Significance of genetic analysis in adult patients with inherited chronic kidney disease

Abstract

Genetic focal segmental glomerulosclerosis (FSGS) is an important but underestimated cause of inherited proteinuric chronic kidney disease (CKD) in adults. We discuss a case of familial CKD due to inverted formin 2 (INF2) gene mutation, where three siblings had disparate phenotypic presentations ranging from CKD with subnephrotic proteinuria to nephrotic-range proteinuria with collapsing FSGS on kidney biopsy over a period of 8 years. The youngest sibling was the index case. The family agreed to undergo genetic testing only after two more siblings were diagnosed with kidney disease. This case highlights how clinical heterogeneity, absence of family history in the index case, initial lack of specific biopsy-proven diagnosis and reluctance to undergo genetic testing can delay the diagnosis of genetic kidney disease in adults.

Background

The genetic causes of familial chronic kidney disease (CKD) are poorly delineated especially in adult patients. Genetic focal segmental glomerulosclerosis (FSGS) is an important cause of familial CKD, but there is significant heterogeneity in the initial clinical presentation, from nephrotic syndrome to subnephrotic proteinuria and even advanced CKD.^{1 2} Familial FSGS is more likely to be autosomal dominant in adolescents and adults compared with children. A kidney biopsy is not always feasible especially with advanced chronic disease. Family history of kidney disease may not always be present especially in the index case, leading to a delay in diagnosis. There is also scepticism about genetic testing for inherited CKD especially in adults. Here we describe an interesting case of familial CKD which highlights these issues in the clinical management of such patients.

Case presentation

Clinical history

A woman in her 20s presented to us with mild pedal oedema and newly diagnosed hypertension. There was no history of joint pain, malar rash, haematuria, hearing loss or visual deficit. She had noticed that she was passing frothy urine.

Family history

The patient has a strong family history of CKD (figure 1). She is the third of five siblings and she became symptomatic 3 years ago. Her youngest brother had been diagnosed with hypertension and CKD (index serum creatinine of 1.7 mg/dL) 10 years ago when he was an adolescent. He had no history of significant oedema and had not undergone kidney biopsy. He presented to us with end-stage kidney disease (ESKD) and underwent renal transplantation 7 years ago with his mother as the donor and currently has stable graft function. Subsequently, the fourth of the five siblings (brother) who was in his early 20s was diagnosed with hypertension and ESKD and died from a sudden cardiac event during dialysis. The family was unwilling to undergo genetic testing at that time. None of the affected patients had any features of neuropathy.

Figure 1.

Pedigree chart showing the distribution of chronic kidney disease in the family.¹¹ Prepared by Soumita Bagchi.

The remaining two brothers are hypertensive, with normal serum creatinine and no urinary abnormality to date. Both of the parents are normotensive and have normal renal function, with no history of consanguinity. There is no history of kidney disease in other second-degree relatives.

Investigations

Initial diagnostic work-up

The patient’s baseline investigations are shown in table 1. Her serum creatinine was 2.5 mg/dL, suggesting kidney dysfunction, with urine protein creatinine ratio of 5.1 g/g, indicating nephrotic-range proteinuria. Her urinary sediment was bland. Her serum albumin was 3.6 g/dL (low normal) and her serum cholesterol was 215 mg/dL (high). Markers for autoimmune disease were normal. Ultrasound showed bilateral normal-sized kidneys with increased echogenicity.

Table 1.

Laboratory parameters of the patient at presentation

Hemoglobin (g/L)	134
Total leukocyte count (103/µL)	8.12
Platelet (/103/µL)	190
Blood urea (mg/dL)	76
Serum creatinine (mg/dL)	2.5
Serum sodium (mEq/L)	137
Serum potassium (mEq/L)	5.6
Total protein/albumin (g/dL)	6.6/3.6
Serum cholesterol (mg/dL)	215
Urine routine microscopy	Protein +3; red blood cells: 1–2/high power field; white blood cell : nil
Urine protein creatinine ratio (g/g)	5.1
ANA/anti-ds DNA*	Negative

* ANA: anti nuclear antibody/anti-ds DNA: anti double stranded DNA antibody

Kidney biopsy

The patient underwent a kidney biopsy (figure 2) which showed FSGS with segmental collapsing phenotype with interstitial fibrosis and tubular atrophy of 30%–35%. Immunofluorescence was negative, while electron microscopy findings were not available.

