A highly informative X-chromosome probe, M27 beta, can be used for the determination of tumour clonality

Clonal hematopoiesis in hematological disorders: Three different scenarios

Clonality studies can establish the single-cell origin of tumors and thus differentiate clonal malignant and premalignant processes from reactive polyclonal processes. Detection of clonal cells may be based on direct tracking of cell lineage-specific sequences or disease-specific somatic mutations identifying the clonal population. Historically, clonal hematopoiesis was defined using the principle of X-chromosome inactivation based on observation that in circulating clonal cells, only one of the active chromosomes was expressed. In myeloproliferative neoplasms (MPNs) virtually all circulating erythrocytes, platelets, and granulocytes are products of single mutated stem cells that preferentially differentiate into the myeloid rather than lymphoid lineage. Thus, clonal differentiated myeloid cells co-exist in circulation with polyclonal long-lived T lymphocytes that originated before the MPN-initiating somatic clonal event. Chronic lymphocytic leukemia (CLL) starts in a differentiating B cell, but other lymphoid lineages and myeloid cells remain polyclonal. Normal T and B cells co-exist with the CLL clone, but are diluted by the massively expanded CLL population, which outnumbers the residual normal cells. Clonal hematopoiesis of undetermined potential (CHIP) has been identified by whole-genome sequencing of healthy individuals. These clones contain a specific somatic mutation previously considered to be disease defining but are detected in only a small proportion of circulating leukocytes, and there is no obvious suppression of normal hematopoietic stem cells. However, more studies are needed to properly define these clones, their persistence or disappearance, and their relative propensity for transforming into leukemias, myeloproliferative neoplasms, or other clonal hematological malignancies.

Screening for clonal hematopoiesis as a predictive marker for development of therapy-related myeloid neoplasia (t-MN) following neoadjuvant therapy for breast cancer: a Southwest Oncology Group study (S0012)

A serious complication associated with breast cancer treatment is the increased risk for development of therapy-related myeloid neoplasms (t-MN). To determine whether dose-intensive adjuvant regimens for breast cancer induce genetic damage to hematopoietic stem cells, defined by the emergence of clonal hematopoiesis, and whether detection of clonal hematopoiesis could be used as an early marker for the subsequent development of t-MN, the Southwest Oncology Group designed a pilot clonality investigation to estimate the incidence of clonal hematopoiesis during and shortly after completion of the dose intensive neoadjuvant regimens for high-risk breast cancer patients. Peripheral blood samples from 274 patients obtained prior to treatment, at time of surgery, and at 6 and 12 months post-surgery were examined by two different clonality assays: the HUMARA (HUMan Androgen Receptor) assay to estimate the incidence of early genetic damage by clonal proliferation, and microsatellite instability (MSI) testing to screen for LOH or defective DNA mismatch repair mechanisms. Clonal hematopoiesis was negative in 93.5% of the samples analyzed. Five patients showed a HUMARA-positive/MSI-negative pattern, and no patients showed a HUMARA-negative/MSI-positive pattern. With a median follow-up of 3.1 years, one patient in our study developed t-AML at 3 years 5 months after randomization. Our results indicate that clonal hematopoiesis assays performed within the 2 years following dose-intensive neoadjuvant therapy failed to identify an emerging clonal hematopoietic stem cell population. Longer clinical follow-up will be necessary to define better the positive predictive value of detecting clonal hematopoiesis in the HUMARA+/MSI- cases.

Clonal Analysis of Agnogenic Myeloid Metaplasia

Agnogenic myeloid metaplasia (AMM) is a chronic myeloproliferative disorder that leads to a sustained proliferation of megakaryocytes and an increase of reticulin fibers within the bone marrow. Blood and bone marrow samples from patients with advanced AMM with fully developed myelofibrosis as well as cases in the cellular phase of the disease were investigated for clonality. Clonality was studied by X-linked restriction length polymorphism in conjunction with DNA methylation patterns. Granulocytes and total bone marrow cells proved to be monoclonal in origin whereas at least a minor portion of the peripheral lymphocytes were not clonally derived. Our findings indicate that the cellular phase of AMM as well as the fully developed disease progressed to myelofibrosis represent a monoclonal proliferation of pluripotent hematopoietic stem cells.

The human androgen receptor X-chromosome inactivation assay for clonality diagnostics of natural killer cell proliferations

Clonality is a frequently exploited characteristic of lymphoid malignancies. However, in the natural killer (NK) cell subset of large granular lymphocyte proliferations, clonality is difficult to prove because of the lack of specific genetic markers, such as immunoglobulin or T-cell receptor gene rearrangements. The human androgen receptor (HUMARA) assay, a polymerase chain reaction-based X-chromosome inactivation assay, is a potential diagnostic tool in these disorders. Although there is much experience with X-chromosome inactivation assays in myeloid proliferations, these assays have found only very limited application in clonality assessment of NK cell proliferations. We applied the HUMARA assay in laboratory diagnostics for detection of clonality in NK cell proliferations. We describe its test performance and report three cases in which clonality of NK cell populations was investigated by use of this assay. Our results demonstrate the usefulness of the HUMARA assay in the diagnostic workup of NK cell proliferations.

Polycythemia vera and its molecular basis: an update

The molecular basis of polycythemia vera is discussed in the context of the JAK2 V617F mutation, in our view the most important advance in understanding the pathogenesis of polycythemia vera. This chapter discusses the nature of the JAK2 V617F mutation including the studies demonstrating its role in erythropoietin independence and hypersensitivity and endogenous erythroid colony formation. The evolving evidence that JAK2 V617F is not specific for polycythemia vera pathogenesis and the development of disease phenotype is presented as well as alternative candidates for pathogenic mutations such as the protein tyrosine phosphatases and SOCS-3. Finally, the clinical correlations and implications of the JAK2 V617F mutation are discussed.

