Abstract: TH-OR065
Primary Membranous Nephropathy: Glomerular RNA Sequencing from Archival Kidney Biopsies
Session Information
- Harnessing Molecular, Machine-Learning, and Genomic Innovations in Pathology
October 25, 2018 | Location: 24A, San Diego Convention Center
Abstract Time: 05:18 PM - 05:30 PM
Category: Pathology and Lab Medicine
- 1502 Pathology and Lab Medicine: Clinical
Authors
- Eikrem, Oystein, University of Bergen, Bergen, Norway
- Koch, Even, University of Bergen, Bergen, Norway
- Knoop, Thomas, Haukeland University Hospital, Bergen, Norway
- Vikse, Bjorn Egil, University of Bergen, Bergen, Norway
- Schordan, Eric, Firalis S.A., Huningue, France
- Debiec, Hanna, Inserm UMR_S1155, Paris, France
- Ronco, Pierre M., Inserm UMR_S1155, Paris, France
- Leh, Sabine, Haukeland University Hospital, Bergen, Norway
- Marti, Hans-Peter, University of Bergen, Bergen, Norway
Background
Our study aim was to expand the usability of archival kidney biopsies with primary membranous nephropathy (MN) by next generation sequencing of glomerular mRNA & lncRNA.
Methods
Formalin-fixed & paraffin-embedded (FFPE) renal biopsies from six female and six male adult patients (mean age 55±16 y, mean proteinuria 2.9±3.5 g/d) from the Norwegian Kidney Biopsy Registry (NKBR) with primary MN were divided into: i) PLA2R antibody positive MN (n=6), and ii) PLA2R antibody negative MN (n=6). In addition, we included iii) normal NBKR control samples (n=8; mean age 27±11 y). All subjects had eGFR>60ml/min/1.73m2. RNA inputs of 0.15-3 ng of total RNA per sample from microdissected glomerular cross-sections (High Pure FFPE Extraction kit, Roche) were used for library preparation (Truseq RNA Exome kit, Illumina) and sequenced as 75 bp paired end on a NextSeq500 by Firalis SA, France. Reads were aligned to Homo sapiens hg38 reference genome using Gencode v.26 for mRNA and LNCipedia 5.0 for lncRNA.
Results
From alignment on their databases, 3473 mRNA & 1719 lncRNA were above a threshold of 2 fragments per kilobase of exon per million reads mapped (FPKM). Principal component analyses and heatmaps with differentially regulated mRNA & lncRNA clustered anti-PLA2R positive and anti-PLA2R negative MN together with some separation from normals (esp. lncRNA). Pathways of renal inflammation and of glomerular injury were upregulated in MN (IPA analyses). Overall, 197 mRNA and 59 lncRNA were differentially regulated comparing MN combined to normal controls. Within the two MN groups, 84 mRNA and 19 lncRNA were differentially expressed. Among these 84 mRNA, subgroups of 12 mRNA (e.g. IGFBP2) and 22 mRNA (e.g. MIF) differed also between normal controls and anti-PLA2R positive or negative MN, respectively. Among the 19 lncRNA, subgroups of 4 and 2 lncRNA differed also between normal controls and anti-PLA2R positive or negative MN, respectively. Thus, these mRNA & lncRNA could represent candidates of diagnostic/prognostic markers and of therapeutic targets if confirmed later.
Conclusion
Sequencing of mRNA & lncRNA from microdissected glomerular cross-sections of FFPE kidney biopsies is feasible and potential biomarker & drug target candidates that discriminate anti-PLA2R positive from anti-PLA2R negative MN were identified.
Funding
- Government Support - Non-U.S.