Abstract
Complement C3 activation is a characteristic finding in membranoproliferative GN (MPGN). This activation can be caused by immune complex deposition or an acquired or inherited defect in complement regulation. Deficiency of complement factor H has long been associated with MPGN. More recently, heterozygous genetic variants have been reported in sporadic cases of MPGN, although their functional significance has not been assessed. We describe a family with MPGN and acquired partial lipodystrophy. Although C3 nephritic factor was shown in family members with acquired partial lipodystrophy, it did not segregate with the renal phenotype. Genetic analysis revealed a novel heterozygous mutation in complement factor H (R83S) in addition to known risk polymorphisms carried by individuals with MPGN. Patients with MPGN had normal levels of factor H, and structural analysis of the mutant revealed only subtle alterations. However, functional analysis revealed profoundly reduced C3b binding, cofactor activity, and decay accelerating activity leading to loss of regulation of the alternative pathway. In summary, this family showed a confluence of common and rare functionally significant genetic risk factors causing disease. Data from our analysis of these factors highlight the role of the alternative pathway of complement in MPGN.
Keywords: complement, membranoproliferative GN (MPGN), immunology
Membranoproliferative GN (MPGN) is a pathologic term describing thickening of the glomerular capillary wall and an increase in mesangial components.1 MPGN has historically been classified by electron microscopy according to the relationship of the electron dense deposits relative to the glomerular basement membrane (MPGN1, dense deposit disease [DDD], and MPGN3).2 Immunofluorescence reveals C3 staining in all types of MPGN; however, many cases also stain for Igs. An increased understanding of the role of complement in the pathogenesis of disease has led to a proposed reclassification of those cases with no or minimal Ig staining as C3 glomerulopathy (C3GN).3–6
Hypocomplementaemia has long been associated with MPGN, and in 1969, C3 nephritic factor (C3Nef) was discovered. It was subsequently shown to be an antibody that stabilized the alternative pathway (AP; C3bBb) convertase,7–10 leading to increased complement turnover. Acquired partial lipodystrophy (APL) has also been reported in patients with MPGN,11 often in association with C3Nef.
Familial forms of MPGN caused by complete deficiency of complement factor H (fH) have been reported.12 In a pedigree with DDD reported by Licht et al.,13 a homozygous mutation resulting in a secreted, functionally inactive fH protein has been described. Additionally, an activating C3 mutation has been reported in a family with DDD.14 More recently, a hybrid CFHR3-1 gene15 and a CFHR116 mutation have been described in familial C3GN. Genetic variants in the complement system have also been described in sporadic MPGN/C3GN in a large cohort of French patients with no family history.17
We examine a family with MPGN and APL previously described by Power et al.18 in 1990 (Figure 1, clinical details in Supplemental Material). Patients 1:2, 2:1, and 2:2 all developed nephrotic syndrome and ESRD, with individuals 1:2 and 2:1 undergoing renal biopsy to confirm MPGN (Figure 1, B–E). Given the family history of MPGN and the low C3 level, patient 2:2 was assumed to have MPGN and did not undergo renal biopsy, although he was diabetic. Patients 1:2, 2:1, and 2:4 developed APL. Historically, patients 1:2, 2:1, and 2:4 all had low C3 levels in keeping with contemporaneous C3Nef results (Supplemental Table 1).
Genetic analysis of this family revealed that all individuals with the renal phenotype (1:2, 2:1, and 2:2) carry a mutation in heterozygosity in the CFH gene. The mutation c.249G>T results in a nonsynonymous substitution in the N-terminal region of fH, p.R83S (Figures 1 and 2A). Patients 2:3 and 2:4 did not carry this mutation.
To determine the structural effects of the R83S mutation, nuclear magnetic resonance (NMR) spectroscopy was used. The overlay of 15N-heteronuclear single quantum coherence spectra (Figure 2B) shows a well dispersed spectrum indicative of a well structured protein for both wild-type (WT; fH1–2WT) and fH1–2R83S. Moreover, differences between the two spectra were relatively few in number and clustered into the intermodular interface (Figure 2, C and D). These observations rule out the suggestion that the R83S substitution significantly disrupted the structure of fH and imply that the protein should be secreted normally in keeping with the normal fH serum level. They suggest that the R83S mutation could elicit its effects through either direct interaction of the R83 side chain with C3bBb or an alteration to the fH1–2 intermodular orientation. Modeling this mutation on a cocrystal structure of fH/C3b19 showed that amino acid (aa) R83 is in direct opposition to C3b, and it would seem most likely that this residue directly participates in the interaction of fH with C3b (Figure 2A).
