Identifying Genomic Alterations Implicated in CAKUT
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of kidney failure in children and young adults worldwide. The clinical consequences of CAKUT are several, from treatments that require specialized nephrology and urology medical and surgical care, to treatment of associated comorbidities, and, eventually dialysis and transplantation. This phenotypically diverse group of disorders is in fact frequently associated with additional extra-urinary comorbidities, such as cardiovascular disease and neurodevelopmental defects, adding to the disease burden for affected children.
Specialists in urology, nephrology, and genomics from NewYork-Presbyterian/Columbia University Irving Medical Center joined with colleagues at major institutions around the world to study the phenotypic spectrum of CAKUT. Their goal was to “identify those genes and allelic variants that are either specific to subcategories of disease or those that have pleiotropic effects across the entire genitourinary tract, and to discover novel cellular pathways that are implicated in kidney and urinary development.”
Advances in genetic research and analysis have begun to provide a more precise understanding of the genetic causes for these conditions. Early disruptions in transcription factors and signaling molecules and pathways can impact full development of the renal system, leading to multiple subphenotypes associated with CAKUT. Understanding the underlying genetic variants that cause these disruptions is key to improving prognosis and paves the way for individualized care. Nevertheless, a molecular-based diagnosis has been possible in the minority of cases, ranging from a few percent to about 20 percent of patients, according to different studies.
The international team, led by Columbia researchers, sought to bolster the availability of a large cohort of deeply phenotyped CAKUT patients and population controls to elucidate the role of specific genetic variants and genes in urinary tract development. In particular, their investigations focused on copy number variations (CNVs), i.e., gain or loss of germline genetic material that can encompass multiple genes at the time. Analysis of CNVs has been an invaluable tool for uncovering the genetic architecture of several pediatric developmental conditions. To accomplish their objectives, the researchers conducted a comprehensive genome-wide analysis of 2,824 samples from patients encompassing common subcategories of CAKUT and 21,498 population controls to compare the prevalence of rare CNVs that intersect genes.
Their findings, published in the January 2019 issue of Nature Genetics, exposed both the presence of a distinct genetic architecture as well as pleiotropic mutations for the different subphenotypes of CAKUT. Specific results included:
- Children with CAKUT had a highly significant higher burden of rare CNVs as compared to controls
- The three largest categories of CAKUT – kidney anomalies, vesicoureteral reflux, and obstructive uropathy – showed distinctly different genomic architecture
- The annotation of CNV-associated genomic disorders (GD) that are known to cause human syndromes resulted in 45 distinct rare CNVs in 112 (4.0 percent) of independent cases compared to 0.6 percent in the control group, placing CAKUT among the conditions that are frequently associated to GD, such as neurodevelopmental delay, cardiac anomalies, and others
- Among CAKUT categories, GDs were present in nearly 10 percent of children with kidney anomalies
- Cases with a known GD-CNV were more likely to have multiple sites of the urinary tract affected and more frequently harbored extrarenal conditions
- Haploinsufficiency is suggested as the main pathogenic mechanism for CAKUT-associated deletion CNVs based on whole exome sequencing in 23 patients with pathogenic microdeletions at 14 independent loci
Among the 45 CAKUT-associated GDs, six loci accounted for 65 percent of the patients with GD-CNVs, identifying regions of the genome that are critical for kidney and urinary tract development. Among these six most prevalent loci, the chromosome 22q11.2 microdeletion (the DiGeorge syndrome locus) was previously characterized in the context of CAKUT by the same investigators (The New England Journal of Medicine, 2017), and the chromosome 16p11.2 microdeletion syndrome appeared as a previously unappreciated frequent cause of CAKUT.
The 16p11.2 microdeletion syndrome has been implicated as a major cause of autism and schizophrenia and found also in other genetic syndromes such as congenital scoliosis, suggesting that gene dosage for transcripts in this region is critical for multiorgan development. The investigative team first validated their findings in an independent cohort of children ascertained at the Children’s Hospital of Philadelphia and confirmed that CAKUT can be recognized in at least 30 percent of individuals with this microdeletion.
In order to identify a genetic driver for the CAKUT phenotypes observed in this syndrome, deletion mapping and prioritization analyses were conducted and TBX6 was recognized as a possible gene. To further elucidate the role of TBX6, the researchers used a mouse allelic series of Tbx6 gene dosage reduction. As first proof of its role in CAKUT, severe Tbx6 transcript reduction resulted in complete penetrance of severe kidney and urinary tract malformations. Interestingly, milder reduction of Tbx6 gene expression, which would more closely mimic the effect of the human microdeletion, resulted in incompletely penetrant and variable CAKUT phenotypes, representing the same subcategories observed in 16p11.2 carriers, i.e., kidney anomalies (hypoplasia and dysplasia), obstructive uropathy, and duplicated collecting systems.
By identifying major susceptibility CNVs for CAKUT and TBX6 as a genetic driver for the 16p11.2 microdeletion syndrome, the study has contributed greatly to expanding the genomic knowledge, advancing the understanding of pediatric malformations of the kidney and urinary tract, and accelerating the pursuit of new therapeutic targets.
The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. Nature Genetics. 2019 Jan;51(1):117-127.
Genetic Drivers of Kidney Defects in the DiGeorge Syndrome. Lopez-Rivera E, Liu YP, Verbitsky M, Anderson BR, Capone VP, Otto EA, Yan Z, Mitrotti A, Martino J, Steers NJ, Fasel DA, Vukojevic K, Deng R, Racedo SE, Liu Q, Werth M, Westland R, Vivante A, Makar GS, Bodria M, Sampson MG, Gillies CE, Vega-Warner V, Maiorana M, Petrey DS, Honig B, Lozanovski VJ, Salomon R, Heidet L, Carpentier W, Gaillard D, Carrea A, Gesualdo L, Cusi D, Izzi C, Scolari F, van Wijk JA, Arapovic A, Saraga-Babic M, Saraga M, Kunac N, Samii A, McDonald-McGinn DM, Crowley TB, Zackai EH, Drozdz D, Miklaszewska M, Tkaczyk M, Sikora P, Szczepanska M, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Darlow JM, Puri P, Barton D, Casolari E, Furth SL, Warady BA, Gucev Z, Hakonarson H, Flogelova H, Tasic V, Latos-Bielenska A, Materna-Kiryluk A, Allegri L, Wong CS, Drummond IA, D'Agati V, Imamoto A, Barasch JM, Hildebrandt F, Kiryluk K, Lifton RP, Morrow BE, Jeanpierre C, Papaioannou VE, Ghiggeri GM, Gharavi AG, Katsanis N, Sanna-Cherchi S. The New England Journal of Medicine. 2017 Feb 23;376(8):742-754. doi: 10.1056/NEJMoa1609009. Epub 2017 Jan 25. PMID: 28121514.
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