HUMARA Gene Research Articles

Intelligence Quotient Variability in Klinefelter Syndrome Is Associated With GTPBP6 Expression Under Regulation of X-Chromosome Inactivation Pattern

Klinefelter syndrome (KS) displays a broad dysmorphological, endocrinological, and neuropsychological clinical spectrum. We hypothesized that the neurocognitive dysfunction present in KS relies on an imbalance in X-chromosome gene expression. Thus, the X-chromosome inactivation (XCI) pattern and neurocognitive X-linked gene expression were tested and correlated with intelligence quotient (IQ) scores. We evaluated 11 KS patients by (a) IQ assessment, (b) analyzing the XCI patterns using both HUMARA and ZDHHC15 gene assays, and (c) blood RT-qPCR to investigate seven X-linked genes related to neurocognitive development (GTPBP6, EIF2S3, ITM2A, HUWE1, KDM5C, GDI1, and VAMP7) and XIST in comparison with 14 (male and female) controls. Considering IQ 80 as the standard minimum reference, we verified that the variability in IQ scores in KS patients seemed to be associated with the XCI pattern. Seven individuals in the KS group presented a random X-inactivation (RXI) and lower average IQ than the four individuals who presented a skewed X-inactivation (SXI) pattern. The evaluation of gene expression showed higher GTPBP6 expression in KS patients with RXI than in controls (p = 0.0059). Interestingly, the expression of GTPBP6 in KS patients with SXI did not differ from that observed in controls. Therefore, our data suggest for the first time that GTPBP6 expression is negatively associated with full-scale IQ under the regulation of the type of XCI pattern. The SXI pattern may regulate GTPBP6 expression, thereby dampening the impairment in cognitive performance and playing a role in intelligence variability in individuals with KS, which warrants further mechanistic investigations.

Molecular Mechanisms of Skewed X-Chromosome Inactivation in Female Hemophilia Patients-Lessons from Wide Genome Analyses.

Introduction: Hemophilia A (HA) is an X-linked bleeding disorder caused by factor VIII (FVIII) deficiency or dysfunction due to F8 gene mutations. HA carriers are usually asymptomatic because their FVIII levels correspond to approximately half of the concentration found in healthy individuals. However, in rare cases, a carrier may exhibit symptoms of moderate to severe HA primarily due to skewed inactivation of her non-hemophilic X chromosome. Aim: The aim of the study was to investigate X-chromosome inactivation (XCI) patterns in HA carriers, with special emphasis on three karyotypically normal HA carriers presenting with moderate to severe HA phenotype due to skewed XCI, in an attempt to elucidate the molecular mechanism underlying skewed XCI in these symptomatic HA carriers. The study was based on the hypothesis that the presence of a pathogenic mutation on the non-hemophilic X chromosome is the cause of extreme inactivation of that X chromosome. Methods: XCI patterns were studied by PCR analysis of the CAG repeat region in the HUMARA gene. HA carriers that demonstrated skewed XCI were further studied by whole-exome sequencing (WES) followed by X chromosome-targeted bioinformatic analysis. Results: All three HA carriers presenting with the moderate to severe HA phenotype due to skewed XCI were found to carry pathogenic mutations on their non-hemophilic X chromosomes. Patient 1 was diagnosed with a frameshift mutation in the PGK1 gene that was associated with familial XCI skewing in three generations. Patient 2 was diagnosed with a missense mutation in the SYTL4 gene that was associated with familial XCI skewing in two generations. Patient 3 was diagnosed with a nonsense mutation in the NKAP gene that was associated with familial XCI skewing in two generations. Conclusion: Our results indicate that the main reason for skewed XCI in our female HA patients was negative selection against cells with a disadvantage caused by an additional deleterious mutation on the silenced X chromosome, thus complicating the phenotype of a monogenic X-linked disease. Based on our study, we are currently offering the X inactivation test to symptomatic hemophilia carriers and plan to expand this approach to symptomatic carriers of other X-linked diseases, which can be further used in pregnancy planning.

