Part One Genetics Of Kidney Disease: The Unexpected Role Of Rare Disorders

Abstract

Hundreds of different genetic causes of chronic kidney disease are now recognized, and while individually rare, taken together they are significant contributors to both adult and pediatric conditions. Traditional genetics approaches relied heavily on identifying large families with multiple affected members and have been fundamental to identifying genetic kidney diseases. With the increased utilization of massively parallel sequencing and improvements to genotype imputation, we can analyze rare variants in large cohorts of unrelated individuals, leading to personalized patient care and significant research advancements. This review evaluates the contribution of rare disorders to patient care and the study of genetic kidney diseases and highlights key advancements that utilize new techniques to improve our ability to identify new gene-disease associations.

Keywords

genetic kidney disease, collapsing analysis, precision medicine, massively parallel sequencing, genomics, chronic kidney disease

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INTRODUCTION

Chronic kidney disease (CKD) is a complex condition that encompasses many individual diseases characterized by abnormalities in kidney structure or function (1). Globally, kidney disease is common, with an estimated prevalence of 9%, and is a major contributor to morbidity and mortality (2). Similar to other common diseases, CKD has relatively high heritability, with broad-sense heritability estimates ranging from 19% to 54% depending on the biomarker utilized (3–5).

Genetic variation can be broadly dichotomized into common variants, present in more than 1% of the alleles of the population [a minor allele frequency (MAF) of >0.01], and rare variants (MAF<0.01) (6–8). The role of common variants in kidney disease has been assessed using genome-wide association studies (GWAS), which have explained only 20% of an estimated 54% heritability in creatinine-based estimated glomerular filtration rate (4). On the other side of the spectrum, rare pathogenic variants are responsible for most Mendelian (monogenic) diseases. There are over 600 Mendelian forms of kidney disease, responsible for 50% of childhood-onset kidney disease; the majority of the causative variants are very rare or private within a specific family (9, 10). Although present at a lower frequency, Mendelian kidney diseases are identified in approximately 10% of adult patients, with the specific diagnostic yield of testing varying based on the individual’s type of kidney disease, family history, age at onset, and extra-renal manifestations (11). Similar to pediatric cases, rare and private variants drive most diagnoses in adult cases. The data on the impact of rare disorders in CKD are now emerging and are consistent with analyses of other complex traits, which have demonstrated that a significant amount of missing heritability is explained by rare protein-altering variants that are not well captured by current genotyping and imputation techniques but can be analyzed using massively parallel sequencing of the exome (exome sequencing, ES) or genome (12, 13).

The rare variants implicated in kidney disease are diverse in their class, inheritance, affected gene, and clinical phenotype. For example, rare structural variants and variations in gene copy number have been linked to the development of congenital anomalies of the kidney and urinary tract (CAKUT), and single-nucleotide variants and small insertions and deletions (indels) have been linked to kidney diseases across the phenotypic spectrum (14, 15). Rare somatic variants have been implicated as a second hit in cyst development in autosomal dominant polycystic kidney disease (ADPKD) and as the driver variants in clonal hematopoiesis of indeterminate potential (CHIP), an age-associated non-malignant condition that may cause an increased risk of kidney failure and complications of CKD (16, 17). Rare mosaic variants also impact the severity of X-linked Alport syndrome, suggesting further complexity in determining the effect of a variant (18).

In this review, we describe the role rare variants play in the genetics of kidney disease. We examine their central place in diagnostic studies, including the implications for patient care and the use of genetic testing in prognostication and treatment. We then explore the typical approaches employed to identify and validate new rare variant associations with disease. We conclude with the investigation of large data sets and the integration of clinical data from electronic health records, which offer opportunities to evaluate genetic effects at a scale that was previously impossible.

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CLINICAL DIAGNOSTIC SETTINGS

Genetic kidney disease is an umbrella term that captures hundreds of rare disorders with an identified genetic cause. To date, over 600 monogenic disorders with kidney and urologic phenotypes have been identified (Figure 1) (19). Almost all these genetic conditions are seen in fewer than 1 in 2,000 people, but cumulatively they represent the fifth most common cause of kidney failure (20). While a few monogenic disorders account for a large fraction of cases, the remaining cases are attributable to a large number of rare disorders. This long tail in the distribution of monogenic kidney diseases has important implications for clinical diagnostic algorithms and gene discovery efforts. Several diagnostic studies have been performed to better define the diagnostic yield and clinical implications of genetic testing in different patient populations with kidney disease. One of the key findings across these studies is that the majority of identified pathogenic variants are very rare, with a maximum (max) MAF of less than 1 × 10–4, or private within a single family.

