Biallelic Novel USP53 Splicing Variant Disrupting the Gene Function that Causes Cholestasis Phenotype and Review of the Literature

Abstract

<b><i>Introduction:</i></b> Hereditary cholestasis is a heterogeneous group of liver diseases that mostly show autosomal recessive inheritance. The phenotype of cholestasis is highly variable. Molecular genetic testing offers an useful approach to differentiate different types of cholestasis because some symptoms and findings overlap. Biallelic variants in <i>USP53</i> have recently been reported in cholestasis phenotype. <b><i>Methods:</i></b> In this study, we aimed to characterize clinical findings and biological insights on a novel <i>USP53</i> splice variant causing cholestasis phenotype and provided a review of the literature. We performed whole-exome sequencing and then confirmed it with Sanger sequencing. In addition, as a result of in silico analyses and cDNA analysis, we showed that the USP53 protein in our patient was shortened. <b><i>Results:</i></b> We report a novel splice variant (NM_019050.2:c.238–1G>C) in the <i>USP53</i> gene via whole-exome sequencing in a patient with cholestasis phenotype. This variant was confirmed by Sanger sequencing and was a result of family segregation analysis; it was found to be in a heterozygous state in the parents and the other healthy elder brother of our patient. According to in silico analyses, the change in the splice region resulted in an increase in the length of exon 2, whereas the stop codon after the additional 3 amino acids (VTF) caused the protein to terminate prematurely. Thus, the mature USP53 protein, consisting of 1,073 amino acids, has been reduced to a small protein of 82 amino acids. <b><i>Conclusion:</i></b> We propose a model for the tertiary structure of USP53 for the first time, and together with all these data, we support the association of biallelic variants of the <i>USP53</i> gene with cholestasis phenotype. We also present a comparison of previously reported patients with <i>USP53</i>-associated cholestasis phenotype to contribute to the literature.

The First Korean Adult Case of Progressive Familial Intrahepatic Cholestasis Type 7 with Novel USP53 Splicing Variants by Next Generation Sequencing

“…USP53, a member of ubiquitin specific proteases involved in deconjugation of ubiquitin and ubiquitin-like protein adducts, is a cysteine protease with complex organizational structures and different functional properties. 8 In animal models, it has been shown that USP53 is a component of the tight junction complex. 9 13 Tight-junction-associated proteins are involved in the survival of auditory hair cells and hearing.…”

“… 6 13 In humans, USP53 has critical roles in many important processes, especially substance transport, membrane permeability, membrane stability, apoptotic processes, repair, and regulation at the transcriptional/translational level. 8 15 The C-terminal domain of USP53 can interact with the tight junction protein 1 (TJP1) and TJP2 heterodimer associated with cholestasis risk. 3 8 16 A total of 19 different USP53 mutations have been reported, including six frameshift mutations, five nonsense mutations, four missense mutations, two indel mutations, one mutation in splicing site, and one small deletion ( Table 1 ).…”

“… 3 4 Liver cholestasis associated with USP53 mutation was first reported in 2019. 4 A total of 32 patients have been reported to date, 3 4 5 6 7 8 9 10 11 many of them in Middle Eastern families. Currently, cholestasis associated with USP53 mutation is considered a novel subtype of PFIC, subtype 7.…”

Ubiquitin‐specific peptidases: Players in bone metabolism

“…Hereditary cholestasis [74,75] Progressive hearing loss [76] CYLD Crohn disease [50] Growth arrest is required for cells to undergo differentiation. 83 However, USP7 overexpression increased cell proliferation, which may be the reason that overexpressed USP7 did not enhance the differentiation of the BMSCs.…”

Genetic alterations and molecular mechanisms underlying hereditary intrahepatic cholestasis

“…USP53 (ubiquitin specific peptidase 53) spliceosome variants can result in the premature termination of the protein, leading to the loss of its functional structure and abnormal metabolic and regulatory interactions. This can contribute to cholestasis in affected individuals ( Gezdirici et al, 2023 ). Jing Zhang et al did discover that USP53 mutations may play a role in some of the phenotypic features observed in cases of TJP2 defect ( Zhang et al, 2020 ).…”