A new sex-specific underlying mechanism for female schizophrenia: accelerated skewed X chromosome inactivation

BackgroundX chromosome inactivation (XCI) is the mechanism by which the X-linked gene dosage is adjusted between the sexes. Evidence shows that many sex-specific diseases have their basis in X chromosome biology. While female schizophrenia patients often have a delayed age of disease onset and clinical phenotypes that are different from those of males, it is unknown whether the sex differences in schizophrenia are associated with X-linked gene dosage and the choice of X chromosome silencing in female cells. Previous studies demonstrated that sex chromosome aneuploidies may be related to the pathogeneses of some psychiatric diseases. Here, we examined the changes in skewed XCI in patients with schizophrenia.MethodsA total of 109 female schizophrenia (SCZ) patients and 80 age- and sex-matched healthy controls (CNTLs) were included in this study. We evaluated clinical features including disease onset age, disease duration, clinical symptoms by the Positive and Negative Syndrome Scale (PANSS) and antipsychotic treatment dosages. The XCI skewing patterns were analyzed by the methylation profile of the HUMARA gene found in DNA isolated from SCZ patient and CNTL leukocytes in the three age groups.ResultsFirst, we found that the frequency of skewed XCI in SCZ patients was 4 times more than that in the age- and sex-matched CNTLs (p < 0.01). Second, we found an earlier onset of severe XCI skewing in the SCZ patients than in CNTLs. Third, we demonstrated a close relationship between the severity of skewed XCI and schizophrenic symptoms (PANSS score ≥ 90) as well as the age of disease onset. Fourth, we demonstrated that the skewed XCI in SCZ patients was not transmitted from the patients’ mothers.LimitationsThe XCI skewing pattern might differ depending on tissues or organs. Although this is the first study to explore skewed XCI in SCZ, in the future, samples from different tissues or cells in SCZ patients might be important for understanding the impact of skewed XCI in this disease.ConclusionOur study, for the first time, investigated skewed XCI in female SCZ patients and presented a potential mechanism for the sex differences in SCZ. Our data also suggested that XCI might be a potential target for the development of female-specific interventions for SCZ.

Use of X-Chromosome Inactivation Pattern to Analyze the Clonality of 14 Female Cases of Kaposi Sarcoma.

BackgroundKaposi sarcoma (KS) has features of both neoplastic growth and hyperplastic proliferation. It is the most common tumor seen in patients with HIV infection. Whether KS is a real tumor or a benign hyperplastic disease is not known.Material/MethodsTissues from KS and cutaneous hemangioma lesion DNA were extracted, and then digested with methylation-sensitive restriction endonuclease HpaII. Human androgen receptor gene (HUMARA) was amplified with PCR method and the product was separated on 10% denaturing polyacrylamide gels and stained with ethylene dibromide (EB) to show the polymorphism of HUMARA. Phosphoglycerate kinase (PGK) was amplified and the product was digested by BStXI, agarose gel and EB stained to show the polymorphism of PGK. Finally, we analyzed the clonality of KS.ResultsIn the 14 patients with KS, heterozygosity of the HUMARA gene was observed in 12 (85.7%) cases. Loss of heterozygosity of HUMARA gene on X-chromosome (without HpaII digestion there were 2 bands, after HpaII digestion there were just 1 of the bands), representing monoclonal origin, was present in 11 cases of Kaposi sarcoma. Heterozygosity of the PGK gene was observed in 5 (35.7%) cases, which all represent monoclonal origin. There was no significant difference according to country, stage, or HIV and HHV-8 (P>0.05).ConclusionsThe current findings suggest that Kaposi sarcoma is a clonal neoplasm, not a reactive proliferation.

Clonality analysis of Kaposi's sarcoma lesions by human androgen receptor assay

Objective To analyze the clonality in Kaposi's sarcoma (KS) lesions by evaluating Xchromosome inactivation pattern in the human androgen receptor (HUMARA) gene.Methods Twenty-five paraffinembedded tissue specimens were collected from female patients with KS (n =15) or cutaneous hemangioma (n =10).DNA was extracted from these specimens,and digested with the methylation-sensitive restriction endonuclease Hpa Ⅱ.PCR was performed to amplify the HUMARA gene,and the amplicons were separated on a 10％ denaturing polyacrylamied gel and stained with ethidium bromide (EB).The loss of heterozygosity of the HUMARA gene was defined as the presence of two DNA fragments before and one fragment after the endonuclease digestion.The clonality in KS lesions was assessed based on the above results.Results Among the 15 patients with KS,13 (86.7％) were heterozygous for the HUMARA gene,of which,92.31％ (12/13) showed loss of heterozygosity of the HUMARA gene on X-chromosome,suggesting a monoclonal origin.Of the 10 patients with hemangioma,9 were heterozygous for the HUMARA gene,and only one lost heterozygosity of the HUMARA gene.The heterozygosity rate for HUMARA gene was significantly different between the patients with KS and hemangioma (P ＜ 0.01).No statistical difference was observed in the clonality status of KS between patients of different nationality,at different stages,or between patients with and without complicated human immunodeficiency virus (HIV) infection (all P ＞ 0.05).Conclusion KS is monoclonal in origin. Key words: Sarcoma, Kaposi; X Chromosome inactivation; Androgen receptor gene; Clonality analysis

