Congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay (CAKUTHED) is a rare autosomal dominant disorder and variants in PBX1 are involved in the etiology of this syndrome. Precise diagnosis is difficult without genetic test. We described a Chinese CAKUTHED patient, whose characteristics were collected from medical records. The potential responsible variants were explored by whole exome sequencing. A heterozygous variant in the PBX1 gene (NM_002585 c.862C>T, p.R288*) was found in the proband, which was confirmed by Sanger sequencing. This heterozygous variant in the PBX1 gene was the molecular pathogenic basis of this disorder. It is necessary to perform a genetic test for diagnosing chronic nephritis with unknown reason.

Congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay (CAKUTHED, OMIM 617641) is an autosomal dominant disorder characterized by different congenital anomalies of the kidney and urinary tract, dysmorphic facial features, and abnormalities of the outer ear [1]. The typical presentations include renal dysfunction and hearing loss. Most patients show developmental delay and intellectual impairment. This disorder is a subtype of congenital anomalies of the kidney and urinary tract (CAKUT), which is a heterogeneous group of abnormalities affecting the kidneys or other structures of the urinary tract.

Mutations in PBX1 are involved in the etiology of CAKUTHED; however, the underlying molecular mechanism is unclear [2]. De novo mutations in PBX1 were first identified as a cause of CAKUT in 2017. Heidet et al. [3] reported 3 unrelated patients with truncating point mutations in the PBX1 gene. Slavotinek et al. [4] identified seven different de novo heterozygous mutations in the PBX1 gene in 8 unrelated patients with CAKUTEHD. Most reported patients were young, with only two adults. Nevertheless, renal presentation was detected in the early lives of all patients. As CAKUTHED is a new disease entity registered on the Online Mendelian Inheritance in Man in 2017, the number of CAKUTHED cases reported previously is rather small. Here we reported a novel variant of PBX1 identified by whole exome sequencing (WES) in a Chinese CAKUTHED patient.

Patients and Clinical Evaluation

A 36-year-old Chinese Han female was admitted to our Department of Nephrology for abnormal renal function. An elevated uric acid level was observed in this patient about 11 years ago, and elevated serum creatinine was noticed 6 years later. As no other related symptoms were noticed, she discontinuously took some renoprotective traditional Chinese medicine. She suffered from sudden sensorineural hearing loss at the age of 18, and developed depression at 29. She had no personal history of severe infectious diseases such as hepatitis and tuberculosis, and she denied a family history of chronic kidney disease or hypertension as well as smoking or drinking.

Her appearance was normal and blood pressure was within the normal range. The blood routine test was normal except for slightly reduced red cell count and hemoglobin (Table 1). Pure tone audiometry was performed to confirm the hearing loss, and moderate to severe hearing loss was confirmed in her ears (Fig. 1). Serum chemistry showed elevated levels of serum creatinine, uric acid, and parathyroid hormone (Table 1). The estimated glomerular filtration rate was 69.0 mL/min/1.73 m2 according to the CKD-EPI equation. Abdominal ultrasound examination showed slightly atrophied kidneys with a size of 9.0 × 3.8 × 1.4 cm on the right side and 9.1 × 4.1 × 1.5 cm on the left side. No abnormality was detected in the liver, pancreas, and spleen by ultrasound examination. To detect anomalies of the kidney and urinary tract, CT urography was performed. However, no obvious abnormality was found except for renal malrotation (Fig. 2).

Table 1.

Patient characteristics at presentation

 Patient characteristics at presentation
 Patient characteristics at presentation
Fig. 1.

Pure-tone audiometry of the proband.

Fig. 1.

Pure-tone audiometry of the proband.

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Fig. 2.

CT scanning showing the renal malrotation.

Fig. 2.

CT scanning showing the renal malrotation.

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To further understand its renal pathology, histopathology study of renal biopsy was performed. Totally, six glomeruli were observed, without sclerosis or matrix hyperplasia. Mild focal tubular atrophy, tubulointerstitial fibrosis, and thickening of basement membrane were observed (Fig. 3). The immunological staining of IgA, IgG, and IgM was slight positive, while immunological staining of C3, C4, C1q, K, and λ was negative. The patient was diagnosed with chronic tubular-interstitial nephritis based on laboratory and histopathology findings. Therefore, angiotensin receptor blocker and traditional Chinese medicine were administered to restore her kidney function and reduce uric acid.

Fig. 3.

Histopathology study of renal biopsy from the proband. PAS staining showed the monolayer epithelium cells and the enlargement of renal tubules. Arrow indicated the focal tubular atrophy.

Fig. 3.

Histopathology study of renal biopsy from the proband. PAS staining showed the monolayer epithelium cells and the enlargement of renal tubules. Arrow indicated the focal tubular atrophy.

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Genetic Analysis

Considering the course of the disease and the unknown reason for chronic nephritis, a genetic test was recommended. Thus, DNA samples from the peripheral blood cells of the proband and her parents were obtained and WES was performed. The isolated genomic DNA was fragmented to 150∼200 bp and subjected to DNA library preparation and sequenced. Totally, the coverage of targets was over 99.7%. The sequencing analysis identified a novel variant of the PBX1 gene in the proband, and the parents were both wildtype (Fig. 4). This variant (NM_002585 c.862C>T, p.R288*) encoded a truncated PBX1 protein. In addition, the variant was excluded from the Single Nucleotide Polymorphism Database (dbSNP) and the Human Genetic Variation Database (HGVD). Sanger sequencing was performed to validate the identified variation (Fig. 4). According to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines, this variant was classified as “pathogenic” (PVS1 + PS2 + PM2). Based on the genetic tests and clinical presentations, this patient was finally diagnosed with CAKUTHED.

