Balanced X-autosome Translocations Research Articles

Premature ovarian insufficiency is associated with global alterations in the regulatory landscape and gene expression in balanced X-autosome translocations

BackgroundPatients with balanced X-autosome translocations and premature ovarian insufficiency (POI) constitute an interesting paradigm to study the effect of chromosome repositioning. Their breakpoints are clustered within cytobands Xq13–Xq21, 80% of them in Xq21, and usually, no gene disruption can be associated with POI phenotype. As deletions within Xq21 do not cause POI, and since different breakpoints and translocations with different autosomes lead to this same gonadal phenotype, a “position effect” is hypothesized as a possible mechanism underlying POI pathogenesis.Objective and methodsTo study the effect of the balanced X-autosome translocations that result in POI, we fine-mapped the breakpoints in six patients with POI and balanced X-autosome translocations and addressed gene expression and chromatin accessibility changes in four of them.ResultsWe observed differential expression in 85 coding genes, associated with protein regulation, multicellular regulation, integrin signaling, and immune response pathways, and 120 differential peaks for the three interrogated histone marks, most of which were mapped in high-activity chromatin state regions. The integrative analysis between transcriptome and chromatin data pointed to 12 peaks mapped less than 2 Mb from 11 differentially expressed genes in genomic regions not related to the patients’ chromosomal rearrangement, suggesting that translocations have broad effects on the chromatin structure.ConclusionSince a wide impact on gene regulation was observed in patients, our results observed in this study support the hypothesis of position effect as a pathogenic mechanism for premature ovarian insufficiency associated with X-autosome translocations. This work emphasizes the relevance of chromatin changes in structural variation, since it advances our knowledge of the impact of perturbations in the regulatory landscape within interphase nuclei, resulting in the position effect pathogenicity.

Allelic and dosage effects of NHS in X-linked cataract and Nance\u2013Horan syndrome: a family study and literature review

Nance–Horan syndrome (NHS) is a rare X-linked dominant disorder caused by mutation in the NHS gene on chromosome Xp22.13. (OMIM 302350). Classic NHS manifested in males is characterized by congenital cataracts, dental anomalies, dysmorphic facial features and occasionally intellectual disability. Females typically have a milder presentation. The majority of reported cases of NHS are the result of nonsense mutations and small deletions. Isolated X-linked congenital cataract is caused by non-recurrent rearrangement-associated aberrant NHS transcription. Classic NHS in females associated with gene disruption by balanced X-autosome translocation has been infrequently reported. We present a familial NHS associated with translocation t(X;19) (Xp22.13;q13.1). The proband, a 28-year-old female, presented with intellectual disability, dysmorphic features, short stature, primary amenorrhea, cleft palate, and horseshoe kidney, but no NHS phenotype. A karyotype and chromosome microarray analysis (CMA) revealed partial monosomy Xp/partial trisomy 19q with the breakpoint at Xp22.13 disrupting the NHS gene. Family history revealed congenital cataracts and glaucoma in the patient’s mother, and congenital cataracts in maternal half-sister and maternal grandmother. The same balanced translocation t(X;19) was subsequently identified in both the mother and maternal half-sister, and further clinical evaluation of the maternal half-sister made a diagnosis of NHS. This study describes the clinical implication of NHS gene disruption due to balanced X-autosome translocations as a unique mechanism causing Nance–Horan syndrome, refines dose effects of NHS on disease presentation and phenotype expressivity, and justifies consideration of karyotype and fluorescence in situ hybridization (FISH) analysis for female patients with familial NHS if single-gene analysis of NHS is negative.

Inactivation of AMMECR1 is associated with growth, bone, and heart alterations.

