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Identifying Compartment-specific Alloimmune Targets After Renal Transplantation by integrated genomics

ABSTRACT: Microarray technology has evolved as a powerful tool over the last decade, to identify biomarkers and study the mechanisms of diseases. We propose a novel application of integrated genomics by combining transcriptional levels with serological antibody profiling after kidney transplantation, with the aim of uncovering the relative immunogenicity of seven different renal compartments after allo-transplantation. Thirty-six paired pre- and post-transplant serum samples were examined from eighteen transplant recipients, across 5,056 protein targets on the ProtoArray V3.0 platform. Normal renal compartment-specific gene expression data from a cDNA platform were re-analyzed and both the cDNA and the ProtoArray platforms were re-annotated to most up-to-date NCBI gene identifiers; 3,835 genes/proteins are measured on both platforms. Antibody levels were ranked for individual patients and the hypergeometric enrichment statistic was applied on mapped compartment-specific expression data. We discovered that after transplantation, in addition to HLA and MICA responses, temporal alloimmune responses are seen against non-HLA antigens specific to different compartments of the kidney, with highest level responses noted against renal pelvis and cortex specific antigens. The renal medulla is of low immunogenicity as none of the outer or inner medulla specific targets generated significant post-transplant antibody responses. Immunohistochemistry confirmed pelvis and cortex specific localizations of selected targeted antigens, supporting the robust nature of this discovery. This study provides a road map of renal compartment-specific non-HLA antigenic targets responsible for generating alloimmune responses, opening the door for clinical correlations with post-transplant dysfunctional states to be determined. Keywords: alloimmune response after kidney transplantation

ORGANISM(S): Homo sapiens

PROVIDER: GSE10452 | GEO | 2008/02/13

SECONDARY ACCESSION(S): PRJNA108005

REPOSITORIES: GEO

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Project description:Microarray technology has evolved as a powerful tool over the last decade, to identify biomarkers and study the mechanisms of diseases. We propose a novel application of integrated genomics by combining transcriptional levels with serological antibody profiling after kidney transplantation, with the aim of uncovering the relative immunogenicity of seven different renal compartments after allo-transplantation. Thirty-six paired pre- and post-transplant serum samples were examined from eighteen transplant recipients, across 5,056 protein targets on the ProtoArray V3.0 platform. Normal renal compartment-specific gene expression data from a cDNA platform were re-analyzed and both the cDNA and the ProtoArray platforms were re-annotated to most up-to-date NCBI gene identifiers; 3,835 genes/proteins are measured on both platforms. Antibody levels were ranked for individual patients and the hypergeometric enrichment statistic was applied on mapped compartment-specific expression data. We discovered that after transplantation, in addition to HLA and MICA responses, temporal alloimmune responses are seen against non-HLA antigens specific to different compartments of the kidney, with highest level responses noted against renal pelvis and cortex specific antigens. The renal medulla is of low immunogenicity as none of the outer or inner medulla specific targets generated significant post-transplant antibody responses. Immunohistochemistry confirmed pelvis and cortex specific localizations of selected targeted antigens, supporting the robust nature of this discovery. This study provides a road map of renal compartment-specific non-HLA antigenic targets responsible for generating alloimmune responses, opening the door for clinical correlations with post-transplant dysfunctional states to be determined. Keywords: alloimmune response after kidney transplantation Plasma profiling using Protein Microarray: Serum antibodies were profiled using Invitrogen ProtoArrayÂ® Human Protein Microarray v3.0 technology (Invitrogen, Carlsbad, CA). This platform contains 5,056 non-redundant human proteins expressed in a baculovirus system, purified from insect cells and printed in duplicate onto a nitrocellulose-coated glass slide. Five mL serum diluted in PBST buffer at 1:150 was applied for 90 minutes onto the Protoarray, after blocking with blocking buffer for 1 hour. The slides were then washed with 5ml fresh PBST buffer, 4 times for 10 minutes each, and probed with secondary antibody (goat anti-human Alexa 647, Molecular Probes, Eugene, OR) for 90 minutes. Finally, after a second washing with PBST buffer, the slides were dried and scanned using a fluorescent microarray scanner (GSI Luminoics Perkin-Elmer scanner). All steps were carried out on a rotating platform at 4 ÂºC. ProtoArray data acquisition and measurement: The slides were scanned at a PMT gain of 60% with a laser power of 90% and a focus point of 0 Î¼m. Fluorescence intensity data were acquired using GenePix Pro 6.0 software (Molecular devices, Sunnyvale, CA) with the appropriate â.galâ file downloaded from the ProtoArray central portal on the Invitrogen website (http://www.invitrogen.com/protoarray) by submitting the barcode of each ProtoArray slide.

Project description:Background: Studies recently support that non-HLA antigens could be additional targets of injury in organ transplant recipients, and MICA was associated with an increased risk of graft loss. Methods: A ProtoArray platform was used to study 37 serum samples from 22 unique patients (15 renal recipients and 7 healthy controls). Thirty paired pre- and post-transplant serum samples were analyzed for detection of de novo post-transplant antibody responses in the 15 patients (10 acute rejection (AR), 5 Stable). Probes on ProtoArray and cDNA platforms (GSE: 3931) were re-annotated and compartment specific gene lists were analyzed using the integrated genomics method. Normal and transplant kidney IHC were performed for MICA antigen localization. Results: Mean MICA-Ab (antibody) signal intensity was significantly higher in transplant patients compared with healthy controls and de novo MICA-Ab were detected in 73% transplant patients. The mean post-transplant signal intensity of MICA-Ab was the highest in C4d+AR. Detection of MICA-Ab responses did not correlate with time post-transplantation, but significantly correlated with decline in graft function over the subsequent year. Integrative genomics predicted localization of the MICA antigen to the glomerulus. IHC confirmed cytoplasmic MICA staining solely in glomerular podocytes in normal kidney. In the transplant kidney, infiltrating mononuclear lymphocytes (T, B and NK) in AR had additional MICA staining. Conclusions: MICA can be highly detected regardless of graft dysfunction or AR. The intensity signal of the MICA antibody correlates with subsequent decline in graft function. The MICA antigen localizes to the glomerulus and infiltrating mononuclear cells in AR. Pre- and post-transplant serum antibodies were profiled for each patient, using the Invitrogen ProtoArrayÂ® Human Protein Microarray v3.0 platform (Invitrogen, Carlsbad, CA). This platform contains 5,056 non-redundant human proteins expressed in a baculovirus system, purified from insect cells and printed in duplicate onto a nitrocellulose-coated glass slide. Each protein is spotted twice on each array, to measure the quality of the signal intensity. Details for experiment processing and analysis follow the previous publication from our group (13). Prospector software was used to retrieve the expression based on immune response profiling of the .gal files.

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Identifying Compartment-specific Alloimmune Targets After Renal Transplantation by integrated genomics

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