Identification of a mutation in complement factor H-related protein 5 in patients of Cypriot origin with glomerulonephritis.

BACKGROUND: Complement is a key component of the innate immune system, and variation in genes that regulate its activation is associated with renal and other disease. We aimed to establish the genetic basis for a familial disorder of complement regulation associated with persistent microscopic haematuria, recurrent macroscopic haematuria, glomerulonephritis, and progressive renal failure.
METHODS: We sought patients from the West London Renal and Transplant Centre (London, UK) with unusual renal disease and affected family members as a method of identification of new genetic causes of kidney disease. Two families of Cypriot origin were identified in which renal disease was consistent with autosomal dominant transmission and renal biopsy of at least one individual showed C3 glomerulonephritis. A mutation was identified via a genome-wide linkage study and candidate gene analysis. A PCR-based diagnostic test was then developed and used to screen for the mutation in population-based samples and in individuals and families with renal disease.
FINDINGS: Occurrence of familial renal disease cosegregated with the same mutation in the complement factor H-related protein 5 gene (CFHR5). In a cohort of 84 Cypriots with unexplained renal disease, four had mutation in CFHR5. Overall, we identified 26 individuals with the mutation and evidence of renal disease from 11 ostensibly unrelated kindreds, including the original two families. A mutant CFHR5 protein present in patient serum had reduced affinity for surface-bound complement. We term this renal disease CFHR5 nephropathy.
INTERPRETATION: CFHR5 nephropathy accounts for a substantial burden of renal disease in patients of Cypriot origin and can be diagnosed with a specific molecular test. The high risk of progressive renal disease in carriers of the CFHR5 mutation implies that isolated microscopic haematuria or recurrent macroscopic haematuria should not be regarded as a benign finding in individuals of Cypriot descent. FUNDING: UK Medical Research Council and Wellcome Trust. Copyright 2010 Elsevier Ltd. All rights reserved.

Introduction

Kidney disease is an important cause of morbidity and mortality worldwide. In many cases, renal injury results from damage caused by the immune system, either in response to microbial infection or because of inappropriate activation of defence mechanisms. The mechanisms that protect the kidney from immunological attack in healthy individuals—and that fail in disease—are not well understood.

The complement system is a key component of host defence, and variation in the genes that regulate complement activation is associated with disease, including age-related macular degeneration, atypical haemolytic uraemic syndrome, and glomerulonephritis. The kidney is especially susceptible to the effects of complement activation, and glomerulonephritis (a leading cause of kidney failure worldwide) is generally characterised by presence of complement within the glomerulus. Typically, complement is accompanied by immunoglobulins, which activate it via the classical pathway. However, complement deposition can occur without immunoglobulin via the complement alternative pathway. This deposition occurs in dense-deposit disease, which is caused by genetic or acquired defects in complement regulation.

Isolated glomerular C3 deposition and inflammation can also arise in the absence of dense-deposit disease. This heterogeneous entity has been termed C3 glomerulonephritis and is often associated with the histological appearance of membranoproliferative glomerulonephritis. Our aim was to investigate an inherited renal disease, which we show is endemic in Cyprus and is characterised by microscopic and synpharyngitic macroscopic haematuria, renal failure, and C3 glomerulonephritis.

Methods

Patients

To detect high penetrance genes leading to kidney disease, we identified multiply affected kindreds of patients from the West London Renal and Transplant Centre (London, UK), prioritising those with an unusual renal condition, syndromic features, or early onset of disease. Family 1 in this report lived in London, UK, and reported ancestry from the Troodos mountains of Cyprus. The index patient from family 2 was referred to us from Cyprus with C3 glomerulonephritis and, because he also came from the Troodos region and C3 glomerulonephritis is very rare, we postulated that he might have the same genetic condition as individuals from family 1. Individuals from both families were tested for evidence of renal disease and underwent genetic analysis, leading to identification of a shared mutation.

To establish the frequency of this genetic mutation, we searched for carriers in two cohorts. We examined DNA for 102 unrelated individuals in the UK 1958 birth cohort and 1015 control participants in the MASTOS study in Cyprus.