To confirm functional significance of the genetic variant, WT (fH1–4WT) and mutant (fH1–4R83S) recombinant proteins, comprising the functional domains of fH (complement control protein modules 1–4 [CCPs 1–4]), were generated. Surface plasmon resonance (SPR) showed that the affinity of fH1–4R83S for C3b is weak compared with fH1–4WT. Using the quantity of fH1–4R83S available (40 μM in the solution flowed over the chip), it was not possible to accurately determine the Kd. It may be estimated that the Kd of the fH1–4R83S–C3b interaction is approximately 75 μM under the same conditions used to measure a Kd of 10.7 μM for fH1–4WT–C3b (Figure 3).
To assess the functional consequences of the impaired binding to C3b, fluid-phase cofactor activity assays were undertaken, showing minimal activity of the fH1–4R83S mutant (Figure 4, A and B). Sheep erythrocyte cell surface assays of cofactor activity confirmed minimal activity of fH1–4R83S compared with fH1–4WT (Figure 4C).
SPR-based decay acceleration assays were then performed, showing markedly reduced function of fH1–4R83S compared with the WT protein (Figure 4D). Sheep erythrocyte cell surface decay acceleration assays confirmed an approximately 75-fold reduction in activity of the mutant protein compared with WT. For fH1–4WT, 50% inhibition of lysis was seen at 5.98 nM, and for fH1–4R83S, 50% inhibition of lysis was seen at 447.5 nM (Figure 4E).
Thus, in this family, we describe a mutation in CFH that segregates with renal disease and results in minimal disruption of structure but leads to a profound loss of complement regulation. Complete fH deficiency or homozygous functionally inactivating mutations in CFH had been reported in cases of MPGN/C3GN previously. This family carries one normally functioning allele and the abnormal allele encoding R83S. More recently, several patients with MPGN1 carrying a heterozygous genetic variant have been reported,17 albeit without functional studies confirming a pathogenic role.
Genotyping of functional nonsynonymous single-nucleotide polymorphisms (SNPs) associated with MPGN20 was subsequently undertaken. In addition to a functionally significant CFH mutation, patients 2:1 and 2:2 had one copy of the CFH H3 haplotype and one CFH H5 haplotype.21 These CFH haplotypes both express a valine at aa 62, which has been shown to be less effective in complement regulation compared with the alternate isoleucine at aa 62.22,23 Likewise, all affected members carried SNPs in C3 (R102G [C3 slow/fast polymorphism]24 /P314L), which have previously been shown to bind fH less strongly, and thus, C3b is less efficiently inactivated.25,26 Both these SNPs, which result in increased AP activity, have been associated with an increased risk of DDD.20
It is interesting to note that, in addition to a functionally significant mutation in CFH and functionally significant SNPs, C3Nef was also detected. C3Nef was first described in 1969 in patients with MPGN and low C3 levels.10 DDD is classically associated with APL, although a recent review suggested that one half of the patients had MPGN1.11 In one series of 26 patients with C3Nef, 18 patients developed MPGN alone, 2 patients had APL alone, and 6 patients had both diseases.24 C3Nef is also found in normal control individuals, which has led to questions about its role in pathogenesis.27 The coexistence of a CFH mutation and C3Nef was also described by Licht et al.13 in DDD and in a case series of MPGN/C3GN by Servais et al.17
It may be hypothesized that C3Nef is partly responsible for the development of renal disease by working in concert with R83S to impair C3 convertase inactivation. However, in the family described herein, C3Nef segregated with APL and not the renal phenotype, which segregates with R83S. We cannot rule out the possibility that individual 2:2 may have been C3Nef-positive at some stage and subsequently, became C3Nef-negative. Clearly, the presence of C3Nef on its own does not result in MPGN in this family, because individual 2:4 does not have renal disease. The familial nature of the APL and C3Nef suggests an underlying genetic predisposition. No genetic variants were found in lipodystrophy-associated genes (Supplemental Table 2); however, all individuals with APL and C3Nef carried the C3 R102G polymorphism previously associated with C3Nef.24 This SNP may have predisposed to generation of C3Nef and consequently, APL. Factor D is highly expressed in adipose tissue and required for formation of the C3 convertase. It has been suggested that loss of fat may be because of C3Nef-induced lysis of adipocytes expressing factor D.28