Fig. 4.

Identification of the novel variant in the CAKUTHED family. a Pedigree of the Chinese family. Affected family members are denoted in black. Arrow indicates the proband. b Direct Sanger sequencing confirmed the heterozygous variant in PBX1 gene.

Fig. 4.

Identification of the novel variant in the CAKUTHED family. a Pedigree of the Chinese family. Affected family members are denoted in black. Arrow indicates the proband. b Direct Sanger sequencing confirmed the heterozygous variant in PBX1 gene.

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PBX1 encodes the pre-B-cell leukemia homeobox transcriptional factor, which belongs to a three-amino-acid-loop-extension (TALE) homeodomain family of transcription factor [5]. It can form nuclear complexes with other TALE proteins that regulate target genes involved in embryogenesis. As an important transcriptional factor, PBX1 is implicated in regulation, cellular differentiation, and tissue expansion. Variants in this gene can lead to different syndromic diseases. A chromosomal translocation, t(1;19) involving this gene and the TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia [6]. Recently, variants in PBX1 have been found to be associated with CAKUTHED syndrome, characterized by multiple congenital defects. These disease-causing variants include partial and complete gene deletions, truncating, splice site and missense variants. In addition, deleterious sequence variants in PBX1 are also found in intellectual impairment and congenital heart disease [4, 7].

CAKUTHED syndrome is a subtype of CAKUT. The differential phenotypes include hearing loss and facial dysmorphism, as well as developmental delay and intellectual disability. Nevertheless, renal presentations are the outstanding feature of CAKUTHED syndrome, frequently leading to end-stage kidney disease. As a syndromic disease, CAKUTHED is usually diagnosed in the early stage of life. Due to the nature of the PBX1 variants, phenotypic heterogeneity can range from subclinical abnormalities to severe malformations. Therefore, it is hard to diagnose the CAKUTHED at the beginning. A 4-year-old Japanese girl was finally diagnosed with CAKUTHED after a genetic test for WES, although her nephropathy had progressively worsened and she developed renal failure at the age of 2 [8]. In our case, renal presentation was found during a routine physical examination at the age of 25, with a serum level of uric acid increased. Meanwhile, the elevated serum creatinine was noticed 5 years later. Actually, hearing loss was evident earlier than renal lesions. As hearing loss is also involved in Alport syndrome, and her renal biopsy did not match features of Alport syndrome, it is difficult for the nephrologist to connect this symptom with renal presentation. Thus, the patient was preliminarily diagnosed with chronic tubular-interstitial nephritis.

Due to the progress of next-generation sequencing, WES has been extensively applied to hereditary diseases, including rare renal diseases. As the cost of WES has been reduced greatly, it shows great potential in clinical application to identify the molecular basis of renal disease, especially for those with unknown etiology. WES can reveal the variants not only in exons but also at the boundary of introns. For instance, a disease-causing variant identified by WES was found to be located in the intron of COL4A5 [9], suggesting that WES is a powerful method for genetic testing. Therefore, our case underwent genetic testing using WES, and a novel variant was found in PBX1 gene, which is associated with CAKUTHED syndrome.

As CAKUTHED syndrome is a subtype of CAKUT, it is not surprising that disease-causing variants are also found in CAKUT patients. Recently, 8 patients with deleterious sequence variants in the PBX1 gene were reported by Slavotinek et al. [4]. One of them harbored the same variant (p.Arg288*) as our case but showed a different phenotype, which might be explained by the age of onset and ethnic difference. In addition, Le Tanno et al. [5] confirmed that PBX1 haploinsufficiency was found in CAKUT patients by using chromosomal microarray analysis. In a cohort of Chinese CAKUT patients, PAX2 was the most commonly mutated gene, while the PBX1 variant was found only in 1 patient [10]. These studies indicated the differential genetic spectrum among ethnic groups. Currently, genotype-phenotype correlations of PBX1 variants are unclear due to the lack of sufficient cases. Therefore, our case helps to understand the phenotype of PBX1-related syndrome and suggests the importance of genetic analysis in all patients with chronic renal failure without a definite diagnosis.

We wish to thank the patient and her family for participation in the study. We also thank the staffs of Chigene (Beijing) Translational Medical Research Center Co. Ltd. for providing next-generation sequencing, analyzing genetic diseases, and discussion.

Written informed consent to participate in the study was obtained from the patient and her parents. The present study was ethically approved by the Ethics Committee of Xinqiao Hospital at Army Medical University (Chongqing, China). All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration. Written informed consents for publication of identifying images and other personal and clinical details were obtained from the patient and her parents. These materials include diagnostic images, treatment and prognostic information, genetic testing results, and other related data used in this report.

The authors have no conflicts of interest to declare.

This work was supported by the Personal Training Program for Clinical Medicine Research of Army Medical University (Grant No. 2018XLC1007).

Weiping Hou: conception and design. Ling Nie, Yan Li, and Tangli Xiao: development of methodology and acquisition of data. Ling Nie, Yan Li, Bo Zhang, and Jinghong Zhao: analysis and interpretation of data. Weiping Hou and Jinghong Zhao: writing and review the manuscript.

The original data of WES are not available according to the Chinese policies of Human Genetic Resource, but the VCF file is available from the corresponding author on reasonable request.

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