We report five individuals with loss-of-function of the X-linked AMMECR1: a girl with a balanced X-autosome translocation and inactivation of the normal X-chromosome; two boys with maternally inherited and de novo nonsense variants; and two half-brothers with maternally inherited microdeletion variants. They present with short stature, cardiac and skeletal abnormalities, and hearing loss. Variants of unknown significance in AMMECR1 in four male patients from two families with partially overlapping phenotypes were previously reported. AMMECR1 is coexpressed with genes implicated in cell cycle regulation, five of which were previously associated with growth and bone alterations. Our knockdown of the zebrafish orthologous gene resulted in phenotypes reminiscent of patients' features. The increased transcript and encoded protein levels of AMMECR1L, an AMMECR1 paralog, in the t(X;9) patient's cells indicate a possible partial compensatory mechanism. AMMECR1 and AMMECR1L proteins dimerize and localize to the nucleus as suggested by their nucleic acid-binding RAGNYA folds. Our results suggest that AMMECR1 is potentially involved in cell cycle control and linked to a new syndrome with growth, bone, heart, and kidney alterations with or without elliptocytosis.

Is the resulting phenotype of an embryo with balanced X-autosome translocation, obtained by means of preimplantation genetic diagnosis, linked to the X inactivation pattern?

To examine if a balanced female embryo with X-autosome translocation could, during its subsequent development, express an abnormal phenotype. Preimplantation genetic diagnosis (PGD) analysis on two female carriers with maternal inherited X-autosome translocations. Infertility center and genetic laboratory in a public hospital. Two female patients carriers undergoing PGD for a balanced X-autosome translocations: patient 1 with 46,X,t(X;2)(q27;p15) and patient 2 with 46,X,t(X;22)(q28;q12.3). PGD for balanced X-autosome translocations. PGD outcomes, fluorescence in situ hybridization in biopsied embryos and meiotic segregation patterns analysis of embryos providing from X-autosome translocation carriers. Controlled ovarian stimulation facilitated retrieval of a correct number of oocytes. One balanced embryo per patient was transferred and one developed, but the patient miscarried after 6weeks of amenorrhea. In X-autosome translocation carriers, balanced Y-bearing embryos are most often phenotypically normal and viable. An ambiguous phenotype exists in balanced X-bearing embryos owing to the X inactivation mechanism. In 46,XX embryos issued from an alternate segregation, der(X) may be inactivated and partially spread transcriptional silencing into a translocated autosomal segment. Thus, the structural unbalanced genotype could be turned into a viable functional balanced one. It is relevant that a discontinuous silencing is observed with a partial and unpredictable inactivation of autosomal regions. Consequently, the resulting phenotype remains a mystery and is considered to be at risk of being an abnormal phenotype in the field of PGD. It is necessary to be cautious regarding to PGD management for this type of translocation, particularly in transferred female embryos.

Incorporation of 5-ethynyl-2'-deoxyuridine (EdU) as a novel strategy for identification of the skewed X inactivation pattern in balanced and unbalanced X-rearrangements.

X-chromosome inactivation occurs randomly in normal female cells. However, the inactivation can be skewed in patients with alterations in X-chromosome. In balanced X-autosome translocations, normal X is preferentially inactivated, while in unbalanced X alterations, the aberrant X is usually inactivated. Here, we present a novel strategy to verify the skewed X inactivation pattern through the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) into cells, in 11 patients: five carriers of balanced X-autosome translocations and six of unbalanced X-chromosome alterations. Since EdU is a labeled nucleoside analog of thymidine, its incorporation during DNA synthesis can reveal late replication regions and the inactive X-chromosome. All EdU findings were validated by the human androgen receptor gene (HUMARA) assay. The late replication regions were easily and quickly visualized in all cells, where inactive Xs are marked with strong green fluorescence. It was observed that the normal X-chromosome was preferentially inactivated in patients with balanced X-autosome translocations; while the aberrant X-chromosome was inactivated in most cells from patients with unbalanced alterations. By performing the fluorescence-based EdU assay, the differences between the active and inactive X-chromosomes are more easily recognizable than by classic cytogenetic methods. Furthermore, EdU incorporation allows the observation of the late replication regions in autosomal segments present in X derivatives from X-autosome translocations. Therefore, EdU assay permits an accurate and efficient cytogenetic evaluation of the X inactivation pattern with a low-cost, easy to perform and highly reproducible technique.