We sought additional individuals in Cyprus by screening for the presence of the mutation in a cohort of 84 Cypriot patients with advanced or end-stage chronic renal disease, either of unknown cause or because of presumed or incompletely characterised glomerulonephritis. A further two families from Cyprus (family 3 and family 4) were tested for the mutation because they had familial renal disease in which other conditions had been sought and excluded. In these families, microscopic and synpharyngitic macroscopic haematuria segregated as an autosomal dominant trait and direct exon sequencing excluded recognised mutations of COL4A3 and COL4A4.

We sought additional individuals in London, UK, by reviewing case records from the West London Renal and Transplant Centre and the Royal Free Renal Unit for potentially affected individuals, looking for histological features consistent with CFHR5 nephropathy. This search identified four further individuals who were shown to have the mutation. One patient had a brother with microscopic haematuria, who was also found to have the mutation (family 5).

Finally, we analysed DNA from 36 individuals with a renal biopsy diagnosis of C3GN (defined as glomerular C3 deposition in the absence of immunoglobulin staining for IgG, IgM, and IgA, and without intramembranous glomerular basement membrane dense deposits) and no recognised family history; 34 individuals were from France (including 19 reported previously) and two were from the UK. Additional single nucleotide polymorphisms (SNPs) were genotyped in three members of five families (CytoSNP 12 panel, Illumina, CA, USA) to define the maximum possible extent of the shared haplotype spanning the locus. Estimation of the probable number of generations since the common affected ancestor of the families was done as previously described. Formal retinal examination was done by an ophthalmologist from Moorfields Eye Hospital, London, UK for two individuals (IV-5 and V-4) from family 1.

The study was approved by the local research ethics committees and participants provided written consent.

Genetic analysis

Individuals from families 1 and 2 were tested for evidence of renal disease, and DNA was extracted from blood or saliva (Oragene, DNA Genotek, Kanata, ON, Canada). Genotypes and haplotypes of 6008 SNPs (Linkage IV panel, Illumina, CA, USA) from these two families were analysed with EasyLINKAGE, PEDCHECK, GENEHUNTER version 2.1, and HAPLOPAINTER. Bidirectional sequencing of the exons of candidate genes was done after PCR amplification (primers available from the authors on request).

CFHR5 internal duplication was assessed by multiplex ligation-dependent probe amplification (MLPA), which was done with unamplified genomic DNA with the P236 A1 ARMD mix 1 (MRC-Holland, Amsterdam, Netherlands). Southern blotting was done with genomic DNA digested with EcoR1 (New England Biolabs, MA, USA). Membranes were probed with a 32P-labelled 371 base pair sequence containing exon 2 of CFHR5. PCR amplification of the CFHR5 duplication insertion point used the primers 5′-TGGAAGCCTGTGGTATAAATGA-3′ and 5′-TCCGGCACATCCTTCTCTAT-3′. Screening PCR to amplify both CFHR5 alleles in a single reaction used the primers 5′-GATTCCATTTGTCAAATATTG-3′, 5′-TCTTCTCCAAAACTATCTAATGTCAA-3′, and 5′-TTTGAATGCTGTTTTAGCTCG-3′.

Serum CFHR5 detection and functional analysis

We used western blotting to detect CFHR5 in serum and recombinant CFHR5 in supernatants using a rabbit polyclonal anti-human-CFHR5 antibody (a gift from J McRae, Immunology Research Centre, Melbourne, Australia). Functional analysis of CFHR5 protein binding to heparin and lysed chicken erythrocytes was done as previously described. Briefly, patient serum was incubated with chicken erythrocytes, which spontaneously activated the alternative pathway resulting in cell lysis and binding of CFHR5 to the disrupted membranes. The relative amounts of unbound CFHR5 protein (supernatant) and bound CFHR5 protein (erythrocyte membrane pellet) were established by western blotting.

Role of the funding source

The funding bodies of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. PHM and MCP had full access to all the data in the study and had final responsibility for the decision to submit for publication.

Results

Renal disease segregated as an autosomal dominant trait in family 1 and family 2 (figure 1). Disease was characterised by persistent microscopic haematuria and episodes of synpharyngitic macroscopic haematuria (within 1–2 days of an upper respiratory tract infection). C3 glomerulonephritis was identified in renal biopsy specimens in affected male and female patients. Glomerular inflammation was variable, but subendothelial and mesangial deposits that were reactive with antibody to C3, but not to C1q, C4, or immunoglobulins, were always present in these patients. Subepithelial deposits were occasionally noted. Figure 2 shows a representative biopsy sample.

