitter supplied) Efforts at finding potential biomarkers of tolerance after kidney transplantation have been hindered by limited sample size, as well as the complicated mechanisms underlying tolerance and the potential risk of rejection after immunosuppressant withdrawal. In this work, three different publicly available genome-wide expression data sets of peripheral blood lymphocyte (PBL) from 63 tolerant patients were used to compare 14 different machine learning models for their ability to predict spontaneous kidney graft tolerance. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLS, XLSX

(Submitter supplied) Operational tolerance after solid organ transplantation is defined as stable graft acceptance without immunosuppression while maintaining normal immunocompetence against immunological insults. However, it is not clear yet which cellular and molecular pathways are driving tolerance in these patients and how this state can be induced in order to improve graft survival. Several transcriptomic analysis have shown that transcription signatures in blood can reflect the immunological state associated with operational tolerance in kidney transplant. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

22 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

17 Samples

Download data: TSV

(Submitter supplied) Survival of solid organ grafts depends on life-long immunosuppression, which results in increased rates of infection and malignancy. Induction of tolerance to allografts would represent the optimal solution for controlling both chronic rejection (CR) and side effects of immunosuppression. Although spontaneous ‘‘operational tolerance’’ can occur in human kidney transplantation, the lack of noninvasive peripheral blood biological markers of this rare phenomenon precludes the identification of potentially tolerant patients in whom immunosuppression could be tapered as well as the development of new tolerance inducing strategies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8798

528 Samples

Download data: GPR

(Submitter supplied) Immunosuppression is needed in HLA identical sibling renal transplantation. We conducted a tolerance trial in this patient cohort using Alemtuzumab induction, donor hematopoietic stem cells, tacrolimus/mycophenolate immunosuppression converted to sirolimus, planning complete drug withdrawal by 24 months post-transplantation. After an additional 12 months with no immunosuppression, normal biopsies and renal function, recipients were considered tolerant. more...

Organism:

Homo sapiens

Type:

Third-party reanalysis; Expression profiling by array

Platforms:

GPL6244 GPL11532

46 Samples

Download data: CEL, TXT

(Submitter supplied) The authors report that in INTERCOM, a prospective international study of 300 kidney transplant biopsies, a microarray-based molecular score for T cell-mediated rejection changed the assessment of 26% of all biopsies, illustrating the potential of precision diagnostics to impact practice.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

306 Samples

Download data: CEL

(Submitter supplied) Histologic diagnosis of T cell-mediated rejection in kidney transplant biopsies has limited reproducibility because it is based on non-specific lesions using arbitrary rules that are subject to differing interpretations. We used microarray results from 403 indication biopsies previously given histologic diagnoses to develop a molecular classifier that assigned a molecular T cell-mediated rejection score to each biopsy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

411 Samples

Download data: CEL

(Submitter supplied) Previously we found that Irf4-deficient T cells were dysfunctional and unable to reject heart allografts and checkpoint blockade treatment could reinvigorate dysfunctional Irf4-deficient T cells and enable them reject heart allografts. But shortly after the reinvigoration those T cells went back to dysfunctional state. TCR-transgenic TEa CD4+ T cells (B6 background) recognize a Balb/c I-Eα allopeptide presented by B6 antigen presenting cells, and were used to assess the effects of immune checkpoint blockades on Irf4-deficient alloreactive T cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

6 Samples

Download data: TXT

(Submitter supplied) The ability to identify a robust means for both pediatric and adult liver transplant recipients for minimization and weaning of immunosuppression is greatly needed. We analyzed 298 samples from pediatric (n=83) and published adult (n=57) liver transplant recipients, and the public available cell or tissue specific samples (n=158). Biomarkers were first identified from the integration of the cross-platform analysis of Stanford pediatric and adult studies and validated in independent samples from UCLA on microarray. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

41 Samples

Download data: TXT

(Submitter supplied) Transplant recipients spontaneously accepting their grafts in the absence of immunosuppression demonstrate the feasibility of attaining allograft tolerance in humans. Previous studies have identified blood transcriptional and cell phenotypic markers specific for either liver or kidney tolerant recipients, but the two settings have not been directly compared yet employing the same platforms. To identify potential similarities in immune parameters between recipients tolerant to different organs, we analyzed blood samples from tolerant and non-tolerant liver and kidney recipients employing whole genome expression microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

72 Samples

Download data: CEL