Limits...
Copy number variation analysis identifies novel CAKUT candidate genes in children with a solitary functioning kidney.

Westland R, Verbitsky M, Vukojevic K, Perry BJ, Fasel DA, Zwijnenburg PJ, Bökenkamp A, Gille JJ, Saraga-Babic M, Ghiggeri GM, D'Agati VD, Schreuder MF, Gharavi AG, van Wijk JA, Sanna-Cherchi S - Kidney Int. (2015)

Bottom Line: Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult.Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes.Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.

View Article: PubMed Central - PubMed

Affiliation: Division of Nephrology, Columbia University, New York, New York, USA.

ABSTRACT

Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large data set of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.

No MeSH data available.


Related in: MedlinePlus

Expression of KIF12 and DLG1 in the developing human kidneyTransversal section through lumbosacral part of human embryo (6th week of development): a) within the nephrogenic zone (nz), KIF12 is weakly expressed in the developing nephron (renal vesicle – rv) and negative in the metanephric mesenchyme (mm). KIF12 is strongly expressed (arrows) in the UB stalk and UB-derived structures, such as the epithelium of collecting ducts (Cd), while the surrounding mesenchyme is negative; b) DAPI nuclear staining; c) merge of a and b; negative isotype control. d) DLG1 is weakly or not expressed in the developing nephron (renal vesicle – rv, metanephric cup - mc) and negative in the metanephric mesenchyme (mm), while it is moderately expressed (arrows) in the epithelium of collecting ducts (Cd); e) DAPI nuclear staining; f) merge of d and f; negative isotype control. Immunostaining of Kif12 and Dlg1, magnification ×40, scale bar 25Xm.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4834924&req=5

Figure 2: Expression of KIF12 and DLG1 in the developing human kidneyTransversal section through lumbosacral part of human embryo (6th week of development): a) within the nephrogenic zone (nz), KIF12 is weakly expressed in the developing nephron (renal vesicle – rv) and negative in the metanephric mesenchyme (mm). KIF12 is strongly expressed (arrows) in the UB stalk and UB-derived structures, such as the epithelium of collecting ducts (Cd), while the surrounding mesenchyme is negative; b) DAPI nuclear staining; c) merge of a and b; negative isotype control. d) DLG1 is weakly or not expressed in the developing nephron (renal vesicle – rv, metanephric cup - mc) and negative in the metanephric mesenchyme (mm), while it is moderately expressed (arrows) in the epithelium of collecting ducts (Cd); e) DAPI nuclear staining; f) merge of d and f; negative isotype control. Immunostaining of Kif12 and Dlg1, magnification ×40, scale bar 25Xm.

Mentions: We evaluated gene expression profiles for all high-priority genes in the developing mouse kidney by using GUDMAP (https://www.gudmap.org/) and GenePaint (www.genepaint.org/) databases. According to these databases, all five genes were expressed in the developing mouse kidney and urinary tract. We subsequently performed localization studies using immunofluorescence antibody staining in the developing embryonic human and mouse kidney at the 6th gestational week and at embryonic day E14.5, respectively. As predicted from data implicating Dlg1 in urinary tract malformations in mice,31 this gene was specifically expressed in the human ureteric bud (UB) (Figure 2) and showed moderate expression in the mouse UB and metanephric mesenchyme (MM) structures (Supplementary Figure 3D). Figure 2A demonstrates strong and specific expression of KIF12 in the human UB stalk at 6th week of gestation and, to a lesser extent, in the mouse MM and developing nephrons at E14.5 (Supplementary Figure 3D). EDA2R, PCDH9, and TRAF7 showed also specific expression in human UB compartment at the 6th week of gestation (Supplementary Figure 3E, G and I) and, to a lesser extent, in the E14.5 mouse embryonic kidney (Supplementary Figure 3F, H and J).


Copy number variation analysis identifies novel CAKUT candidate genes in children with a solitary functioning kidney.

Westland R, Verbitsky M, Vukojevic K, Perry BJ, Fasel DA, Zwijnenburg PJ, Bökenkamp A, Gille JJ, Saraga-Babic M, Ghiggeri GM, D'Agati VD, Schreuder MF, Gharavi AG, van Wijk JA, Sanna-Cherchi S - Kidney Int. (2015)

Expression of KIF12 and DLG1 in the developing human kidneyTransversal section through lumbosacral part of human embryo (6th week of development): a) within the nephrogenic zone (nz), KIF12 is weakly expressed in the developing nephron (renal vesicle – rv) and negative in the metanephric mesenchyme (mm). KIF12 is strongly expressed (arrows) in the UB stalk and UB-derived structures, such as the epithelium of collecting ducts (Cd), while the surrounding mesenchyme is negative; b) DAPI nuclear staining; c) merge of a and b; negative isotype control. d) DLG1 is weakly or not expressed in the developing nephron (renal vesicle – rv, metanephric cup - mc) and negative in the metanephric mesenchyme (mm), while it is moderately expressed (arrows) in the epithelium of collecting ducts (Cd); e) DAPI nuclear staining; f) merge of d and f; negative isotype control. Immunostaining of Kif12 and Dlg1, magnification ×40, scale bar 25Xm.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834924&req=5

Figure 2: Expression of KIF12 and DLG1 in the developing human kidneyTransversal section through lumbosacral part of human embryo (6th week of development): a) within the nephrogenic zone (nz), KIF12 is weakly expressed in the developing nephron (renal vesicle – rv) and negative in the metanephric mesenchyme (mm). KIF12 is strongly expressed (arrows) in the UB stalk and UB-derived structures, such as the epithelium of collecting ducts (Cd), while the surrounding mesenchyme is negative; b) DAPI nuclear staining; c) merge of a and b; negative isotype control. d) DLG1 is weakly or not expressed in the developing nephron (renal vesicle – rv, metanephric cup - mc) and negative in the metanephric mesenchyme (mm), while it is moderately expressed (arrows) in the epithelium of collecting ducts (Cd); e) DAPI nuclear staining; f) merge of d and f; negative isotype control. Immunostaining of Kif12 and Dlg1, magnification ×40, scale bar 25Xm.
Mentions: We evaluated gene expression profiles for all high-priority genes in the developing mouse kidney by using GUDMAP (https://www.gudmap.org/) and GenePaint (www.genepaint.org/) databases. According to these databases, all five genes were expressed in the developing mouse kidney and urinary tract. We subsequently performed localization studies using immunofluorescence antibody staining in the developing embryonic human and mouse kidney at the 6th gestational week and at embryonic day E14.5, respectively. As predicted from data implicating Dlg1 in urinary tract malformations in mice,31 this gene was specifically expressed in the human ureteric bud (UB) (Figure 2) and showed moderate expression in the mouse UB and metanephric mesenchyme (MM) structures (Supplementary Figure 3D). Figure 2A demonstrates strong and specific expression of KIF12 in the human UB stalk at 6th week of gestation and, to a lesser extent, in the mouse MM and developing nephrons at E14.5 (Supplementary Figure 3D). EDA2R, PCDH9, and TRAF7 showed also specific expression in human UB compartment at the 6th week of gestation (Supplementary Figure 3E, G and I) and, to a lesser extent, in the E14.5 mouse embryonic kidney (Supplementary Figure 3F, H and J).

Bottom Line: Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult.Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes.Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.

View Article: PubMed Central - PubMed

Affiliation: Division of Nephrology, Columbia University, New York, New York, USA.

ABSTRACT

Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large data set of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.

No MeSH data available.


Related in: MedlinePlus