Histopathological and clonal study of combined lobular and ductal carcinoma of the breast

Lobular carcinoma in situ (LCIS) clinically constitutes a risk factor for the subsequent development of either invasive lobular carcinoma (ILC) or invasive ductal carcinoma (IDC). In order to approach the possibility of this common precursor of both ILC and IDC, we investigated combined lobular and ductal carcinomas. Thirty-two cases of lobular carcinoma were picked up out of 773 cases of operated breast carcinomas. The histopathological detailed re-examination using immunostain of E-cadherin and β-catenin revealed a rather high frequency of combined lobular carcinomas than previous reports. Clinicopathologically, combined lobular carcinomas were younger and smaller than pure lobular carcinomas, and the cytological atypia was relatively low. These results suggested that combined lobular carcinomas could be detected in the earlier stage of breast cancer. Furthermore, the lobular and ductal components of combined carcinomas coexisted in the neighborhood and were distributed contiguously. The immunohistochemical phenotypes of both components were accorded in most combined cases. A genetic analysis using methylation-specific PCR on the HUMARA gene demonstrated that the same allele was inactivated in both lobular and ductal components in all detectable cases of combined carcinoma. Therefore, it is reasonable to assume that both lobular and ductal components of combined carcinomas are clonal and derived from the LCIS as the common precursor lesion, which may contradict the conventional concept that the lobular and ductal carcinomas arise from distinct differentiation pathways.

Partial Reversal of the Methylation Pattern of the X-linked Gene HUMARA during Hematopoietic Differentiation of Human Embryonic Stem Cells

Human embryonic stem cells (hESCs) can be induced to differentiate towards hematopoiesis with high efficiency. In this work, we analyzed the methylation status of the X-linked HUMARA (human androgen receptor) gene in hematopoietic cells derived from hESC line H9 before and after induction of hematopoietic differentiation. All passages of H9 and H9-derived hematopoietic cells displayed homogenous methylation pattern with disappearance of the same allele upon HpaII digestion. This pattern persisted in the great majority of different hematopoietic progenitors derived from H9, except in 11 of 86 individually plucked colonies in which an equal digestion of the HUMARA alleles has been found, suggesting that a methylation change occurring at this locus during differentiation. Interestingly, quantification of X inactive-specific transcript (XIST) RNA in undifferentiated H9 cell line and day 14 embryoid bodies (EB) by RT-PCR did not show any evidence of XIST expression either before or after differentiation. Thus, during self-renewal conditions and after induction of commitment towards the formation of EB, the methylation pattern of the HUMARA locus appears locked with the same unmethylated allele. However, hematopoietic differentiation seems to be permissive to the reversal of methylation status of HUMARA in some terminally differentiated progenitors. These data suggest that monitoring methylation of HUMARA gene during induced differentiation could be of use for studying hESC-derived hematopoiesis.

Mucinous nonneoplastic cyst of the pancreas: apomucin phenotype distinguishes this entity from intraductal papillary mucinous neoplasm

Mucinous nonneoplastic cyst of the pancreas is a newly described and rare cystic lesion with unknown histogenesis. It is defined as a cystic lesion lined with mucinous epithelium, supported by hypocellular stroma and not communicating with the pancreatic ducts. It is very challenging to differentiate this lesion from other cystic mucinous neoplasms of the pancreas such as branch-duct intraductal papillary mucinous neoplasm by morphology. In this study, a total of 436 pancreatic specimens resected between 2002 and 2007 in our institution were reviewed. Fifteen (3.4%, 15/436) mucinous nonneoplastic cysts were identified. They included 3 males and 12 females, with a median age of 60 years. Forty-six percent of cases (7/15) occurred in pancreatic head, 27% (4/15) in neck, 7% (1/15) in body, and 20% (3/15) in tail. The size of lesions ranged from 0.5 to 3.5 cm in greatest dimension. In most cases (12/15, 80%), mucinous nonneoplastic cyst was associated or adjacent to acinar-ductal mucinous metaplasia. These morphologic data indicate that mucinous nonneoplastic cyst is not really a rare disease and may originate from acinar-duct mucinous metaplasia histogenestically. Furthermore, apomucin immunostains of mucinous nonneoplastic cyst showed MUC1 expressed in 27% (4/15) cases, MUC5AC in 67% (10/15 cases), and MUC2 was were negative in all cases, whereas intraductal papillary mucinous neoplasm (n = 17; 5 main duct type, 12 branch-duct type) showed focal and weak MUC1 positivity in 18% (3/17) cases, MUC2 positivity in 71% (12/17) cases, and all intraductal papillary mucinous neoplasm (17/17) were MUC5AC positive. The clonality assay with the HUMARA gene revealed that the mucinous nonneoplastic cysts were of polyclonal origin. For the first time, using HUMARA assay, we demonstrate the nonneoplastic nature of these cysts and further characterize morphologic and immunophenotypic properties that allow differentiation from intraductal papillary mucinous neooplasm.

