CAH-X Syndrome: Genetic and Clinical Profile

Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia

Congenital Adrenal Hyperplasia (CAH), one of the most common inherited disorders, is caused by defects in adrenal steroidogenesis. It is potentially lethal if untreated and is associated with multiple comorbidities, including fertility issues, obesity, insulin resistance, and dyslipidemia. CAH can result from variants in multiple genes, but the most frequent cause is deletions and conversions in the segmentally duplicated RCCX module, which contains the CYP21A2 gene and a pseudogene. The molecular genetic test to identify pathogenic alleles is cumbersome, incomplete, and available from a limited number of laboratories. It requires testing parents for accurate interpretation, leading to healthcare inequity. Less severe forms are frequently misdiagnosed, and phenotype/genotype correlations incompletely understood. We explored whether emerging technologies could be leveraged to identify all pathogenic alleles of CAH, including phasing in proband-only cases. We targeted long-read sequencing outputs that would be practical in a clinical laboratory setting. Both HiFi-based and nanopore-based whole-genome long-read sequencing datasets could be mined to accurately identify pathogenic single-nucleotide variants, full gene deletions, fusions creating non-functional hybrids between the gene and pseudogene ("30-kb deletion"), as well as count the number of RCCX modules and phase the resulting multimodular haplotypes. On the Hi-Fi data set of 6 samples, the PacBio Paraphase tool was able to distinguish nine different mono-, bi-, and tri-modular haplotypes, as well as the 30-kb and whole gene deletions. To do the same on the ONT-Nanopore dataset, we designed a tool, Parakit, which creates an enriched local pangenome to represent known haplotype assemblies and map ClinVar pathogenic variants and fusions onto them. With few labels in the region, optical genome mapping was not able to reliably resolve module counts or fusions, although designing a tool to mine the dataset specifically for this region may allow doing so in the future. Both sequencing techniques yielded congruent results, matching clinically identified variants, and offered additional information above the clinical test, including phasing, count of RCCX modules, and status of the other module genes, all of which may be of clinical relevance. Thus long-read sequencing could be used to identify variants causing multiple forms of CAH in a single test.

Genetics in Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency and Clinical Implications

Of all congenital adrenal hyperplasia (CAH), 95% to 99% is 21-hydroxylase deficiency (21OHD), an autosomal recessive disease. 21OHD is due to an insufficiency of 21-hydroxylase enzyme, which is encoded by the CYP21A2 gene and involved in cortisol and aldosterone production. The clinical presentation differs widely from severe classic to mild nonclassic CAH. 21OHD represents one of the most complex and at the same time intriguing topics in human genetics and its molecular diagnosis involves ongoing challenges. To provide a meticulous presentation of the topic, we searched the past and present literature, including original articles and reviews from PubMed, ScienceDirect, Web of Science, Embase, and Scopus, using search terms for genetics of 21OHD, 21OHD variants, molecular diagnosis of 21OHD, and 21OHD genetic testing. We offer a comprehensive review focusing on recent developments, new concepts, and conclusions.

Bone Densitometry Parameters in Females with Ehlers-Danlos Syndrome-Does the Hypermobile Subtype Increase the Risk of Low Bone Mass in Patients with Ehlers-Danlos Syndrome?

Background: The purpose of this study was to assess bone densitometry parameters in patients with classical and hypermobile Ehlers-Danlos syndrome (EDS) and to determine whether the hypermobile subtype increases the risk of low bone mass, which is particularly important in this patient group, since the genetic mutation responsible for this subtype is still unknown. Material and Methods: In order to conduct this study, we collaborated with the EDS society in Poland. A total of 30 females of reproductive age who were included in the study were divided into two groups: Group 1-those with classical EDS (n = 9) and Group 2-those with hypermobile EDS (n = 21). Routine laboratory test results, bone turnover markers, and densitometry parameters were evaluated and compared. Results: The study groups showed no differences in terms of densitometry parameters or markers of calcium-phosphate metabolism. A multivariate logistic analysis demonstrated no increase in the risk of low bone mass (defined as a Z-score lower than -2) in patients with hypermobile EDS (OR 0.067 [95% Cl 0.0-20.927]; p = 0.356). Conclusions: The hypermobile subtype of EDS does not increase the risk of low bone mass; there were no significant differences between patients with hypermobile EDS and those with classical EDS in terms of either densitometry parameters or markers of calcium-phosphate metabolism. Although patients with hypermobile EDS are not at a higher risk of developing low bone mineral density, they should be regularly monitored for any calcium and phosphate metabolism abnormalities.

Long-Read Sequencing Solves Complex Structure of CYP21A2 in a Large 21-Hydroxylase Deficiency Cohort

CONTEXT

Genetic testing for 21-hydroxylase deficiency (21-OHD) is always challenging. The current approaches of short-read sequencing and multiplex ligation-dependent probe amplification (MLPA) are insufficient for the detection of chimeric genes or complicated variants from multiple copies. Recently developed long-read sequencing (LRS) can solve this problem.

OBJECTIVE

To investigate the clinical utility of LRS in precision diagnosis of 21-OHD.