Figure 2.

(A) Representative histology image showing glomerulus with collapsing phenotype with segmental tuft collapse and overlying podocytic hypertrophy and hyperplasia. Adjacent tubulointerstitial chronicity with associated lymphomononuclear infiltrate is also noted (periodic acid Schiff’s stain 200×). (B) Silver stain better highlighting the segmentally collapsed tuft with prominent overlying podocytes around the tuft filling the Bowman’s space (Jones methenamine silver stain 200×). Images provided by Dr Adarsh Wamanrao Barwad.

Genetic testing

Clinical exome assay by next generation sequencing in the patient’s sister revealed a heterozygous missense mutation in exon 2 of the inverted formin 2 (INF2) gene (chr14:g.104701582G>A; depth: 126×) that results in the amino acid substitution of serine for glycine at codon 73 (p.Gly73Ser; ENST00000392634.9); this was further validated by Sanger sequencing. Subsequently, her youngest sibling, who is a renal transplant recipient, was also found to have the same mutation by Sanger sequencing. The mutation was not detected in the eldest sibling and in both parents. The second sibling did not agree to genetic testing.

Clinical exome sequencing involves examining 1% of the genome which codes for exons and splice junctions for disease-causing mutations in patients who are suspected to have an inherited disease. This is based on the premise that majority of pathogenic (disease-causing) variants are located in this region, thus making it a cost-effective approach to genetic testing. It may sometimes give a false negative report in patients with known familial disease phenotype due to genetic heterogeneity, current lack of knowledge about all disease-causing genetic mutations and inherent flaws in the test technology.³

Differential diagnosis

Other genetic causes of familial FSGS were considered in the differential diagnosis.

Treatment

The patient was managed with supportive treatment, including optimisation of blood pressure and renin angiotensin system blockade with angiotensin converting enzyme (ACE) inhibitor therapy.

Outcome and follow-up

The patient’s kidney ailment subsequently progressed to ESKD and she is currently on maintenance haemodialysis.

Discussion

Genetic FSGS in adults

Monogenic causes of FSGS are more common in children and adolescents compared with adults. Adult-onset genetic FSGS is often underestimated, with significant variability in clinical presentation, from nephrotic syndrome to subnephrotic proteinuria and CKD.^{1 2} In addition to mutations in podocyte genes like INF2, ACTN4, TRPC6 and CD2AP, glomerular membrane abnormality due to COL4A mutation is also an important cause of genetic FSGS in adults.⁴ Genetic testing is often deferred in adults with FSGS, especially when family history is lacking, often leading to unnecessary use of immunosuppression, to which they usually do not respond, thus progressing to ESKD. However, unlike primary FSGS, genetic FSGS cases are less likely to recur after kidney transplantation.

INF2 mutation

Mutation in the INF2 gene was identified as a genetic cause of FSGS in 2010.⁵ INF2 belongs to the formin subfamily of actin regulatory proteins and plays an important role in maintaining the stability of podocyte actin cytoskeleton essential for preserving the integrity of the glomerular filtration barrier. INF2 mutations account for 9%–16% of autosomal dominant cases of FSGS in adults.^5–9 It has incomplete penetrance, and INF2-related disease usually presents in the second/third decade of life, with progression to ESKD by third to fourth decade. It may also manifest in children. Wide variability in age of presentation has been reported, as seen in this family. Patients present with isolated proteinuria or nephrotic syndrome with progressive kidney disease with or without Charcot-Marie-Tooth syndrome. This family had three siblings who developed CKD over 8 years with disparate presentations, with the youngest presenting first, thus highlighting the clinical heterogeneity associated with this disease. Kidney biopsy usually shows FSGS not otherwise specified, but collapsing phenotype seen in our patient has been reported infrequently.⁸ In the absence of genetic testing, diagnosis may be delayed if the patient presents with advanced CKD and kidney biopsy is not feasible.⁹

