Molecular cloning of human adenosine deaminase gene sequences

A history of pediatric immunology

Immunology has played a prominent role in the history of medicine. Pediatric immunologists have focused on immune aberrations in pediatric disorders, particularly those involving host defense mechanisms. These efforts have paid rich dividends in terms of fundamental knowledge of the immune system and major therapeutic advances, including 1) i.v. immunoglobulin therapy, 2) hematopoietic stem cell transplantation, and 3) gene therapy. Pediatric immunology as an organized discipline emerged in the early 1950s, when pediatricians and their basic scientist colleagues began to focus on clinical and basic research related to immunodeficiency. Since then, key organizations and infrastructure have been developed to support this research and the clinical care of immunodeficient patients. We review here the evolution of contemporary pediatric immunology, particularly in North America, from its roots in 19th-century Europe to its current expression as one of the fundamental scientific and clinical disciplines of pediatrics.

Red blood cell enzymes and their clinical application

Red blood cell enzyme activities are measured mainly to diagnose hereditary nonspherocytic hemolytic anemia associated with enzyme anomalies. At least 15 enzyme anomalies associated with hereditary hemolytic anemia have been reported. Some nonhematologic disease can also be diagnosed by the measurement of red blood cell enzyme activities in the case in which enzymes of red blood cells and the other organs are under the same genetic control. Progress in molecular biology has provided a new perspective. Techniques such as the polymerase chain reaction and single-strand conformation polymorphism analysis have greatly facilitated the molecular analysis of erythroenzymopathies. These studies have clarified the correlation between the functional and structural abnormalities of the variant enzymes. In general, the mutations that induce an alteration of substrate binding site and/or enzyme instability might result in markedly altered enzyme properties and severe clinical symptoms.

T lymphocyte-directed gene therapy for ADA- SCID: initial trial results after 4 years

In 1990, a clinical trial was started using retroviral-mediated transfer of the adenosine deaminase (ADA) gene into the T cells of two children with severe combined immunodeficiency (ADA- SCID). The number of blood T cells normalized as did many cellular and humoral immune responses. Gene treatment ended after 2 years, but integrated vector and ADA gene expression in T cells persisted. Although many components remain to be perfected, it is concluded here that gene therapy can be a safe and effective addition to treatment for some patients with this severe immunodeficiency disease.

Recent progress in the molecular genetic analysis of erythroenzymopathy

During the relatively recent period in which normal genes for most red cell enzymes have been isolated, the techniques of molecular biology have been applied to the studies of erythroenzymopathy. Single nucleotide substitutions have been identified in aldolase, triosephosphate isomerase, glucose 6-phosphate dehydrogenase, and adenylate kinase variants by the cloning and nucleotide sequence of the patients' genes. Up to now, all of the enzyme-deficient variants which have been investigated have been caused by point mutations. An exception is a hemolytic anemia secondary to increased adenosine deaminase (ADA) activity. Red cell ADA activity increases on the order of a hundred-fold in affected individuals. The basic abnormality appears to result from overproduction of structurally normal enzyme due to abnormal transcriptional or translational efficiency.

Structural and functional analysis of the murine adenosine deaminase gene

We describe the structural and functional analysis of cosmid clones that span the entire murine adenosine deaminase gene. Functional analysis indicated that these clones are capable of encoding murine adenosine deaminase activity when introduced into human cell lines. Structural analysis revealed that the gene consists of 12 exons distributed over approximately 25 kb. The exact size of each exon and the sequence of each exon/intron junction were determined. The results show that the 1056-nucleotide open reading frame for adenosine deaminase extends from exon 1 to exon 11, and that exon 12 contains untranslated sequences only. During the course of these investigations, we discovered that a gene encoding an abundant 1.3-kb polyadenylated transcript overlaps the 3' end of the murine adenosine deaminase gene and is transcribed from the opposite strand.

Development of molecular approaches to estimating germinal mutation rates. I. Detection of insertion/deletion/rearrangement variants in the human genome