Lessons from familial myeloproliferative disorders

By definition, myeloproliferative disorders (MPDs) are caused by an acquired somatic mutation of a hematopoietic progenitor/stem cell and have sporadic occurrence. However, well-documented families exist with first-degree relatives acquiring one or several MPDs. It is reasonable to assume that the germ-line mutation(s) or genetic background must facilitate or predispose for one or several somatic mutation(s) that lead to the MPD that is indistinguishable from the sporadic form. This is best documented in familial polycythemia vera (PV), which appears to be inherited as an autosomal dominant disorder with incomplete penetrance. However, there are also families wherein members develop any combination of MPDs, including PV, essential thrombocythemia (ET), chronic myelocytic leukemia (CML), and idiopathic myelofibrosis (IMF). A separate group of familial diseases is the familial thrombocythemias, wherein germ-line mutations in the genes for thrombopoietin or its receptor, MPL, cause polyclonal hereditary thrombocythemia, which may be clinically indistinguishable from ET. Patients with the congenital polycythemic condition "primary familial and congenital polycythemia" (PFCP) have characteristically decreased erythropoietin (Epo) levels similar to PV, hypersensitive erythroid progenitors, and low Epo levels; as such, this condition is often confused with PV. Therefore, PFCP will also be discussed here, while other congenital polycythemic states such as the Chuvash polycythemia that have elevated or inappropriately normal Epo levels will be omitted from this review in view of their distinct phenotype and unique laboratory features.

Molecular analysis of clonality of sporadic angiomyolipoma

Angiomyolipoma, which consists of three intimately intermixed components, smooth muscle, blood vessels, and adipose tissue, is variably considered a hamartoma, a choristoma or a true neoplasm. This study has investigated the clonality of sporadic angiomyolipomas in seven women, each with a single lesion, by determining the pattern of X-chromosome inactivation. Polymerase chain reaction (PCR) amplification of the highly polymorphic human androgen receptor gene (HUMARA) was performed on the DNA extracted from the paraffin-embedded lesional tissue microdissected to sample the admixed smooth muscle and blood vessel component (SMC/BV) and the adipose tissue component. All seven patients were heterozygous for HUMARA polymorphism upon amplification of undigested DNA from non-lesional tissue and were therefore informative for further analysis. In all patients, lesional DNA, representative of the components, was predigested with HpaII restriction enzyme for amplification of the methylated allele. In six patients, the lesions were clonal, while in one, polyclonal. The polyclonal lesion was small and had less than 20 per cent SMC/BV component. Microdissected SMC/BV component was clonal in 6/7 lesions; the scanty SMC/BV in the remaining lesion did not yield amplifiable DNA. Microdissected adipose tissue was polyclonal in all seven lesions. Angiomyolipomas are three clonal lesions due to a clonal smooth muscle cell and blood vessel component, while the polyclonal adipose tissue is probably metaplastic or reactive.

Field cancerization, clonality, and epithelial stem cells: the spread of mutated clones in epithelial sheets

There has been considerable debate about the origin of human tumours, whether they arise from a single cell and are clonal populations or whether there needs to be some sort of co-operativity between cells for the neoplastic process to begin. Current theories subscribe to the clonal view, where a series of mutations in one cell begins a process of selection and clonal evolution leading to the development of the malignant phenotype. This review approaches this problem by asking how mutated clones, once established, spread through tissues before becoming overtly invasive. While there is substantial evidence in favour of independent origins of each tumour from a unique mutated clone, there are instances where such clones expand and remain cohesive, often involving a large area of tissue. The main example is the movement of mutated clonal crypts through the colorectal epithelium, by the process of crypt fission. In passing, the clonal architecture of early, pre-invasive lesions is examined, often with some surprising results.

Amelogenin dosage compensation in carcinoma of colon, lung, liver and kidney, is not a marker of clonality in males

The analysis of patterns of X-chromosome inactivation is becoming increasingly utilized as a marker of clonal composition of tissues from women. To date, however, no analogous system has been found for the study of clonality in tissue from men. In the current study, the methylation patterns for portions of the amelogenin genes are tested, which are encoded on both the X- and Y-chromosome (AMGX and AMGY). The polymerase chain reaction (PCR) was used to amplify portions of AMGX and AMGY from genomic DNA of carcinomas of the colon, lung, liver and kidney, as well as from matched normal somatic tissues. The amplification target included Alu I methylation sensitive restriction endonuclease sites as well as a 189 bp sequence which is present in AMGX but is absent in AMGY. Polymerase chain reaction amplification of AMGX and AMGY was successful using genomic DNA from both tumour and normal control tissue in 24 of the 26 cases. Pretreatment of genomic DNA with Alu I blocked amplification of AMGX in all cases from both normal tissue and tumour. This indicates that AMGX and AMGY undergo a non-random pattern of methylation in both normal tissues and in tumours, precluding their use as a marker of clonality. Methylation of Alu I sites in AMGY suggests that the amelogenin genes undergo dosage compensation, which raises the possibility that the expression of amelogenin is not restricted to the development of the tooth bud but may also play some other role in various tissues of the body.

Cytogenetic and molecular genetic demonstration of polyclonality in an acinic cell carcinoma

The paradigm that human malignancies are monoclonal has been questioned during recent years by the finding of unrelated, cytogenetically aberrant clones in short-term cultures from certain tumour types, notably carcinomas of the breast, skin and upper aerodigestive tract. In order to analyse whether cytogenetically unrelated clones are also unrelated at the molecular level, we analysed the X-chromosome inactivation status in cell cultures from a cytogenetically highly polyclonal acinic cell carcinoma of the parotid gland. By using cell cultures dominated by a single abnormal clone, obtained through in vitro culturing for 3-5 passages, we showed that the different clones must indeed have originated from different cells.