Genetic mechanisms leading to primary amenorrhea in balanced X-autosome translocations

To map the X-chromosome and autosome breakpoints in women with balanced X-autosome translocations and primary amenorrhea, searching candidate genomic loci for female infertility. Retrospective and case-control study. University-based research laboratory. Three women with balanced X-autosome translocation and primary amenorrhea. Conventional cytogenetic methods, genomic array, array painting, fluorescence in situ hybridization, and quantitative reverse transcription-polymerase chain reaction. Karyotype, copy number variation, breakpoint mapping, and gene expression levels. All patients presented with breakpoints in the Xq13q21 region. In two patients, the X-chromosome breakpoint disrupted coding sequences (KIAA2022 and ZDHHC15 genes). Although both gene disruptions caused absence of transcription in peripheral blood, there is no evidence that supports the involvement of these genes with ovarian function. The ZDHHC15 gene belongs to a conserved syntenic region that encompasses the FGF16 gene, which plays a role in female germ line development. The break in the FGF16 syntenic block may have disrupted the interaction between the FGF16 promoter and its cis-regulatory element. In the third patient, although both breakpoints are intergenic, a gene that plays a role in the DAX1 pathway (FHL2 gene) flanks distally the autosome breakpoint. The FHL2 gene may be subject to position effect due to the attachment of an autosome segment in Xq21 region. The etiology of primary amenorrhea in balanced X-autosome translocation patients may underlie more complex mechanisms than interruption of specific X-linked candidate genes, such as position effect. The fine mapping of the rearrangement breakpoints may be a tool for identifying genetic pathogenic mechanisms for primary amenorrhea.

Autism Spectrum Disorder in a Girl with aDe NovoX;19 Balanced Translocation

Balanced X-autosome translocations are rare, and female carriers are a clinically heterogeneous group of patients, with phenotypically normal women, history of recurrent miscarriage, gonadal dysfunction, X-linked disorders or congenital abnormalities, and/or developmental delay. We investigated a patient with a de novo X;19 translocation. The six-year-old girl has been evaluated due to hyperactivity, social interaction impairment, stereotypic and repetitive use of language with echolalia, failure to follow parents/caretakers orders, inconsolable outbursts, and persistent preoccupation with parts of objects. The girl has normal cognitive function. Her measurements are within normal range, and no other abnormalities were found during physical, neurological, or dysmorphological examinations. Conventional cytogenetic analysis showed a de novo balanced translocation, with the karyotype 46,X,t(X;19)(p21.2;q13.4). Replication banding showed a clear preference for inactivation of the normal X chromosome. The translocation was confirmed by FISH and Spectral Karyotyping (SKY). Although abnormal phenotypes associated with de novo balanced chromosomal rearrangements may be the result of disruption of a gene at one of the breakpoints, submicroscopic deletion or duplication, or a position effect, X; autosomal translocations are associated with additional unique risk factors including X-linked disorders, functional autosomal monosomy, or functional X chromosome disomy resulting from the complex X-inactivation process.

Switch in X-inactivation in a JAK2 V617F-negative case of polycythemia vera with two acquired X-autosome translocations

We report a JAK2 V617F-negative case of polycythemia vera with two acquired balanced X-autosome translocations and no history of previous exposure to chemo/radiotherapy. The patient's first clone carried a novel translocation t(X;15)(q24;q13) as a sole abnormality. The second clone exhibited an additional translocation, t(X;20)(q13;q13.3), which is a rare recurrent abnormality in myeloid malignancies. This is the first report of a hematological disorder with both X chromosomes being translocated. Late replication studies revealed a switch in X-inactivation from the X chromosome involved in t(X;15) (first clone) to the X chromosome involved in the t(X;20)(q13;q13.3) (second clone). The inactivation of the translocated X chromosomes could provide potential for the inactivation of the adjacent autosomal regions, resulting in epigenetic gene silencing.

