Evidence of pathogenicity of a mutation in 3' untranslated region causing mild haemophilia A.

INTRODUCTION: Despite the high mutation detection rate, in a small group of haemophilia A patients, using current screening methods, no causal mutation in F8 can be detected. In such cases, the causal mutation might be in the non-coding sequences of F8. AIM: Rarely, mutations in non-coding sequences reveal a pivotal role. Here, we analysed a mild haemophilia A patient harbouring a mutation in the 3' untranslated region (UTR) of F8 and elucidated the molecular mechanism leading to haemophilia phenotype. METHODS: To find the causal mutation, the complete F8 genomic region was analysed by next generation sequencing. The effect of the identified alteration on F8 expression was evaluated in silico and analysed for the splicing effect at mRNA level. Moreover, in vitro studies using a luciferase reporter system were performed to functionally analyse the mutation. RESULTS: We identified an alteration in the 3' UTR (c.*56G>T) as the only change in F8 gene. Pedigree analysis showed a segregation pattern for three affected members for the presumptive mutation. Moreover, the variant was predicted in silico to create a new donor splice site, which was also detected at mRNA level, resulting in a 159 bp deletion in 3' UTR of F8. Finally, the variant showed reduced expression of the gene reporter firefly luciferase in cell line expression analysis. CONCLUSION: Our results advocate the patient specific c.*56G>T base change in the 3' UTR to be a disease-associated mutation leading to alternative splicing explaining the mild haemophilia A phenotype.

Novel characterization of a breakpoint in F8: an individualized approach to gene analysis when PCR and MLPA results contradict.

Haemophilia A is an X-linked bleeding disorder caused by heterogeneous mutations in the F8 gene. Two inversion hotspots in intron 22 and intron 1, as well as point mutations, small insertions and deletions in the F8 gene account for causal mutations leading to severe haemophilia A. Rarely, novel molecular mechanisms lead to a haemophilia A phenotype which cannot be completely characterized by routine molecular diagnostic methods. Here, we characterized the molecular abnormality in a boy with a severe haemophilia A phenotype. On investigation by PCR and DNA sequencing, exon 18 of F8 repeatedly failed to amplify. However, analysis by multiplex ligation-dependent probe amplification demonstrated the presence of exon 18 sequence, suggesting a more complex rearrangement than a single exon deletion. The analysis of exon 18 and its flanking regions by inverse PCR revealed a complex mutation comprising insertions of extragenic sequences from Xq28 along with a partial duplication of exon 18. Based on the successful analysis and characterization of the familial breakpoint, we developed a PCR-based diagnostic approach to detect this defect in family members in whom no diagnostic test could be offered until this time.

Genetic testing in bleeding disorders.

The aim of molecular genetic analysis in families with haemophilia is to identify the causative mutation in an affected male as this provides valuable information for the patient and his relatives. For the patient, mutation identification may highlight inhibitor development risk or discrepancy between different factor VIII assays. For female relatives, knowledge of the familial mutation can facilitate carrier status determination and prenatal diagnosis. Recent advances in understanding mutations responsible for haemophilia and methods for their detection are presented. For reporting of such mutations, participation in external quality assessment ensures that essential patient and mutation details are routinely included and that pertinent information is incorporated in the interpretation.

Maternal methylation imprints on human chromosome 15 are established during or after fertilization.

Prader-Willi syndrome (PWS) is a neurogenetic disorder that results from the lack of transcripts expressed from the paternal copy of the imprinted chromosomal region 15q11-q13 (refs. 1,2). In some patients, this is associated with a deletion of the SNURF-SNRPN exon 1 region inherited from the paternal grandmother and the presence of a maternal imprint on the paternal chromosome. Assuming that imprints are reset in the germ line, we and others have suggested that this region constitutes part of the 15q imprinting center (IC) and is important for the maternal to paternal imprint switch in the male germ line. Here we report that sperm DNA from two males with an IC deletion had a normal paternal methylation pattern along 15q11-q13. Similar findings were made in a mouse model. Our results indicate that the incorrect maternal methylation imprint in IC deletion patients is established de novo after fertilization. Moreover, we found that CpG-rich regions in SNURF-SNRPN and NDN, which in somatic tissues are methylated on the maternal allele, are hypomethylated in unfertilized human oocytes. Our results indicate that the normal maternal methylation imprints in 15q11-q13 also are established during or after fertilization.