Figure 1

Pedigrees of two ostensibly unrelated families from the Troodos mountain region, Cyprus, showing haplotypes at region of maximum linkage on chromosome 1

Green boxes are haplotypes (HapMap coordinates 192344247 to 201027281).

Figure 2

Renal biopsy sample of patient V-4 from family 1

(A) Periodic acid-Schiff stain of glomerulus demonstrating mesangial hypercellularity (arrow). (B) Immunoperoxidase stain for C3 showing granular staining on the capillary wall. (C and D) Electron micrographs showing prominent mesangial electron-dense deposits (black arrow), subendothelial deposits (arrowheads), and occasional subepithelial deposits (white arrow).

In family 1, a genome-wide SNP-based analysis that used an autosomal dominant model and scored all patients with haematuria as affected established linkage to an 18 cM (centimorgan) region of chromosome 1q31–32 (logarithm of the odds [LOD] score 2·22). With the addition of family 2, the combined LOD score was 3·40 (figure 3). A haplotype of 17 SNPs spanning 8·74 cM within the linked region was shared by all affected members of both families, which is consistent with inheritance of an allele at this locus from a common ancestor (figure 1). This haplotype (HapMap coordinates 192344247 to 201027281) included complement factor H (CFH) and CFH-related (CFHR) 1–5 genes. Sequencing of CFH and two of the CFH-related genes (CFHR1 and CFHR5) in patients V-4 and IV-5 (both family 1) did not reveal any mutations.

Figure 3

Genome-wide single-nucleotide polymorphism-based analysis

LOD=logarithm of the odds.

MLPA analysis detected a heterozygous deletion of CFHR1 and CFHR3 in three members of family 2 (figure 4), which did not segregate with renal disease and is a polymorphism present in 14·2% of healthy controls. MLPA analysis also showed heterozygosity for a previously unreported duplication of exons 2 and 3 of CFHR5 in affected individuals from family 1 (IV-5 and V-4) and family 2 (II-1 and III-2), but not in the unaffected individual in family 2 (II-2) (figure 4). The CFHR5 internal duplication was confirmed, and its size established, by Southern hybridisation of genomic DNA with CFHR5 exon 2. The boundary of the duplication was identified by resequencing a PCR product (figure 5). Figure 5 shows an additional 6·3 kbp fragment on Southern blot analysis in affected individuals from family 1 (IV-5 and V-4) and family 2 (II-1 and III-2). This band was not present in two unrelated control individuals or in an unaffected individual from family 2 (II-2), in whom only the expected 7·9 kbp band was seen. With a reverse primer positioned in CFHR5 exon 2 and a forward primer in intron 3, there was no amplification from wild-type DNA (as expected). The duplication of exons 2 and 3 in DNA with the mutation led to a product of 4·8 kbp with these primers. Sequencing of this product confirmed the position and size of the duplication. A diagnostic PCR test was then designed with three primers which gave a 298 bp product from the wild-type allele and an additional 222 bp product from the allele with the CFHR5 internal duplication. The 222 bp product was seen in affected but not unaffected members of families 1 and 2 (figure 6).

Figure 4

Multiplex ligation-dependent probe amplification analysis of CFH and CFHR genes using genomic DNA from five individuals from families 1 and 2

Figure 5

Southern blot of EcoR1-digested genomic DNA from two unrelated controls (C1 and C2) and five individuals from families 1 and 2, probed with exon 2 of CFHR5

Arrows show orientation of PCR primers. Numbered black rectangles are CFHR5 exons. Double-headed arrows are EcoR1 restriction fragments. Red triangle shows the duplicated region.

Figure 6

Diagnostic PCR test for CFHR5

Arrowhead shows one 298 bp product in the wild-type allele and arrows shows the 222 bp product in the allele associated with CFHR5 internal duplication.

With this diagnostic PCR, we did not detect a CFHR5 internal duplication in 102 randomly selected participants from the UK 1958 birth cohort. The CFHR5 internal duplication was only detected in one individual of 1015 control participants in the MASTOS study (for whom no clinical or personal details were available). The CFHR5 internal duplication is therefore a rare allele in the Cypriot population.

