Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients
2016-02-29
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GEO Accession Number GSE86884
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Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients
Published Date
2016-02-29
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Israni, Ajay
isran001@umn.edu
isran001@umn.edu
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Genomics Data
Human Subjects Data
Genomics Data
Human Subjects Data
Abstract
This is the FPKM and clinical covariate data from a paper in PLOS One. These data will be useful for future researchers to study gene expression patterns over time before and after immunosuppression and kidney transplantation. We removed subject names and any other identifiers in order to de-identify the subjects.
Description
We performed RNA sequencing (RNAseq) on peripheral blood mononuclear cells (PBMCs) to identify differentially expressed gene transcripts (DEGs) after kidney transplantation and after the start of immunosuppressive drugs. RNAseq is superior to microarray to determine DEGs because it's not limited to available probes, has increased sensitivity, and detects alternative and previously unknown transcripts. DEGs were determined in 32 adult kidney recipients, without clinical acute rejection (AR), treated with antibody induction, calcineurin inhibitor, mycophenolate, with and without steroids. Blood was obtained pre-transplant (baseline), week 1, months 3 and 6 post-transplant. PBMCs were isolated, RNA extracted and gene expression measured using RNAseq. Principal components (PCs) were computed using a surrogate variable approach. DEGs post-transplant were identified by controlling false discovery rate (FDR) at < 0.01 with at least a 2 fold change in expression from pre-transplant. The top 5 DEGs with higher levels of transcripts in blood at week 1 were TOMM40L, TMEM205, OLFM4, MMP8, and OSBPL9 compared to baseline. The top 5 DEGs with lower levels at week 1 post-transplant were IL7R, KLRC3, CD3E, CD3D, and KLRC2 (Striking Image) compared to baseline. The top pathways from genes with lower levels at 1 week post-transplant compared to baseline, were T cell receptor signaling and iCOS-iCOSL signaling while the top pathways from genes with higher levels than baseline were axonal guidance signaling and LXR/RXR activation. Gene expression signatures at month 3 were similar to week 1. DEGs at 6 months post-transplant create a different gene signature than week 1 or month 3 post-transplant. RNAseq analysis identified more DEGs with lower than higher levels in blood compared to baseline at week 1 and month 3. The number of DEGs decreased with time post-transplant. Further investigations to determine the specific lymphocyte(s) responsible for differential gene expression may be important in selecting and personalizing immune suppressant drugs and may lead to targeted therapies.
Referenced by
Dorr C, Wu B, Guan W, Muthusamy A, Sanghavi K, Schladt DP, et al. (2015) Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients. PLoS ONE 10(5): e0125045.
http://dx.doi.org/10.1371/journal.pone.0125045
http://dx.doi.org/10.1371/journal.pone.0125045
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This is Version 2 of the data. It replaces Version 1:
http://conservancy.umn.edu/handle/11299/177631.1
http://conservancy.umn.edu/handle/11299/177631.1
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This study was funded by National Institute for General Medical Sciences' Pharmacogenomics Research Network for the project titled "Precision Immune Suppression. The PRECISE Study. Genomics of Transplantation" that was awarded to Pamala A. Jacobson and Baylor College of Medicine Human Genome Sequencing Center. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Suggested citation
Dorr, Casey; Wu, Baolin; Guan, Weihua; Muthusamy, Amutha; Sanghavi, Kinjal; Schladt, David; Maltzman, Jonathan; Scherer, Steven; Brott, Marcia; Matas, Arthur; Jacobson, Pamala; Oetting, William; Israni, Ajay. (2016). Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients. Retrieved from the Data Repository for the University of Minnesota (DRUM), http://dx.doi.org/10.13020/D6KS3R.
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