Purine metabolism in childhood acute lymphoblastic leukemia: biochemical markers for diagnosis and chemotherapy

Assessment of gene set analysis methods based on microarray data

Gene set analysis (GSA) incorporates biological information into statistical knowledge to identify gene sets differently expressed between two or more phenotypes. It allows us to gain an insight into the functional working mechanism of cells beyond the detection of differently expressed gene sets. In order to evaluate the competence of GSA approaches, three self-contained GSA approaches with different statistical methods were chosen; Category, Globaltest and Hotelling's T(2) together with their assayed power to identify the differences expressed via simulation and real microarray data. The Category does not take care of the correlation structure, while the other two deal with correlations. In order to perform these methods, R and Bioconductor were used. Furthermore, venous thromboembolism and acute lymphoblastic leukemia microarray data were applied. The results of three GSAs showed that the competence of these methods depends on the distribution of gene expression in a dataset. It is very important to assay the distribution of gene expression data before choosing the GSA method to identify gene sets differently expressed between phenotypes. On the other hand, assessment of common genes among significant gene sets indicated that there was a significant agreement between the result of GSA and the findings of biologists.

Comparison of univariate and multivariate gene set analysis in acute lymphoblastic leukemia

BACKGROUND

Gene set analysis (GSA) incorporates biological with statistical knowledge to identify gene sets which are differentially expressed that between two or more phenotypes.

MATERIALS AND METHODS

In this paper gene sets differentially expressed between acute lymphoblastic leukaemia (ALL) with BCR-ABL and those with no observed cytogenetic abnormalities were determined by GSA methods. The BCR-ABL is an abnormal gene found in some people with ALL.

RESULTS

The results of two GSAs showed that the Category test identified 30 gene sets differentially expressed between two phenotypes, while the Hotelling's T2 could discover just 19 gene sets. On the other hand, assessment of common genes among significant gene sets showed that there were high agreement between the results of GSA and the findings of biologists. In addition, the performance of these methods was compared by simulated and ALL data.

CONCLUSIONS

The results on simulated data indicated decrease in the type I error rate and increase the power in multivariate (Hotelling's T2) test as increasing the correlation between gene pairs in contrast to the univariate (Category) test.

Serum adenosine deaminase and total superoxide dismutase activities before and after surgical removal of cancerous laryngeal tissue

In this study, pre- and post-operative serum activities of adenosine deaminase (ADA) and total superoxide dismutase (SOD) enzymes were measured in patients with squamous cell laryngeal cancer. Activities of both enzymes were found to be higher in cancerous patients compared to the controls. No significant differences were found however between pre- and post-operative values for both enzymes in the patient group. It has been suggested that ADA and SOD enzymes leak from the cancerous laryngeal tissues into the blood stream. The absence of differences between pre- and post-operative serum enzyme activities has two possible explanations: Firstly, removal of previously released enzymes from the blood stream takes a much longer period than one month; and secondly, cancerous laryngeal tissue is not the only source of the enzymes mentioned even after removal of cancerous tissue by surgical operation, other sources such as adjacent tissues and/or metastatic tissues etc, still release these enzymes into the blood stream.

Studies on the incorporation of precursors into purine and pyrimidine nucleotides via 'de novo' and 'salvage' pathways in normal lymphocytes and lymphoblastic cell-line cells

The incorporation of radioactive precursors into purine and pyrimidine nucleotides via 'de novo' and 'salvage' pathways was measured in normal lymphocytes, resting as well as proliferating, and lymphoblastic cell-line cells (MOLT-3). Lymphocytes stimulated with anti-CD3 were taken as actively proliferating lymphocytes (35% in the S-phase, 40 h after stimulation). The incorporation of the precursors in the purine and pyrimidine ribonucleotides was measured by a combination of anion-exchange high-performance liquid chromatography (HPLC) and on-line radioactivity measurement. The actively proliferating normal lymphocytes and MOLT-3 cells incorporated 30-500 times more of the various precursors in the ribonucleotides compared to normal resting lymphocytes. The imbalance in the nucleotide pool found in proliferating normal and lymphoblastic cells was reflected in the incorporation pattern of the various precursors. The activities of the branch-point enzymes IMP dehydrogenase and CTP synthetase most likely determine the differences in the composition of the nucleotide pools between resting and proliferating cells.