METHODS

In the cohort of 832 patients with 21-OHD, the current approaches provided the precise molecular diagnosis for 81.7% (680/832) of cases. LRS was performed to solve the remaining 144 cases with complex chimeric variants and 8 cases with variants from multiple copies. Clinical manifestations in patients with continuous deletions of CYP21A2 extending to TNXB (namely CAH-X) were further evaluated.

RESULTS

Using LRS in combination with previous genetic test results, a total of 16.9% (281/1664) CYP21A1P/CYP21A2 or TNXA/TNXB chimeric alleles were identified in 832 patients, with CYP21A1P/CYP21A2 accounting for 10.4% and TNXA/TNXB for 6.5%. The top 3 common chimeras were CYP21 CH-1, TNX CH-1, and TNX CH-2, accounting for 77.2% (217/281) of all chimeric alleles. The 8 patients with variants on multiple copies of CYP21A2 were accurately identified with LRS. The prevalence of CAH-X in our cohort was 12.1%, and a high frequency of connective tissue-related symptoms was observed in CAH-X patients.

CONCLUSION

LRS can detect all types of CYP21A2 variants, including complex chimeras and pathogenic variants on multiple copies in patients with 21-OHD, which could be utilized as a first-tier routine test for the precision diagnosis and categorization of congenital adrenal hyperplasia.

Congenital Adrenal Hyperplasia

We describe congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency, which is the most common primary adrenal insufficiency in children and adolescents. In this comprehensive review of CAH, we describe presentations at different life stages depending on disease severity. CAH is characterized by androgen excess secondary to impaired steroidogenesis in the adrenal glands. Diagnosis of CAH is most common during infancy with elevated 17-hydroxyprogesterone levels on the newborn screen in the United States. However, CAH can also present in childhood, with late-onset symptoms such as premature adrenarche, growth acceleration, hirsutism, and irregular menses. The growing child with CAH is treated with hydrocortisone for glucocorticoid replacement, along with increased stress doses for acute illness, trauma, and procedures. Mineralocorticoid and salt replacement may also be necessary. Although 21-hydroxylase deficiency is the most common type of CAH, there are other rare types, such as 11β-hydroxylase and 3β-hydroxysteroid dehydrogenase deficiency. In addition, classic CAH is associated with long-term comorbidities, including cardiometabolic risk factors, impaired cognitive function, adrenal rest tumors, and bone health effects. Overall, early identification and treatment of CAH is important for the pediatric patient.

Genetic Characterization of a Cohort of Italian Patients with Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency

INTRODUCTION

Defects in the steroid 21-hydroxylase gene (CYP21A2) cause 21-hydroxylase deficiency (21OHD), the main cause of congenital adrenal hyperplasia (CAH). The disease shows a broad spectrum of clinical forms, ranging from severe or classical (salt wasting, SW, and simple virilizing, SV), to mild late onset or nonclassical (NC). 21OHD affects 1 in 15,000 in its severe classic form and 1 in 200-1000 in its mild NC form. There are many studies reporting the frequency of CYP21A2 pathogenic variants in different populations; however, few of them provide comprehensive information about Italian patients. Here, we present genetic results from a cohort of 245 unrelated Italian individuals with clinical diagnosis of CAH due to 21OHD.

METHODS

A specific polymerase chain reaction (PCR) protocol combined with Sanger sequencing was used for CYP21A2 analysis. The multiplex ligation-dependent probe amplification (MLPA) assay was employed for copy number variation (CNV) determination.

RESULTS

One hundred fourteen (46.5%) of the index cases had the NC form, 57 (23.3%) had the SV form, and 74 (30.2%) presented the SW form of the disease. The most prevalent variant found in NC patients was the p.Val282Leu (51.3%), while the most frequent variants in the classical form were p.Ile173Asn (8.6%) and c.293-13C>G (26.0%). In our study, the frequency of large rearrangements was 15.3%, with CAH-X alleles representing 40% of all DEL/CONV. In addition, 12 alleles carried rare variants, and 1 had a novel variant p.(Arg342Gln). We observed phenotype-genotype correlation in 94.7% of cases. A complete concordance was observed in Groups 0 (enzyme activity completely impaired) where all patients had the SW form as expected. In Group A (0-1% residual enzyme activity), 78.4% of patients had the anticipated SW form while 21.6% were diagnosed with the SV form. Within Group B (~ 2% residual enzyme activity), 93.4% of patients exhibited SV form and 6.5% SW disease. Finally, 92.6% and 7.4% of patients belonging to Group C (enzyme partially impaired to ~ 20-60% residual activity) exhibited NC and SV phenotypes, respectively.

CONCLUSION

This work, representing a comprehensive genetic study, expanded the CYP21A2 variants spectrum of Italian patients with 21OHD and could be helpful in prenatal diagnosis and genetic counseling.

Long-Term Outcomes of Congenital Adrenal Hyperplasia

A plethora of negative long-term outcomes have been associated with congenital adrenal hyperplasia (CAH). The causes are multiple and involve supra-physiological gluco- and mineralocorticoid replacement, excess adrenal androgens both intrauterine and postnatal, elevated steroid precursor and adrenocorticotropic hormone levels, living with a congenital condition as well as the proximity of the cytochrome P450 family 21 subfamily A member 2 (CYP21A2) gene to other genes. This review aims to discuss the different long-term outcomes of CAH.