Monoallelic Methylation of the Human Androgen Receptor Gene as Detected by the HUMARA Clonality Assay Does Not Consistently Reflect X-Chromosome Inactivation and Is Therefore Unreliable for Assessment of Clonal Hematopoiesis.

Abstract 4566Even in the absence of a disease specific chromosomal marker, clonality can be assessed in somatic tissues of female origin by using assays based on the pattern of X-chromosome inactivation. The most widely used technique for quantifying X-chromosome inactivation is the HUMARA method that is based on the putative role of DNA methylation at CpG sites close to trinucleotide repeats in exon 1 in silencing of the AR locus. However, using the HUMARA method, we and others have observed that approximately 30% of healthy elderly volunteers appear to have clonal hematopoiesis. This observation is at odds with the concept that normal hematopoiesis is a polyclonal process, suggesting that the finding of monoclonality or oligoclonality in a high percentage of healthy volunteers by using the HUMARA method, is a technical artifact. To address this issue, we developed a clonality assay based on gene expression of five X-linked polymorphic genes and found no evidence of clonal hematopoiesis in healthy elderly volunteers, although we confirmed extreme skewing of X inactivation (consistent with monoallelic methylation of AR) in 30% of the study subject when analyzed by HUMARA (Swierczek et al., Blood 2008). In the present studies, we have validated the accuracy and reproducibility of our quantitative transcription-based clonality assay (qTCA) using two different methods for quantifying gene expression and compared the results with those obtained using the HUMARA method. DNA and RNA were extracted from peripheral blood samples from 31 healthy female volunteers (age in years as follows: range, 22-55; mean, 35; median, 34). RNA was reverse transcribed (RT) and analyzed by using our qTCA in which expression of three polymorphic genes (MPP1, IDS and FHL1), that are subject to X inactivation, is quantified by allele-specific, real-time RT-PCR. Based on DNA analysis, 25 of the 31 (80%) volunteers were polymorphic for at least one of the test genes. Results are reported as the percentage of each of the two single nucleotide polymorphisms (SNPs) that is present in the sample (e. g., 60% A; 40% G). PCR primers are designed to provide maximum discrimination between SNPs with >13 PCR cycles (i. e., 13 log2) separating true-positive from false-positive amplification. Aliquots of the isolated RNA from the test samples were sent to an independent investigator (JJ), at a separate institution, who was blinded to the results of our qTCA, and the allele ratio was determined by using a different technique (quantitative pyrosequencing). Comparison of the results, confirmed the accuracy and reproducibility of the two methods with coefficients of correlation for each gene as follows: (MPP1, r=0.9385; IDS, r=0.8565; FHL1, r=0.8657). One of the 25 informative females (4%) showed extreme skewing (SNP ratio >75%:25%) of X inactivation by both methods. Based on allelic differences in the number of CAG repeats, 29/31 participants were informative in the HUMARA. Among most of the samples, a good correlation was observed between the pattern of X chromosome inactivation as determined by HUMARA and that determined by both qTCA and quantitative pyrosequencing, however, 8/29 (27%) samples analyzed by the HUMARA showed extreme skewing of allele methylation (ratio >75%:25%). Of the 8 subjects with extreme skewing, 3 were homozygous (i. e., non-informative) for all of the X-chromosome polymorphic genes used in the qTCA. Samples from the 5 informative participants were analyzed by using the qTCA, and, in contrast to the HUMARA results, only one subject showed extreme skewing of the SNP ratio (the same subject as identified in the original qTCA). We also quantified HUMARA gene expression using the difference in the number of exon 1 CAG repeats between the two AR alleles as the polymorphic marker. These experiments showed that, of the 8 volunteers with skewing of X inactivation based on HUMARA, 5 had skewing of AR allele expression and 3 had expression of both AR alleles, indicating that the correlation between DNA methylation at the AR locus and AR mRNA transcription is inconsistent. In conclusion, we found a good correlation between the HUMARA and qTCA in some females; however, this was not the case in many healthy females both elderly and young. These experiments demonstrate the accuracy and reproducibility of the qTCA and confirmed that this technique is not subject to the artifact of aberrant skewing of X-inactivation due to monoallelic methylation of AR that limits the applicability and value of the HUMARA. Disclosures:No relevant conflicts of interest to declare.