An update on clonality, cytokines, and viral etiology in Langerhans cell histiocytosis

Many etiologies have been proposed for Langerhans cell histiocytosis (LCH). Recent scientific studies have clearly provided new insights into the etiology and pathogenesis of the disease. The possible role of viruses has not been completely negated, but no viral genomes have been consistently detected in LCH lesions. Other studies do not indicate that LCH arises from a primary defect in the immune system, although altered immune responses and immune dysfunction may play a role in the pathophysiology of the disease. Definitive results have been gained from molecular studies of clonality, however. These have definitively established that LCH is a clonal histiocytic disease rather than a reactive polyclonal disorder.

Pathogenetic Aspects of Myelodysplastic Syndromes

The myelodysplastic syndromes (MDS) are acquired clonal disorders of the bone marrow. They were clearly defined in morphological terms by the French-American-British (FAB) group in 1982, as five conditions each with their own diagnostic criteria, but with the shared characteristics of ineffective blood cell production in one or more cell line, morphological dysplasia and a variable propensity to evolve into acute myeloid leukaemia (AML). In clinical practice patients typically present in old age with macrocytic anaemia, cytopenias, monocytosis and accumulation of marrow blast cells leading in time to fatal bone marrow failure or AML. To date treatment is unable to alter the natural history of MDS except in those few individuals who are able to undergo allogeneic progenitor cell transplantation.

Giant cell tumor of tendon sheath is a polyclonal cellular proliferation

Giant cell tumor of tendon sheath (GCTTS) is a common soft tissue tumor. Immunophenotypical evidence suggests it is of synovial cell origin. There is controversy regarding the underlying nature of this lesion, specifically whether it is a neoplastic or nonneoplastic (ie, reactive or hyperplastic) process. Karyotypic abnormalities have been identified in GCTTS and interpreted as evidence of neoplasia, although the finding of similar karyotypic abnormalities in unequivocally nonneoplastic proliferations raises questions about using such findings to define a neoplasm. In an attempt to resolve this uncertainty, a polymerase chain reaction (PCR)-based assay for methylation of the X-linked human androgen receptor gene (HUMARA) was used to assess whether GCTTS is a clonal or polyclonal proliferation. DNA was isolated from formalin-fixed, paraffin-embedded tissue blocks from eight cases of digital GCTTS in female subjects; two cases of hepatocellular carcinoma (HCC) were used as clonal controls. Seven of eight cases of GCTTS were informative, and each showed a polyclonal proliferation, whereas both cases of HCC were clonal. Our results indicate that GCTTS is a nonneoplastic proliferation, if one accepts that a population of cells forming a tumorous mass must show clonality to be classified as a neoplasm. Our results emphasize that simple karyotypic abnormalities do not define a neoplasm. It remains to be determined whether GCTTS is a reactive or hyperplastic process.

Clonality analysis in tumours of women by PCR amplification of X-linked genes

Modifications have been made to two polymerase chain reaction (PCR) methods for clonality analysis based on the inactivation patterns of two highly polymorphic X-linked genes encoding the androgen receptor (AR) and monoamine oxidase A (MAOA). These methods have been used to examine the clonal nature of frozen tissues from 42 tumours and 25 non-tumour controls from female subjects. Unbalanced inactivation patterns of the genes, which indicate monoclonality, were frequently observed in tumours of heterozygous (informative) cases (18/35 = 51.4 per cent for the AR gene, 9/30 = 30 per cent for the MAOA gene, and 21/38 = 55.2 per cent for both). Among 23 informative non-tumour controls, only one (4.3 per cent), a reactive lymph node, showed skewing in the AR gene. Successful detection of monoclonality was found to depend on the proportion of tumour cells in the tissues examined. None of the AR or MAOA informative cases containing less than 50 per cent of tumour cells showed imbalance in inactivation patterns. With more than 50 per cent of tumour cells in the samples, 66.6 per cent (18/27) of AR and 39.1 per cent (9/23) of MAOA informative cases showed allelic imbalance, with a combined frequency of 72.4 per cent (21/29) of both genes. Our results demonstrate that the methods described are useful for clonal analysis of tissue samples from female patients.

Assessment of Clonality and Its Relevance in Acute Myeloid Leukaemia and Bone Marrow Transplantation

The study of clonality in females is a useful tool in assessing states of neoplastic cell expansion in myeloid malignancies and remission status after chemotherapy and bone marrow transplant. Various experimental techniques have been developed based on the Lyon Hypothesis of X chromosome inactivation in females. Specific enzymes are utilised to distinguish active from inactive X chromosomes, distinctive patterns of which are then visualised by Southern blotting or more recently PCR. A valuable contribution to the nature of myeloid malignancies has been gained by these means.

X-chromosome inactivation is mostly random in placental tissues of female monozygotic twins and triplets

Patterns of X-chromosome inactivation in chorion, amnion, and cord from 79 pairs of twins were examined. Seven sets of triplets were included in the analysis, both as twin pairs and triplets. Twins were stratified as dizygotic (DZ), monozygotic (MZ), monochorionic, and dichorionic and were selected for birth weight discordance, discordance for congenital anomalies, twin-twin transfusion syndrome, and various patterns of vascular anastomosis. X-inactivation was predominantly symmetric. Chorion was the most likely tissue to show asymmetric X-inactivation and was found most frequently in MZ dichorionic twins. There was no correlation of X-inactivation pattern with the selected clinical criteria. This study does not confirm that asymmetric X-inactivation in embryonic tissues is a common phenomenon in female twins, including monozygotic twins.

Factor VIII gene inversions in severe hemophilia A patients

The mutations causing hemophilia A are very heterogeneous with the exception of a large inversion involving intron 22 in the factor VIII (FVIII) gene which appears to be the underlying defect in approximately 45% of all severely affected patients (FVIII < or = 1%). In these patients it is thought that the factor VIII gene is disrupted within intron 22 due to inappropriate recombination of FVIIIA with one of 2 homologous regions upstream of the factor VIII gene resulting in a large (approximately 500 kb) inversion. The inversion can be detected by Southern blot analysis and greatly enhances the accuracy of genetic counselling services available to families with severe hemophilia A. We report here the presence of this mutation in a study of 27 unrelated families with severe hemophilia. The factor VIII inversion was identified in 12 of 27 (44%) severe hemophilia A patients and has been successfully used for direct carrier analysis and prenatal diagnosis.

