Clinical and biochemical characteristics of patients with ornithine transcarbamylase deficiency and in silico analysis of OTC gene

Abstract

Background: This study seeks to elucidate the clinical and biochemical features of Ornithine transcarbamylase deficiency (OTCD), a pleomorphic congenital hyperammonemia disorder with a non-specific clinical phenotype. Additionally, the research aims to analyze the mutation spectrum of the OTC gene and its potential association with phenotype, as well as to perform an in silico analysis of novel OTC variants to elucidate their structure-function relationship.

Methods: In this study, we conducted a retrospective analysis of the clinical and biochemical features of 12 patients with OTCD and examined their metabolite profiles. Additionally, we reviewed existing literature to explore the range of mutations in the OTC gene and their possible associations with phenotypic outcomes. Furthermore, we employed the high ambiguity-driven protein-protein docking (HADDOCK) algorithm and protein-ligand interaction profiler (PLIP) to predict the pathogenicity of these mutations and elucidate the underlying mechanisms of pathogenesis in novel variants of the OTC gene.

Results: Nine cases, all of which were male, presented with early onset, while two cases, all of which were female, exhibited late onset. Additionally, one male case was asymptomatic. The ages of the patients at the time of diagnosis ranged from 1 day to 12 years. Peak plasma ammonia levels were found to be higher in patients with early onset compared to those with late onset. Molecular analyses identified a total of 12 different mutations, including two novel mutations (V323G and R320P). In silico analysis indicated a potential difference in affinity between wild-type and mutant OTCase, with V323G and R320P mutations leading to a decreased binding ability of OTCase to the substrate, potentially disrupting its function.

Conclusion: This study broadened the genetic variation spectrum of OTCD and provided substantial evidence for genetic counselling to affected families. Additionally, we elucidated variant data of OTC in Chinese patients through comprehensive literature review. Given the ongoing uncertainty surrounding the genotype-phenotype correlation of OTCD, the results of our in silico analysis can contribute to a deeper understanding of this complex, rare, and severe genetic disorder.

Keywords: OTC; Gene variants; In Silico snalysis; Ornithine transcarbamylase defciency.

Fig. 1

Comparison of biochemical data between diferent phenotypes of OTCD Chinese patients in references. EO, early-onset; LO, late-onset; Lac, lactic acid; ALT, alanine aminotransferase; AST, glutamic-oxalacetic transaminase, TBIL, total bilirubin. **** P<0.0001, ***P<0.001, **P<0.01, *P<0.05, ns P ≥ 0.05

Fig. 2

Comparison of biochemical data between diferent phenotypes and gender of OTCD Chinese patients in references. EO, early-onset; LO, late-onset; Lac, lactic acid; ALT, alanine aminotransferase; AST, glutamic-oxalacetic transaminase, TBIL, total bilirubin. **** P<0.0001, ***P<0.001, **P<0.01, *P<0.05, ns P ≥ 0.05

Fig. 3

Representations of the wild-type structure of OTC protein and the location of the mutation site. The cyan color labels the ORN-binding/equatorial structural domains and the orange color labels the CP-binding/polar structural domains. In the further enlarged image, the upper part indicates the mutation at site 320 and the lower part indicates the mutation at site 323, where wild-type residues are labeled in green and mutant residues are labeled in yellow and blue

Fig. 4

Representations of the protein-ligand interactions of OTC wild-type and mutant-type structures. The PAO molecule was labeled in yellow, interacting residues of wild-type proteins were labeled in green, interacting residues of R320P mutant proteins were labeled in orange, and interacting residues of V323G mutant proteins were labeled in blue

Fig. 5

Analysis of molecular dynamics simulation results. (a) Showing the RMSD of the wild-type and mutant structures. (b) Showing the hydrogen bonding number of the wild-type and mutant structures. (c) Demonstration of RMSF of wild-type and mutant structures. black color in (a), (b) and (c) indicates wild-type structure, red color indicates R320P mutant structure and green color indicates V323G mutant structure. (d), (e) and (f) show the wild-type and mutant structures after 100 ns simulation. The gold structure is the wild-type initial structure, and the transparent green color of (d) Fig. indicates the wild-type protein structure after kinetic simulation, where the highlighted part (residues 110–130, 264–280) corresponds to the RMSF peak part. (e) Figure Transparent pink indicates the structure of R320P mutant after kinetic simulation, where the highlighted part (residues 100–135, 264–284, 310–330) corresponds to the RMSF peak part. (f) Figure Transparent gray indicates the V323G mutant structure after kinetic simulation, where the highlighted part (residues 110–130, 264–283) corresponds to the RMSF peak part