We then screened a cohort of 84 patients in Cyprus with advanced or end-stage renal failure. This screening identified one female and three male patients with the mutation, none of whom reported ancestry in the Troodos mountains. Families 3 and 4 were identified by testing Cypriot families with unexplained haematuria, and the CFHR5 duplication was identified in all seven individuals affected with microscopic or synpharyngitic macroscopic haematuria, but not in five unaffected relatives. A renal biopsy had been taken from one individual from these families and showed C3 glomerulonephritis. Neither of these families could trace their ancestry to the Troodos mountains region. The review of case records from two renal units in London followed by DNA testing identified three men and one woman of Cypriot descent with CFHR5 nephropathy. In one of these cases a brother with microscopic haematuria was also tested and found to have the CFHR5 mutation (family 5). Although not ostensibly related to family 1 or family 2, paternal ancestry was from the same valley in the Troodos Mountains.

The table summarises available clinical data for all the individuals we showed had the CFHR5 mutation or who were obligate carriers. In all affected men, there was progressive renal impairment with end-stage renal disease between the ages of 40 and 69 years. Renal impairment was less common in affected women than in affected men (p=0·0016; table).

Table

Clinical and pathological findings in CFHR5 nephropathy

		Male	Female	Total
Individuals with CFHR5 mutation		14	12	26
	With microscopic haematuria	11/11	11/11	22/22
Obligate carriers with impaired renal function		3/3	0/0	3/3
Confirmed affecteds and obligate carriers with impaired renal functionn*		13/16†	2/12	15/28
Affecteds with synpharyngitic macroscopic haematuria		5/8	2/4	7/12
Biopsy findings in affected individuals
	Mesangial matrix expansion	6/6	2/3	8/9
	Increased glomerular cellularity	6/6	2/3	8/9
	Segmental capillary wall thickening	6/6	2/3	8/9
	Glomerular staining for C3	6/6	3/3	9/9
	Glomerular staining for C1q, IgA, IgG, or IgM	0/6	0/3	0/9
	Subendothelial electron-dense deposits	6/6	3/3	9/9
	Mesangial electron-dense deposits	6/6	3/3	9/9
	Scanty subepithelial electron-dense deposits	4/6	3/3	7/9
CFHR512123-9 detected in serum		7/7	4/4	11/11
Normal serum C3, C4, CFH, and CFI		9/9	5/5	14/14
Negative for C3NeF		2/2	2/2	4/4
Normal retinal appearance‡		1/1	1/1	2/2
Self-reported visual impairment		0/8	0/7	0/15
Additional ungenotyped first-degree relatives with impaired renal function		5	0	5

Data are number/number of confirmed affecteds and obligate carriers of CFHR5 duplication for whom data were available. CFHR5=complement factor H-related protein 5. CFH=complement factor H. CFI=complement factor I. C3NeF=C3 nephritic factor.

p=0·0016 men versus women, Fisher's exact test.

One patient's DNA and urine was analysed, but no data on renal function were available.

From fundoscopic examination by ophthalmologist.

These findings suggest that the newly identified CFHR5 duplication accounts for a substantial proportion of renal disease in Cyprus and is not confined to the Troodos mountain region. Further genotyping of SNPs showed a haplotype extending from 1·4 cM upstream to 4·7 cM downstream of the mutation that cosegregated with the CFHR5 internal duplication in the five families tested, which is consistent with inheritance of the mutation by all affected individuals from an original founder. By contrast, none of the 36 individuals with biopsies showing C3 glomerulonephritis from the UK and France had the CFHR5 mutation.

CFHR5 is a 65 kDa plasma protein consisting of nine short consensus repeat (SCR) domains (repeating units that are characteristic of CFH and CFHR proteins). Duplication of exon 2 (encoding SCR1) and exon 3 (encoding SCR2), predicted a novel CFHR5 protein with duplicated SCR domains 1 and 2 (figure 7). Western blotting of serum samples from affected individuals detected the normal CFHR5123-9 (superscript numbers denote SCRs) protein, and a slow migrating protein that was consistent with the predicted molecular weight of CFHR512123-9 (figure 7).