1. Pediatric Conditions

Genetic diseases were originally thought to be mostly pediatric, so earlier diagnostic studies focused on evaluating pediatric patients (11, 21). One such study used ES to evaluate 187 pediatric patients with steroid-resistant nephrotic syndrome and identified a genetic cause in 49 (26%) cases and 77 diagnostic variants (22). Interestingly, despite the recessive inheritance of these conditions, all variants were extremely rare; 32 (42%) were absent from the literature, 39 (51%) were absent from Exome Aggregation Consortium (ExAC), and a further 25 (32%) had a max MAF of less than 1 × 10−4. One exception is a pediatric steroid-resistant nephrotic syndrome caused by variants in NPHS2, which offers an interesting example of the interaction of common and rare variants in the disease. NPHS2 p.R229Q is the most commonly identified pathogenic variant in this patient population, with a max MAF in ExAC of 0.029. However, the NPHS2 p.R229Q variant does not cause disease when present in the homozygous state and is only pathogenic when paired with certain other rare NPHS2 variants (23). In the cited study, the deleterious variants found in trans to NPHS2 p.R229Q in affected individuals were always rare and often private, with NPHS2 p.E264Q being the most common in ExAC, having a max MAF of 0.003. Similarly, the evaluation of genetic causes of CAKUT in 232 families identified 32 different causative variants in 32 cases (14%) affecting 22 genes with 16 (50%) of these variants absent from the literature and 28 (88%) very rare or absent from the Genome Aggregation Database (gnomAD) (24).

2. Broadening to Adult Patients

ES has been used to evaluate diverse patient populations with kidney disease, including individuals with adult-onset disease. The largest study to do so included 3,315 individuals with CKD from any cause, of whom 2,144 had developed kidney failure and 2,837 were adults at study entry (15). This study identified a molecular diagnosis in 307 individuals (9.1%) leading to the diagnosis of 66 different Mendelian kidney diseases. The study identified 343 diagnostic variants, of which 340 99%) are rare in gnomAD. Most variants were either very rare, with a max MAF of less than 1 × 10−4 (n = 84, 24%), or private (n = 229, 67%) (Figure 2a).

3. Impacts of a Genetic Diagnosis

One of the key findings of diagnostic studies is that most genetic diagnoses directly impact patient care, even with the limited number of targeted treatments currently available. Groopman et al. (15) found that a genetic diagnosis led to a clinical impact in 89% of cases, including in 76% of cases where a genetic kidney disease was suspected before testing. These clinical impacts were retrospectively assessed and ranged from informing prognosis to changing transplant and treatment decisions. Importantly, a genetic diagnosis in patients with CKD of unknown etiology clarified the cause of kidney disease in all cases, carried prognostic implications for 77%, initiated targeted subspecialty care for 77%, and changed therapy for 62%. Prospective data supporting the clinical utility of genetic testing for kidney disease were recently published on 204 patients with suspected genetic kidney disease who underwent ES. A direct clinical impact was reported for 47 (59%) probands with a genetic diagnosis and 73 (91%) families (25). Clinical impacts included the prevention of 10 kidney biopsies, changes to treatment plans in 16 cases, and altered surveillance in 35 that were again driven by rare variants (Figure 2b).

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4. Prognosis

The variability in the clinical presentation of genetic forms of kidney diseases has complicated the provision of prognostic information to patients, even when a genetic cause is identified. In addition, the majority of pathogenic variants associated with kidney disease are very rare or private within a family, which limits our ability to provide prognosis based on individual variants. Nevertheless, genotype–phenotype correlations have been part of human genetics since its inception, often using generalizable variant characteristics such as the type of effect on the protein, the properties of the altered amino acid, or the position of the variant within the protein. In nephrology, the two most mature applications of this approach look at ADPKD and Alport syndrome. For patients with ADPKD, the PROPKD (predicting renal outcomes in polycystic kidney disease) scoring system has been developed and validated to predict an individual’s median age at kidney failure by integrating clinical and variant data (26). Truncating variants in PKD1 carry the highest risk of kidney failure, followed by nontruncating PKD1 variants, then variants in PKD2, and it also appears that nontruncating in-frame insertions and deletions in PKD1 that alter the protein length carry a higher risk than missense variants (27). Similarly, for patients with Alport syndrome, nonsense variants carry the most severe prognosis while splicing and missense variants portend intermediate and mild phenotypes, respectively. Other factors such as the position of the variant within the gene, its position relative to noncollagenous interruptions, and the substituting amino acid have also been shown to impact patient prognosis (28–30). Future tools may also include predictive information from both common and rare variants to improve their power (31). The availability of larger data sets would allow the integration of more variants, and ideally more distinct families with the same variants, into the development of robust prognostic tools to allow for better predictions. Such tools could significantly impact clinical trials, as participants could be stratified based on the expected progression of their disease.

