Identifying the genes involved in CD4+ T cell mediated-acute allograft rejection
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE14540 | GEO | 2010/03/01
SECONDARY ACCESSION(S): PRJNA111627
REPOSITORIES: GEO
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Project description:Acute allograft rejection is a leading cause for the failure of organ allotransplantation. Identifying the genes involved in the rejection process provides clues to study the mechanisms, and to provide specific gene targets for monitoring, predicting and preventing acute allograft rejection. Using a mice model of skin acute allograft rejection and SAGE method, we analyzed gene expression in the CD4+ T cells of the mice, the cell type known to play critical roles in acute allograft rejection. Our study identifies 402 SAGE tags significantly different from these from the control. From these SAGE tags, we identified 91 increasingly and 85 decreasingly expressed genes, and many genes have not been linked with acute allograft rejection before. Functional classification of these genes shows that apoptosis, transcription regulation, cell growth and maintenance and signal transduction are among the most frequently changed functional groups. Our study provides a genome-wide view for the genes involving acute allograft rejection in the CD4+ T cells, and indicates that acute allograft rejection involves multiple genes in different functional categories. The genes identified from the study provide candidates for further studying the mechanisms and for monitoring, predicting and preventing acute allograft rejection. Female mice of 6-10 week age were used for the study. BALB/c mice (H-2d) and BALB/c severe combined immunodeficient (SCID) mice were from the animal facility of Shandong University (Jinan, China). C57BL/6 (H-2b, B6) were from Vitalriveri Co. ltd (Beijing, China). Mice were maintained in a pathogen-free animal environment during the experimental process. The use of mice for the study was approved by the Institutional Animal Experimental Committee, and animal care and surgical procedures were performed in compliance with the standard animal experimental protocols of Shandong University School of Medicine. The process of generating skin acute allograft rejection followed the established procedure (12). Briefly, dorsal skin of C57BL/6 was transplanted onto the dorsal thorax of BALB/c SCID mice under sterile condition (allotransplant). As a control, dorsal skin of BALB/c mice was transplanted to BALB/c SCID mice (autotransplant). After 28 days of transplantation, CD4+ T cells were harvested from the spleens of BALB/c mice by using the mouse CD4+ T cells enrichment columns (R&D) with the purity >90% as measured by flow cytometry and 8x106 purified CD4+ T cells were adoptively injected into each transplanted mice via the lateral tail vein. The skin graft in each transplanted mice was then monitored daily. The skin graft was considered to fully reject when more than 50% of the skin became necrosis. SAGE Analysis Upon 14 days post CD4+ T cell transferring, CD4+ T cells were collected from the spleens of five mice in each group with adaptive CD4 T cell transferring using the same process described above. Total RNA was extracted from the purified cells by using Trizol reagent (Invitrogen) and mRNA was purified from the total RNA using oligo dT beads (Invitrogen). cDNA was synthesized by using MMLV reverse transcriptase and oligo(dT) primers (MBI-add full name). SAGE libraries from 4 allotransplant and autotransplant groups were constructed following the standard procedure (13). For each SAGE library, 1,200 sequences were collected through an ABI 3730 DNA sequencer (Applied BioSystems). SAGE tags were extracted from the sequences by using the SAGE2000 software (Invitrogen).
2010-02-28 | E-GEOD-14540 | biostudies-arrayexpress
Project description:Purpose: to explore the function and mechanism of acute rejection in vascularized composite allotransplantation Method: tRF & tiRNA profiles of acute rejection in vascularized composite allotransplantation were generated by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using SYBR Green assays. Results:Sequencing was used to screen expression profiles and predict target genes. Compared with the control group, there were significant differences in the expression levels of 16 tRFs & tiRNAs, including 5 up-regulated target genes and 11 down-regulated target genes. Bioinformatics analysis and RT-qPCR revealed potential up regulation of tRFs & tiRNAs(tiRNA-1-33-Gly-GCC-1, tiRNA-1-34-Glu-CTC-1, tRF-1-32-Gly-GCC-2-M2) and down regulation of tRFs & tiRNAs (tRF-59:75-Gln-CTG-2-M2, tRF-59:76-Val-AAC-1-M2). Conclusion: In conclusion, it is speculated that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA induced acute rejection by regulating CACNA1D gene in MAPK signaling pathway. This provides a new insight into the mechanism and therapeutic targets of acute rejection.