Purine de novo synthesis as the basis of synergism of methotrexate and 6-mercaptopurine in human malignant lymphoblasts of different lineages

Methotrexate (MTX) causes an inhibition of purine de novo synthesis (PDNS), resulting in increased intracellular availability of 5-phosphoribosyl-1-pyrophosphate (PRPP) in human malignant lymphoblasts with an active PDNS. Normal bone marrow cells and peripheral blood lymphocytes lack this capacity. The increased levels of PRPP can be used for enhanced incorporation of 6-mercaptopurine (6MP), indicating a potential time-, sequence- and dose-dependent synergism of both drugs. The effects of 0.02 microM and 0.2 microM MTX on the PDNS of MOLT-4 (T-), RAJI (B-) and KM-3 (non-B-non-T-) human malignant lymphoblasts were studied with respect to PRPP levels, aminoimidazolecarboxamide ribonucleosidemonophosphate (AICAR) levels and the incorporation of labeled glycine into purine metabolites. These results were correlated with the activity of the PDNS (labeled glycine incorporation) and the purine salvage pathway (labeled hypoxanthine incorporation) in untreated cells. Inhibition of PDNS by 0.02 microM MTX was complete in KM-3 cells with a moderately active PDNS and salvage pathway. RAJI cells, with a relatively low PDNS and high salvage pathway, demonstrated an incomplete, but increasing inhibition of PDNS, whereas inhibition of PDNS in MOLT-4 cells with both pathways active was minimal and recovered in time. Treatment with 0.2 microM MTX resulted in a complete inhibition of PDNS in all cell lines. After treatment with MTX an enhanced incorporation of labeled hypoxanthine and 6MP was noticed, confirming the potential rescue from MTX cytotoxicity by hypoxanthine and a potential synergism of MTX and 6MP on cytotoxicity. The enhanced incorporation of 6MP was more obvious in RAJI and KM-3 cells in comparison with MOLT-4 cells. These data demonstrate the important role of both the activities of the PDNS and the purine salvage pathway in malignant lymphoblasts of different subclasses with respect to the synergism of MTX and 6MP.

Enzymes of purine metabolism in lymphoid neoplasms, clinical relevance for treatment with enzyme inhibitors

A few enzymes of the purine degradative pathway have proved valuable in diagnosis and treatment of lymphomas and lymphocytic leukemia. Of particular interest are the enzymes adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP) and ecto-5'-nucleotidase (5NT). Intact activities of ADA and PNP have been shown to be vital for lymphoid cells. During development, lymphoid precursors go through remarkable changes in the concentrations of these enzymes and the neoplasms derived from them show a "frozen" biochemical profile similar to the corresponding normal cell of origin. Knowledge of the role of these enzymes has led to the pharmacological use of enzyme inhibitors for the specific treatment of lymphoid neoplasms. This review concerns the enzymatic make-up of normal and neoplastic lymphocytes and exploitation of this knowledge for the treatment of lymphomas. Special emphasis will be put on the clinical use of an ADA-inhibitor, deoxycoformycin.