Clonal nature of odontogenic tumours

Although clonal origin is an essential step in the comprehension of neoplasias, there have been no studies to examine whether odontogenic tumours are derived from a single somatic progenitor cell. The purpose of this study was to investigate the clonal origin of odontogenic tumours. Fresh samples of seven ameloblastomas, two odontogenic mixomas, two adenomatoid odontogenic tumour, one calcifying odontogenic cyst, one calcifying epithelial odontogenic tumour (CEOT) and six odontogenic keratocyst (OKC) of female patients were included in this study. After DNA extraction, the HUMARA gene polymorphism assay was performed. Most of the informative odontogenic lesions studied (12 out of 16) showed a monoclonal pattern. Among the polyclonal cases, two were OKC, one CEOT and one odontogenic mixoma. Our results suggest that most odontogenic tumours are monoclonal.

Clonality of large regenerative nodules in liver cirrhosis.

The role of the large regenerative nodule (RN) in hepatocarcinogenesis is not clear, although the incidence of hepatocellular carcinoma (HCC) is high in cirrhotic liver. This study was aimed at clarifying the preneoplastic nature of large RN without atypia. We analyzed the clonality of HCCs and large RNs, ranging in size from 0.6 to 1.2 cm, of cirrhotic liver by X-linked human androgen receptor (HUMARA) gene assay, using the principle of random X chromosome methylation and inactivation in females. Eleven cases of HCC and five cases of large RN without atypia from ten female patients were selected. All HCCs, large RNs and paired non-tumorous tissue from adjacent liver were selectively microdissected from deparaffinized hematoxylin and eosin stained slides. Genomic DNA was isolated and digested with Hha I. Polymerase chain reaction (PCR) amplification of the HUMARA gene was performed using a PCR mixture containing [alpha-32P]-dCTP. The PCR products were separated by gel electrophoresis and analysed by autoradiography. HUMARA was informative in nine out of ten female patients. In the informative 10 HCCs from nine patients, 9 HCCs were monoclonal and one case was polyclonal. The HCC case that showed polyclonality contained many inflammatory cells in the tumor. All of the large RNs were polyclonal. No allelic loss of chromosome 18q was present in the large RNs in constrast to the 3 out of 7 HCCs, which showed allelic deletion in chromosome 18q. We conclude that all or most of the cells composing the large RNs without atypia are polyclonal and the size of a nodule may not be important in hepatocarcinogenesis. This clonality assay may be informative for the differentiation between regenerative and preneoplastic nodules in cirrhotic liver.

Validation of a Novel Clonality Assay in Patients with Clonal Hematologic Disorders

Clonality assays, based on X-chromosome inactivation, discriminate active from inactive alleles. They are useful in the diagnosis and assessment of therapeutic response in clonal hematologic disorders, especially in absence of an identifiable somatic mutations. Skewing of X-chromosome allelic-usage, based on preferential methylation of one of the HUMARA alleles, was reported as evidence of clonal hematopoiesis in ~30% elderly women, precluding the use of this assay in elderly patient (>65 years of age). Using a quantitative, transcriptionally-based clonality assay, we did not detect clonal hematopoiesis in >200 healthy non-elderly women. In view of the susceptibility of aging hematopoietic stem cells to epigenetic dysregulation, we reinvestigated the issue of clonality in forty elderly women (age 65–92, mean 81.3 years), using a novel, quantitative qPCR transcriptional clonality assay. In this assay, mRNA transcribed from five X-chromosome polymorphic genes expressed in peripheral blood neutrophils is quantified by real time, allele specific RT-PCR. We did not detect clonal hematopoiesis in any of the elderly women. However, using HUMARA assay, 30% of these elderly women were detected to have monoallelic methylation of the HUMARA gene locus, consistent with previously reported literature. We concluded that our novel transcriptional clonality assay is suitable for evaluation of clonal hematopoiesis in all women including elderly women (Swierczek S, Agarwal N et al. Blood 2008, July 18 epub). Using this novel assay, we detected clonal hematopoiesis in 31 out of 32 well characterized patients with myeloproliferative disorders:polycythemia vera (all fourteen patients were clonal by our assay and all were JAK2V617F positive),essential thrombocytosis (nine out of ten patients were clonal by our assay, one out of ten patients was cMPLW515L positive, seven out of ten were JAK2 V617F positive; however one subject with low JAK2 V617F allelic burden was polyclonal by our assay), andprimary myelofibrosis (all eight patients were clonal by our assay and two of them were positive for JAK2V617F).In addition, we detected clonal hematopoiesis in 4 patients with unexplained anemia (two eventually evolved in to myelodysplastic syndrome), and in one patient with persistent leukocytosis (eventually found to be cMPLW515L positive). Using our assay we did not detect clonal hematopoiesis in 10 patients with reactive or secondary erythrocytosis, thrombocytosis or leukocytosis. We conclude that our novel transcriptional clonality assay is suitable for detection of clonal hematopoiesis in patients with clonal hematologic disorders, especially in patients lacking known somatic mutation. Studies to detect an emerging clone in milieu of polyclonal hematopoiesis (such as seen in PNH or early stages of clonal hematological disorders) by comparison of X-chromosome allelic usage ratio in myeloid cells and in T lymphocytes are underway.