Heterozygous large deletions of Factor 8 gene in females identified by multiplex PCR-LC.

Haemophilia A is the most common X-linked recessive bleeding disorder. In 5% of severely affected patients the mutations responsible for the disease are large deletions encompassing from one exon to the complete Factor 8 (F8) gene. Large deletions in a male haemophilic patient are easily detected by the absence of the corresponding PCR product. However, in female carriers, identification of the various heterozygous large deletions is difficult representing a major limitation to accurate carrier diagnosis. The deletion is masked by the presence of the second allele that serves as template for the PCR reaction. Quantitative PCR can differentiate between the presence of one or two alleles. Here we report an assay based on multiplex amplification of several exons of the F8 gene of various length and subsequent quantitative evaluation of the amplicons by liquid chromatogphy (LC). Using this approach we achieved an accurate classification of 16 female carriers and eight non-carriers for deletions in the F8 gene in 19 investigated families. One mother and one grandmother were classified as non-carriers, underlining the high de novo mutation rate of large deletions in female germ cells. The large deletions in three families were confirmed by fluorescent in situ hybridization. In conclusion, the multiplex PCR-LC technique represents a rapid, simple and reliable method for detection of heterozygous large deletions in female carriers.

Familial hydatidiform molar pregnancy: the germline imprinting defect hypothesis?

Imprinting is the uniparental expression of a set of genes. Somatic cells carry two haploid sets of chromosomes, one maternal and one paternal, while germ cells contain only one of the two forms of chromosomes, male or female. This implies that during early embryogenesis the cells committed for developing the future germ cell lineage, the primordial germ cells, which are diploid, have to undergo a total chromosome reprogramming process. This process is delicately controlled during gametogenesis to ensure that males and females have only their respective form of gametes. The machinery involved in this process is yet poorly defined. Familial hydatidiform molar (HM) pregnancy is an abnormal form of pregnancy characterized by hydropic degeneration of placental villi and abnormal, or absence of, embryonic development. To date, the molecular defect causing this condition is unknown. However, in a few studied cases, the presence of paternal methylation patterns on the maternal chromosomes was observed. In this chapter, we summarize what is known about methylation aberrations in HMs and examine more closely the proposed hypothesis of a maternal germline imprinting defect.

Analysis of mRNA in hemophilia A patients with undetectable mutations reveals normal splicing in the factor VIII gene.

BACKGROUND: haemophilia A (HA) is characterized by partial or total deficiency of factor VIII (FVIII) protein activity. It is caused by a broad spectrum of mutations in the FVIII gene. Despite tremendous improvements in mutation screening methods, in about 2% of HA patients no DNA change could be found, even after sequencing the whole coding part of the FVIII gene including the flanking splice sites, as well as the promotor and the 3' UTR regions. OBJECTIVES, PATIENTS AND METHODS: In the present study we performed a detailed RNA analysis of three groups of patients. The first included control patients with known splicing defects, the second included two patients with already identified nucleotide changes close to splicing sites, that could potentially alter the normal splicing process, and a third group of 11 unrelated patients whose genomic DNA have already been screened for mutations by DHPLC and direct sequencing with no mutation being identified. RESULTS: Both candidate splice site mutations were shown to result in either skipping or alternative splicing of at least one exon, therefore these DNA changes must be considered as causal for the patients' HA phenotype. In contrast, no abnormalities on the RNA level were observed in any of 11 unrelated patients without mutations in the FVIII gene. CONCLUSIONS: These findings exclude mutations that could be located deep in the introns and affecting either normal splicing or lead to mechanisms causing some unknown rearrangements of the FVIII gene. In fact, our results point to the presence of still unknown factor(s) causing HA, which might be either allelic or in the close proximity of the FVIII gene or non-allelic associated with other genetic loci that are involved in the processing of the FVIII protein.

F8 genetic analysis strategies when standard approaches fail.

