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Series GSE240778 Query DataSets for GSE240778
Status Public on Feb 28, 2024
Title Transciptomic signature of chronic antibody-mediated kidney rejection traited by extracorporeal photopheresis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background: The benefit of extracorporeal photopheresis on the course of kidney transplant rejection is unknown. The aim of our study was to investigate the variations in transcriptomics on graft biopsies when extracorporeal photopheresis was used to treat chronic humoral rejection after kidney transplantation.
Methods: we retrospectively analyzed the mRNA expression of 770 genes of interest in graft biopsies performed before and after treatment. Eight patients received an average of 23 extracorporeal photopheresis sessions over 4 months between the two biopsies.
Results: Transcriptomic analysis of the graft biopsies identified a significant (adjusted p-value< 0.05) increase in CAV1 mRNA in all patients and a significant decrease in CD19, IL21, PAX5, and SFTPA2 mRNAs in 7 of 8 patients.
Conclusions: In patients treated with extracorporeal photopheresis for chronic humoral rejection after renal transplantation, omic analysis of repeated biopsies shows a reduction in fibrotic and inflammatory transcriptomic signatures.
Overall design It is a retrospective single-center, pilot, case series of 8 kidney transplant recipients with biopsy-proven cABMR according to Banff classification and treated by ECP therapy between 2016 and 2020 at Lille University Hospital, France.
Half of the patients met the criteria for active cABMR and the other half for inactive cABMR, but all them had a microvascular inflammation score (g+ptc) greater than or equal to 2. ECP procedure was based on an induction phase with 2 ECP sessions per week during the first 6 weeks, then one session weekly from week 6 to 12 and a maintenance phase with two ECP sessions monthly until repeated biopsy. Each patient had biopsy-proven cABMR and systematic biopsy after three months of ECP treatment. Ten-µm-thick sections were obtained from frozen or alcohol-formalin-acetic acid (AFA) fixed-paraffin embedded tissue-block to collect the 300 ng of RNA required for analyses. RNA was isolated and extracted using the tissue RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany), and then concentration was assessed with the NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). 300ng of total RNA from each sample was then hybridized to the nCounter® Human Organ Transplant Panel (NanoString Technologies, Seattle, WA, USA). This panel evaluates the expression of 758 target genes and 12 internal reference genes for data normalization. Expression data were normalized and analyzed with the nSolver Analysis Software (version 4.0.70).
Arnaud Lionet and Marine Van triempon participated in pateint care; Martin Figeac and Céline Villenet performed the transcriptomic analysis, jean baptiste Gibier performed the histologic analysis.
Citation(s) 38380348
Submission date Aug 14, 2023
Last update date Feb 28, 2024
Contact name frédéric leprêtre
Organization name Lille University
Department CHU of Lille, CBP
Lab plateforme de génomique fonctionnelle et structurale
Street address Boulevard du Pr Leclercq
City lille
ZIP/Postal code 59037
Country France
Platforms (1)
GPL30305 NanoString Human Organ Transplant Panel
Samples (16)
GSM7709145 graft_before.treatment_Bo.
GSM7709146 graft_after.treatment_patBo
GSM7709147 graft_before.treatment_patDu1
BioProject PRJNA1005233

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE240778_Normalized_signals.txt.gz 30.5 Kb (ftp)(http) TXT
GSE240778_RAW.tar 160.0 Kb (http)(custom) TAR (of RCC)
Processed data included within Sample table
Processed data are available on Series record

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