Identification of Polycystic Kidney Disease 1 Like 1 Gene Variants in Children With Biliary Atresia Splenic Malformation Syndrome

Abstract

Biliary atresia (BA) is the most common cause of end-stage liver disease in children and the primary indication for pediatric liver transplantation, yet underlying etiologies remain unknown. Approximately 10% of infants affected by BA exhibit various laterality defects (heterotaxy) including splenic abnormalities and complex cardiac malformations-a distinctive subgroup commonly referred to as the biliary atresia splenic malformation (BASM) syndrome. We hypothesized that genetic factors linking laterality features with the etiopathogenesis of BA in BASM patients could be identified through whole-exome sequencing (WES) of an affected cohort. DNA specimens from 67 BASM subjects, including 58 patient-parent trios, from the National Institute of Diabetes and Digestive and Kidney Diseases-supported Childhood Liver Disease Research Network (ChiLDReN) underwent WES. Candidate gene variants derived from a prespecified set of 2,016 genes associated with ciliary dysgenesis and/or dysfunction or cholestasis were prioritized according to pathogenicity, population frequency, and mode of inheritance. Five BASM subjects harbored rare and potentially deleterious biallelic variants in polycystic kidney disease 1 like 1 (PKD1L1), a gene associated with ciliary calcium signaling and embryonic laterality determination in fish, mice, and humans. Heterozygous PKD1L1 variants were found in 3 additional subjects. Immunohistochemical analysis of liver from the one BASM subject available revealed decreased PKD1L1 expression in bile duct epithelium when compared to normal livers and livers affected by other noncholestatic diseases. Conclusion: WES identified biallelic and heterozygous PKD1L1 variants of interest in 8 BASM subjects from the ChiLDReN data set; the dual roles for PKD1L1 in laterality determination and ciliary function suggest that PKD1L1 is a biologically plausible, cholangiocyte-expressed candidate gene for the BASM syndrome.

Figure 1.. Construction of the set of 2,016 genes of interest (GOI).

To explore the potential contribution of ciliary and ciliopathy gene variants underlying the BASM phenotype, a collated set of ciliopathy and biliary GOI was derived from 4 large comprehensive data sets: (1) Cildb – a knowledgebase for centrosomes and cilia (27, 49); (2) Simon Fraser University (SFU) Ciliome Database – a summary of ciliomic studies (31); (3) MCIL1 – Emory Genetics Laboratory Ciliopathies Sequencing Panel; and (4) MM340 – Emory Genetics Laboratory Neonatal and Adult Cholestasis Sequencing Panel.

Figure 2.

A.) The number of reported laterality features per participant. Representation of the number of laterality features (–6) per participant expressed as a percentage of the total cohort (n in parentheses). Note that the majority of participants (48) had two or more laterality defects. Four of the 67 participants had isolated renal anomalies. B.) The 6 categorical types of reported laterality features. The most common reported abnormalities of left-right patterning in the 67 BASM participants expressed as a percentage of the total cohort (n in parentheses). The majority had splenic abnormalities or intestinal malrotation, with substantial overlap in the types of anomalies between participants. Abbreviation: IVC, inferior vena cava.

Figure 3.. Schematic depiction of the PKD1L1 variants in this report.

Exonic regions affected by each variant are noted among the 58 PKD1L1 exons. Adapted from (50).

Figure 4.. PKD1L1 expression in bile duct epithelium.

Immunohistochemical detection of PKD1L1 in human liver tissue from: A) Subject 1; and representative regions from patients with B) carbamoyl phosphate synthetase deficiency; C) hepatoblastoma; and D) Alagille syndrome (with absence of portal tract bile ducts). E-G are from serial sections of liver tissue from a normal 3-day-old infant: E) hematoxylin and eosin staining; immunostaining with F) keratin 7 and G) PKD1L1. Bile duct profiles are highlighted and enlarged in E-G. Note robust PKD1L1 expression in cholangiocytes from two livers affected by hepatocellular disease and normal pediatric liver tissue (B, C, G), absence in Alagille syndrome (D), and weak/absent expression in Subject 1(A).