Hematopoiesis is not clonal in healthy elderly women

AbstractClonality assays, based on X-chromosome inactivation, discriminate active from inactive alleles. Skewing of X-chromosome allelic usage, based on preferential methylation of one of the HUMARA alleles, was reported as evidence of clonal hematopoiesis in approximately 30% of elderly women. Using a quantitative, transcriptionally based clonality assay, we reported X-chromosome–transcribed allelic ratio in blood cells of healthy women consistent with random X-inactivation of 8 embryonic hematopoietic stem cells. Furthermore, we did not detect clonal hematopoiesis in more than 200 healthy nonelderly women. In view of the susceptibility of aging hematopoietic stem cells to epigenetic dysregulation, we reinvestigated the issue of clonality in elderly women. Forty healthy women (ages 65-92 years; mean, 81.3 years) were tested by a novel, quantitative polymerase chain reaction (qPCR) transcriptional clonality assay. We did not detect clonal hematopoiesis in any of the tested subjects. We also tested DNA from the same granulocyte samples using the methylation-based HUMARA assay, and confirmed previous reports of approximately 30% extensively skewed or monoallelic methylation, in agreement with likely age-related deregulated methylation of the HUMARA gene locus. We conclude that the transcriptionally based X-chromosome clonality assays are suitable for evaluation of clonal hematopoiesis in elderly women.

Cryptic mosaicism involving a second chromosome X in patients with Turner syndrome

The high abortion rate of 45,X embryos indicates that patients with Turner syndrome and 45,X karyotype could be mosaics, in at least one phase of embryo development or cellular lineage, due to the need for the other sex chromosome presence for conceptus to be compatible with life. In cases of structural chromosomal aberrations or hidden mosaicism, conventional cytogenetic techniques can be ineffective and molecular investigation is indicated. Two hundred and fifty patients with Turner syndrome stigmata were studied and 36 who had female genitalia and had been cytogenetically diagnosed as having "pure" 45,X karyotype were selected after 100 metaphases were analyzed in order to exclude mosaicism and the presence of genomic Y-specific sequences (SRY, TSPY, and DAZ) was excluded by PCR. Genomic DNA was extracted from peripheral blood and screened by the human androgen receptor (HUMARA) assay. The HUMARA gene has a polymorphic CAG repeat and, in the presence of a second chromosome with a different HUMARA allele, a second band will be amplified by PCR. Additionally, the CAG repeats contain two methylation-sensitive HpaII enzyme restriction sites, which can be used to verify skewed inactivation. Twenty-five percent (9/36) of the cases showed a cryptic mosaicism involving a second X and approximately 14% (5/36), or 55% (5/9) of the patients with cryptic mosaicism, also presented skewed inactivation. The laboratory identification of the second X chromosome and its inactivation pattern are important for the clinical management (hormone replacement therapy, and inclusion in an oocyte donation program) and prognostic counseling of patients with Turner syndrome.

G6PD deficiency from lyonization after hematopoietic stem cell transplantation from female heterozygous donors

To determine whether during hematopoietic stem cell transplantation (HSCT), X-chromosome inactivation (lyonization) of donor HSC might change after engraftment in recipients, the glucose-6-phosphate dehydrogenase (G6PD) gene of 180 female donors was genotyped by PCR/allele-specific primer extension, and MALDI-TOF mass spectrometry/Sequenom MassARRAY analysis. X-inactivation was determined by semiquantitative PCR for the HUMARA gene before/after HpaII digestion. X-inactivation was preserved in most cases post-HSCT, although altered skewing of lyonization might occur to either of the X-chromosomes. Among pre-HSCT clinicopathologic parameters analyzed, only recipient gender significantly affected skewing. Seven donors with normal G6PD biochemically but heterozygous for G6PD mutants were identified. Owing to lyonization changes, some donor-recipient pairs showed significantly different G6PD levels. In one donor-recipient pair, extreme lyonization affecting the wild-type G6PD allele occurred, causing biochemical G6PD deficiency in the recipient. In HSCT from asymptomatic female donors heterozygous for X-linked recessive disorders, altered lyonization might cause clinical diseases in the recipients.