Figure 7

Western blot of serum with a polyclonal anti-CFHR5 antibody for detection of CFHR5

In affected patients there is a slower migrating band consistent with the predicted molecular weight of CFHR512123-9. Duplicated short consensus repeat domains are shown in green. *Initial aminoacid sequence in the duplicate SCR1 differs from the original SCR1, as described in the text.

Although the initial aminoacid sequence of the wild-type SCR1 is Glu-Gly-Thr-Leu-Cys-Asp (with the first glutamic acid encoded by exon 1), the duplicated SCR1 is encoded only by exon 2 and therefore is predicted not to have this glutamic acid. Splicing of exon 3 upstream of the exon 2 sequence results in a change in the initial codon of the duplicated SCR1 so that the second aminoacid in the sequence is arginine rather than glycine. Hence, the initial aminoacid sequence of the duplicated SCR1 is predicted to be Arg-Thr-Leu-Cys-Asp. The rest of the duplicated SCR1 aminoacid sequence and entire duplicated SCR2 aminoacid sequence is identical to wild-type CFHR5.

The physiological role of CFHR5 is not known; the plasma concentration is estimated to be 3–6 μg/mL, which is approximately 1% of that of the well characterised complement regulator CFH. CFHR5 has been shown to co-localise with complement deposits in diseased human kidneys and binds to surface-bound activated C3 (termed C3b). We showed that mutant CFHR512123-9 protein bound less effectively than did wild-type protein to two sources of surface-bound complement; complement-lysed erythrocyte membranes (figure 8) and glomerular-bound mouse complement (webappendix p 1).

Figure 8

Functional analysis of CFHR5 proteins

(A) Western blot of bound and unbound CFHR5 to complement-lysed erythrocyte membranes. (B) Quantitative data from three experiments analysing binding to complement-lysed erythrocyte membranes.

Previous in-vitro investigations have reported that CFHR5 shares some of the complement regulatory activities of CFH; CFHR5 can be a cofactor for the proteolytic inactivation of complement C3b by the plasma enzyme complement factor I, although its activity is weak by comparison with that of CFH. We confirmed that both the wild-type CFHR5 and mutant CFHR512123-9 proteins have complement factor I cofactor activity; in both cases the activity is substantially weaker than that reported for CFH. The mutant CFHR512123-9 protein did not have reduced activity compared with wild-type in this assay; perhaps surprisingly, complement factor I cofactor activity was increased (webappendix p 2).

Discussion

We provide evidence for an inherited renal disease, endemic in Cyprus, that is characterised by microscopic and synpharyngitic macroscopic haematuria, renal failure, and C3 glomerulonephritis, and show that affected individuals have an internal duplication within the gene for complement factor H-related protein 5 (CFHR5). We term this disease CFHR5 nephropathy.

Isolated microscopic haematuria is a common presentation that in the absence of urinary tract abnormalities, proteinuria, or renal impairment is usually believed to be benign, and with present guidelines is not investigated by renal biopsy. However, this study shows that isolated microscopic haematuria can be the presenting feature of progressive renal disease, with implications for patients and their families. Furthermore, analysis of data suggests that familial isolated microscopic haematuria attributable to heterozygous mutations in COL4A3 and COL4A4 is also associated with progressive chronic kidney disease. Taken together, these findings underscore the importance of any history of renal disease in the family and the value of renal biopsy and genetic investigations in this setting.

CFHR5 nephropathy has several noteworthy clinical features. First, the risk of progressive renal impairment is more common in men than in women. Second, since Berger's original description, repeated episodes of synpharyngitic haematuria have been regarded as almost diagnostic of IgA nephropathy; CFHR5 nephropathy should now be thought of as a differential diagnosis. Third, although retinopathy is a well recognised feature of dense-deposit disease, with affected individuals developing ocular drusen at a young age, clinically significant visual impairment was not a feature of CFHR5 nephropathy. This finding is consistent with a study that reported no association between CFHR5 polymorphisms and risk of age-related macular degeneration. However, because formal ophthalmological assessment was only done for two affected individuals in this study, we cannot exclude the presence of subclinical ocular disease in CFHR5 nephropathy.