Langerhans'-cell histiocytosis (histiocytosis X)--a clonal proliferative disease

BACKGROUND

The lesions of Langerhans'-cell histiocytosis (histiocytosis X), a proliferative histiocytic disorder of unknown cause, contain histiocytes similar in phenotype to dendritic Langerhans' cells. The disease ranges in severity from a fatal leukemia-like disorder to an isolated lytic lesion of bone. Intermediate forms of the disease are usually characterized by multiorgan involvement, diabetes insipidus, and a chronic course.

METHODS

To determine whether Langerhans' histiocytosis is a polyclonal reactive disease or a clonal disorder, we used X-linked polymorphic DNA probes (HUMARA, PGK, M27 beta[DXS255], and HPRT) to assess clonality in lesional tissues and control leukocytes from 10 female patients with various forms of the disease. Lymphoid clonality was also assessed by analysis of rearrangements at immunoglobulin and T-cell-receptor gene loci.

RESULTS

The HUMARA assay detected clonal cells in the lesions of 9 of the 10 patients: 3 patients had acute disseminated disease, 3 had unifocal disease, and 3 had intermediate forms. The percentage of clonal cells closely approximated the percentage of CD1a-positive histiocytes in each lesion. Clonality was also confirmed in two of nine cases with the PGK or M27 beta probe. Extreme constitutional lyonization precluded assessment of clonality in the 10th case. Lymphoid clonality was ruled out in all cases.

CONCLUSIONS

The detection of clonal histiocytes in all forms of Langerhans'-cell histiocytosis indicates that this disease is probably a clonal neoplastic disorder with highly variable biologic behavior. Thus, genetic mutations that promote clonal expansion of Langerhans' cells or their precursors may now be identified.

Clonal analysis of human adrenocortical carcinomas and secreting adenomas

OBJECTIVES

Adrenocortical tumours in man are characterized mainly on biochemical, anatomical and histological grounds which establish their secretory pattern and, with some uncertainty, their benign or malignant nature. To study further these tumours and eventually to shed some light on their pathogenesis, we determined their clonal composition.

METHODS

Clonal composition was determined by X-chromosome inactivation analysis on tumour and leucocyte DNA using three markers: M27 beta, phospho-glycero-kinase (PGK) and hypoxanthine-phosphoribosyl transferase (HPRT) with 88, 33 and 27% heterozygosity rates respectively.

PATIENTS

Clonal analysis was performed on 25 tumours from 19 heterozygous female patients: four had a carcinoma, 14 had a single secreting adenoma, and one had autonomous bilateral macronodular hyperplasia with Cushing's syndrome (seven adenomas examined).

RESULTS

The malignant tumours had patterns indicative of monoclonality. The single adenomas displayed contrasting results with patterns indicative of monoclonality in eight cases, and patterns indicative of polyclonality in six cases; monoclonal adenomas were larger and had a higher prevalence of nuclear pleomorphism than the apparently polyclonal adenomas. In the patient with bilateral macronodular hyperplasia, different clonal patterns were present in different adenomas: whereas a clear monoclonal pattern was observed in the three adenomas of the right gland, in which the active X-allele was not always the same, in two interpretable adenomas of the left gland, a moderately skewed pattern suggested a partial monoclonal component.

CONCLUSIONS

These data show that adrenocortical carcinomas are monoclonal and suggest that adenomas may arise from a single cell or from more than one cell under the putative action of local growth factors. In adenomas, which until now had appeared homogeneous, this genetic heterogeneity may reflect different pathophysiological mechanisms or it may represent different stages of a common multistep process exceptionally occurring in a single patient with bilateral macronodular hyperplasia.

Pyridoxine-refractory congenital sideroblastic anaemia with evidence for autosomal inheritance: exclusion of linkage to ALAS2 at Xp11.21 by polymorphism analysis

A son and daughter of unaffected parents had transfusion dependent, pyridoxine-refractory sideroblastic anaemia from birth. Their haemoglobin levels were 4.3 and 6.4 g/dl, respectively. delta-Aminolaevulinate synthase activity in erythroblasts from fractionated marrow of the sister was 135 pmol delta-aminolaevulinate formed/10(6) erythroblasts/hour (normal range = 110-650 pmol). While mutations of the erythroid-specific delta-aminolaevulinate synthase gene (ALAS2) at Xp11.21 have been reported in patients with X linked sideroblastic anaemia, sequence analysis of the ALAS2 gene in the son did not identify any mutations in the coding region, the intron/exon boundaries, or the 1 kb 5' promoter region. A useful polymorphism was found in the 3' region of the ALAS2 gene, a G to A transition, 220 nt 3' of the AATAAA polyadenylation signal. Mismatch PCR at this site and subsequent discrimination by XmnI restriction analysis of 148 alleles identified the gene frequency of this polymorphism to be 25%. Analysis of the inheritance of this intragenic polymorphism showed that the affected sibs received different maternal alleles at the ALAS2 locus, excluding mutations in this gene as the cause of their sideroblastic anaemia. Furthermore, the absence of a dimorphic erythrocyte population in the mother, coupled with the demonstration of random X inactivation in her peripheral leucocytes, showed that the mother was not the carrier of any X linked sideroblastic anaemia mutation. These results strongly suggest that the sideroblastic anaemia in this family is an autosomal recessive trait.