In the initial report of this family, the term MPGN1 was used because of the heavy staining of IgM and less intense IgG staining in patient 1:2.18 Contemporary immunofluorescence is not available to reassess this pathology in the light of new classifications.6,29 Immune complexes may have triggered complement activation, unmasking the latent genetic complement defect. Alternatively, Igs may have deposited nonspecifically in areas of sclerosis and scarring.30 Genetic variants in AP genes have been detected among individuals with MPGN1.17 In this family, having definitively established the abnormal control of complement activation in disease, the term C3GN could be used, which was suggested by Pickering et al.6
In summary, in this family, we describe a mutation in CFH, which results in minimal disruption of structure but leads to a profound loss of complement regulation and segregates with renal disease. Members of the family with MPGN also carry functionally significant C3GN risk polymorphisms. It is likely that the cosegregation of these risk factors causes insufficient control of the AP, resulting in MPGN.
Concise Methods
The study was approved by Newcastle and North Tyneside 1 Research Ethics Committee, and informed consent was obtained in accordance with the Declaration of Helsinki.
Complement Assays
C3 and C4 levels were measured by rate nephelometry (Beckman Coulter Array 360). fH and factor I levels were measured by radioimmunodiffusion (Binding Site).
Genetic Analysis
Mutation screening of CFH, CFI, CFB, MCP, and C3 was undertaken using Sanger sequencing.31–35 Genotyping of the following SNPs, CFH 2332C>T (rs3753394); CFH c.184G>A, isoleucine at aa 62 V (rs800292); CFH c.1204C>T, H402Y (rs1061170); CFH c.2016A>G, Q672Q (rs3753396); and CFH c.2808G>T, E936D (rs1065489), was used to determine the CFH haplotypes. Screening for genomic disorders affecting CFH, CFHR1, CFHR2, CFHR3, and CFHR5 was undertaken using multiplex ligation-dependent probe amplification as previously described.36 For investigation of APL genetics, whole-exome sequencing was used (Supplemental Material).
Production and Purification of Proteins
Clones of Pichia pastoris strain KM71H producing WT (fH1–4WT) and mutant (fH1–4R83S) fH in the setting of CCPs 1–4 were generated as described previously.37 In brief, the R83S point mutation was generated in a pPICZαB (Invitrogen) vector containing residues 19–263 of fH, with a C-terminal 6× His tag and an N-terminal myc tag (EQKLISEEDL), using the QuikChange site-directed mutagenesis kit (Stratagene) with the following primers: (f) gggttgctcttaatccattaaggaaatgtcagaaaagTccctgtggacatcctggagatactcc; (r)ggagtatctccaggatgtccacagggActtttctgacatttccttaatggattaagagcaaccc. Fidelity was confirmed by bidirectional Sanger sequencing. KM71H cells were transformed using electroporation, selected by zeocin, and screened for protein expression.
Protein expression was carried out in a 3-L BioFlo 115 Biofermenter (New Brunswick). A starter culture was transferred into 1 L basal fermentor salts (0.095% [wt/vol] calcium sulfate, 1.82% [wt/vol] potassium sulfate, 1.5% [wt/vol] magnesium sulfate heptahydrate, 0.42% [wt/vol] potassium hydroxide, 2.7% [vol/vol] phosphoric acid, and 2.5% [vol/vol] glycerol) enriched with 1% (wt/vol) casein aa, 0.5% (wt/vol) PTM1 salts, and 0.5% (vol/vol) antifoam A (Sigma-Aldrich). After the initial batch-fed glycerol was exhausted, glycerol feeds were maintained for 24 hours at 30°C. The cells were allowed to starve for 4 hours before recombinant expression was induced with 0.75% methanol containing 0.5% (wt/vol) PTM1 salts. After 3 days at 15°C with methanol feeds, the supernatant was removed and filtered, and its pH was adjusted to 7.4.