Most mutations in the INF2 gene cluster in exons 3 and 4, but mutations in exon 2 have also been identified.^5–8 Our patients had a heterozygous missense mutation in exon 2, resulting in amino acid substitution of serine for glycine at codon 73 (p.Gly73Ser; ENST00000392634.9), which is very rare and has been previously reported in only one family.⁸ Considering that both parents did not have the mutation suggests this was possibly a type of germline mosaicism.

Challenges in genetic testing in CKD

Genetic diseases account for 10%–15% of cases of ESKD in adults, suggesting the need to do genetic testing in patients with a family history of CKD or features suspicious of an inherited disease. Identifying a genetic cause has significant therapeutic implications. It helps avoid unnecessary expensive treatment like immunosuppression with associated adverse events in patients with genetic FSGS. Screening of family members facilitates genetic counselling, early diagnosis, timely initiation of supportive treatment and monitoring, thus improving long-term outcomes. Genetic testing is also crucial to prevent asymptomatic family members who may harbour the disease-causing mutation from being inadvertently considered as potential kidney donors for transplantation. Despite this, multiple factors have prevented the integration of genetic testing into the diagnostic work-up of patients with CKD.¹⁰ There is a knowledge gap about the genetic causes of CKD in adults and testing is considered to have limited utility in patient management in the absence of targeted therapy both by patients and treating nephrologists. Absence of a family history in the index case may lead to delay in testing, especially in adults. A high index of suspicion for a genetic cause of kidney disease is required in adolescents or young adults presenting with unexplained CKD. This case brings forth these practical issues which may hamper early diagnosis in these patients. Our understanding of the inherited causes of CKD is still evolving, which makes interpretation of certain mutations uncertain, and deficiencies in testing methods occasionally lead to false negative reports even in well-established cases of familial disease. The cost of these tests is a concern especially in low and middle-income countries like India in the absence of universal healthcare. Further research is required to develop affordable testing technology with better diagnostic yield to make them more accessible. Cost utility analysis of genetic testing in kidney disease, especially in adults, is warranted to interpret its role especially in resource-limited nations.

Patient’s perspective.

I had seen one of my brothers develop kidney disease, undergo dialysis and get a kidney transplantation over the last few years. It has been a very challenging and turbulent time for my family. During this period another brother also developed the same illness. Unfortunately he had advanced kidney failure at the time of diagnosis despite not having any complaints in the past and succumbed to his illness before he could get a kidney transplant. Our parents realized that this may be something which runs in families but had difficult time accepting this as there was no history of kidney disease in their extended family. However, they were getting my elder brothers and myself tested regularly for evidence of kidney disease. Based on their past experience, they took appropriate medical advice as soon as I was detected to have hypertension and so the definite cause of kidney disease could be identified. But I failed to respond and progressed to kidney failure and am currently requiring regular hemodialysis. I hope to be able to undergo a kidney transplant in the future. I think research is needed to identify specific treatment for these diseases as it affects young people and hampers their future.

Learning points.

• This case highlights how a specific diagnosis of a genetic cause of CKD may be delayed due to multiple factors

• Families are often reluctant to undergo genetic testing if there is a lack of targeted disease-specific therapy.

• The cost of genetic testing may be a deterrent, especially in resource limited countries where patients often have to pay for these investigations.

• A strong index of suspicion is required when evaluating adolescents or young adults with CKD and parents as well as siblings should be screened for kidney disease

• Timely detection of the mutation and disease in relatives is essential to exclude them as potential kidney donors and for early initiation of supportive therapy

Ethics statements

Patient consent for publication

Obtained.