2022-07-20 | GSE190008 | GEO
Project description:Background. The lack of noninvasive biomarkers of rejection remains a challenge in the accurate monitoring of deeply buried nerve allografts and precludes optimization of therapeutic intervention. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation with or without immunosuppression. Methods. Balb/c mice were randomized into 3 experimental groups, that is, (1) untreated isograft (Balb/c → Balb/c), (2) untreated allograft (C57BL/6 → Balb/c), and (3) allograft (C57BL/6 → Balb/c) with FK506 immunosuppression. A 1-cm Balb/c or C57BL/6 donor sciatic nerve graft was transplanted into sciatic nerve gaps created in recipient mice. At 1, 3, 7, 10, and 14 d after nerve transplantation, nerve grafts, whole blood, and sera were obtained for miRNA expression analysis with an miRNA array and subsequent validation with quantitative PCR.
2014-07-01 | GSE48971 | GEO
Project description:Background. The lack of noninvasive biomarkers of rejection remains a challenge in the accurate monitoring of deeply buried nerve allografts and precludes optimization of therapeutic intervention. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation with or without immunosuppression. Methods. Balb/c mice were randomized into 3 experimental groups, that is, (1) untreated isograft (Balb/c → Balb/c), (2) untreated allograft (C57BL/6 → Balb/c), and (3) allograft (C57BL/6 → Balb/c) with FK506 immunosuppression. A 1-cm Balb/c or C57BL/6 donor sciatic nerve graft was transplanted into sciatic nerve gaps created in recipient mice. At 1, 3, 7, 10, and 14 d after nerve transplantation, nerve grafts, whole blood, and sera were obtained for miRNA expression analysis with an miRNA array and subsequent validation with quantitative PCR.
2014-07-01 | GSE48969 | GEO
Project description:Predicting Acute Cardiac Allograft Rejection Using Donor and Recipient Gene Expression
| PRJNA150525 | ENA
Project description:Compromised renal function after renal allograft transplantation often results in anemia in the recipient. Molecular mechanisms leading to anemia during acute rejection are not fully understood; inadequate erythropoietin production and iron deficiency have been reported to be the main contributors. To increase our understanding of the molecular events underlying anemia in acute rejection, we analyzed the gene expression profiles of peripheral blood lymphocytes (PBL) from four pediatric renal allograft recipients with acute rejection and concurrent anemia, using DNA microarrays containing 9000 human cDNA clones (representing 7469 unique genes). In these anemic rejecting patients, an 'erythropoiesis cluster' of 11 down-regulated genes was identified, involved in hemoglobin transcription and synthesis, iron and folate binding and transport. Additionally, some alloimmune response genes were simultaneously down-regulated. An independent data set of 36 PBL samples, some with acute rejection and some with concurrence of acute rejection and anemia, were analyzed to support a possible association between acute rejection and anemia. In conclusion, analysis using DNA microarrays has identified a cluster of genes related to hemoglobin synthesis and/or erythropoeisis that was altered in kidneys with renal allograft rejection compared with normal kidneys. The possible relationship between alterations in the expression of this cluster, reduced renal function, the alloimmune process itself, and other influences on the renal transplant awaits further analysis.
2005-11-01 | E-SMDB-2730 | biostudies-arrayexpress
Project description:Liver transplantation is the only lifesaving therapy for patients with irreversible liver failure, and 30% of the recipients experience acute rejection in the first 12 months following transplantation. Acute rejection is diagnosed by core needle biopsy and noninvasive methods for predicting acute rejection could improve clinical care. MicroRNAs (miRNAs) are emerging as biomarkers of clinically significant events. We investigated whether circulating extracellular miRNA profiles in sera matched to liver allograft biopsies predict human liver allograft status. Small RNA sequencing and TaqMan low-density array analysis of RNA from biopsy matched sera identified that liver specific miR-122, and miRs -885, -210, -194, 193b, -192, -148a, -34a and -22 distinguish patients with acute rejection biopsies from those with biopsies without rejection features (false discovery rate of <0.15). We measured absolute levels of these informative 9 miRNAs using quantitative real-time PCR assays. Receiver-operating-characteristic (ROC) curve analysis of circulating levels of miRNA levels validated that all 9 miRNAs discriminate patients with acute rejection in their biopsies from those without rejection in their biopsies (P <0.01 to P<0.0001). A parsimonious diagnostic signature of miR-122 and miR-194 was diagnostic of acute rejection with a sensitivity of 79% (95% confidence interval [CI], 49% to 95%) and a specificity of 88% (95% CI, 64% to 99%) (area under the curve, 0.91; 95% CI, 0.81 to 1.00; P<0.001 by ROC curve analysis). Our findings suggest that a molecular signature of miR-122 and miR-194 in serum offers a noninvasive means of diagnosing acute rejection including mild forms in human liver allografts.
