January 3, 2018
In the past few years, we have learned a lot about the genetics of kidney and urinary tract malformations. In this paper, we review recent advances in the field and discuss opportunities and challenges ahead.
December 5, 2017
Patients with chronic kidney disease (CKD) often have a family member who is also affected. In addition, many of them present late in the course of disease such that their nephrologist just cannot pinpoint the underlying cause of kidney failure using traditional diagnostic methods. We performed a pilot study of whole exome sequencing in 92 patients with CKD to determine whether it can help in the diagnosis and management. We identified the causal mutation in 24% of patients, including many patients with CKD of unknown cause. In most cases, the genetic diagnosis had a clinical impact such as targeted surveillance and sometimes changes in therapy. In addition we found mutations in PARN in patients with tubulo-interstitial nephropathy, identifying a new cause of kidney disease. These findings indicate significant opportunities for introducing DNA sequencing and precision medicine for the diagnosis and management of patients with kidney disease. Based on these findings, we are performing larger studies to pinpoint the utility of genomic diagnostics for CKD.
November 2, 2017
Congenital malformations of the kidney are the most common cause of renal failure in children. In collaboration with the Sanna-Cherchi lab, we used whole exome sequencing (WES) in 202 children with congenital kidney malformation and identified biallelic mutations in SLIT3 and heterozygous loss of function mutatIons in GREB1L as two new genetic forms of the disease. While inactivation of Slit3 in mice has been shown to cause kidney and other organ malformations, the function of GREB1L is not known. CRISPR-Cas9 induced mutations of the zebrafish ortholog, performed in the Davis and Katsanis labs, produced pronephric defects, demonstrating that zebrafish will be very useful for studying GREB1L function. These findings demonstrate the utility of exome-wide association studies to discover new genes and biological pathways underlying kidney diseases.
March 27, 2017
It is increasingly recognized that children with chronic kidney disease (CKD) are at increased risk for neurocognitive impairment. It has been hypothesized that this finding is secondary to the metabolic and psychosocial burden imposed by chronic kidney disease. We had previously shown that 7 to 10% of children with CKD have a genomic disorder that predisposes to neuropsychiatric disorders, suggesting a genetic link between CKD and neurocognitive impairment. We therefore examined the association of neurocognitive scores and the presence of genomic disorders children enrolled in the Chronic Kidney Disease in Children Study (CKiD). We found that genomic disorders are associated with lower IQ, and greater anxiety and depression scores and poorer executive functioning in children with CKD, independent of other risk factors for neurocognitive impairment such as kidney function or blood pressure. These findings clarify association of CKD with neurocognitive co-morbidities in pediatric CKD, indicating that in a subset of children, poorer neurocognitive performance is attributable to the presence of a genomic disorder that simultaneously impairs kidney function and neurocognitive development. These data call for early identification of genomic disorders in children with CKD and indicate that interventions independent of CKD treatment will be required to address neurocognitive impairment in this population.
March 24, 2016
Fatty liver disease is becoming the most common cause of end-stage liver failure. It is not known why some people are more prone to fat accumulation and subsequent liver injury. In collaboration with the Worman lab, we studied why some strains of mice develop liver injury whereas others were perfectly healthy on the same high fat diet. We conducted a genome wide association study to pinpoint loci predisposing to various fatty liver associated traits, taking advantage of publicly available data. We identified the Sel1l locus as the major contributor to variation in serum bile acid levels and other related metabolic traits, such as cholesterol in blood and and in liver. Examination of Sel1l haploinsufficient mice confirmed that SEL1L influences bile acid levels after exposure to high fat diet. We further showed that loss of Sel1l affects hepatocyte homeostasis via modulation of HNF1A and HNF4A levels, two transcription factors that have been implicated in the pathogenesis of Maturity-Onset Diabetes of the Young (MODY) and bile acid homeostasis. These findings identify a new gene involved in bile acid metabolism, and nominate SEL1L as candidate gene for fatty liver disease and related metabolic traits such as hypercholesterolemia and diabetes in humans.
April 20, 2015
In the US, children with end-stage renal disease have a one-year mortality rate of 35 per 1,000 patient years. Pediatric Chronic Kidney Disease (CKD) results in an increased morbidity from anemia, hypertension, cardiovascular complications, and it is often accompanied with neurodevelopmental and cognitive deficits. However, we often cannot make a precise diagnosis of the underlying disease, due to late referral or overlap in clinical presentation of different disorders.