An important pathological consideration was that most of the individuals who were biopsied initially had a histological diagnosis of membranoproliferative glomerulonephritis type 1. Review led to recognition that these abnormalities were C3 glomerulonephritis, which is an entity described in a French report of 19 patients that did not identify families with more than one affected individual. In that series, men were not more severely affected than were women, synpharyngitic macroscopic haematuria was not reported, and microscopic haematuria was absent in seven of 19 (37%) patients at diagnosis. By contrast, CFHR5 nephropathy is an inherited disease, characterised by synpharyngitic macroscopic haematuria (noted in seven [58%] of the affected individuals tested; see table) and microscopic haematuria (all affected individuals tested). Thus, CFHR5 nephropathy constitutes a distinct clinical entity that is associated with the histological category C3 glomerulonephritis. Abnormalities in other complement genes were identified in a subset of the patients in the French report, suggesting that different mechanisms of complement dysregulation can lead to much the same histological appearances.

The CFHR5 mutation is a copy number variation (ie, a duplication or deletion of a segment of DNA), which is not detectable with standard exon-based sequencing. Copy number variations arise through non-allelic recombination events that are more common in regions of complex genomic architecture such as the CFH and CFHR1–5 gene cluster.

The extent of the shared haplotype suggests that affected members of the families inherited the mutation from a common ancestor about 16 generations ago, and our identification of additional cases and affected families in the Cypriot population implies the existence of a substantial number of individuals with CFHR5. The high penetrance of haematuria (all 22 mutation carriers tested; see table), the wide geographical distribution of ancestry within Cyprus, and the presence of affected individuals in the UK suggests that this disease will account for a substantial proportion of renal disease affecting inhabitants of the island and their descendants worldwide. Population-based studies need to be done to quantify this proportion; we examined only a small cohort of Cypriots with advanced or end-stage renal disease, either of unknown cause or attributed to presumed or incompletely characterised glomerulonephritis. In the US renal data system, about 25% of patients with advanced renal disease would fit into this category.

Although CFHR5 nephropathy seems to be a common cause of renal disease in the Cypriot population, we did not detect this specific CFHR5 mutation in 36 cases of sporadic C3 glomerulonephritis from France and the UK. Whether this geographical disparity is the effect of ascertainment bias, positive selection for the allele within Cyprus (perhaps because of the presence of an endemic infectious disease), or genetic drift within the island's population is not known. So far, mutations in other complement regulatory genes and the presence of C3 nephritic factor have been reported in a few cases of C3 glomerulonephritis; other genetic abnormalities of CFHR5 might exist.

The mutation we identified in CFHR5 provides a robust genetic marker for a novel hereditary nephritis, and screening for the mutation is a reliable clinical test. However, our understanding of how the mutation causes the disease is incomplete and we do not exclude the possibility that another mutation within the 6·1 cM-shared haplotype could exist. We propose that CFHR5 is important in complement processing within the kidney, and that the CFHR5 mutation impairs the ability of CFHR5 to achieve this. Our model is consistent with the previous finding that wild-type CFHR5 co-localises with complement within the kidney in renal disease.

Our in-vitro functional studies show that the mutant CFHR512123-9 protein binds to surface-bound complement (on erythrocytes and mouse glomeruli) substantially less well than does wild-type CFHR5. Western blot analysis of serum from affected individuals showed greater intensity for mutant CFHR512123-9 protein than for wild-type CFHR5 (figure 7); an in-vivo finding that would be consistent with a defect in recruitment of the mutant protein from the circulation to interact with surface-bound complement. However, CFHR5 is not a straightforward loss of functional allele, because it produces a circulating protein that shows enhanced complement factor I cofactor activity in vitro compared with wild-type CFHR5.

In laboratory models of C3 dysregulation, excessive production of inactivated C3b (iC3b) by complement factor I is important for the initiation of renal injury; complement factor I cofactor activity of CFHR512123-9 could lead to an increase in iC3b in the glomerulus. More studies will be necessary to elucidate fully the biological role of CFHR5 and the pathophysiology of C3 glomerulonephritis in CFHR5 nephropathy. The central role of abnormal complement deposition in this disease suggests that inhibition of the terminal complement pathway (for instance with the humanised anticomplement C5 monoclonal antibody eculizumab, which is effective for treatment of paroxysmal nocturnal haemoglobinuria) might be of therapeutic benefit in CFHR5 nephropathy and clinical studies are needed to address this issue.