2019-06-30 | GSE69579 | GEO
Project description:We have analyzed the pattern of gene expression in human primary CD34(+) stem/progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 x 10(6) CD34(+) cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. By using the generation of longer sequences from SAGE tags for gene identification (GLGI) method, we identified the correct gene for 385 of 440 high-copy SAGE tags that matched multiple genes and we generated 198 novel 3' expressed sequence tags from 138 high-copy novel SAGE tags. We observed that many different SAGE tags were derived from the same genes, reflecting the high heterogeneity of the 3' untranslated region in the expressed genes. We compared the quantitative relationship for genes known to be important in hematopoiesis. The qualitative identification and quantitative measure for each known gene, expressed sequence tag, and novel SAGE tag provide a base for studying normal gene expression in hematopoietic stem/progenitor cells and for studying abnormal gene expression in hematopoietic diseases. Keywords: other
2005-03-01 | GSE2346 | GEO
Project description:CONTEXT Slowly progressive chronic tubulo-interstitial damage jeopardizes long-term renal allograft survival. Both immune and non-immune mechanisms are thought to contribute, but the most promising targets for timely intervention have not been identified. OBJECTIVE In the current study we seek to determine the driving force behind progressive histological damage of renal allografts, without the interference of donor pathology, delayed graft function and acute graft rejection. DESIGN We used microarrays to examine whole genome expression profiles in renal allograft protocol biopsies, and analyzed the correlation between gene expression and the histological appearance over time. The gene expression profiles in these protocol biopsies were then compared with gene expression of biopsies with acute T-cell mediated rejection. PATIENTS Human renal allograft biopsies (N=120) were included: 96 rejection-free protocol biopsies and 24 biopsies with T-cell mediated acute rejection. RESULTS In this highly cross-validated study, we demonstrate the significant association of established, ongoing and future chronic histological damage with regulation of adaptive immune gene expression (T-cell and B-cell transcript sets) and innate immune response gene expression (dendritic cell, NK-cell, mast cell and granulocyte transcripts). We demonstrate the ability of gene expression analysis to perform as a quantitative marker for ongoing inflammation with a wide dynamic range: from subtle subhistological inflammation prior to development of chronic damage, over moderate subclinical inflammation associated with chronic histological damage, to marked inflammation of Banff-grade acute T-cell mediated rejection. CONCLUSION Progressive chronic histological damage after kidney transplantation is associated with significant regulation of both innate and adaptive immune responses, months before the histological lesions appear. This study therefore corroborates the hypothesis that quantitative inflammation below the diagnostic threshold of classic T-cell or antibody-mediated rejection is associated with early subclinical stages of progressive renal allograft damage. We used microarrays to examine whole genome expression profiles in renal allograft protocol biopsies, and analyzed the correlation between gene expression and the histological appearance over time. The gene expression profiles in these protocol biopsies were then compared with gene expression of biopsies with acute T-cell mediated rejection. Human renal allograft biopsies (N=120) were included: 96 rejection-free protocol biopsies and 24 biopsies with T-cell mediated acute rejection.
2011-12-10 | E-GEOD-25902 | biostudies-arrayexpress
Project description:Acute renal allograft rejection is an important complication in kidney transplantation. Accurate diagnosis of rejection events is necessary for timely response and treatment. We illustrate the usefulness and biological relevance of selected multivariate approaches to detect rejection from genomic and proteomic signals. The data was used to study gene expression changes using whole genome microarray analysis of peripheral blood from subjects with acute rejection (n=20) and non-rejecting controls (n=20) to obtain insight into the molecular and biological causation of acute renal allograft rejection when combined with proteomics (iTRAQ) data for the same patients/time-points.
2014-04-26 | GSE46474 | GEO