CFH and CFHR Copy Number Variations in C3 Glomerulopathy and Immune Complex-Mediated Membranoproliferative Glomerulonephritis.

Rossella Piras,Marina Noris,Matteo Breno,Ariela Benigni,Richard J H Smith,Caterina Mele,Giuseppe Remuzzi,Paola Cuccarolo,Marta Alberti,Roberta Donadelli,Elisabetta Valoti,Paraskevas Iatropoulos,Elena Bresin

doi:10.3389/fgene.2021.670727

Abstract

C3 Glomerulopathy (C3G) and Immune Complex-Mediated Membranoproliferative glomerulonephritis (IC-MPGN) are rare diseases characterized by glomerular deposition of C3 caused by dysregulation of the alternative pathway (AP) of complement. In approximately 20% of affected patients, dysregulation is driven by pathogenic variants in the two components of the AP C3 convertase, complement C3 (C3) and Factor B (CFB), or in complement Factor H (CFH) and Factor I (CFI), two genes that encode complement regulators. Copy number variations (CNVs) involving the CFH-related genes (CFHRs) that give rise to hybrid FHR proteins also have been described in a few C3G patients but not in IC-MPGN patients. In this study, we used multiplex ligation-dependent probe amplification (MLPA) to study the genomic architecture of the CFH-CFHR region and characterize CNVs in a large cohort of patients with C3G (n = 103) and IC-MPGN (n = 96) compared to healthy controls (n = 100). We identified new/rare CNVs resulting in structural variants (SVs) in 5 C3G and 2 IC-MPGN patients. Using long-read single molecule real-time sequencing (SMRT), we detected the breakpoints of three SVs. The identified SVs included: 1) a deletion of the entire CFH in one patient with IC-MPGN; 2) an increased number of CFHR4 copies in one IC-MPGN and three C3G patients; 3) a deletion from CFHR3-intron 3 to CFHR3-3′UTR (CFHR34–6Δ) that results in a FHR3-FHR1 hybrid protein in a C3G patient; and 4) a CFHR31–5-CFHR410 hybrid gene in a C3G patient. This work highlights the contribution of CFH-CFHR CNVs to the pathogenesis of both C3G and IC-MPGN.

Highlights

Membranoproliferative glomerulonephritis (MPGN) is a heterogeneous group of rare glomerular diseases associated with complement dysregulation, which leads to the deposition of 90–180 mg/dl (C3) and its cleavage products in glomeruli
One hundred ninety-nine patients with primary C3 Glomerulopathy (C3G) or ICMPGN were recruited from the Italian Registry of MPGN (ICMPGN: n = 96, 48.2%; C3G: n = 103, 51.8%, including C3 glomerulonephritis (C3GN): n = 74; dense deposit disease type (DDD): n = 29), 159 of whom have been described in a previous study (Iatropoulos et al, 2018)
C4: 10–40 mg/dl; Normal plasma sC5b-9 levels: ≤400 ng/ml; Normal serum/plasma factor H (FH) levels: ≥193 mg/L; rare variants (RVs), rare variant defined as genetic variant in coding and splicing regions of complement genes already related to C3G- immune-complex-mediated MPGN (IC-MPGN) (CFH, CFI, CD46, CFB, C3, and THBD) with minor allele frequency (MAF) in the gnomAD database

Summary

Introduction

Membranoproliferative glomerulonephritis (MPGN) is a heterogeneous group of rare glomerular diseases associated with complement dysregulation, which leads to the deposition of C3 and its cleavage products in glomeruli. Current classification is based on glomerular deposits detected by immunofluorescence (IF) microscopy (Pickering et al, 2013). Cases with glomerular C3 staining in combination with significant immunoglobulin (IgGs) deposition are defined as immune-complex-mediated MPGN (IC-MPGN). Electron microscopy (EM) allows further differentiation of C3G into either dense deposit disease type (DDD), which is characterized by intramembranous highly electron-dense deposits, or C3 glomerulonephritis (C3GN), in which the deposits are less dense and have mesangial and/or subendothelial and subepithelial localization (Pickering et al, 2013; Hou et al, 2014)

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