Aberrant ribonucleotide pattern in lymphoid cells from patients with chronic lymphocytic leukaemia or non-Hodgkin lymphoma

The intracellular purine and pyrimidine ribonucleotide concentrations were determined in lymphoid cells from peripheral blood of 16 patients with chronic lymphocytic leukaemia (CLL) and from peripheral blood and/or lymphoid tissue of 18 patients with non-Hodgkin lymphoma (NHL). Compared to normal peripheral lymphocytes, the lymphoid cells from CLL patients contained lower, and those from NHL patients higher amounts of nucleotides. The lymphoid cells of NHL patients showed an imbalance in the nucleotide pool compared to either normal resting peripheral or proliferating tonsillar lymphocytes. The lymphoid cells of patients with CLL showed an imbalance only when compared to normal, resting peripheral lymphocytes. The abnormalities in the nucleotide pools involved decreased ratios of purine:pyrimidine, adenine:guanine and uracil:cytosine nucleotides. Lymphocytes from CLL and NHL patients contained increased amounts (relative and/or absolute) of UDP sugars, and NHL lymphocytes also showed a changed composition of the UDP sugars. Analysis of the ribonucleotides in the lymphoid cells provides useful information for the differential diagnosis of patients suspected of having CLL or NHL, and may be valuable for the design of new chemotherapeutic regimens.

Low cytidine deaminase levels in human hematopoietic cell lines

Purine and pyrimidine enzyme profiles of human cell lines have been investigated. A novel observation was the finding that most of the cell lines showed very low or undetectable levels of cytidine (deoxycytidine) deaminase, while they possessed pyrimidine 5'-nucleotidase, cytidine and deoxycytidine kinase activities. Most cell lines showed high levels of adenosine deaminase and purine nucleoside phosphorylase activities and low levels of purine 5'-nucleotidase. We propose that high adenosine deaminase and purine nucleoside phosphorylase activities and low cytidine deaminase activity may be of importance for immature hematopoietic cells in order to ensure a balanced synthesis of the DNA precursors.

Purine degradative enzymes and immunological phenotypes in chronic B-lymphocytic leukaemia: indications that leukaemic immunocytoma is a separate entity

Investigations of the purine degradative enzymes adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP), and ecto-5'-nucleotidase (5'NT) have been shown to be of value in defining subsets of lymphoid malignancies. We have studied the activities of these enzymes in the circulating malignant cells of 35 patients with chronic B lymphocytic leukaemia and have correlated the biochemical data with immunological phenotypes. Classification of the cases into those without evidence of secretory activity ('true' CLL, 14 patients) and those with cytoplasmic immunoglobulin (CIg) ('immunocytoma'; 21 patients) revealed that immunocytomas are phenotypically and biochemically associated with more mature features. Malignant cells without CIg were characterized by low activities of ADA, PNP and 5'NT. In malignant cells with evidence of secretory activity (immunocytoma), low activity of ADA was also observed, but the activities of PNP and 5'NT were relatively high and approached the range of normal B lymphocytes. The differences in PNP (P less than 0.05) and in 5'NT (P less than 0.01) between these two groups were significant. Phenotypically the cells without CIg were predominantly associated with IgM (+k light chains) as surface membrane immunoglobulin (SmIg) whereas expression of IgG was more often observed in the leukaemic cells with CIg. No correlation between enzyme patterns and the stage of the disease was apparent. Thus both biochemical and immunological criteria show that cases of CLL vary within a range of maturity and that those with CIg might be more mature in the B cell axis. The present study emphasizes the value of purine enzyme studies in defining subsets of B cell neoplasia.

Abnormal nucleotide pattern in the eosinophils of a patient with acute lymphoblastic leukemia associated with eosinophilia

In this article we present a patient with acute lymphoblastic leukemia (ALL) associated with eosinophilia, in which the eosinophilia preceded a meningeal and bone-marrow relapse of ALL. We analysed the purine and pyrimidine nucleotide content of the eosinophils (92% pure) and compared the nucleotide pattern with that of eosinophils from healthy donors and from patients with eosinophilia not associated with leukemia. The ratios of purine:pyrimidine and of uracil:cytosine nucleotides were decreased compared with those in eosinophils from healthy donors and from patients with eosinophilia with other aetiologies. The total nucleotide concentration was increased, especially the concentration of UDP-sugars and pyrimidine nucleotides. The decrease in these ratios and the increase in concentration of the nucleotides and the UDP-sugars were also detected in leukemic cells of patients with ALL (de Korte et al., Leukemia Res. 10, 389-396 (1986) compared to normal lymphocytes. We suggest a malignant character of the eosinophils in our patient with ALL associated with eosinophilia, in contrast with the non-malignant state suggested previously for these cells.

