DNA methylation profiling of kidney transplant recipients
Ontology highlight
ABSTRACT: Targeted bisulfite sequencing data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- kidney transplant(Tx) was generated to study 1) methylation difference between pre- and postTx, 2) methylation difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, 3) immune response regarding Tx and immunosuppression prophylaxes, and 4) how the gene expression and DNA methylation are associated.
Project description:Targeted bisulfite sequencing data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- lung transplant(Tx) was generated to study 1) methylation difference between pre- and postTx, 2) methylation difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, and 3) immune response regarding Tx and immunosuppression prophylaxes.
Project description:RNA-seq data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- kidney transplant(Tx) was generated to study 1) gene expression difference between pre- and postTx, 2) gene expression difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, 3) immune response regarding Tx and immunosuppression prophylaxes, and 4) how the gene expression and DNA methylation are associated.
Project description:To study the gene expression dynamics in cytomegalovirus (CMV) DNAemic patients after kidney transplantation, we performed RNA sequencing (RNAseq) on 31 DNAemic patients at 4 timepoints (baseline, 1 week post-DNAemia, 1 month post-DNAemia, and a long-term timepoint 9-18 months post-DNAemia) matched with 31 non-DNAemic patients at 2 timepoints (baseline and long-term).
Project description:We used Affymetix HG Focus GeneChip to measure the expression levels of HIV seronegative and seropositive individuals in human PBMCs in vivo. GSM39104 -GSM39115 are HIV seronegative samples; GSM39116-GSM39137 are HIV seropositive but drug naive samples; GSM39138-GSM39147 are HIV seropositive samples used to test serostatus biomarker; GSM39148-GSM39170 are HIV seropositive individuals whose CD4 cells decrease over time; GSM39171-GSM39187 are HIV seropositive individuals whose CD4 cells increase over time; GSM39188-GSM39190 are HIV seropositive samples used to test CD4 cell increase/decrease over time.
Project description:<p>High-throughput linking of T cell receptor (TCR) sequences to their binding antigens is vital for immune profiling, yet challenging. We present Tetramer associated TCR Sequencing (TetTCR-Seq) to address this challenge. Binding is determined using a library of DNA-barcoded antigen tetramers that are rapidly and inexpensively generated using an in vitro transcription/translation platform. We included CMV+ donors (CMV seropositive donors who are infected with Cytomegalovirus) to screen for CMV specific TCRs.</p>
Project description:Infection with cytomegalovirus is characterised by very strong and sustained T cell responses in peripheral blood. These expansions increase even further with age and research suggests CMV-specific T cells may contribute towards development of accelerated immune senescence and vascular disease in elderly people. In this study we compared the transcriptional profile of CD4+ T cells specific for two CMV-derived epitopes to that of CD4+CCR7-CD45RA- (effector memory) T cells of CMV-seronegative individuals. The aim was to get a better understanding of the nature of these virus-specific T cells and how they may contribute to immunopathology.
Project description:The CD8+ T cell compartment of human cytomegalovirus (CMV) seropositive individuals characteristically contains a high proportion of cells that expresses Natural Killer Cell Receptors (NKR) which may contribute to the surveillance of virus-infected cells. To test if this enhanced expression is a direct and immediate result of CMV infection we used DNA microarrays to analyse putative changes in RNA-expression level of 39 NKRs in CMV-specific CD8+ T cells of renal transplant recipients experiencing primary CMV infection. Already in the acute phase of infection 29 NKRs were induced of which 19 remained high 1 year after cessation of viral replication. Activating and inhibitory NKRs were induced to a similar extent. Detailed longitudinal flowcytometric analyses confirmed NKR changes at the protein level. Strikingly, a strong induction of CD94 on CD3+ T cells was observed with surface expression of activating CD94dimNKG2C dimers appearing before inhibitory CD94brightNKG2A ones. After the acute phase of infection, the balance between inhibitory and activating receptors did not change. Thus, CMV infection induces a rapid and lasting change in the expression of NK receptors on human CD8+ T cells. Keywords: primary cytomegalovirus infection, human, CD8+ T cells, NKR, latent infection, chronic infection CMV-specific CD8+ T cells were isolated at three different stages (peak, 1 year p.i, latent) from three CMV seropositive individuals. Total RNA for each stage was pooled and compared with pooled RNA of naive CD8+ T-cells from healthy controls. For quality control naive CD8+ T-cells were compared with naive CD8+ T-cells. The experiment was performed in dye-swap.