JAK2 Mutation in Granulocytes and Platelets and X-Chromosome Gene-Based Clonal Analysis in Chronic Myeloproliferative Disorders.

BCR/ABL-negative chronic myeloproliferative disorders (CMPDs) are considered to arise in a pluripotent progenitor cell. High prevalence of a point mutation in Janus Kinase 2 (JAK2) exon12 gene (JAK2-V617F) in CMPDs has been observed in many reports. Since most studies, however, are restricted mainly in granulocyte lineage, information about the JAK2 gene status in other cell lineage is limited. Heparinized peripheral blood was obtained from 49 patients with polycythemia vera (PV), 109 with essential thrombocytosis (ET), and 5 with chronic idiopathic myelofibrosis (CIMF). After centrifugation, platelets were collected from the upper plasma layer. The remaining blood layer was subjected to Ficoll-Hypaque density gradient centrifugation. Granulocytes were obtained from the pellet and T-cells recovered from the interface were further positively selected using either anti-CD3 or anti-CD4 immunoconjugated magnetic beads (Miltenyi Biotec, Germany). After DNA and RNA extraction, PCR amplified JAK2 exon 12 gene was sequenced to check the presence of JAK2-V617F mutation. Furthermore, X-chromosome linked clonal analysis using human androgen receptor (HUMARA) gene was carried out in 58 females. Correlation between the mutation status and clinical data was analyzed using statiscal software R (The R Development Core team). In PV, the frequency of JAK2-V617F mutation in granulocytes and platelets was 72.3 % and 74.3%, respectively (p-value 0.844). In ET, this mutation rate was 51.9% in granulocytes and 73% in platelets and the difference was significant (p-value 0.005). In all CMPDs, the cases showing JAK2-V617F mutation in granulocytes always had the mutation in platelets as well, but in one case of PV and 11 cases of ET, the JAK2-V617F mutation was observed only in platelets. T cell fraction was negative for JAK2-V617F mutation in all cases examined. White blood cell count was significantly higher in cases of JAK2-V617F mutation in their platelets compared to that in cases without this mutation (12.6 × 109/l vs. 9.2 × 109/l), but hemoglobin level and platelet count did not differ between the two groups (14.9g/l vs. 14.6 g/l, 81.4 × 109/l vs. 95.2 × 109/l). In addition, cases showing this mutation in platelets were more likely to be associated with thrombosis than cases showing the wild type gene (p-value 0.018). On clonal analyses using the HUMARA gene, 6/8 patients with PV, 15/27 patients with ET, and 1/1 patient with CIMF demonstrated a monoclonal pattern in their granulocytes. Interestingly, in 23 cases showing the JAK2-V617F mutation, 7 patients showed the polyclonal HUMARA pattern; in 13 cases without mutation, 7 showed the monoclonal HUMARA pattern. The discrepancy of JAK2-V617F mutation rate between platelets and granulocytes in ET suggests that analysis of platelet fraction is advantageous for detecting the mutation. This finding also suggests that the JAK2 mutation could be involved only in megakaryocyte lineage in some ET patients. HUMARA analysis confirmed that some ET patients with monoclonal disease lack the JAK2-V617F mutation, which is consistent with previous reports.

Glucose-6-Phosphate Dehydrogenase Deficiency in Female Octogenarians, Nanogenarians, and Centenarians

Age-related skewing of X-chromosome inactivation leading to glucose-6-phosphate dehydrogenase (G6PD) deficiency in elderly women in a population with prevalent G6PD gene mutations was investigated. G6PD activity was measured biochemically. G6PD mutations were detected by polymerase chain reaction (PCR) and allele-specific extension, and analyzed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and Sequenom MassARRAY. X-chromosome inactivation was quantified by semiquantitative PCR for the HUMARA gene, before and after HpaII digestion. In 173 women (median age: 90 years; range, 80-107 years), 18 heterozygotes for G6PD mutations were identified. Three heterozygotes were G6PD deficient, owing to skewed X-chromosome inactivation affecting the wild-type allele. Fifteen heterozygotes, with skewing apparently affecting the mutant alleles, had normal but significantly lower G6PD levels. At 1.73%, G6PD deficiency was significantly more frequent than expected from population screening at birth. Due to skewed X-chromosome inactivation, elderly women in populations with prevalent G6PD mutations are at risk of G6PD deficiency.