It was applied to a 5-ml His trap column (GE Healthcare) at 4°C, and the protein was eluted with 500 mM imidazole followed by size exclusion chromatography on Superdex 200 (GE Healthcare). Protein identity was confirmed by mass spectrometry. Protein concentrations were calculated using absorbance at 280 nm and calculated extinction coefficients (47,870 M−1⋅cm−1).
NMR analysis was performed in the context of a previously generated fragment of fH22 (CCPs 1 and 2; residues 19–142) using QuikChange with the primers above as previously described; 15N-labeled samples of both WT and mutant were prepared by using (15NH4)2SO4 (Isotec) as the sole source of nitrogen during cell growth. Protein expression was carried out using baffled shaker flasks. A starter culture was transferred into three flasks (each containing 1 L buffered minimal glycerol) and incubated at 30°C for 48 hours. Protein expression was then induced daily with 0.5% methanol feeds for 72 hours. Purification of this fragment from supernatant after centrifugation of the cell pellet was achieved by cation-exchange chromatography at pH 4.0 (SP Sepharose Fast Flow; Sigma-Aldrich). Additional purification steps followed using size exclusion chromatography on Superdex 200 (GE Healthcare) and reverse-phase high-performance liquid chromatography (Supelco Discovery BIO Wide Pore C5 Column; Supelco, Inc.).
NMR Spectroscopy
NMR spectra were acquired on an 800-MHz Bruker Avance III spectrometer fitted with a TCI cryogenic probe. Two-dimensional 1H-15N-heteronuclear single quantum coherence spectra were acquired at 37°C with 100 µM samples of the fH1–2 proteins in 20 mM deuterated sodium acetate (pH 4.5) containing 10% (vol/vol) D2O and 0.02% (wt/vol) NaN3. Resonance assignments were determined where possible by comparison with the previously assigned WT spectrum.22 Chemical shift differences between the fH1–2WT and fH1–2R83S proteins were determined using the CCPNMR Analysis Suite of Programs. Normalized log values of the chemical shift differences were entered into the B factor field of the Protein Data Bank file (2RLP) and plotted onto cartoon representations of the representative structure of fH1–2 WT using Pymol (http://www.pymol.org/).38
Binding Affinity for C3b by SPR
The binding affinities of the fH1–4WT and fH1–4R83S were monitored by SPR using a Biacore ×100 instrument (GE Healthcare); 500 resonance units of human C3b (CompTech) were immobilized on a Biacore series CM5 sensor chip (GE Healthcare) using standard amine coupling.37 The reference surface of the chip was prepared by performing a mock coupling in the absence of any protein. Experiments were performed at 25°C and a 30-μl/min flow rate. Duplicate injections (concentrations of 0.5–40 μM) were performed in 10 mM Hepes-buffered saline, 3 mM EDTA, and 0.05% (vol/vol) surfactant p20 (GE Healthcare). A contact time of 90 seconds was used (sufficient for achieving steady-state conditions for all samples) followed by a dissociation period of 600 seconds. Chips were regenerated between sample injections with two 45-second injections of 1 M NaCl (pH 7.0). Data were processed using the BIAevaluation 4.1 software (GE Healthcare). Data from the reference cell and a blank (buffer) injection were subtracted, and dissociation constants were calculated using a steady-state affinity model from the background-subtracted traces.
Measurement of Decay Acceleration Activity by SPR
Decay accelerating activity was measured in real time using a Biacore ×100 instrument as described previously.37 Briefly, 2300 resonance units C3b were immobilized using standard amine coupling to the CM5 sensor chip. Subsequently, a mixture of factor B (500 nM) and factor D (60 nM) was flowed (10 μl/min) over the surface for 120 seconds to form the AP convertase.
The convertase was allowed to decay naturally for 210 seconds, fH1–4WT or fH1–4R83S (in running buffer of Hepes-buffered saline containing 0.5% [vol/vol] surfactant P20 and 1 mM MgCl2 [temperature at 25°C]) was flowed across the surface for 60 seconds, and convertase decay was visualized in real time. Between injections, surfaces were regenerated using a 45-second injection of 1 μM purified fH (CompTech) followed by a 45-second injection of 1 M NaCl (pH 7.0). Data were evaluated using BIAevaluation 4.1 (GE Healthcare). As a control, the construct was also flowed over the bare surface, and binding data were subtracted from the decay sensogram.
