Diversity of theCYP21P-Like Gene inCYP21Deficiency

Ehlers-Danlos Syndromes, Joint Hypermobility and Hypermobility Spectrum Disorders

Ehlers-Danlos syndrome is an umbrella term for a clinically and genetically heterogeneous group of hereditary soft connective tissue disorders mainly featuring abnormal cutaneous texture (doughy/velvety, soft, thin, and/or variably hyperextensible skin), easy bruising, and joint hypermobility. Currently, musculoskeletal manifestations related to joint hypermobility are perceived as the most prevalent determinants of the quality of life of affected individuals. The 2017 International Classification of Ehlers-Danlos syndromes and related disorders identifies 13 clinical types due to deleterious variants in 19 different genes. Recent publications point out the possibility of a wider spectrum of conditions that may be considered members of the Ehlers-Danlos syndrome community. Most Ehlers-Danlos syndromes are due to inherited abnormalities affecting the biogenesis of fibrillar collagens and other components of the extracellular matrix. The introduction of next-generation sequencing technologies in the diagnostic setting fastened patients' classification and improved our knowledge on the phenotypic variability of many Ehlers-Danlos syndromes. This is impacting significantly patients' management and family counseling. At the same time, most individuals presenting with joint hypermobility and associated musculoskeletal manifestations still remain without a firm diagnosis, due to a too vague clinical presentation and/or the lack of an identifiable molecular biomarker. These individuals are currently defined with the term "hypermobility spectrum disorders". Hence, in parallel with a continuous update of the International Classification of Ehlers-Danlos syndromes, the scientific community is investing efforts in offering a more efficient framework for classifying and, hopefully, managing individuals with joint hypermobility.

Domestication Effects on Stress Induced Steroid Secretion and Adrenal Gene Expression in Chickens

Understanding the genetic basis of phenotypic diversity is a challenge in contemporary biology. Domestication provides a model for unravelling aspects of the genetic basis of stress sensitivity. The ancestral Red Junglefowl (RJF) exhibits greater fear-related behaviour and a more pronounced HPA-axis reactivity than its domesticated counterpart, the White Leghorn (WL). By comparing hormones (plasmatic) and adrenal global gene transcription profiles between WL and RJF in response to an acute stress event, we investigated the molecular basis for the altered physiological stress responsiveness in domesticated chickens. Basal levels of pregnenolone and dehydroepiandrosterone as well as corticosterone response were lower in WL. Microarray analysis of gene expression in adrenal glands showed a significant breed effect in a large number of transcripts with over-representation of genes in the channel activity pathway. The expression of the best-known steroidogenesis genes were similar across the breeds used. Transcription levels of acute stress response genes such as StAR, CH25 and POMC were upregulated in response to acute stress. Dampened HPA reactivity in domesticated chickens was associated with changes in the expression of several genes that presents potentially minor regulatory effects rather than by means of change in expression of critical steroidogenic genes in the adrenal.

Molecular analysis of the CYP21A2 gene in Chinese patients with steroid 21-hydroxylase deficiency

OBJECTIVE

21-Hydroxylase deficiency (21-OHD) is the most common cause of congenital adrenal hyperplasia (CAH), a family of autosomal recessive disorders involving impaired cortisol synthesis. This study aimed to design a reliable and rational approach for identifying mutations in the CYP21A2 gene and to characterize the molecular basis of 21-OHD in 30 Chinese patients.

DESIGN AND METHODS

Copy number variations were investigated by multiplex ligation-dependent probe amplification (MLPA). Locus-specific polymerase chain reaction (PCR)/restriction endonuclease analysis was then used to verify CYP21A2 rearrangement products and prevent allele dropout. Direct sequencing of rearrangement products was performed to further refine recombination breakpoint locations. Direct sequencing of the entire CYP21A2 gene was used to detect microconversions.

RESULTS

We successfully characterized 60 CYP21A2 alleles from 30 patients with genetic defects. The most common one was intron 2 splice mutation (38.3%). Eighteen alleles with large gene deletions/conversions were identified, which accounted for nearly one-third (30.0%) of the genetic defects. Among these, three types of CYP21A1P/CYP21A2 chimeric genes (CH-1, CH-2, and CH-4) were characterized. Two novel CYP21A2 rearrangement genes were revealed and further demonstrated to be located downstream of the TNXB gene.

CONCLUSIONS

Our results indicate that the stepwise diagnostic procedure involving MLPA analysis, locus-specific PCR/restriction endonuclease analysis, and direct DNA sequencing can provide detailed genetic information about Chinese 21-OHD patients, which is helpful for characterizing structural rearrangements of CYP21A2.

Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

The human RCCX is a common multiallelic copy number variation locus whose number of segments varies between one and four in a chromosome. The monomodular form normally comprises four functional genes, but in duplicated RCCX segments generally only the gene-encoding complement component C4 produces a protein. C4 genes can code either for a C4A or a C4B isotype protein and exhibit dichotomous size variation. Distinct RCCX variants show association with numerous diseases; however, identification of the basis of these associations is often challenging, not least because the RCCX is localized in the major histocompatibility complex (MHC) region, a genomic area characterized by exceedingly long-range linkage disequilibrium. Here we present a detailed analysis on RCCX variants and their relationship with so-called 'ancestral' or 'conserved extended' MHC haplotypes in healthy Caucasians. In addition to former investigations, precise order and size of all C4A and C4B genes were determined even in trimodular RCCX structures. Considering C4 copy numbers, length, isotype specificity and CYP21A2 copy numbers, we have identified 15 distinct RCCX variants and described the RCCX structures involved in 29 repeatedly occurring MHC haplotypes. The findings should become a useful tool for future RCCX- and MHC-related disease association studies.

Analysis of the CYP21A1P pseudogene: indication of mutational diversity and CYP21A2-like and duplicated CYP21A2 genes

The CYP21A1P gene downstream of the XA gene, carrying 15 deteriorated mutations, is a nonfunctional pseudogene that shares 98% nucleotide sequence homology with CYP21A2 located on chromosome 6p21.3. However, these mutations in the CYP21A1P gene are not totally involved in each individual. From our analysis of 100 healthy ethnic Chinese (i.e., Taiwanese) (n=200 chromosomes) using the polymerase chain reaction (PCR) products combined with an amplification-created restriction site (ACRS) method and DNA sequencing, we found that approximately 10% of CYP21A1P alleles (n=195 chromosomes) presented the CYP21A2 sequence; frequencies of P30, V281, Q318, and R356 in that locus were approximately 24%, 21%, 11%, and 34%, respectively, and approximately 90% of the CYP21A1P alleles had 15 mutated loci. In addition, approximately 2.5% (n=5 chromosomes) showed four haplotypes of the 3.7-kb TaqI-produced fragment of the CYP21A2-like gene and one duplicated CYP21A2 gene. We conclude that the pseudogene of the CYP21A1P mutation presents diverse variants. Moreover, the existence of the CYP21A2-like gene is more abundant than that of the duplicated CYP21A2 gene downstream of the XA gene and could not be distinguished from the CYP21A2-TNXB gene; thus, it may be misdiagnosed by previously established methods for congenital adrenal hyperplasia caused by a 21-hydroxylase deficiency.

Novel deletion alleles carrying CYP21A1P/A2 chimeric genes in Brazilian patients with 21-hydroxylase deficiency

BACKGROUND

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency is caused by deletions, large gene conversions or mutations in CYP21A2 gene. The human gene is located at 6p21.3 within a locus containing the genes for putative serine/threonine Kinase RP, complement C4, steroid 21-hydroxylase CYP21 tenascin TNX, normally, in a duplicated cluster known as RCCX module. The CYP21 extra copy is a pseudogene (CYP21A1P). In Brazil, 30-kb deletion forming monomodular alleles that carry chimeric CYP21A1P/A2 genes corresponds to ~9% of disease-causing alleles. Such alleles are considered to result from unequal crossovers within the bimodular C4/CYP21 locus. Depending on the localization of recombination breakpoint, different alleles can be generated conferring the locus high degree of allelic variability. The purpose of the study was to investigate the variability of deleted alleles in patients with 21-hydroxylase deficiency.

METHODS

We used different techniques to investigate the variability of 30-kb deletion alleles in patients with 21-hydroxylase deficiency. Alleles were first selected after Southern blotting. The composition of CYP21A1P/A2 chimeric genes was investigated by ASO-PCR and MLPA analyses followed by sequencing to refine the location of recombination breakpoints. Twenty patients carrying at least one allele with C4/CYP21 30-kb deletion were included in the study.

RESULTS

An allele carrying a CYP21A1P/A2 chimeric gene was found unusually associated to a C4B/C4A Taq I 6.4-kb fragment, generally associated to C4B and CYP21A1P deletions. A novel haplotype bearing both p.P34L and p.H62L, novel and rare mutations, respectively, was identified in exon 1, however p.P30L, the most frequent pseudogene-derived mutation in this exon, was absent. Four unrelated patients showed this haplotype. Absence of p.P34L in CYP21A1P of normal controls indicated that it is not derived from pseudogene. In addition, the combination of different approaches revealed nine haplotypes for deleted 21-hydroxylase deficiency alleles.

CONCLUSIONS

This study demonstrated high allelic variability for 30-kb deletion in patients with 21-hydroxylase deficiency indicating that a founder effect might be improbable for most monomodular alleles carrying CYP21A1P/A2 chimeric genes in Brazil.