Haemophilia A is a common X-linked recessive disorder caused by mutations in F8 leading to deficiency or dysfunction of coagulant factor VIII (FVIII). Despite tremendous improvements in mutation screening methods, in a small group of patients with FVIII deficiency suffering from haemophilia A, no DNA change can be found. In these patients, analysis reveals no causal mutations even after sequencing the whole coding region of F8 including the flanking splice sites, as well as the promoter and the 3' untranslated region (UTR). After excluding the mutations mimicking the haemophilia A phenotype in interacting partners of the FVIII protein affecting the half life and transport of the protein, mutations or rearrangements in non-coding regions of F8 have to be considered responsible for the haemophilia A phenotype. In this review, we present the experiences with molecular diagnosis of such cases and approaches to be applied for mutation negative patients.

Deep intronic 'mutations' cause hemophilia A: application of next generation sequencing in patients without detectable mutation in F8 cDNA.

BACKGROUND: In a small group of typical hemophilia A (HA) patients no mutations in the F8 coding sequence (cDNA) could be found. In the current study, we performed a systematic screening of genetic and non-genetic parameters associated with reduced FVIII:C levels in a group of mostly mild HA (only one moderate) patients with no detectable mutations in F8 cDNA. METHODS: We determined FVIII and VWF activity and antigen levels and performed VWF-FVIII binding (VWF:FVIIIB) and VWF-collagen binding assays (VWF:CB) as well as VWF multimer analysis. VWF was completely sequenced to exclude mutations. The F8 locus, including the introns, was sequenced using overlapping long-range PCRs (LR-PCRs) combined with a next generation sequencing (NGS) approach. Moreover, the F8 mRNA was analyzed quantitatively and qualitatively by real-time PCR (qRT) and overlapping reverse transcription (RT) PCRs, respectively. RESULTS: All VWF tests were normal. The LR-PCRs demonstrated the integrity of the F8 locus. Eight unique polymorphisms were found in the patients, with two being recurrent. Furthermore, RT-PCRs analysis confirmed that two of the unique variants create detectable new cryptic splice sites in the patients that result in the introduction of intronic DNA sequences into the mRNA and create premature stop codons. CONCLUSION: By systematically excluding all possible causes of HA, we could with great certainty conclude that deep intronic mutations in F8, although rare, cause abnormal mRNA splicing, leading to mild HA.

Identification of a third rearrangement at Xq28 that causes severe hemophilia A as a result of homologous recombination between inverted repeats.

BACKGROUND: Intrachromosomal homologous recombination between inverted repeats on the X chromosome account for about half of severe hemophilia A cases. Repeats in F8 intron 1 and intron 22 can recombine with homologous inverted repeats located about 200 kb upstream and 500 kb downstream of F8, respectively, resulting in partial sequence inversion of the F8 open reading frame and, subsequently, no functional protein production. OBJECTIVES: In the present study, we characterize a third novel homologous recombination at Xq28 consistent with absence of F8 transcription that we previously reported for the affected chromosome of the index patient as well as his mother and sister. RESULTS: The rearrangement occurs between a repeat in F8 intron 1 (Int1R-1) and an inverted identical repeat (Int1R-2d) in intron 2 of a duplicated copy of IKBKG located about 386 kb upstream of F8. The rearrangement was confirmed by Southern blot and inverse PCR and results in failure of PCR amplification across Int1R-1. CONCLUSION: We developed a PCR-based diagnostic method that can be used to screen for this genetic rearrangement in cases of severe hemophilia A for which mutations cannot be identified.

Sequencing of the factor 8(F8) coding regions in 10 Turkish hemophilia A patients reveals three novel pathological mutations, and one rediagnosis of von Willebrand's disease type 2N.

The most common cause for severe cases of hemophilia A is the homologous recombination involving intron 22 and related sequences outside the F8 gene. F8 coding regions of the gene including the exon/intron junctions were sequenced in 10 Turkish hemophilia A patients all of whom have been typed negative for intron 22 inversion and who did not have a detectable change by DGGE analysis. Pathological changes including two novel deletions (c. 205del CT and c. 3699del ACAT), one novel missense mutation (9546A) and two recurrent missense mutations were observed in five patients. The c. 2110C > T is another novel pathological change affecting exonic splicing enhancer site in two patients. One of the remaining three patients had a recurrent vWD type 2N mutation in the F8 binding site of the vWF (C788R). The S1269S polymorphism (c. 3864A > C) detected phenotype. Conclusively, sequencing of the promoter and the coding regions of 10 hemophilia A patients contributes four novel pathological mutations to the F8 mutations list and reveals a rediagnosis of hemophilia A but is still not sufficient to confirm hemophilia A phenotype in two patients.