Project description:We used Affymetix HG Focus GeneChip to measure the expression levels of HIV seronegative and seropositive individuals in human PBMCs in vivo. GSM39104 -GSM39115 are HIV seronegative samples; GSM39116-GSM39137 are HIV seropositive but drug naive samples; GSM39138-GSM39147 are HIV seropositive samples used to test serostatus biomarker; GSM39148-GSM39170 are HIV seropositive individuals whose CD4 cells decrease over time; GSM39171-GSM39187 are HIV seropositive individuals whose CD4 cells increase over time; GSM39188-GSM39190 are HIV seropositive samples used to test CD4 cell increase/decrease over time. Keywords: other
Project description:Competition between antigen-specific T cells for peptide:MHC (p:MHC) complexes shapes the ensuing T cell response. T cells also compete for access to antigen presenting cells (APCs), which results in competition between T cells of different antigen specificities and is referred to as cross-competition. When both mechanisms are in place, a memory T cell population specific for just a single epitope can effectively limit de novo antigen-specific T cell responses. Whether human cytomegalovirus (CMV)-specific T cell responses prevent other de novo T cell responses is unknown, but of interest in a transplant context as well as the development of CMV-based vaccines. We assessed the extent of T cell competition and cross-competition in a cohort of non-myeloablative hematopoietic stem cell transplant (nmHSCT) patients. In our cohort, HSCT donors and recipients were CMV-seronegative and -positive, respectively, thus providing genetically distinct memory and naïve T cell populations. We used single-cell transcriptomics to track donor versus recipient-derived T cell clones. We found that recipient-derived CMV-specific memory T cells outcompeted donor-derived responses of identical specificity; however, expansion of other donor-derived T cell clones still occurred averaging 24 rounds of cell division. The transcriptional programs between expanding donor and recipient-derived cells were largely congruent and consistent with an effector T cell response. Our data further indicated that the composition of the T cell compartment changed due to expanding and contracting clones in the first 90 days post-nmHSCT. Overall, our data suggest that CMV-specific memory T cells compete for p:MHC but not APC access during CMV reactivation.
Project description:The CD8+ T cell compartment of human cytomegalovirus (CMV) seropositive individuals characteristically contains a high proportion of cells that expresses Natural Killer Cell Receptors (NKR) which may contribute to the surveillance of virus-infected cells. To test if this enhanced expression is a direct and immediate result of CMV infection we used DNA microarrays to analyse putative changes in RNA-expression level of 39 NKRs in CMV-specific CD8+ T cells of renal transplant recipients experiencing primary CMV infection. Already in the acute phase of infection 29 NKRs were induced of which 19 remained high 1 year after cessation of viral replication. Activating and inhibitory NKRs were induced to a similar extent. Detailed longitudinal flowcytometric analyses confirmed NKR changes at the protein level. Strikingly, a strong induction of CD94 on CD3+ T cells was observed with surface expression of activating CD94dimNKG2C dimers appearing before inhibitory CD94brightNKG2A ones. After the acute phase of infection, the balance between inhibitory and activating receptors did not change. Thus, CMV infection induces a rapid and lasting change in the expression of NK receptors on human CD8+ T cells. Keywords: primary cytomegalovirus infection, human, CD8+ T cells, NKR, latent infection, chronic infection