To shed light on the genetic component of pediatric CKD we performed chromosomal microarrays to detect genomic imbalances in 419 children enrolled in the Chronic Kidney Disease in Children (CKiD) Prospective Cohort Study and compared them to 21,575 control individuals, including children. Genomic disorders were present in 4.5% of children with CKD compared to 0.45% of controls. An additional 2.9% of CKiD participants carried novel, likely pathogenic genomic imbalances that would have been reportable in a clinical setting. Importantly, we observed genomic imbalances with diagnostic value across the whole clinical spectrum of pediatric CKD. In some instances the genomic finding confirmed the clinical diagnosis, as exemplified by deletion of the CTNS gene in children with cystinosis; in other instances the genomic lesion was unsuspected and either reclassified or refined the diagnosis.
Thus many children with CKD may have an undiagnosed genetic disorder, and implementation of genetic testing with chromosomal microarray (and perhaps genome sequencing in the near future), will help with making a precise diagnosis of disease and developing personalized workup and therapy.
We will need to study larger populations to validate these findings in an independent CKD population before we can recommend routine genetic testing in all children with CKD. However, based on this paper and or our prior publication, it is clear that patients with CKD due to kidney malformations (renal aplasia/hypoplasia/dysplasia) have the highest risk of having a genomic imbalance and should be considered for DNA microarrays now, and genome sequencing in the near future.
This study also serves as proof of principle that Nephrology may be ideally positioned to spearhead the adoption of genomic diagnostics in the pediatric clinical practice: Perinatal imaging and lab tests are routinely performed to assess kidney development and function, and detection of CKD could become an indication to search for genomic imbalances to achieve personalized medical interventions at an early stage.
October 12, 2014
Our latest genetic study of IgA nephropathy (IgAN) is now published in Nature Genetics! This is the largest GWAS of IgAN published to date, involving over 20,000 individuals of European and East Asian ancestry. We identified several new genome-wide significant associations, including ITGAM-ITGAX, VAV3, DEFA and CARD9 loci. We also replicated all previously reported signals. Interestingly, nearly all IgAN loci are either directly associated with risk of inflammatory bowel disease or maintenance of the intestinal epithelial barrier and response to mucosal pathogens. The geospatial distribution of risk alleles is highly suggestive of polygenic adaptation, and genetic risk correlates strongly with variation in local pathogens, particularly helminth diversity, suggesting a possible role for host-intestinal pathogen interactions in shaping the genetic landscape of IgAN. We hypothesize that high genetic risk of IgAN in East Asian populations might represent a consequence of protective adaptations against endemic intestinal worm infections. Our study also points to the key role of intestinal immunity in the pathogenesis of this common form of nephritis.
July 17, 2013
Some things are meant to be. After all, out of over 20,000 genes in the human genome, only DSTYK, (a.k.a. “Dusty protein kinase") shares its name with Dusty, the beloved family dog of Katelyn Burgess, the talented student who spent two years doing research on congenital malformations of the kidney and urinary tract in our lab. So when Katelyn first detected a splice-site mutation in DSTYK in a Sardinian family with these congenital defects, we were sure we were on to something good.
Left panel: Dusty the dog can usually be found on the front porch of Katleyn’s house. Right panel: The DSTYK protein (red label) is heavily expressed in the ureteric bud and metanephric mesenchyme during early nephrogenesis and colocalizes with FGF receptors 1 and 2 (green). Blue: E-Cadherin.
Congenital malformations of the kidney and urinary tract are the major cause of pediatric end-stage renal failure. Familial forms occur in about 10% of the cases, mostly with autosomal dominant mode of inheritance. Gene identification for dominant diseases with incomplete penetrance and small pedigree size has been proven extremely challenging.
In this study we performed genome-wide linkage analysis coupled with whole-exome sequencing to identify a mutation in DSTYK, predicted to result in an in-frame deletion of 9 highly conserved aminoacids. Resequencing of 311 additional patients identified mutations in 7 other individuals (2.3%). Among these mutations one, a premature termination mutation at the 8th amino acid, suggests loss-of-function as pathogenic mechanism. DSTYK is expressed in the epithelia of all major organs and morpholino knock-down in zebrafish resembles inactivation of fibroblast growth factor (FGF) signaling. Consistent with these data, DSTYK is expressed in the ureteric bud and metanephric mesenchyme during early nephrogenesis and colocalizes with FGF receptors 1 and 2. RNA silencing of DSTYK transcript n human embryonic kidney cells abrogates FGF-dependent ERK phosphorylation.
These data discover dominant mutations in DSTYK in 2.3% of patients with urinary tract malformations, and identify a novel positive effector of FGF signaling during embryonic kidney development.