Phenotype in X chromosome rearrangements: pitfalls of X inactivation study

X inactivation pattern in X chromosome rearrangements usually favor the less unbalanced cells. It is correlated to a normal phenotype, small size or infertility. We studied the correlation between phenotype and X inactivation ratio in patients with X structural anomalies. During the 1999-2005 period, 12 X chromosome rearrangements, including three prenatal cases, were diagnosed in the Laboratoire de Cytogénétique of Strasbourg. In seven cases, X inactivation ratio could be assessed by late replication or methylation assay. In three of seven cases (del Xp, dup Xp, t(X;A)), X inactivation ratio and phenotype were consistent. The four other cases showed discrepancies between phenotype and X inactivation pattern: mental retardation and dysmorphism in a case of balanced X-autosome translocation, schizophrenia and autism in two cases of XX maleness and MLS syndrome (microphthalmia with linear skin defects) in a case of Xp(21.3-pter) deletion. Discrepancies between X inactivation ratio and phenotype are not rare and can be due to gene disruption, position effect, complex microrearrangements, variable pattern of X inactivation in different tissues or fortuitous association. In this context, the prognostic value of X inactivation study in prenatal diagnosis will be discussed.

Phenotypic effects of balanced X-autosome translocations in females: a retrospective survey of 104 cases reported from UK laboratories.

Females with balanced X-autosome translocations are a clinically heterogeneous group of patients in which X breakpoint position and replication behaviour may influence phenotypic outcome. This study reviewed all cases reported by UK cytogenetics laboratories over a 15-year period (1983-1997). Publication bias was avoided by reviewing all reported cases. One hundred and four female carriers were identified, 62 of who were probands. By reason for referral, these were: multiple congenital abnormalities and/or developmental delay (MCA/DD): 26 (42%); gonadal dysfunction: 22 (35%); phenotypically normal with or without recurrent miscarriage (NRM): 9 (15%); recognized X-linked syndrome: 5 (8%). The information obtained was compared with published data and with data from the authors' own laboratories of female patients with balanced autosome-autosome translocations (n=115). We concluded that: (1) MCA/DD cases were significantly over-represented compared to previous published data (P<0.005) and were more common than in female probands with balanced autosome-autosome translocations (P<0.05). (2) MCA/DD cases showed random breakpoint distribution along the X chromosome (P>0.05). MCA/DD cases with subtelomeric breakpoints at Xp22 or Xq28 were not always associated with deviation from the expected pattern of X-inactivation where this was known. De novo cases were significantly more likely to be assigned as MCA/DD than any other category (P<0.005). (3) Gonadal dysfunction (GD) was invariably associated with a 'critical region' breakpoint, Xq13-q26, (20/22 probands). However, 7/44 (16%) of patients surveyed had breakpoints within Xq13-Xq26 and proven fertility. (4) Recognized 'X-linked syndrome' cases were significantly under-represented (P<0.001) compared to previous published data.

The X Chromosome and Recurrent Spontaneous Abortion: The Significance of Transmanifesting Carriers