Cofactor Assay in Fluid Phase
Kinetic fluid-phase assays were used to measure cofactor activity for factor I–mediated proteolytic cleavage of C3b.37 Factor I, fH, and C3b were all purchased from CompTech; 3 μl C3b (5.68 μM), 4.5 μl factor I (1.14 μM), and 5 μl fH1–4 (0.75 μM) were made up to a final volume of 15 μl in PBS. For the positive control reaction, 5 μl purified fH (6.45 μM) was used, and for the negative control, 5 μl PBS was used. The mixture was incubated at 37°C for 15, 30, 60, and 120 minutes, and the reaction was stopped by the addition of 2× lamelli reducing buffer to a final volume of 30 μl and heated to 95°C for 5 minutes. The products of the reaction were then separated by SDS-PAGE and transferred to nitrocellulose membrane. The C3b α- and β-chain fragments were visualized using rabbit anti-C3 antibody (1:5000; Abcam, Inc.) and goat anti-rabbit horseradish peroxidase (1:5000; Abcam, Inc.) secondary and chemoluminescence substrate (Thermo Fisher Scientific).
Measuring Decay Acceleration on Sheep Erythrocytes
C3b-coated sheep erythrocytes were prepared as described previously.23 Cells were resuspended to 2% (vol/vol) in AP buffer (5 mM sodium barbitone [pH 7.4], 150 mM NaCl, 7 mM MgCl2, and 10 mM EGTA). The AP convertase was formed on the cell surface by incubating 50 μl cells with an equal volume of AP buffer containing factor B (40 μg/ml) and factor D (0.4 μg/ml; CompTech) at 37°C for 15 minutes. Cells (100 μl) were incubated with 50 μl concentration range fH1–4WT and fH1–4R83S in PBS/20 mM EDTA for 15 minutes. Lysis was developed by adding 50 μl 4% (vol/vol) normal human serum depleted of factor B and fH23 in PBS/20 mM EDTA and incubating at 37°C for 60 minutes. To determine the amount of lysis, cells were pelleted by centrifugation, and hemoglobin release was measured at 410 nm (A410). Controls included 0% lysis (buffer only) and 100% lysis (0.1% [vol/vol] Nonidet P-40). Percentage of inhibition from lysis was calculated by the formula (A410[buffer only]−A410[fH])/A410[buffer only]×100%.
Measuring Cofactor Activity on Sheep Erythrocytes
To test cofactor activity,37 washed C3b-coated sheep erythrocyte cells were resuspended to 2% (vol/vol) in AP buffer and incubated with an equal volume of a range of concentrations of fH1–4WT and fH1–4R83S and 2.5 μg/ml factor I (CompTech) for 8 minutes at 25°C. After three washes in AP buffer, a 50-μl aliquot of cells (2%) was mixed with 50 μl AP buffer containing factor B (40 μg/ml) and factor D (0.4 μg/ml) and then incubated for 15 minutes at 25°C to form AP convertase on the remaining C3b. Lysis was developed by adding 50 μl 4% (vol/vol) normal human serum depleted of factor B and fH in PBS/20 mM EDTA and incubating at 37°C for 10 minutes. Percentage of inhibition from lysis was calculated by the formula (A410[buffer only]−A410[fH])/A410[buffer only]×100%.
Disclosures
A.R., T.H.J.G., and D.K. have received honoraria for consultancy work from Alexion Pharmaceuticals.
Supplementary Material
Acknowledgments
The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under Grant 305608 (EURenOmics). This work was supported by Kidney Research UK Grant RP29/2010, including a grant from the Rosetrees Trust. E.K.S.W. is a Medical Research Council clinical training fellow. G.S.R. is funded by Instituto Nacional de Ciência e Tecnologia de Medicina Molecular—Universidade Federal de Minas Gerais. A.R. and D.K. are Wellcome Trust intermediate clinical fellows. D.A. was funded by the Wellcome Trust.
Footnotes
Published online ahead of print. Publication date available at www.jasn.org.
This article contains supplemental material online at http://jasn.asnjournals.org/lookup/suppl/doi:10.1681/ASN.2013070732/-/DCSupplemental.
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