Analysis of clonality in archival tissues by polymerase chain reaction amplification of PGK-1

Clonality of archival formalin-fixed tissue sections was analyzed by polymerase chain reaction amplification of a portion of the X-linked phosphoglycerate kinase (PGK-1) gene. Amplification was successful in 29 of 36 cases of uterine endometrioid adenocarcinoma. Five of these cases, including both tumor and control tissue from the same patients, were heterozygous for the BstXI polymorphic site of the PGK-1-amplified product, permitting analysis of clonality. Pretreatment of the DNA with HpaII blocked amplification of one of the two PGK-1 alleles from four of five cases of tumor, indicating the clonal pattern of X chromosome inactivation in these cases. In contrast, in DNA from paired control tissues HpaII pretreatment had no effect, indicating a random pattern of X chromosome inactivation in normal tissue. One of the cases of endometrioid adenocarcinoma contained a high proportion (45%) of nontumor cells, precluding the determination of clonality. We conclude that polymerase chain reaction amplification can be used for the determination of the pattern of X chromosome inactivation in formalin-fixed tissue sections. Such an approach makes it feasible to include specimens from archival tissue collections in the analysis of clonality.

Use of X-linked clonal analysis in acute promyelocytic leukemia

X-linked clonal analysis (XLCA) either using Glucose-6-phosphate dehydrogenase (G-6-P-D) polymorphisms or restriction fragment length polymorphisms (RFLP) and methylation analysis has provided considerable understanding of haematologic malignancy. Acute Promyelocytic Leukemia (APL) is characterized by a unique cytogenetic translocation t(15;17), frequent achievement of remission without a preceding phase of marrow hypocellularity after induction chemotherapy and a high rate of clinical response to all-trans retinoic acid (ATRA). In limited studies XLCA has provided insight into the pathogenesis and mechanism of drug action in this disease.

Clonal haematopoiesis in children with acquired aplastic anaemia

The methylation pattern of three X-linked genes, phosphoglycerate kinase (PGK), hypoxanthine phosphoribosyl transferase (HPRT) and DXS255 detected by hypervariable M27 beta probe, was analysed to determine the proportion of aplastic anaemia (AA) with clonal haematopoiesis in Japanese children. Methylation analysis was performed on DNA from separated granulocytes and compared to that of bone marrow derived fibroblasts to exclude selective lyonization in all somatic cells. Of 20 female patients examined, the methylation pattern of at least one gene was informative in granulocyte DNA from 18 patients (90%). Of these, 8/20 patients (40%) were heterozygous for PGK, 8/18 (44%) were heterozygous for HPRT and 17/18 (94%) were heterozygous for DXS255. In 14/18 patients both alleles were equally methylated. Four patients exhibited a unilateral methylation pattern in their granulocytes. The same unilateral pattern was again demonstrated in fibroblasts from two of the four patients suggesting that in the latter one X chromosome was selectively inactivated in all of the somatic cells. The remaining two patients showed a unilateral methylation pattern that was restricted to their granulocytes, suggesting the existence of true clonal haematopoiesis. They responded well to antilymphocyte globulin (ALG) and presently have no evidence of a clonal disorder such as myelodysplastic syndrome (MDS) or paroxysmal nocturnal haemoglobinuria (PNH). Although these results indicate that some children with AA exhibit clonal haematopoiesis, analysis of a greater number of subjects will be required to establish the clinical value of clonal haematopoiesis in patients with AA.

Clonality of chronic neutrophilic leukaemia associated with myeloma: analysis using the X-linked probe M27 beta

AIMS

To determine whether myeloid proliferation was monoclonal or polyclonal in a woman with chronic neutrophilic leukaemia and myeloma.

METHODS

The X-linked probe, M27 beta was used to determine the clonality of the neutrophil population by analysis of restriction fragment length polymorphisms and X inactivation pattern.

RESULTS

A polyclonal pattern of X inactivation was obtained for the neutrophil population in this patient.

CONCLUSION

The myeloid expansion in chronic neutrophilic leukaemia associated with myeloma represents a polyclonal reactive response to the plasma cell clone rather than a co-existent myeloproliferative disorder.

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.

Karyotypic analysis in primary myelodysplastic syndromes

Cytogenetics has provided new insights into the biology and pathogenesis of myelodysplastic syndromes. In patients with refractory anemia, it has provided proof of clonality and has helped differentiate chronic myelomonocytic leukemia from chronic myeloid leukemia. As a prognostic tool, cytogenetics has been predictive of duration of survival and leukemic transformation. However, its role as an independent prognostic factor compared with recent prognostic scoring systems remains to be determined. New techniques such as fluorescent in situ hybridization using chromosome-specific DNA probes may expand the usefulness of cytogenetics. The prognostic impact of cytogenetics may not be fully realized until more effective treatments become available.

The hypervariable DXS255 locus contains a LINE-1 repetitive element with a CpG island that is extensively methylated only on the active X chromosome

The DXS255 locus at Xp11.22 is highly polymorphic due to a 26-bp variable number of tandem repeats (VNTR) motif. In previous studies, one of the MspI sites flanking the VNTR manifested a correlation between methylation and X chromosome inactivation. Here we show, by DNA sequence analysis, that this MspI site is located within the CpG island at the 5' end of a LINE-1 element, which is 2.5 kb from the VNTR. The methylation status of the CpG island was assessed in Southern blotting experiments using the methylation-sensitive enzymes HpaII, HhaI, and BssHII. All these sites were completely methylated on active X chromosomes, consistent with previously reported findings of full methylation of LINE-1 elements throughout the genome. However, on inactive X chromosomes these sites were predominantly unmethylated, although patterns were found to be heterogeneous. The results suggest that LINE-1 elements on the inactive X chromosome are not suppressed by full methylation of their CpG islands. The differential methylation of the DXS255 CpG island provides the basis for a highly informative X inactivation analysis system.