If, as we have argued, a subset of female carriers of X-linked recessive lethal traits are genetically predisposed to spontaneous abortion, and if such carriers can reliably be ascertained via their skewed pattern X chromosome inactivation, it becomes possible to test the hypothesis that X-linked recessive lethal traits are a significant cause of RSA in the general population. Intrinsic to this argument are the assumptions that the trait is cell autonomous—that is, that it causes death or growth disadvantage to the cells with the mutant X active and that hemizygous males survive at least until the pregnancy is clinically observable through a positive bHCG test.To test this hypothesis, we have initiated a case-control study wherein we compare the frequency of highly skewed X chromosome inactivation in women with two or more unexplained spontaneous abortions to the frequency in female controls (Lanasa et al. 1998xSee all References1998). The women characterized with idiopathic RSA have undergone a complete evaluation to rule out any of the known causes of RSA described above (Stephenson 1996xFrequency of factors associated with habitual abortion in 197 couples. Stephenson, MD. Fertil Steril. 1996; 66: 24–29Abstract | Full Text PDF | PubMedSee all References1996). The controls are women from the same demographic region, with no known history of spontaneous abortion; furthermore, the cases and controls are age-distribution matched, so that the distribution of ages between the two groups is the same. Defining skewed X inactivation as preferential use of one X chromosome in ≥90% of peripheral leukocytes, we have found 7 (14.6%) of 48 to have skewed X inactivation. In contrast, only 1 (1.5%) of 68 control females exhibit this extent of nonrandom X inactivation. This finding is statistically significant, with P < .01 (Fisher's exact test, one-tailed).The frequency of nonrandom X inactivation is somewhat lower (1.5%) in our control group than has been reported previously. Other groups have estimated that the frequency of skewed inactivation (at the level of ≥90% silencing of one copy of the chromosome) as 3.2% (Gale et al. 1997xAcquired skewing of X-chromosome inactivation patterns in myeloid cells of the elderly suggests stochastic clonal loss with age. Gale, RE, Fielding, AK, Harrison, CN, and Linch, DC. Br J Haematol. 1997; 98: 512–519Crossref | PubMedSee all References1997) or 3.5% (Plenge et al. 1997xA promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation. Plenge, RM, Hendrich, BD, Schwartz, C, Arena, JF, Naumova, A, Sapienza, C, Winter, RM et al. Nat Genet. 1997; 17: 353–356Crossref | PubMed | Scopus (189)See all References1997) in women of the same age in the population at large. Although case-control comparisons across studies may be perilous, it is interesting to note that, even when these higher estimates of skewing frequency are used for the control group, the frequency we observe in our group of RSA-affected women remains significant at the level of P < .05 (Fisher's exact test, one-tailed).Although the results presented here are clearly preliminary, it is interesting to speculate about the frequency of X-linked recessive lethal traits in the general population. Given a frequency of idiopathic RSA of 1 in 250 in the general population, and an affection rate of ∼1 in 7 in our case population, the population prevalence of X-linked lethals leading to RSA could be as high as 1 in 1,750. In fact, our ascertainment methodology will miss a large number of carriers, since, on average, a carrier would have to become pregnant five times to show two spontaneous abortions. Furthermore, there is great selective pressure against such traits. As X-linked recessive lethal traits can be passed on only to daughters, the carrier frequency should be halved in each generation. If 1 in 1,750, in fact, approximates the carrier frequency, then the new mutation rate must be 1 in 3,500. Since the highest-known single-gene–mutation rate is that of dystrophin at 1 in 10,000, a mutation rate of 1 in 3,500 indicates extensive genetic heterogeneity. This is consistent with the hypothesis that there are a significant number of vital genes on the X chromosome.RSA is a major women's health concern. As the application of molecular genetics to RSA advances, it will be possible to begin characterizing those genes that cause spontaneous abortion in the recessive state. The X chromosome inactivation assay affords a methodology by which female carriers of X-linked recessive lethal defects can be identified. Over time, then, by assembling familial pedigrees, the individual causative genes can be identified. The X-inactivation assay should become an important diagnostic tool in the clinical evaluation of women with RSA, as secondary skewed X inactivation will be the common denominator by which carriers of X-linked recessive lethal traits can be identified.