Feb 21, 2013
Birth defects are a major cause of childhood morbidity and mortality. The Danforth mouse, known for its characteristically foreshortened tail, is a classic model of birth defects involving the musculoskeletal, gastrointestinal, and genitourinary systems. This mouse was first described in 1930 but the underlying causal mutation remained elusive until recently. In 2012 we localized the mutation to a 42.8-kb segment on chromosome 2, and subsequently identified the mutation as an 8.5-kb transposon upstream of Pancreas Specific Transcription Factor, 1a (Ptf1a). This insertion disrupts a highly conserved Ptf1a regulatory domain, causing increased and temporally premature Ptf1a expression. Most important for elucidating the mutant phenotype, we found that this mutation caused ectopic expression of Ptf1a in the notochord, hindgut, and mesonephros of the mouse; affecting the embryonic tissues that give rise to organ defects in the Danforth mouse. Our data provide a striking example of how a mutation in a noncoding, regulatory region can produce dysregulation of gene expression, resulting in profound developmental defects. These data highlight the critical role of noncoding elements in coordination of gene expression in the vertebrate genome and demonstrate the need to include regulatory mutations when searching for the cause of human birth defects.
Nov 15, 2012
In this study we examined whether large genomic imbalances (copy-number variants or CNVs) contribute to congenital kidney malformations, one of the most common forms of birth defects. We found that large rare CNVs are considerably more common among 522 individuals with renal hypodysplasia or agenesis compared to >13,000 population controls. Strikingly, the majority of the known CNV disorders detected in this study have previous associations with developmental delay or neuropsychiatric diseases. Altogether, up to 16.6% of individuals with kidney malformations had a molecular diagnosis attributable to a copy-number disorder, strongly suggesting that a search for copy number variants should be considered as a first diagnostic step in this patient population.
June 21, 2012
In this study we analyzed 12 IgAN case-control cohorts comprising of over 10,000 individuals. We confirmed that our previously discovered GWAS loci were significant contributors to disease risk. In addition, we identified two novel independent susceptibility alleles within the MHC region and a new genetic interaction between two loci on different chromosomes. Combining the data across all cohorts, we developed a genetic risk score that explained nearly 5% of variation in disease risk and predicted a northward risk gradient in Europe. This revealed a previously unrecognized increase in IgAN–attributable kidney failure in Northern European countries. We also created an online risk score calculator that assess individual genetic risk in relationship to the worldwide average.
June 16, 2012
Considering highly variable clinical course, early identification of individuals at risk of renal disease progression represents one of the major challenges in the field of IgA nephropathy. Recently, we completed a clinical study assessing the risk of end stage renal disease in IgAN. The study involved 619 biopsy-diagnosed patients from Shanghai, China. The best independent predictors of progression to end stage renal disease were eGFR, systolic blood pressure, hemoglobin, and serum albumin levels at the time of diagnosis. Based on these observations, we developed a 4-variable equation of a clinical progression risk score. Our score explained nearly 22% of the total variance in the primary outcome (need for renal replacement therapy). Clinically, the risk of progression can now be assessed using our new web-based calculator.
March 13, 2011
We completed a large GWAS for IgAN involving a total of 5,966 participants of Chinese and European ancestry. In this study, we identified five independent susceptibility loci that are common in the populations studied. Interestingly, some of the alleles that protect against IgAN impart increased risk for other autoimmune or infectious diseases, suggesting complex selective pressures shaping the spectrum of allelic frequencies at these loci. Moreover, our discoveries provide novel insights into the pathogenesis of IgAN.
November 15, 2010
Adriamycin is a commonly used chemotherapeutic agent that also produces significant tissue damage and induces Adriamycin nephropathy in specific mouse inbred strains. We found that sensitivity to nephropathy was produced by a mutation in the Prkdc gene, which encodes a critical nuclear DNA double-stranded break repair protein. We determined that Prkdc participates in mtDNA regulation and demonstrated genetic interaction with Mpv17, which encodes a mitochondrial protein mutated in human mtDNA depletion syndromes. Our findings implicate mtDNA damage in the development of Adriamycin toxicity and identify Prkdc as a modifier gene in mtDNA depletion syndromes and a component of the mitochondrial genome maintenance pathway.
April 20, 2009
We performed expression quantitative trait locus (eQTL) analysis of podocyte genes in HIV- 1 transgenic mice to gain insight into genetic susceptibility to HIV-1-associated nephropathy (HIVAN). In 2 independent crosses, we found that transcript levels of the podocyte gene Nphs2 were controlled by an ancestral cis-eQTL and by 2 trans-eQTLs that localized to the nephropathy susceptibility loci HIVAN1 and HIVAN2. Transregulation of podocyte genes was observed in the absence of HIV-1 or glomerulosclerosis, while presence of the HIV-1 transgene interfered with transregulation, demonstrating effects of gene-environment interactions on disease. These data demonstrate that transcript levels of Nphs2 and related podocyte-expressed genes are networked and suggest that the genetic lesions introduced by HIVAN susceptibility alleles perturb this regulatory pathway and transcriptional responses to HIV-1, increasing susceptibility to nephropathy.