X inactivation as a mechanism of selection against lethal alleles: further investigation of incontinentia pigmenti and X linked lymphoproliferative disease

Thirty-one females with incontinentia pigmenti (IP), 42 controls, and 11 females from four families segregating for X linked lymphoproliferative disease (XLP) were studied for evidence of skewed X inactivation by analysis of methylation at sites in the HPRT, PGK, and M27 beta (DXS255) regions of the X chromosome. Extensive skewing of X inactivation was present in blood from 4/42 (9.5%) control females and 11/31 (35%) of those with IP. This frequency of skewed inactivation was seen in both familial and sporadic cases of IP. Analysis of inactivation in mother/daughter pairs, both affected and control subjects, showed no familial consistency of pattern, arguing against specific mutations being associated with particular patterns of inactivation. In the only informative family where both mother and daughter were affected by IP and showed skewed inactivation, the IP mutation was on the active X chromosome. This argues against cell selection during early embryogenesis being the explanation for the skewed inactivation observed. These data confirm that skewed inactivation of one X is observed in lymphocytes from a significant minority of normal females, and is seen with raised frequency in IP heterozygotes. It is not, however, a universally observed phenomenon, and the relationship of X inactivity to the IP mutation appears to be complex. In the case of XLP, though skewed X inactivation patterns are seen in most disease carriers, the frequency with which this phenomenon occurs in normal females renders it an unreliable diagnostic marker for XLP carriers.

Ph-negative and bcr-negative atypical chronic myelogenous leukemia: biological features and clinical outcome

We report the clinical, hematologic, cytogenetic, and molecular characteristics of 13 patients with Philadelphia-negative (Ph-), bcr-negative atypical chronic myelogenous leukemia (CML). In the majority of cases, the phenotypic features at presentation resembled those of typical CML. However, these patients presented with a higher median age, lower median hemoglobin levels, and lower leukocyte and platelet counts than patients with Ph-positive CML. Cytogenetic analysis showed an abnormal karyotype in only one case. Southern blot investigation, using probes exploring the entire M-bcr region, demonstrated the absence of genomic bcr-abl rearrangements. The assessment of clonality in five patients (study of X-methylation patterns in females heterozygous at the DXS255 locus) indicated the proliferation of a monoclonal cell population. Disease evolution was mostly characterized by bone marrow failure, extramedullary infiltrates, and poor response to chemotherapy, without evidence of overt acute transformation. Our observations suggest that some hematologic and clinical features and the modalities of disease progression are presently the most helpful factors in distinguishing these bcr/abl-negative patients from those with typical bcr+CML. The differences existing also with chronic myelomonocytic leukemia (CMMoL), allow the consideration of ph-/bcr- CML as a separate entity, the nature of which remains to be elucidated.

Clonal lymphocytes are detectable in only some cases of MDS

Clonal analysis of lymphocytes from patients with myelodysplastic syndrome (MDS) has been carried out using X-chromosome inactivation patterns detected by the probe M27 beta, and by polymerase chain reaction amplification of the immunoglobulin heavy chain gene hypervariable region, CDR3. Of 32 female patients heterozygous for M27 beta only seven (22%) demonstrate monoclonality of peripheral blood lymphocytes. 12 (37%) give unequivocal polyclonal results and the remaining cases give patterns of X-inactivation which cannot be interpreted either way. A study of 68 MDS patients showed five (7%) with a population of B-cells with a monoclonal rearrangement of CDR3 compared with none out of 60 normal individuals, none out of 15 with B-non Hodgkin lymphoma (B-NHL) in remission and 19 out of 25 (75%) of cases of B-chronic lymphocytic leukaemia (B-CLL). Monoclonal lymphocytes were found by both techniques in only two females with MDS. We conclude that the presence of polyclonal lymphocytes is a common finding in patients with MDS.

Clonal analysis of human tumors with M27 beta, a highly informative polymorphic X chromosomal probe

The clonality of human tumors can be studied by X inactivation/methylation analysis in female patients heterozygous for X-linked DNA polymorphisms. We present a detailed study on clonal tumor analysis with M27 beta, a highly informative probe detecting a polymorphic X chromosomal locus, DXS255. The polymorphism detected at this locus is due to variable numbers of tandem repeats. The rate of constitutional heterozygosity detected by M27 beta was 88%. Normal tissue from gastrointestinal mucosa and thyroid showed random, hence polyclonal, patterns. Nonrandom clonal X inactivation was detected in all 22 malignant neoplasms that had been shown to be clonal by other DNA markers, such as antigen receptor gene rearrangements or clonal loss of heterozygosity at 17p and other loci. 16/48 normal blood leukocyte samples (33%) showed considerably skewed X inactivation patterns. Comparison of blood leukocytes and normal tissue indicated that in a given individual, X inactivation patterns may be tissue specific. M27 beta was used to study the clonal composition of 13 benign thyroid nodules from 12 multinodular goiters with rapid recent growth, traditionally termed "adenomas." Nine of them were clonal, whereas four nodules and tissue from a case of Graves' goiter were not, indicating that some, but not all, such thyroid nodules may represent true clonal neoplasms. The M27 beta probe permits one to study the clonal composition by the X inactivation approach of a wide variety of solid tumors from most female patients. As a control, normal tissue homologous to the tumor type of interest is preferable to DNA from blood leukocytes, since the latter may show nonrandom X inactivation patterns in a fairly high proportion of cases. M27 beta may, therefore, be of limited use for the clonal analysis of neoplasms derived from hematopoietic cells.

Molecular analysis of clonality in plasma cell dyscrasias

It has been suggested that multiple myeloma, generally considered a neoplastic disorder of mature plasma cells, may arise from a pluripotent haemopoietic stem cell. The possibility that circulating lymphocytes derive from the same neoplastic progenitor has been tested in a large number of studies in the past few years, as proof of the interest that this subject is raising among scientists, and also of its elusiveness. We studied a group of 29 patients with plasma cell dyscrasias in order to evaluate clonality of haemopoietic cell populations. The X-linked markers hypoxantine phosphoribosyltransferase (HPRT) and phosphoglycerate kinase (PGK) disclosed no monoclonal component in seven heterozygous women. Analysis of immunoglobulin gene rearrangement with four probes showed a germline configuration in samples from 25/29 patients. Only four bone marrow samples from subjects with aggressive disease had rearranged C mu sequence; one had rearrangement of JH and C mu.

