Identification of compound heterozygous patients with primary hyperoxaluria type 1: clinical evaluations and in silico investigations

Biallelic Variant in the AGXT Gene in a Family Segregating Primary Hyperoxaluria; Accurate Genetic Diagnosis and Carrier Detection

AIM

Autosomal recessive primary hyperoxalurias (PH) are genetic disorders characterised by elevated oxalate production. Mutations in genes involved in glycoxylate metabolism are the underlying cause of PH. Type 1 PH (PH1) results in malfunctioning of alanine-glyoxylate aminotransferase enzymes of liver due to a change in the genetic sequence of alanine-glyoxylate aminotransferase (AGXT) gene. We encountered a large family segregating genetic disease of high oxalate kidney stones. A genetic analysis was carried out with the aim to identify underlying genetic defect.

METHODS

A large family with multiple affected individuals was recruited for this study. An extensive clinical evaluation, followed by genetic analysis, was carried out. Due to the heterogeneous nature of the disease, two members of the family having disease symptoms were subjected to whole exome sequencing (WES). Variants were annotated, filtered, and prioritised using various bioinformatic tools to detect disease associated genetic defects.

RESULTS

Unbiased and hypothesis-free WES data analysis was performed. Raw reads (fastq files) were mapped to the reference genome and duplicates were removed. Variants were annotated, filtered, and prioritised. A low-frequency missense variant (c. 1049G>A) in the AGXT gene was considered the candidate variant. This variant replaces the highly conserved glycine amino acid with aspartate (p.Gly350Asp). The variant is destabilising for protein-protein interaction based on predicted change in binding free energy (ΔΔG). All members having disease phenotype were found homozygous to the mutation. Both parents and unaffected individuals in a family are heterozygous for the variant.

CONCLUSION

Identification of pathogenic variant in the AGXT gene, in this family, provides genotype-phenotype correlation and permits accurate clinical diagnosis as well as carrier detection. Moreover, this variant extends the AGXT mutation spectrum in a different population and highlights the clinical significance and diagnostic relevance of the variant.

Expanding the Genetic Spectrum of AGXT Gene Variants in Egyptian Patients with Primary Hyperoxaluria Type I

Introduction: Approximately 80% of primary hyperoxaluria cases are caused by primary hyperoxaluria type 1 (PH1, OMIM# 259900), which is characterized by pathogenic variants in the AGXT gene, resulting in deficiency of the liver-specific enzyme alanine-glyoxylate aminotransferase (AGT). This leads to increased production of oxalate, which cannot be effectively eliminated from the body, resulting in its accumulation primarily in the kidneys and other organs. Subjects and Methods: This study included 17 PH1 Egyptian patients from 12 unrelated families, recruited from the Inherited Kidney Disease Outpatient Clinic and the Dialysis Units, Cairo University Hospitals, during the period from January 2018 to December 2019, aiming to identify the pathogenic variants in the AGXT gene. Results: Six different variants were detected. These included three frameshift and three missense variants, all found in homozygosity within the respective families. The most common variant was c.121G>A;p.(Gly41Arg) detected in four families, followed by c.725dup;p.(Asp243GlyfsTer12) in three families, c.33dup;p.(Lys12Glnfs156) in two families, and c.731T >C;p.(Ile244Thr), c.33delC;p.(Lys12Argfs34), and c.568G>A;p.(Gly190Arg) detected in one family each. Conclusion: Consanguineous Egyptian families with history of renal stones or renal disease suspicious of primary hyperoxaluria should undergo AGXT genetic sequencing, specifically targeting exons 1 and 7, as variants in these two exons account for >75% of disease-causing variants in Egyptian patients with confirmed PH1.

Next-generation sequencing in identification of pathogenic variants in primary hyperoxaluria among 21 Egyptian families: Identification of two novel AGXT gene mutations

Background

Primary hyperoxaluria (PH) is a rare heterogeneous, autosomal recessive disorder of glyoxylate metabolism. It is characterized by excessive hepatic production of oxalate resulting in a wide spectrum of clinical, imaging, and functional presentation. The characteristic features of PH comprise of recurrent urolithiasis, renal stones, and/or nephrocalcinosis. Three known types of PH have been identified PH1, PH2, and PH3. Pathogenic variants in AGXT, GRHPR, and HOGA1 cause the phenotypic expression of PH.

Methods

In this study, we describe the clinical and genetic findings of 22 patients from 21 unrelated Egyptian families with the distinctive clinical features of PH. A thorough clinical evaluation followed by an NGS custom panel of AGXT, GRHPR, and HOGA1 genes was done.

Results

Two novel mutations (p.Gly27Glu and p.Gln256Serfs*17) and six previously reported mutations (p.Lys12Glnfs*156, p.Lys12Argfs*34, p.Ile244Thr, p.Asn22Ser, p.Pro11Leu, and p.Ile340Met) were identified in AGXT gene. The NGS panel results were validated thereafter using Sanger sequencing.