Inhibitor development in correlation to factor VIII genotypes.

Alloantibodies (inhibitors) against factor VIII (FVIII) develop in 20-30% of patients with severe haemophilia A and render classical FVIII substitution therapy ineffective. Several studies have shown that genetic factors, the type of FVIII gene mutation and immune response genes (e.g. the Major Histocompatibility Complexes), influence the risk of inhibitor formation. In particular, the type of FVIII gene mutation has proven to be a decisive risk factor. Patients with severe molecular gene defects (e.g. large deletions, nonsense mutations, intron-22 inversion) and no endogenous FVIII synthesis have a 7-10 times higher inhibitor prevalence than patients with milder molecular gene defects (e.g. missense mutations, small deletions, splice site mutations). To date, at least 10 distinct classes of mutations have been shown which have differing risks of associated inhibitor formation. A challenging observation in inhibitor patients is the heterogeneity of the antibody epitopes with respect to their number and their specificity. At least five epitopes in the FVIII molecule have been identified that constitute the targets for antibodies in most inhibitor patients. These epitopes are located in the ar3 region and the A2, A3, C1, C2 domains which correspond to the functional binding sites of the ligands of the FVIII protein. At present, the determinants of the characteristics of these epitopes and the subsequent inhibitor titre are unknown. A relationship of the mutation site and the epitope localization has been shown for some individual patients with mild haemophilia A. However, in severely affected haemophilia A patients, the influence of patient genetics on inhibitor titre and epitope specificity has yet to be elucidated.

Intron 22 inversions in the Turkish haemophilia A patients: prevalence and haplotype analysis.

In about half of the severe haemophilia A cases, the disease is caused by an inversion that split the F.VIII gene into two parts separated by approximately 300-400 kb. Herein, we show that in the Turkish population this inversion mutation accounts for 29% of 141 haemophilia A cases and 42% of severe cases. Most of the inversions are of the distal type (72%) whereas nine were of the proximal type (28%). Haplotype analysis using 4 markers in the F.VIII gene did not reveal a single haplotype associated with the inversion. However, the pre- valence of one haplotype: HindIII (-) - Int13 (CA)20 - Int22 (CA + CT)26 - XbaI (-) is higher in the inversion patients. Since founder effect is excluded for the inversion patients, our results suggest that some as yet unknown factor(s) may make these alleles more prone for the inversion. However, a bias due to the low number of studied cases cannot be excluded.

Intron 22-specific long PCR for the Xba I polymorphism in the factor VIII gene.

The Xba I polymorphic site in the factor VIII gene is present in the int22h-1 region which is found in two other copies (int22h-2 and int22h-3) distal to the gene. Previously the polymorphic status of the Xba I locus was studied by either Southern blot or PCR that amplified all three copies. Here we report the use of a long PCR that specifically amplifies the intragenic site in intron 22, making use of this marker an easy and reliable assay. Moreover, about 25% of previously uninformative Turkish haemophilia A families examined with three markers proved to be informative for linkage analysis, using the Xba I polymorphism.

Analysis of the two microsatellite repeat polymorphisms of the factor VIII gene in the Turkish population.

DNA-based diagnosis of haemophilia A has previously been carried out by linkage analysis using two highly informative markers, Hind III RFLP and St14 VNTR, for affected Turkish families. In the present study the number and frequency of the microsatellite alleles at introns 13 and 22 in the factor VIII (FVIII) gene were analysed in order to increase the rate of informative females and accuracy of linkage analysis. Six alleles were observed at both loci. The two most frequent alleles of each locus were the same as the two common alleles found in Anglo-Americans. The comparison of heterozygosity of both microsatellite loci showed that the Turkish population is slightly less polymorphic than Anglo-Americans but more polymorphic than Chinese, Slavs and Uzbekians. The additional use of the two microsatellite repeat polymorphisms with the previously established informative markers has been accepted as the most effective strategy in DNA diagnosis by linkage analysis for the assessment of haemophilia A carriers and affected fetuses in the Turkish population. The modifications adopted in this study for the multiplex PCR analysis of the microsatellite repeat polymorphism eliminated the use of radioactivity and sequencing gels, reducing cost and labour.

Methylation profiles of DXPas34 during the onset of X-inactivation.

X chromosome inactivation is controlled by the cis-acting X-inactivation centre (Xic). In addition to initiating inactivation, Xic, which includes the XIST: gene, is involved in both a counting process that senses the number of X chromosomes and the choice of X chromosome to inactivate. Controlling elements lying 3' to XIST: include the DXPas34 locus. Deletion of DXPas34 in undifferentiated embryonic stem (ES) cells eliminates expression of both XIST: and the antisense transcript TSIX:, thought to initiate from a CpG island lying close to, but telomeric to, the DXPas34 locus itself. Deletion of DXPas34 leads to non-random inactivation on ES cell differentiation and disrupts imprinted X-inactivation in vivo. In order to investigate the role of methylation at DXPas34 in the initial steps of X-inactivation, we studied its methylation status during pre- and post-implantation embryonic development and ES cell differentiation, using the bisulphite sequencing technique. Analysis of the methylation status of both the DXPas34 locus and the associated downstream CpG island shows that extensive hypermethylation of the DXPas34 locus is a relatively late event in differentiation and embryogenesis. We conclude that methylation of DXPas34 cannot be the X chromosome imprint, nor can it be involved in the parent-of-origin effects associated with deletion of the DXPas34 locus and the neighbouring CpG island.

Bisulfite-based methylation analysis of imprinted genes.

Genomic imprinting is an epigenetically controlled form of gene regulation leading to the preferential expression of one parental gene copy. To date, approximately 40 imprinted genes have been described that are exclusively or predominantly expressed from either the paternal or the maternal allele (www.mgu.har.mrc.ac.uk/imprinting/implink.html). Changes in the imprinted expression of such genes result in developmental abnormalities; in the human they are associated with several diseases and various types of cancer (1-3).

De novo factor VIII gene intron 22 inversion in a female carrier presents as a somatic mosaicism.

The intron 22 inversion represents the most prevalent factor VIII gene defect in severe hemophilia A, accounting for about 40% of all mutations. It is hypothesized that the inversion mutations occur almost exclusively in germ cells during meiotic cell division by intrachromosomal recombination between 1 of 2 telomeric copies of the Int22h region and its intragenic homologue. The majority of inversion mutations originate in male germ cells, where the lack of bivalent formation may facilitate flipping of the telomeric end of the single X chromosome. This is the first intron 22 inversion that presents as a somatic mosaicism in a female, affecting only about 50% of lymphocyte and fibroblast cells of the proposita. Supposing a post-zygotic de novo mutation as the usual cause of somatic mosaicism, the finding would imply that the intron 22 inversion mutation is not restricted to meiotic cell divisions but can also occur during mitotic cell divisions, either in germ cell precursors or in somatic cells. (Blood. 2000;96:2905-2906)

Sequence conservation and variability of imprinting in the Beckwith-Wiedemann syndrome gene cluster in human and mouse.

In human and mouse most imprinted genes are arranged in chromosomal clusters. This linked organization suggests coordinated mechanisms controlling imprinted expression. We have sequenced 250 kb in the centre of the mouse imprinting cluster on distal chromosome 7 and compared it with the orthologous Beckwith-Wiedemann gene cluster on human chromosome 11p15.5. This first comparative imprinting cluster analysis revealed a high structural and functional conservation of the six orthologous genes identified. However, several striking differences were also discovered. First, compared with the mouse the human sequence is approximately 40% longer, mostly due to insertions of two large repetitive clusters. One of these clusters encompasses an additional gene coding for a homologue of the ribosomal protein L26. Second, pronounced blocks of unique direct repeats characteristic of imprinted genes were only found in the human sequence. Third, two of the orthologous gene pairs Tssc4/TSSC4 and Ltrpc5/LTRPC5 showed apparent differences in imprinting between human and mouse, whereas others like Tssc6/TSSC6 were not imprinted in either organism. Together these results suggest a significant functional and structural variability in the centre of the imprinting cluster. Some genes escape imprinting in both organisms whereas others exhibit tissue- and species-specific imprinting. Hence the control of imprinting in the cluster appears to be a highly dynamic process under fast evolutionary adaptation. Intriguingly, whereas imprinted genes within the cluster contain CpG islands the non-imprinted Ltrpc5 and Tssc6/TSSC6 do not. This and additional comparisons with other imprinted and non-imprinted regions suggest that CpG islands are key features of imprinted domains.