Eleven X Chromosome Breakpoints Associated with Premature Ovarian Failure (POF) Map to a 15-Mb YAC Contig Spanning Xq21

Eleven balanced X-autosome translocations associated with premature ovarian failure (POF) were mapped to a YAC contig spanning most of Xq21 and constructed between the DXS223 and DXS1171 loci. The contig corresponds to a genomic region of about 15 Mb and contains the whole X-Y homologous region. The most proximal and most distal breakpoints associated with POF were mapped 15 Mb apart. The remaining breakpoints were localized along this large region, in the X-specific and in the X-Y homologous region. Four of the YACs contained two breakpoints in the same or in flanking STS intervals. Our results confirm the cytological findings and suggest that a minimum number of eight different genes in Xq21 may be involved with ovary development. Interruption of such loci could be the cause of POF.

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.(ABSTRACT TRUNCATED AT 250 WORDS)

Balanced structural changes involving the human X: effect on sexual phenotype.

Reports of 107 cases (89 females and 18 males) with balanced X-autosome translocations and 11 cases with pericentric inversions (and their families) have been reviewed. Of the 78 informative females, 36 were infertile and had an X-breakpoint in the segment Xq13-26. Thus the existence of the critical segment has been amply confirmed by this review. However the finding of three normal fertile females with deletion of a part or the whole of this segment suggests that it is not the break in the critical segment, as was first thought, but rather the contact between loci in the critical segment and loci external to it that is responsible for the abnormal sexual phenotype. Six females were exceptions to the critical region hypothesis. The X-breakpoints in these were in the critical region and yet each had had one or more children. Three of the six women (two inversions and one translocation carriers) were not wholly normal as they suffered from menstrual cycle disorder, secondary sterility and/or early menopause. Four of the six (including the three true exceptions) had a breakpoint in band Xq22. It is possible that there are two critical segments within Xq13-26 separated by a small segment in band Xq22. Seven of the nine adult male carriers of the balanced X-autosome translocations were infertile. Even from this limited number of cases it appears that male carriers of X-autosome translocations are likely to suffer from a disturbance of spermatogenesis as is the case in mouse and drosophila. Male carriers of X-inversions do not necessarily suffer from infertility. Results from one family with X-inversion suggest that some sort of a position effect in the X affecting the sexual phenotype may also be operating in the male.

539 PRESUMPTIVE EVIDENCE FOR THE PRESENCE OF 2 ACTIVE X CHROMOSOMES IN A BALANCED X-AUTOSOLL TRANSLOCATION

In human somatic cells, X chromosomes in excess of one are late replicating. In balanced X-autosome translocation, the general rule is that the normal X is late replicating. We are reporting the first such translocation in which there is no late replicating X in 1/3 of cells analyzed. A 6-year-old girl with the Beckwith-Wiedemann syndrome has a balanced, de novo, X;1 translocation (G-banded karyotype is 46,X,t(X;1) (Xpter→ Xq26::1q12→ lqter; lpter→ 1q12::Xq26→ Xqter). Using the BrdU terminal pulse method followed by acridine orange or Hoechst 33258 stain and giemsa in 2 successive lymphocyte cultures, the normal X was identified as late replicating in approximately 66% of metaphases. In the remaining 34% of cells, neither the normal X nor the Xt appeared to be late replicating. In these cells, regions of chromosomes 4 and 13, known to be late replicating, are clearly identifiable. In no case did the small Xq portion in the reciprocal translocation chromosome appear as late replicating. This finding serves as presumptive evidence for the presence of 2 active X chromosomes in a balanced X-autosome translocation. Supported in part by NIH grants # RR75 and CA 19834

Balanced reciprocal X-4 translocation in a female patient with early secondary amenorrhea

Balanced translocations involving an X chromosome and an autosome have been infrequently reported. A patient with a balanced X-autosome translocation 46,X,rcp(X;4)(q26;q21) who exhibited early secondary amenorrhea and gonadal dysgenesis is described. In an effort to explain the varied phenotypic expressions encountered in female cases of balanced X-autosome translocations, evidence will be provided to suggest an extension of the minimal limits of the “critical region” in the long arm of the X chromosome from A-B, as described by Sarto and associates,7 to new minimal limits C-D.