Non-skewed X-inactivation may cause mental retardation in a female carrier of X-linked α-thalassemia/mental retardation syndrome (ATR-X): X-inactivation study of nine female carriers of ATR-X

X-linked alpha-thalassemia/mental retardation syndrome (ATR-X) is a syndromic form of X-linked mental retardation. We investigated the X-inactivation status of nine female ATR-X carriers by methylation-specific PCR of the HUMARA gene. Six carriers demonstrated a skewed X-inactivation pattern (>90:10) and one showed a non-skewed pattern (72:28), while two were uninformative because of homozygosity for the CAG repeat polymorphic alleles in the HUMARA. Only the carrier mother who showed non-skewed X-inactivation had moderate mental retardation. These findings suggest that mutations in ATRX may cause mental retardation in females, if the X chromosome carrying mutated ATRX is not properly inactivated.

Clonality in Granulocytes Detected by an Improved HUMARA Assay: A Good Prognostic Marker in Bone Marrow Failure Patients Exhibiting Chromosomal Abnormalities of Indefinite Significance.

Some patients with aplastic anemia (AA) and approximately 40% of patients with refractory anemia (RA) of myelodysplastic syndrome exhibit karyotypic abnormalities in bone marrow dividing cells. Although some of the patients undergo evolution to acute myeloid leukemia (AML), others follow a clinical course similar to AA patients without chromosomal abnormalities. Except for several abnormalities such as −7 and 5q-, the clinical significance of such chromosomal abnormalities in bone marrow failure patients remains unclear. We recently developed a reliable HUMARA assay capable of detecting a clonal population in granulocytes which constitutes 30% or more of total granulocytes (Blood . 2003; 102:1211–1216). Studying correlation between chromosomal abnormalities and the presence of clonality may help in understanding the pathogenetic role of chromosomal abnormalities in AA and RA. We thus analyzed 50 acquired AA and 28 RA female patients who were heterozygous for the HUMARA gene. Chromosomal abnormalities such as add(5)(q13), 9q–9q+ and del(7)(q14q22) were found in 8% of AA and 21% of RA patients. Clonality was detected in 38% of AA patients and 39% of RA patients. Incidence of chromosomal abnormalities in patients with clonality (27%) was higher than that in patients without clonality (4%, p<0.01). In two AA patients who respectively exhibited add(5)(q13) in 10% and +8 in 38% dividing cells, clonality was not detected and these abnormal clones became undetectable at the time of subsequent bone marrow examination. Clonality was detected in the other 2 AA patients respectively exhibiting 9q–9q+ in 40% and del(7)(q14q22) in 25% dividing cells, and in all 5 RA patients respectively exhibiting +8 in 10%, del(5)(q13q31), dup(1)(q32q12) in 90%, del(5)(q13), add(11)(q23), inv(9) in 65% and X,-X in 100% of dividing cells. None of the 50 AA patients including 2 patients with clonality and chromosomal abnormalities underwent evolution to AML during 2-year follow up while one of 28 RA patients who exhibited del(5)(q13q31) progressed to AML. The proportion of clonal granulocytes in total granulocytes estimated by the HUMARA assay remained unchanged in most patients with clonality except for the transformed one. These data indicate that the chromosomal abnormality in bone marrow dividing cells is not necessarily associated with presence of clonal granulocyte population in peripheral blood and that detection of clonality in granulcytes in bone marrow failure patients with chromosomal abnormalities of indefinite significance is useful in predicting prognosis of these patients.

Wiskott–Aldrich syndrome in a female with skewed X-chromosome inactivation

Wiskott–Aldrich syndrome (WAS) is an X-linked recessive disorder characterized by immunodeficiency, eczema, and thrombocytopenia with small platelets. The phenotype of affected males is usually severe, although female carriers of the disorder have no clinical signs of the genetic defect. This is explained by the preferential selection of the normal, nonmutated X-chromosome, as the active allele in hematopoietic cells. In the present article we describe a female case of WAS, with a G-to-A transition in the WASP gene at nucleotide 291. She displays mild thrombocytopenia, with both normal and small-sized platelets. A methylation analysis of the HUMARA gene showed a nonrandom X-chromosome inactivation pattern in which the X-chromosome carrying the normal WASP gene was preferentially inactivated, leaving the mutant gene active. Thus, our results suggest that skewed X-inactivation, favoring the WASP-mutated allele, is the mechanism underlying the WAS phenotype of this girl. Moreover the results alert us to the fact that particular females, with a family history of WAS, may develop certain signs of the disease.