Projects | Overview
Whole-exome sequencing (WES) finds a CKD-related mutation in approximately 20% of patients presenting with CKD before 25 years of age. Although provision of a molecular diagnosis could have important implications for clinical management, evidence is lacking on the diagnostic yield and clinical utility of WES for pediatric renal transplant recipients. To determine the diagnostic yield of WES in pediatric kidney transplant recipients, we recruited 104 patients who had received a transplant at Boston Children’s Hospital from 2007 through 2017, performed WES, and analyzed results for likely deleterious variants in approximately 400 genes known to cause CKD. Nearly one third of pediatric renal transplant recipients had a genetic cause of their kidney disease identified by WES. Knowledge of this genetic information can help guide management of both transplant patients and potential living related donors.
Chronic kidney diseases (CKD) take one of the highest tolls on human health, and their prevalence continuously rises. Steroid-resistant nephrotic syndrome (SRNS) is the 2nd most frequent cause of CKD before 25 yrs. By focal segmental glomerulosclerosis (FSGS) it inevitably leads to CKD with a 33% recurrence risk in a renal transplant. The pathogenesis of SRNS is unknown and no curative treatment is available. For SRNS, the primary causes (etiology) and disease mechanisms (pathogenesis) have been a conundrum for decades. However, identification of full-penetrance single-gene causes of NS (e.g. podocin) has implicated the renal glomerular podocyte at the center of the pathogenesis.
Nephronophthisis-related ciliopathies (NPHP-RC) are a group of inherited diseases that affect genes encoding proteins that localize to primary cilia or centrosomes. With few exceptions, ciliopathies are inherited in an autosomal recessive manner, and affected individuals manifest early during childhood or adolescence. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. The phenotypes of NPHP-RC are very diverse, and include cystic-fibrotic kidney disease, brain developmental defects, retinal degeneration, skeletal deformities, facial dimorphism, and, in some cases, laterality defects, and congenital heart disease. Mutations in the same gene can give rise to diverse phenotypes depending on the mutated allele. At the same time, there is broad phenotypic overlap between different monogenic genes. The identification of monogenic causes of ciliopathies has furthered the understanding of molecular mechanism and cellular pathways involved in the pathogenesis.
Congenital anomalies of the kidneys and urinary tract (CAKUT)
Chronic kidney disease (CKD) takes a high toll on human health, requiring dialysis or renal transplantation for survival. Before age 30 years ~50% of CKD is caused by CAKUT. However, its pathogenesis remains obscure. Deep insights into mechanisms of human CAKUT recently came from discovery of 44 monogenic genes that, if mutated, cause CAKUT. 22 of these genes were discovered by whole exome sequencing (WES) and functionally characterized in the applicant’s laboratory. We demonstrated by WES in CAKUT cohorts that causative monogenic mutations can be detected in >13-21% of cases, with similar detection rates in adult onset CKD due to CAKUT (JASN 29:2348, 2018; KI 95:914, 2019). We discovered a potential novel CAKUT gene in 8% of families. In addition, we showed that specific mutations in CAKUT genes illicit a broad phenotypic spectrum ranging from isolated to syndromic CAKUT (JASN 28:69, 2017). Our findings may have future consequences for diagnostics, prevention, and personalized therapy of children and adults with CAKUT. Monogenic causes of CAKUT coalesce around distinct signaling pathways.
Urinary stone disease (USD), one of the most frequent human diseases, afflicts 1/11 individuals in their lifetime. Pain, stone recurren-ce, and potential loss of renal function impose a severe health burden on patients. Nephrolithiasis can be associated with nephrocalcinosis. However, surprisingly little is known about etiology and pathogenesis of USD, and prevention and therapy are limited. Recently, by high-throughput exon sequencing of a large USD cohort we made the surprising discovery that in a remarkable ~20% of children and 11% of adults with USD we detected a causative monogenic mutation (recessive or dominant) in one of 30 USD candidate genes (Halbritter J Med Genet 49:756, 2012). We confirmed these results in 2 additional cohorts by whole exome sequencing (WES), showing that important consequences for prognosis/prophylaxis, and treatment of USD result from mutation detection (Braun cJASN 11:664, 2016; Daga Kidney Int, in press 2017). Furthermore, by WES we discovered mutations in SLC26A1 (Gee AJHG 98:1228, 2016) and in OXGR1 (unpublished) as 2 novel causes of USD, suggesting that many monogenic causes of USD are yet to be discovered. Our proposed discovery and functional characterization of known and novel single-gene causes of USD will likely transform the diagnostics, prognosis, prevention, treatment, and our mechanistic understanding of USD.
Midaortic syndrome (MAS) is a rare cause of severe childhood hypertension characterized by narrowing of the abdominal aorta in children and is associated with extensive vascular disease. It may occur as part of a genetic syndrome, such as neurofibromatosis, or as consequence of a pathological inflammatory disease. However, most cases are considered idiopathic. We hypothesized that in a high percentage of these patients, a monogenic cause of disease may be detected by evaluating whole exome sequencing data for mutations in 1 of 38 candidate genes previously described to cause vasculopathy. We studied a cohort of 36 individuals from 35 different families with MAS by exome sequencing. In 15 of 35 families (42.9%), we detected likely causal dominant mutations. In 15 of 35 (42.9%) families with MAS, whole exome sequencing revealed a mutation in one of the genes previously associated with vascular disease (NF1, JAG1, ELN, GATA6, and RNF213). Ten of the 15 mutations have not previously been reported. This is the first report of ELN, RNF213, or GATA6 mutations in individuals with MAS. Mutations were detected in NF1 (6/15 families), JAG1 (4/15 families), ELN (3/15 families), and one family each for GATA6 and RNF213. Whole exome sequencing can provide conclusive molecular genetic diagnosis in a high fraction of individuals with syndromic or isolated MAS. Establishing an etiologic diagnosis may reveal genotype/phenotype correlations for MAS in the future and should, therefore, be performed routinely in MAS.