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5. Treatment

Diagnostic studies have shown that obtaining a genetic diagnosis can have a direct impact on treatment (Table 1). Examples include the use of high-dose coenzyme Q10 (CoQ10) supplementation for patients with nephrotic syndrome and diagnostic variants within the CoQ10 pathway (COQ2, COQ6, ADCK2/COQ8B, PDSS2, MTTL1) and the use of xanthine oxidase inhibitors for patients with APRT (adenine phosphoribosyltransferase) deficiency (32, 33). A genetic diagnosis can limit exposure to ineffective treatments; for example, when a genetic cause of the nephrotic syndrome is identified, immunosuppression is usually not used, as the majority of genetic nephrotic syndrome cases will not respond and these treatments carry significant risks (34). Future studies should assess the benefits of avoiding adverse effects, such as reduced infection and cancer risks from limiting immunosuppression due to genetic testing. Moreover, the ability to detect undiagnosed patients with monogenic diseases can help with risk stratification in clinical trials to optimize power and reduce exposure to side effects.

An ultimate goal is to develop curative treatments. One of the most advanced examples in nephrology is the application of gene therapy for Fabry disease (35). Fabry disease is caused by over 1,000 different variants in the GLA gene, most very rare or private, that lead to reduced α-galactosidase A activity and the accumulation of glycosphingolipids (36). The standard treatment for this disease is enzyme replacement therapy (ERT), which requires regular infusions and can lead to treatment-limiting anti-drug antibodies. However, in a pilot safety study, five males with classical Fabry disease due to very rare missense variants who were stably treated with ERT were treated with gene therapy (35). They underwent lentivirus-mediated ex vivo gene therapy where hematopoietic stem/progenitor cells were transduced with a functional GLA gene, then reintroduced via an autologous hematopoietic stem cell transplant. These patients demonstrated a durable normalization of leukocyte α-galactosidase A activity and stable glycosphingolipid levels that allowed three (60%) of them to discontinue their ERT, with a reasonable adverse event profile. This study gives us hope that with further refinement, curative treatments may be available for more of our patients.

The Fabry disease also provides other interesting examples of personalized therapy, including chaperone therapy and treatment decisions for female patients. A common mechanism of disease in this condition is altered protein trafficking leading to a reduction in enzyme activity. Migalastat is a chaperone molecule that restores enzyme function and shows clinical efficacy similar to ERT in 35–50% of individuals with an amenable variant but has no effect in individuals with nonamenable variants (37, 38). This variant specificity makes genetic testing a key step in optimizing therapy for patients with Fabry disease. It was long thought that, due to the X-linked nature of the disease, females were unaffected carriers; however, it is now clear that many females are affected and that there is a complex interplay between the specific variant characteristics and skewed X inactivation that leads to highly heterogeneous clinical presentations (39). This has complicated the decision of when and how to treat female Fabry disease patients, as some individuals benefit from therapy but we lack tools to predict response before patients are symptomatic, highlighting an area in need of further research.

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Other targeted therapies are becoming available for patients with genetic kidney diseases, using new techniques like RNA interference (RNAi), antisense-oligonucleotides (ASO), and CRISPR-Cas9. RNAi has shown great promise for the treatment of genetic kidney diseases, with positive phase III trials using patisiran to treat hereditary transthyretin amyloidosis due to TTR variants and lumasiran to treat primary hyperoxaluria type 1 due to AGT variants (40, 41). These treatments have been designed to be variant agnostic, allowing them to be used to treat individuals with a variety of different rare variants. CRISPR-Cas9 has been studied in a small cohort of individuals with transthyretin amyloidosis and was shown to reduce serum TTR production through targeted gene knockdown using an in vivo delivery technique (42). Exon-skipping ASO treatment of truncating COL4A5 variants has been shown in mice to induce clinical and histologic improvements by altering the protein effect to an in-frame exon deletion (43). This may become a treatment option for patients with a variety of rare truncating COL4A5 variants that typically cause severe disease but have yet to be studied in humans. Therapeutic approaches for APOL1-associated nephropathy include using ASO treatments to reduce APOL1 expression and the use of small-molecule inhibitors of APOL1 to reduce its function (44). These targeted and personalized therapies are likely to be applied to different genetic diseases and offer our patients hope for better treatments in the future.

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Mark D. Elliott,1,2,3 Hila Milo Rasouly,1,2 and Ali G. Gharavi1,2,3

1 Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; email: ag2239@columbia.edu

2 Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA

3 Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA