Functional disomies of the X chromosome influence the cell selection and hence the X inactivation pattern in females with balanced X-autosome translocations: A review of 122 cases

We reviewed 122 cases of balanced X-autosome translocations in females, with respect to the X inactivation pattern, the position of the X break point and the resulting phenotype. In 77% of the patients the translocated X chromosome was early replicating in all cells analysed. The break points in these cases were distributed all along the X chromosome. Most of these patients were either phenotypically normal or had gonadal dysgenesis, some had single gene disorders, and less than 9% had multiple congenital anomalies and/or mental retardation. In the remaining 23% of the cases the translocated X chromosome was late replicating in a proportion of cells. In these cells only one of the translocation products was reported to replicate late, while the remaining portion of the X chromosome showed the same replication pattern as the homologous part of the active, structurally normal X chromosome. The analysis of DNA methylation in one of these cases confirmed noninactivation of the translocated segment. Consequently, these cells were functionally disomic for a part of the X chromosome. The presence of disomic cells was highly prevalent in translocations with break points at Xp22 and Xq28, even though spreading of X inactivation onto the adjacent autosomal segment was noted in most of these cases. This suggests that selection against cells with a late replicating translocated X is driven predominantly by a functional disomy X, and that the efficiency of this process depends primarily on the position of the X break point, and hence the size of the noninactivated region. Since the persistence of cells with a late replicating translocated X was usually associated with mental retardation and other abnormalities, it is concluded that the outcome of the selection process against the functional disomy X is the major determinant of the clinical status in most patients with balanced X-autosome translocations.     

Mental retardation in association with a balanced X-autosome translocation and random inactivation of the X chromosomes

A woman whose karyotype shows an apparently balanced reciprocal translocation, 46,X, t(Xq +; 10q —) is described. She is profoundly mentally retarded and shows minor physical abnormalities with normal sexual development. There is a random pattern of late replication of the normal X and the X involved in the translocation, whereas in most balanced X-autosome translocations there is preferential inactivation of the normal X.     

X chromosome inactivation and the diagnosis of X linked disease in females.

In studies of female patients with suspected deficiency of the E1 alpha subunit of the pyruvate dehydrogenase complex, we have found that X inactivation ratios of 80:20 or greater occur at sufficient frequency in cultured fibroblasts to make exclusion of the diagnosis impossible in about 25% of cases. Pyruvate dehydrogenase E1 alpha subunit deficiency is an X linked inborn error of metabolism which is well defined biochemically and is unusual in that most heterozygous females manifest the condition. The diagnosis is usually established by measurement of enzyme activity and the level of immunoreactive protein and these analyses are most commonly performed on cultured fibroblasts from the patients. Skewed patterns of X chromosome inactivation make it impossible to exclude the diagnosis if the normal X chromosome is expressed in the majority of cells. While most of the observed variation appears to be the expected consequence of random X inactivation, it may be further exaggerated by sampling and subsequent expansion of the cells for analysis.     

Autism spectrum disorder in females with ARHGEF9 alterations and a random pattern of X chromosome inactivation

Proper function of GABAergic synapses depends upon the postsynaptic compartment anchoring of neurotransmitter receptors to the membrane by gephyrin and collybistin (Cb). In humans, Cb is encoded by ARHGEF9 on Xq11.1. ARHGEF9 alterations, some inherited from unaffected mothers, have been reported in males with autism, seizures and severe neurodevelopmental abnormalities. In females, a spectrum of mild to moderate phenotype has been detected. We report two unrelated females with autism and mild intellectual disability. High resolution X-chromosome microarray analysis revealed de novo intragenic deletions in ARHGEF9 of 24?kb and 56?kb involving exons 5–8 and exons 3–8 and leading to truncated forms of collybistin. Peripheral blood samples revealed random X-chromosome inactivation in both patients. To explain phenotypic variability in female patients, we propose a model for disruption of collybistin and various irregular interactions in post-synaptic neurons based on X inactivation patterns. Our findings highlight the importance of ARHGEF9 integrity and suggest further research on its correlation with autism and neurobehavioral problems.     

X chromosome inactivation pattern in female carriers of X linked hypophosphataemic rickets.

X linked hypophosphataemia (XLH) results from an abnormality of renal tubular phosphate reabsorption. The disorder is inherited as an X linked dominant trait and the gene has been mapped to Xp22.1-p22.2. A candidate gene (PEX) has recently been isolated. The most striking clinical features are growth retardation and skeletal abnormalities. As expected for X linked dominant disorders, females are less affected. However, such a gene dosage effect does not exist for renal phosphate reabsorption. Preferential X chromosome inactivation has been proposed as a possible explanation for this lack of gene dosage. We have examined the X inactivation pattern in peripheral blood cells from 12 females belonging to seven families with XLH using PCR analysis at the androgen receptor locus. The X inactivation pattern in these patients did not differ significantly from the pattern in 30 healthy females. The X inactivation pattern in peripheral blood cells does not necessarily reflect the X inactivation pattern in renal cells. However, the finding of a normal distribution of X inactivation in peripheral blood cells indicates that the similarity in the renal handling of phosphate in male and female patients is not related to a ubiquitous preferential X inactivation.     

Assessing the inactivation pattern in chromosome X among symptomatic carriers and women with haemophilia

X chromosome inactivation is a stochastic event that occurs early in female embryo development to achieve dosage compensation with males. Certain genetic mechanisms affect the normal process causing a skewed X inactivation pattern which has clinical relevance in female carriers of X-linked recessive disorders, like haemophilia. The most commonly used assay to evaluate the X inactivation pattern is the PCR amplification of the human androgen receptor gene (HUMARA). The use of this technique in bleeding carriers and women with haemophilia allows identifying if their hemorrhagic symptoms are due to an unfavourable lyonization. Furthermore, these studies are important for understanding the X chromosome inactivation process in humans.     

Deletions and translocations involving the distal short arm of the human X chromosome: review and hypotheses.

In this review we describe the various types of chromosomal abnormalities found in the distal short arm of the human X chromosome and the most common clinical features associated with each type, emphasizing the underlying molecular mechanisms. The study of these patients has significant implications for identifying the disease genes involved.     

Characterization and use of somatic cell hybrids with interspecific translocations involving the human X chromosome

Two hybrid cell lines, whose only human material was a portion of the X translocated on to a mouse chromosome, have been characterized by cytogenetics, in situ hybridization and Southern blotting. In one hybrid (HORL911R8B) the region Xpter to Xq2(2–4) was identified. In the other (PIP) the single human fragment was found to contain sequences from two separate X chromosomal regions (corresponding approximately to Xp11.4–Xp22.1 and Xq26–Xqter). These two hybrids in combination with a third (WAG 8) retaining Xqter to Xp21 as a human X-autosome translocation chromosome, form a mapping panel for rapid subregional assignments to the human X chromosome. This mapping panel has been used to provide information about the order of DNA sequences derived from the X chromosome and to provide an assignment for an anonymous DNA segment, M201γ, to Xp11.4–Xp21.1.     

X chromosome replication patterns in a case of X;9 balanced translocation.

A case of X;9 balanced translocation in a female with amenorrhoea is reported. The X breakpoint was at Xq21, inside the 'critical region'. The normal X was consistently late replicating in blood lymphocytes and skin and ovary fibroblasts.     

Role of chromosome aberrations in recurrent abortion: a study of 269 balanced translocations

We have studied a sample of 5,445 couples in which the woman was ascertained to have had two or more spontaneous abortions: 396 from our Cytogenetics Unit (present series) and 5,049 from the literature (literature series). In approximately 5% of these couples one of the members was a carrier of a balanced translocation, either reciprocal (2/3 of cases) or Robertsonian (1/3). In 1% of the couples there were other chromosome anomalies, mostly gonosomal aneuploidies or mosaicisms. A pericentric inversion of the heterochromatic region of chromosome 9 was present in 3% of the couples of the present series and in 1% of the literature series. The number of female carriers exceeded significantly that of males. The probability for one member of the couple to be a carrier increased with the number of abortions at the time of ascertainment, but it does not seem modified by the concomitant presence of term pregnancies. The analysis of the cytogenetic findings in 80 cases of Robertsonian and 156 cases of reciprocal translocations suggests that some chromosomes are preferentially involved, and that in reciprocal translocations the breakpoints are not distributed at random on the chromosome arms. There is an excess of breakpoints on chromosomes 6, 7, and 22 and a dearth on chromosome 12. This distribution is significantly different from that of a sample of reciprocal translocations ascertained for a malformed child. In both samples the breakpoints seem associated with fragile sites more frequently than expected by chance. An analysis of the potential and effective chromosome imbalance suggests that in subjects with unbalanced chromosomes survival is correlated with a minimum imbalance.     

Molecular cytogenetic analysis of a de novo balanced X;autosome translocation: Evidence for predominant inactivation of the derivative X chromosome in a girl with multiple malformations

We report on the characterization of a de novo, apparently balanced translocation t(X;15)(p11.3;q26) detected in a girl with multiple congenital malformations. Replication banding studies on Epstein-Barr virus transformed peripheral blood lymphocytes revealed non-random X chromosome inactivation with predominant inactivation of the derivative X chromosome. Using chromosomal fluorescence in situ hybridization (FISH), we located the breakpoints to a 30 kb region on the short arm of the X chromosome band p11.3 and to a 160 kb region defined by BAC RP11-89K11 on the long arm of chromosome 15. Our data suggest that the disruption/disturbance of plant homeo domain (PHD) zinc finger gene KIAA0215 or of another gene (RGN, RNU12, P17.3, or RBM10) in the breakpoint region on the X chromosome is not well tolerated and leads to the selection of cells with an active non-rearranged X chromosome.     

Isodicentric X chromosome in a moderately tall patient with gonadal dysgenesis: lack of effect of functional centromere on inactivation pattern.

An isodicentric X chromosome (46, X idic (X)(pter leads to qter::qter leads to pter)) with a single functioning centromere was found in all lymphocytes and fibroblasts examined from a female patient 171.5 cm in height presenting with primary amenorrhoea. Replication of the abnormal chromosome was consistently late. In some cells the pattern was asymmetrical but the asymmetry did not appear to relate to the position of the active centromere.     

Molecular and cytogenetic analysis of the spreading of X inactivation in X;autosome translocations

We have performed detailed studies of the spreading of X inactivation in five unbalanced human X;autosome translocations. Using allele-specific RT-PCR we observed long-range silencing of autosomal genes located up to 45 Mb from the translocation breakpoint, directly demonstrating the ability of X inactivation to spread in cis through autosomal DNA. Spreading of gene silencing occurred in either a continuous or discontinuous fashion in different cases, suggesting that some autosomal DNA is resistant to the X inactivation signal. This spread of inactivation was accompanied by, but not dependent upon, CpG island methylation. Observations of late-replication, histone acetylation and histone methylation show that X inactivation can spread in the absence of cytogenetic features normally associated with the inactive X. However, the distribution of histone modifications which distinguish the inactive X are more accurate cytogenetic measures of the spread of X inactivation than late-replication. Overall, despite remarkable variation in the spread of X inactivation among the five cases there was good correlation between the pattern of gene silencing and the attenuation of clinical phenotype associated with each partial autosomal trisomy. We discuss our observations in the context of hypotheses which address the spread of X inactivation.     

Mutations of the PTPN11 gene in therapy-related MDS and AML with rare balanced chromosome translocations

Activating mutations of the PTPN11 gene encoding the SHP2 tyrosine phosphatase is the most common genetic abnormality in juvenile myelomonocytic leukemia and is sporadically observed in myelodysplasia (MDS) and acute myeloid leukemia (AML). An unselected series of 140 patients with therapy-related MDS or AML were investigated for mutations of PTPN11 in Exons 3, 4, 8, and 13. Four cases had mutations of the gene; three of these had deletions or loss of chromosome arm 7q. Two cases had rare balanced translocations to chromosome band 21q22 with rearrangement of the RUNX1 gene and the other two patients had rare balanced translocations to chromosome band 3q26 with rearrangement of the EVI1 gene. The findings support cooperation between so called Class I and Class II mutations in leukemogenesis.     

Segregation of a totally skewed pattern of X chromosome inactivation in four familial cases of Rett syndrome without MECP2 mutation: implications for the disease

BACKGROUND—Rett syndrome is a neurodevelopmental disorder affecting only girls; 99.5% of Rett syndrome cases are sporadic, although several familial cases have been reported. Mutations in the MECP2 gene were identified in approximately 70-80% of sporadic Rett syndrome cases.
METHODS—We have screened the MECP2 gene coding region for mutations in five familial cases of Rett syndrome and studied the patterns of X chromosome inactivation (XCI) in each girl.
RESULTS—We found a mutation in MECP2 in only one family. In the four families without mutation in MECP2, we found that (1) all mothers exhibit a totally skewed pattern of XCI; (2) six out of eight affected girls also have a totally skewed pattern of XCI; and (3) it is the paternally inherited X chromosome which is active in the patients with a skewed pattern of XCI. Given that the skewing of XCI is inherited in our families, we genotyped the whole X chromosome using 32 polymorphic markers and we show that a locus potentially responsible for the skewed XCI in these families could be located on the short arm of the X chromosome.
CONCLUSION—These data led us to propose a model for familial Rett syndrome transmission in which two traits are inherited, an X linked locus abnormally escaping X chromosome inactivation and the presence of a skewed XCI in carrier women.


Keywords: Rett syndrome; skewed X chromosome inactivation; X chromosome; MECP2     

X inactivation analysis in a female with hypomelanosis of Ito associated with a balanced X;17 translocation: evidence for functional disomy of Xp.

X inactivation analysis was performed on normal and hypopigmented skin samples obtained from a female with hypomelanosis of Ito associated with a balanced whole arm X;17 translocation. Severe skewing of X inactivation resulting in inactivity of the intact X was found in blood and cultures of both types of skin, but analysis of DNA prepared directly from hypopigmented skin showed significant inactivation of the translocated X, inconsistent with the usual mechanism of phenotypic expression in X;autosome translocations. In addition, dual colour FISH analysis using centromere specific probes for chromosomes X and 17 showed that the breakpoints on both chromosomes lie within the alphoid arrays, making interruption of a locus on either chromosome unlikely. While partial variable monosomy of loci on chromosome 17p cannot be excluded as contributing to the phenotype in this patient, it is argued that the major likely factor is partial functional disomy of sequences on Xp in cell lineages that have failed to inactivate the intact X chromosome.     

Fragile-X syndrome and skewed X-chromosome inactivation within a family: a female member with complete inactivation of the functional X chromosome

Fragile X syndrome is the most common form of inherited mental retardation. It is caused by the increase in length of a stretch of CGG triplet repeats within the FMR1 gene. A full mutation (> 200 repeats) leads to methylation of the CpG island and silencing of the FMR1 gene. We present here two sisters that are compound heterozygotes for a full mutation and a 53 repeat intermediate allele, one of them showing mental retardation and clinical features of an affected male (speech delay, hyperactivity, large ears, prominent jaw, gaze aversion), while the other is borderline normal (mild delay). Southern blot and FMRP expression analysis showed that the sister with mental retardation had the normal FMR1 gene totally methylated and no detectable protein, while her sister had 70% of her cells with the normal FMR1 gene unmethylated and normal FMRP levels. We found that the observed phenotypic differences between both sisters who are cytogenetically normal, are caused by extreme skewed X-chromosome inactivation. Analysis of the extended family showed that most of the other female family members that carry a pre-mutation or a full mutation showed some degree of skewing in their X-chromosome inactivation. The presence of several family members with skewed X inactivation and the direction and degree of skewing is inconsistent with a mere selection during development, and suggests a genetic origin for this phenomenon.