title: Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients.
abstract: 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.
authors.affiliation: Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America; Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Casey
authors.initials: C
authors.lastname: Dorr
authors.affiliation: Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Baolin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Weihua
authors.initials: W
authors.lastname: Guan
authors.affiliation: Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America.
authors.forename: Amutha
authors.initials: A
authors.lastname: Muthusamy
authors.affiliation: College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Kinjal
authors.initials: K
authors.lastname: Sanghavi
authors.affiliation: Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America.
authors.forename: David P
authors.initials: DP
authors.lastname: Schladt
authors.affiliation: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America.
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Maltzman
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Dallas, Texas, United States of America.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Scherer
authors.affiliation: College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Marcia J
authors.initials: MJ
authors.lastname: Brott
authors.affiliation: Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Matas
authors.affiliation: College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Pamala A
authors.initials: PA
authors.lastname: Jacobson
authors.affiliation: College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: William S
authors.initials: WS
authors.lastname: Oetting
authors.affiliation: Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America; Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America; Department of Epidemiology and Community Health, University of Minnesota School of Medicine, Minneapolis, Minnesota, United States of America.
authors.forename: Ajay K
authors.initials: AK
authors.lastname: Israni
mesh_terms: D000328:Adult; D064591:Allografts / Q000276:immunology; D001483:Base Sequence; D065095:Calcineurin Inhibitors / Q000627:therapeutic use; D005260:Female; D015870:Gene Expression / Q000235:genetics; D005786:Gene Expression Regulation / Q000187:drug effects* / Q000235:genetics; D006801:Humans; D007168:IMP Dehydrogenase / Q000037:antagonists & inhibitors; D007165:Immunosuppression Therapy / Q000379:methods*; D007166:Immunosuppressive Agents / Q000627:therapeutic use*; D016030:Kidney Transplantation; D007963:Leukocytes, Mononuclear / Q000166:cytology / Q000276:immunology*; D008297:Male; D008875:Middle Aged; D009173:Mycophenolic Acid / Q000031:analogs & derivatives / Q000627:therapeutic use; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics; D066027:Transplant Recipients
chemical_list: D065095:Calcineurin Inhibitors; D007166:Immunosuppressive Agents; D007168:IMP Dehydrogenase; D009173:Mycophenolic Acid