Imbalance in the ribonucleotide pools of lymphoid cells from acute lymphoblastic leukemia patients

The intracellular purine and pyrimidine ribonucleotide concentrations were determined in the lymphoid cells from peripheral blood and/or bone-marrow of 29 patients with acute lymphoblastic leukemia (ALL), as well as in the mononuclear cells from peripheral blood of 12 patients with ALL in remission. The lymphoid cells of ALL patients showed an imbalance in the nucleotide pool compared with normal lymphocytes, whereas the nucleotide pool of mononuclear cells from patients with ALL in remission had normal values. The imbalance in the lymphoid cells from ALL patients involved decreased ratios of purine:pyrimidine, adenine:guanine and uracil:cytosine nucleotides, and an increased amount, together with a changed composition, of the UDP sugars. When compared with tonsil-derived B lymphocytes and thymocytes, ALL lymphoid cells have an increased amount (absolute and relative) and a change composition of the UDP sugars. Significant differences were found between the mean values for the immunologically defined subgroups of ALL and between the mean values for patients with a high or a low percentage of blast cells. However, individual patients cannot be classified according to their nucleotide pattern, because of the overlapping ranges. The results of this study may be useful for the design of new therapeutic regimens.

Nucleotide profiles of normal human blood cells determined by high-performance liquid chromatography

An anion-exchange high-performance liquid chromatography method has been used to quantitate the intracellular purine and pyrimidine nucleotides in extracts of pure lymphocytes, monocytes, neutrophils, eosinophils, erythrocytes, and platelets isolated from the blood of healthy human donors. For accurate and reproducible measurements of the nucleotide profiles in different types of pure leukocytes, the cell suspensions have to be free of platelets and erythrocytes. Incubation of the purified leukocytes for 1 h at 0 degrees C did not alter the nucleotide concentrations but reduced the interdonor variation to 10%. Incubation of purified lymphocytes for 1 h at 37 degrees C caused considerable changes in the relative concentrations of the adenine, guanine, uracil, and cytosine nucleotides. During this incubation the cell viability, the cell number, and the ATP:ADP ratio decreased. Incubation of monocytes and granulocytes for 1 h at 37 degrees C caused considerable loss of cells and/or cell death. For erythrocytes and platelets reproducible nucleotide concentrations were obtained after extraction of freshly isolated cells. During storage of erythrocytes, both at 0 degrees C and at 37 degrees C, a decrease in the ATP:ADP ratio was detected. In all cell types the predominant nucleotides were purine nucleotides, especially adenosine triphosphate. The relative concentrations of the adenine, guanine, uracil, and cytosine nucleotides were very reproducible per cell type and appeared to be characteristic for each cell type. The total nucleotide content was nearly the same for all cell types except erythrocytes, when expressed per microgram of protein. The described methods for purification and storage of blood cells will be useful for comparison of blood cells from healthy donors with those of patients, for example, leukemia patients, in which deviations of the purine and pyrimidine metabolic enzymes have already been described.