Childhood polyclonal T cell lymphocytosis with neutropenia: effects of antilymphocyte globulin and granulocyte colony stimulating factor in vitro and in vivo

The pathogenesis of the neutropenia that occurs in some patients with chronic T cell lymphocytosis is not well understood. We have investigated a 15-year-old girl with this syndrome. Initial committed bone marrow progenitor numbers (CFUgm) were low but markedly increased in vitro following T cell depletion. Similarly a transient correction of neutropenia was observed following in vivo lymphocyte depletion with antilymphocyte globulin. A sustained neutrophil recovery was achieved with daily therapy using recombinant human granulocyte colony stimulating factor (rhG-CSF) despite persistence of the lymphocytosis; during successful therapy CFUgm numbers remained low, and were not increased by the in vitro addition of rhG-CSF. These observations suggest the possibility of an inhibitory regulatory mechanism specifically acting on neutrophil granulopoiesis.

Gene mutations in myelodysplasia

The myelodysplastic syndrome is a paradigm of human preleukaemia. Normal haemopoiesis is progressively displaced by an abnormal clone derived from a mutated stem cell. The initial mutation is unknown but its occurrence may be related to the overall load of random mutations which are a consequence of both intrinsic DNA defects and external mutagens. Evolution of the pathological population is marked by an increasing load of genetic lesions at the molecular and cytogenetic levels. Ras mutations can be detected in the blood of about 50% of MDS patients. Fms mutations are less common but these lesions can be found both in patients and in haematologically normal subjects who have previously received cytotoxic therapy suggesting that they can occur early in the preleukaemic process. Clonal haemopoiesis in the absence of either ras or fms mutations can occur in these subjects. The data suggest the inability of mutant ras or fms genes alone to produce observable preleukaemic changes but that subjects with these mutations may be predisposed to future MDS. Ras mutations are a common accompaniment of a wide variety of malignancies and experimental transfection of the mutant gene can induce a malignant phenotype in cultured cells. There are many possible mechanisms for this transformation which may be relevant in a clinical context. Experimentally observed effects include a direct influence on the cell cycle, the induction of drug resistance and the stimulation of autocrine growth factor production. It may eventually be possible to define which gene mutations are important in conferring a malignant state, which determine phenotype and which are of incidental significance.

Clonality of cell populations in refractory anaemia using combined approach of gene loss and X-linked restriction fragment length polymorphism-methylation analyses

We have used X-linked restriction fragment length polymorphism (RFLP)-methylation and gene deletion analyses to investigate the nature of the progenitor cell of origin in the myelodysplastic syndromes (MDS). Gene deletion studies were performed on the granulocyte and T-lymphocyte fractions of six women with refractory anaemia (RA) and either a partial deletion of the long arm of chromosome 5 (5q-) or monosomy 7. All six showed gene loss in the granulocyte but not the T-lymphocyte fractions, indicating monoclonality of the granulocytes but not the T-lymphocytes. In order to further investigate this finding, we subsequently performed X-RFLP-methylation studies using the probe M27 beta, and also a probe for the phosphoglycerate kinase (PGK) gene. These studies have confirmed the monoclonality of the granulocytes and the polyclonality of the T-lymphocytes in these cases. Our findings suggest that in this group of patients with MDS the T-lymphocytes were not involved in the disorder, and furthermore, in the one case where B-lymphocytes were also available, that the progenitor cell of origin was restricted to the myeloid lineage.

Differential methylation at the 5' and the 3' CCGG sites flanking the X chromosomal hypervariable DXS255 locus

The degree of methylation at the 5' and 3' CCGG sequences flanking the variable number of tandem repeat (VNTR) region of the DXS255 locus at Xp11.22 was analysed separately in several haematopoietic cell lineages. The 5' CCGG site on active chromosomes was found to be completely methylated in B and T lymphocytes and granulocytes. Methylation of the 5' site on inactive X chromosomes differed between females (0%-60%), but was consistent in different cell lineages obtained from individual females. In contrast, methylation at the 3' CCGG site on active chromosomes was found to vary in B lymphocytes (40%-100%), whereas complete methylation was found in T lymphocytes and granulocytes. The extent of methylation on inactive X chromosomes was found to differ significantly between B lymphocytes (17%), T lymphocytes (54%) and granulocytes (82%). Thus, methylation at the 5' CCGG site seems to be primarily related to the status of X chromosome inactivation, whereas methylation at the 3' CCGG site is mainly subject to cell-lineage-specific influences.

Discordance of muscular dystrophy in monozygotic female twins: evidence supporting asymmetric splitting of the inner cell mass in a manifesting carrier of Duchenne dystrophy

In 1990, Richards et al. reported dramatically skewed lyonization in a set of female monozygotic twins heterozygous for Duchenne muscular dystrophy (DMD). The skewed inactivation pattern was symmetrical in opposite directions, one twin being affected with DMD, the other one being normal. Here, we report an additional set of female monozygotic twins heterozygous for a mutation at the dystrophin locus. Similarly, one shows a manifesting carrier phenotype while one is normal. However, unlike the previous report, we find a skewed X inactivation pattern only in the affected twin, while the normal twin showed a random X inactivation pattern. Our results lend considerable experimental support for the models of twinning and X inactivation recently outlined by Nance in 1990, in that these twins probably represent asymmetric splitting of the inner cell mass (ICM): The affected twin likely arose when a small proportion of the ICM split off after lyonization had occurred. In this situation, the original ICM could give rise to the normal twin with random lyonization, while the newly split cells would experience catch-up growth and lead to the affected twin. Genetic studies of this family showed that the specific dystrophin gene mutation was an exon duplication that arose sporadically in the paternally derived X chromosome.