Conclusion

Our results extend the number of AGXT mutations identified so far and emphasize the important role of genetic testing in providing proper counseling and patients management.

Clinical analysis of 13 children with primary hyperoxaluria type 1

A retrospective statistical analysis of primary hyperoxaluria type 1 (PH1) in children from June 2016 to May 2019 was carried out to discover its clinical and molecular biological characteristics. Patients were divided into two groups (infant and noninfant) according to clinic type. There were 13 pediatric patients (male:female = 6:7) with PH1 in the cohort from 11 families (four of which were biological siblings from two families), whose median age of symptom onset was 12 months and median confirmed diagnosis age was 14 months. Infant type (6 patients) was the most common type. The infant type mortality rate (100%) was higher than the noninfant (14.3%) (p = 0.029). The incidence of renal failure in infant patients was 67%, while the noninfant was 14.3%. 8 of 10 patients with nephrocalcinosis (NC) (76.92%, 10/13) were diagnosed by radiological imaging examinations, including X-ray (3 patients), CT (4 patients) and MRI (1 patient). NC was an independent risk factor for renal insufficiency [OR 3.33, 95% CI (0.7-1.2)], p < 0.05). Nine types of AGXT gene mutations were found; 1 type, c.190A > T, were first reported here. The most common AGXT gene mutation was c.679_680del, which occurred in exon 6 (5 patients). The infant type is the most common type of pediatric PH, with a relatively higher ratio of renal failure at symptom onset and poor prognosis. NC is an independent risk factor leading to renal failure, and radiological imaging examination is recommended for patients with abnormal ultrasound examination to identify NC. AGXT gene detection is important for the diagnosis and treatment of PH1 in children.

Pharmacogenetics of advanced lung cancer: Predictive value of functional genetic polymorphism AGXT Pro11Leu in clinical outcome?

INTRODUCTION

AGXT gene codes for the enzyme alanine glyoxylate aminotransferase, which is involved in hepatic peroxisomal metabolism of platinum-based chemotherapeutic agents. The association of genetic variant AGXT rs34116584 on the clinical outcome and response to chemotherapy of patients with non-small cell lung cancer (NSCLC) remains to be established. Our aim was to evaluate the association of functional AGXT gene polymorphism in NSCLC progression, considering as primary and secondary endpoint, progression free survival (PFS) and overall survival (OS), respectively.

METHODS

Genotyping of theAGXT rs34116584 genetic polymorphism was performed by mass spectrometry on 168 DNA samples from patients with NSCLC (stages IIIA-IVB). Univariate survival analysis included the study of Kaplan-Meier curves with the Log-Rank test, while Cox regression was used as a multivariate analysis.

RESULTS

Multivariate analysis showed shorter PFS for T carriers [HR=2.0, 95% CI, 1.4-3.0, p<0.0001] and shorter OS [HR=1.8, 95% CI, 1.1-3.0, p=0.017] globally, as well as in a subgroup of patients (n=144) treated with first line platinum-based chemotherapy [HR=2.0, 95% CI, 1.3-3.1, p=0.001] and [HR=1.8, 95% CI, 1.1-3.1, p=0.026], respectively.

CONCLUSION

This polymorphism seems to have an impact on NSCLC progression, opening new perspectives for its inclusion as a pharmacogenetic predictor of response to platinum-based chemotherapy.

Oxalobacter formigenes treatment combined with intensive dialysis lowers plasma oxalate and halts disease progression in a patient with severe infantile oxalosis

BACKGROUND

Infantile oxalosis, the most devastating form of primary hyperoxaluria type 1 (PH1), often leads to end-stage renal disease (ESRD) during the first weeks to months of life.

CASE-DIAGNOSIS

Here, we report the outcome of the therapeutic use of Oxalobacter formigenes (Oxabact OC5; OxThera AB, Stockholm, Sweden) in a female infant with PH1 who exhibited severely elevated plasma oxalate (Pox) levels, pronounced nephrocalcinosis, anuretic end-stage renal disease, and retinal oxalate deposits. Following the diagnosis of PH1 at an age of 8 weeks, a combined regimen of daily peritoneal dialysis, daily pyridoxine treatment and hemodialysis (3 times a week) was unable to reduce the pronounced hyperoxalemia. After the addition of Oxalobacter formigenes therapy to the otherwise unchanged treatment regimen, Pox levels first stabilized and subsequently declined from 130 μmol/L to around 80 μmol/L. Nephrocalcinosis and retinal deposits stabilized. Oxalobacter formigenes treatment was well-tolerated and no related adverse events were observed. The patient showed nearly age-appropriate growth and development and received successful combined liver-kidney transplantation at the age of two years.

CONCLUSIONS

Treatment with O. formigenes combined with intensive dialysis led to reduction of Pox, stabilization of systemic oxalosis, and improvement in the clinical disease course. O. formigenes treatment may be an option for reduction of oxalosis in infantile patients with insufficient response to conservative treatments until combined liver-kidney transplantation can be performed.

Genetics and genomic medicine in Tunisia

Genetics and genomic medicine in Tunisia.