CFH and CFHR Copy Number Variations in C3 Glomerulopathy and Immune Complex-Mediated Membranoproliferative Glomerulonephritis
Rossella Piras, Matteo Breno, Elisabetta Valoti, Marta Alberti, Paraskevas Iatropoulos, Caterina Mele, Elena Bresin, Roberta Donadelli, Paola Cuccarolo, Richard J. Smith, Ariela Benigni, Giuseppe Remuzzi, Marina Noris
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 ( CFHR3 4 – 6 Δ) that results in a FHR3-FHR1 hybrid protein in a C3G patient; and 4) a CFHR3 1 – 5 -CFHR4 10 hybrid gene in a C3G patient. This work highlights the contribution of CFH-CFHR CNVs to the pathogenesis of both C3G and IC-MPGN.