Primary thrombocythaemia: diagnosis and management

Since PT is more likely than reactive thrombocytosis to be complicated by thromboembolic manifestations, the differential diagnosis is important. A combination of positive clinical and laboratory criteria probably represents the most useful diagnostic method at present, although a molecular biological approach may prove to be of value in females in the future. Treatment to suppress the megakaryocytic proliferation is suggested in all patients, since even young patients are not immune to major complications, and treatment may possibly delay long-term myelofibrotic transition. Acute haemorrhage should be treated by platelet transfusions, with or without platelet apheresis and with rapid control of the count by hydroxyurea. Vascular occlusive lesions should be treated with aspirin, with or without platelet apheresis and with hydroxyurea. Busulphan is suggested as the drug of choice for long-term therapy in patients over 40 years of age while hydroxyurea is proposed below this age. The place of interferon-alpha therapy has not yet been established but may have a particular role in women of child-bearing age.

Variable X-chromosome DNA methylation patterns detected with probe M27 beta in a series of lymphoid and myeloid malignancies

In this study the X chromosome probe M27 beta was used to investigate DNA methylation at the DXS255 locus and hence X inactivation status and determination of tumour clonality in blood, bone marrow and biopsy tissue involved with morphologically and phenotypically defined lymphoid and myeloid disease from 14 female patients along with uninvolved bone marrow from two control individuals. Thirteen out of 16 individuals (81%) were restriction fragment length polymorphism (RFLP) heterozygous for DXS255. DNA methylation status could not be assessed in the three DXS255 homozygous individuals. In eight DXS255 heterozygous individuals clonality was clearly demonstrated using M27 beta and in six of these cases independent analysis using T cell receptor (TcR) and immunoglobulin (Ig) gene probes confirmed the presence of clonal tumour cell populations. In the two controls, polyclonality was inferred from M27 beta probe analysis. In the remaining three cases (all acute lymphoblastic leukaemia (ALL)) both DXS255 X chromosome sequences appeared to be methylated. Clonality in these cases was demonstrated by TcR or Ig monoclonal gene rearrangements. These data demonstrate the value of the M27 beta probe for determining tumour clonality in a number of cases with lymphoid and myeloid disease but indicate that there may not always be a complete correlation between DNA methylation. X inactivation status and tumour clonality in certain lymphoid neoplasms, restricting the use of this probe in clonality studies. Correlations between DNA methylation, X inactivation status and stage of normal and neoplastic T and B cell development require further investigation.

Recent advances in the molecular analysis of inherited disease

Many important human genes have been cloned during the last ten years. In some cases, using reverse genetic techniques [Orkin, S. H. (1986) Cell 47, 845-850], disease-causing genes have been isolated whose product was previously unknown. Important examples include the dystrophin protein which, when mutated, gives rise to either Duchenne or Becker muscular dystrophy [Koenig, M., Hoffman, E. P., Bertelson, C. J., Monaco, A. P., Feener, C. and Kunkel, L. M. (1987) Cell 50, 509-517; Monaco, A. P., Bertelson, C. J., Liechti-Gallati, S. & Kunkel, L. M. (1988) Genomics 2, 90-95; Koenig, M., Monaco, A. P. & Kunkel, L. M. (1988) Cell 53, 219-228] and the cystic fibrosis transmembrane conductance regulator (CFTR) [Riordan, J. R., Rommens, J. M., Kerem, B.-S., Alon, N., Rozmahel, R., Grzelczak, Z., Zielenski, J., Lok, S., Plavsic, N., Chou, J.-L., Drumm, M. L., Ianuzzi, M. C., Collins, F. S. & Tsui, L.-C. (1989) Science 245, 1066-1073]. Recently the technology for systematically detecting single base-pair changes by chemical methods, enzymatic methods or direct DNA sequencing has greatly expanded and simplified. In addition to providing structural information about these clinically important genes and information on disease-causing mutations, these studies have led to an increased understanding of mechanisms of mutation, to the discovery of novel genetic mechanisms and to important clinical applications of carrier detection and pre-natal diagnosis. The recent rapid progress has been made possible by the development of DNA amplification using the polymerase chain reaction (pcr) invented by Saiki and colleagues [Saiki, R. K., Chang, C-A., Levenson, C. H., Warren, T. C., Boehm, C. D., Kazazian, H. H. & Ehrlich, H. A. (1988) N. Engl. J. Med. 319, 537-541].

Molecular biology and leukaemia diagnosis

The diagnosis and classification of leukaemia started with simple morphological examination and now embraces use of special stains, cytochemistry and immunophenotyping. Genetic studies have progressed from karyotyping to detection of genetic changes within genes. The methods described in this chapter are still at an early stage of development and, so far, have provided relatively little in the way of an extension of available diagnostic information. Sometimes the methods provide extensions to existing techniques, for example by the detection of bcr rearrangements in patients who have CML or ALL but do not have a detectable Philadelphia chromosome. Another example is retrospective diagnosis of gene rearrangements using DNA from slide preparations. However, it should be noted that it has only very recently been shown that there is likely to be a causal relationship between the Ph chromosome and leukaemia. Daley et al (1990) induced CML in mice by bone marrow transplantation of cells infected with a retrovirus encoding P210bcr/abl and Heisterkamp et al (1990) produced mice transgenic for a BCR/ABL P190 DNA construct and showed that the progeny died of acute leukaemia (mostly ALL). We have not summarized studies of the incidence of activated oncogenes such as RAS in leukaemia and myelodysplasia. Such oncogenes appear to be involved in many tumours and may well indicate either a predisposition to cancer or a particular stage of malignancy, but their analysis does not at present help in making a diagnosis. It is likely that, as we understand more about the nature of the malignant process, we shall be able to use genetic techniques to enhance considerably both diagnostic and prognostic precision.