Comparing the Southern blot method and polymerase chain reaction product analysis for chimeric RCCX detection in CYP21A2 deficiency

The 3.2-kb TaqI-produced fragment of the CYP21A1P pseudogene and the 3.7-kb TaqI-produced fragment of the functional CYP21A2 gene exist on chromosome 6p21.3. We used the polymerase chain reaction (PCR) product and Southern blot method with TaqI endonuclease digestion to identify a chimeric RCCX module in two unrelated patients with congenital adrenal hyperplasia (CAH). After TaqI cleavage, the PCR product analysis revealed that patient 1 with the chimeric CYP21A1P/CYP21A2 gene in one allele and IVS2-12A/C>G in combination with the 707-714del mutation in the other allele produced a configuration of 3.2- and 2.4-kb fragments. Patient 2, who carried IVS2-12A/C>G in combination with the 707-714del mutation in one allele and the chimeric TNXA/TNXB gene in the other allele, presented with 3.2- and 2.3-kb fragments. However, Southern blot analysis showed that patients 1 and 2 produced 3.2-, 2.4-, and 2.5-kb fragments. We conclude that the chimeric CYP21A1P/CYP21A2 gene, IVS2-12A/C>G in combination with the 707-714del mutation, and the chimeric TNXA/TNXB gene cannot be distinguished by the Southern blot method. Conversely, the chimeric TNXA/TNXB gene was identified in the PCR product analysis due to the appearance of the 2.37-kb fragment, which indicates the occurrence of the chimeric TNXA/TNXB formation extending to the boundary of TNXA in the RCCX region.

21-hydroxylase genotyping in Australasian patients with congenital adrenal hyperplasia

Mutations in CYP21 (21-hydroxylase) lead to congenital adrenal hyperplasia (CAH). We genotyped 26 probands with CAH by PCR-sequencing the entire CYP21 gene. 25/26 had homozygous or compound heterozygous mutations. The frequencies of mutations were similar to other populations with deletion/hybrid, I2 G splice and I172N the most common. Five patients with a I172N allele predicting simple-virilising CAH had a salt-wasting phenotype. Two other probands also had a more severe phenotype than predicted by genotype. Two families had both non-classic and salt-wasting phenotypes arising from combinations of three deleterious alleles. Two novel CYP21 alleles were detected: D106N and a large deletion encompassing CYP21 and adjacent pseudogene. Two rare CYP21 alleles were also found. Three of these four novel/rare alleles were only detected as a result of sequencing the entire CYP21 gene. Entire CYP21 sequencing will increase the number of mutations detected in CAH, and in combination with functional studies should contribute a greater understanding of phenotype-genotype correlations.

Diversity of the CYP21A2 gene: a 6.2-kb TaqI fragment and a 3.2-kb TaqI fragment mistaken as CYP21A1P

The 3.7- and 3.2-kb fragments produced by TaqI digestion are respective crucial markers of the CYP21A2 and CYP21A1P genes for the analysis of the RCCX module in chromosome 6p21.3. Herein, we report two distinct CYP21A2 haplotypes. One occurred in a CAH patient with a 6.2-kb TaqI fragment caused by a mutation at the TaqI site (TCGA) located downstream of the CYP21A2 gene, and the other was a parent in a suspected CAH family with a 3.2-kb TaqI fragment resulting from a 156-bp fragment conversion of the CYP21P promoter sequence which led to the production of a TaqI site at nt -209 and two additional CYP21A1P nucleotides at nt -198 (C>T) and -188/-189 (T insertion). From further sequencing analysis, the promoter region of the 3.2-kb allele showed four normal transcriptional sequences positioned at nt -126C, -113G, -110T, and -103A. However, other nucleotides such as at nt -294T, -293A, and -282A were unchanged. We concluded that the 6.2-kb TaqI fragments of the CYP21A2 haplotype may lead to an incorrect result in the analysis between CYP21A2 and CYP21A1P. The formation of the 3.2-kb TaqI fragment allele which can be mistaken for the CYP21A1P gene may be caused by small-scale conversions of the CYP21A1P gene located between nt -126C and -282A. Therefore, the CYP21A2 haplotype not only presents a 3.7-kb TaqI fragment but also may possibly exist in multiple forms including both 6.2- and 3.2-kb fragments.

Identification of the size and antigenic determinants of the human C4 gene by a polymerase chain-reaction-based amplification method

The human C4 complement components of the C4 locus are encoded by two genes, C4A and C4B, located on chromosome 6p21.3 of the major histocompatibility complex of the human leukocyte antigen class III region. The size difference between the two genes is due to the presence of HERV-K (C4), an endogenous retroviral sequence (6.7 kb long), in intron 9 of the long C4 gene. Whether the C4 is the long (L) or short (S) gene was determined by the Southern blot method, and the antigenic determinants in residues 1,054-1,106 of Rodgers and Chido were generally identified by immunoblot analysis. Herein, we explore a polymerase chain reaction (PCR) amplification method for directly determining the size of C4 loci adjacent to the respective RP1 and RP2 genes and antigenic determinants by DNA sequencing. From the results of this study, we concluded that all of the C4 genes adjacent to the RP1 gene presented the long gene. In addition, 47% of the C4 genes adjacent to the RP2 gene were the short gene and 53% were the long gene. This result was consistent with that of the Southern blot analysis. The PCR method is practical for identifying the C4 genotype and can be used to detect other polymorphisms among variants of C4 genes.