Biochemical enzyme analysis in acute leukaemia

This report summarises the current knowledge regarding the clinical utility of biochemical enzyme markers for both diagnostic and therapeutic purposes in acute leukaemia. The enzymes studied most extensively in this field are terminal deoxynucleotidyl transferase, adenosine deaminase, 5'-nucleotidase, purine nucleoside phosphorylase, and acid phosphatase, esterase, hexosaminidase isoenzymes. For each enzyme, the quantitative and qualitative characteristics in various immunologically defined subclasses of acute leukaemia are described. The quantitative evaluation of enzyme activities represents an adjunctive classification technique which should be incorporated into the multivariate analysis, the "multiple marker analysis." By qualitative characterisation pronounced heterogeneity of leukaemia subsets is uncovered. The application of 2'-deoxycoformycin, a specific inhibitor of adenosine deaminase, and the potential usefulness of two other enzymes as targets for treatment with selective agents is discussed. The concept that gene products expressed at certain developmental stages of normal cells can similarly be detected in leukaemic cells (which therefore seem to be "frozen" or "arrested" at this particular maturation/differentiation stage) is supported by the results obtained in enzyme studies. Besides their practical clinical importance for classification and treatment of acute leukaemias, biochemical enzyme markers constitute a valuable research tool to disclose biological properties of leukaemic cells.

Prognostic value of 5'nucleotidase in acute lymphoblastic leukemia with the common-ALL phenotype

5'-Nucleotidase (5'NT) is an enzyme found on the surface membrane of leukemic cells with the c-ALL phenotype. We studied 79 children with acute lymphoblastic leukemia (ALL). Thirty six of them had the c-ALL phenotype. Within this c-ALL group, ten had 5'-NT positive leukemic cells. Clinical data were available in 33 c-ALL cases. Sex, age and initial white blood cell count were comparable between 5'NT positive and 5'NT negative c-ALL cases. In the 5'NT positive group the probability of complete continuous remission was significantly lower than in the 5'NT negative group (p less than 0.05).

Enzymological studies in chronic lymphocytic leukemia

Adenosine deaminase (ADA), 5'nucleotidase (5'NT), ecto-5'NT, purine nucleoside phosphorylase (PNP), hypoxanthine-guanine phosphoribosyltransferase (HGPRT), adenine phosphoribosyltransferase (APRT), adenosine kinase (AK), AMP-deaminase (AMPD) and adenylate kinase (AdKin) activities were assayed in peripheral blood lymphoid cells from 20 patients with B-cell type chronic lymphocytic leukemia (CLL). Significantly decreased mean activities of ADA, 5'NT, ecto-5'NT, PNP and AMPD were observed when comparing B-CLL lymphoid cells with control peripheral blood lymphocytes (PBL). AK and AdKin activities however, were found to be higher in B-CLL. Relatively wide ranges of ADA and 5'NT activity were observed. In patients with paraproteinaemia, 5'NT activity was found to be relatively high and in the range of the activities in normal PBL. ADA activity seemed to be slightly higher in patients without paraproteinaemia. No correlation could be found between the enzyme activities and the number of cells rosetting with sheep erythrocytes or bearing surface immunoglobulin (sIg). A relationship was suggested between 5'NT activity and Ig production.

Purine metabolism in relation to leukemia and lymphoid cell differentiation

A number of inborn errors of purine metabolism have been associated with immunodeficiency diseases. From studies to the possible mechanism(s) leading to the defects in the immune system, it appeared that the accumulation of deoxyATP and deoxyGTP and the subsequent inhibition of ribonucleotide reductase played an important role. The inhibition of methylation pathways through the accumulation of s-adenosylmethionine seems to be a second valid concept. The amount to which certain subtypes of lymphoid cells were affected by the enzyme deficiencies was strongly related to the enzymatic make-up of the cells. Lymphoid cells from different maturation stages could be affected in a specific way, depending on the different enzyme activities of these cells. Studies on human lymphoblastic leukemias showed that, related to the immunological subtype, the different leukemias could be characterized by a different enzymatic make-up. In this paper we discuss the possibilities for a specific enzyme directed chemotherapy, directed against specific subtypes of human lymphoblastic leukemias. Experimental evidence indicates that for example the adenosine deaminase inhibitor 2'deoxycoformycin can be used as a specific drug against acute lymphoblastic leukemia with the T cell phenotype.