DNA from 130 individuals was studied with up to 18 (primarily cDNA) probes for the frequency of variants in this initial experiment to determine the feasibility of this approach to screening for germinal gene mutations. This approach, a modification of the usual restriction enzyme mapping strategy, focuses on the detection of insertion/deletion/rearrangement (I/D/R) variants, because the DNA is digested with only two restriction enzymes before transfer to membranes and hybridization with an extensive series of unrelated probes. Some 4000 noncontiguous, independent DNA fragments ("loci"), functional loci, pseudogenes or anonymous fragments, (a total of approximately 77,400 kb) were screened. 19 different classes and 31 copies of presumably I/D/R variants were detected while 4 different classes and 24 individuals exhibiting base substitution variants were observed. 18 of the 19 I/D/R classes were rare variants, that is, each were observed at a frequency, within this population, of less than 0.01; 3 of the base substitution classes existed at polymorphic frequencies and only 1 was a rare variant. 10 of the I/D/R classes, occurring in a total of 18 individuals, were detected with probes which are not known to be associated with repetitive elements. This is a variant frequency for I/D/R variants without known repetitive elements of 0.15 classes and 0.23 copies for each 1000 kb screened; this would extrapolate to 1600 such variant sites in the genome of each individual. Within the context of a mutation screening program, the rare variants, either with or without repetitive elements, would have a higher probability of being de novo mutations than would polymorphic variants; this former group would be the focus of family studies to test for the heritability of the allele (fragment pattern). Sufficient DNA probes are available to screen a significant portion of the human genome for genetic variation and de novo mutations of this type.

Ecto-enzyme activity of human erythrocyte adenosine deaminase

Adenosine deaminase is found primarily in the cytoplasm of many cell types. In the human erythrocyte, about 30 per cent of the total adenosine deaminase activity is membrane associated, and about two-thirds of this is inactivated by treatment of intact erythrocytes with the nonpenetrating reagent diazotized sulfanilic acid, without affecting lactate dehydrogenase, a soluble cytoplasmic enzyme. This indicates that within the cell membranes, the catalytic site of about two-thirds of the adenosine deaminase faces the external medium, i.e., ecto adenosine deaminase. Localization of adenosine deaminase activity at the cell membrane is demonstrated directly by electron microscopy by use of the substrate 6-Chloropurine ribonucleoside, which is dechlorinated by adenosine deaminase to produce Cl-, which is precipitated at its locus of formation by added Ag+, and the precipitated AgCl converted into the electron dense Ag0 upon exposure to light. From the Hydropathic Profile of the amino acid sequence of adenosine deaminase it is evident that there are two hydrophobic domains of sufficient length to span a biological membrane, and it is proposed that these domains could function to anchor the enzyme to the membrane. The importance of adenosine deaminase is indicated by the fatal immuno-deficiency which results from untreated genetic adenosine deaminase deficiency. It may be important to determine whether the amount of ecto adenosine deaminase activity is better suited to assess the clinical status of adenosine deaminase deficient patients that the currently used total cellular enzyme activity.

Separation of human from mouse and monkey adenosine deaminase by ion-exchange chromatography following retroviral-mediated gene transfer

A method for the chromatographic separation of human adenosine deaminase (ADA) from murine and monkey ADA is described. This procedure was developed in order to detect the expression of low or moderate levels of human ADA following retroviral-mediated gene transfer of cloned human ADA gene sequences into both mouse and monkey cells. Protein separation was achieved on a Mono Q (HR 5/5) anion-exchange column using the Pharmacia fast protein liquid chromatography system and was found to be a highly reproducible method yielding enzymatically active protein. An increasing linear gradient extending from 0.05 to 0.5 M potassium chloride (pH 7.5) was used to elute the enzyme. Under these conditions, most human ADA does not bind to the column and elutes in the low-salt buffer (0.05 M KCl), while murine ADA elutes at 0.12 M KCl and monkey ADA at 0.15 M KCl. The column fractions were assayed for ADA activity, and the characteristic isozyme banding patterns for human, mouse, and monkey ADA were confirmed by starch gel electrophoresis. This procedure allows the rapid and reproducible separation of human ADA from that of other species and yields partially purified enzymatically active protein.

The induction of class I HLA by interferon-alpha is independent of the cell cycle, but the expression is enhanced by a G1/S block

The induction of class I HLA expression by interferon-alpha (IFN-alpha) was studied in lymphoid cells arrested or traversing different stages of the cell cycle. Exponential cultures of MOLT-4 cells and the MOLT-4 cell variant YHHH were treated with the cell cycle inhibitors aphidicolin and colcemid to obtain cell populations arrested in G1/S and G2/M, respectively, and also cells traversing from S to M and vice versa. Cytofluorimetry with the monoclonal antibody YTH/76.3 (which specifically detects those class I molecules which are most susceptible to IFN-alpha induction) was used to quantitate the class I HLA response to IFN-alpha. The results showed that the response to IFN-alpha is not restricted to a given stage of the cell cycle. These studies also revealed that when the cells were arrested at G1/S, the absolute level of class I HLA expression was enhanced 2-3-fold, both in the presence or absence of either IFN-alpha or IFN-gamma. Therefore, even when absolute levels changed, the ratio of IFN-induced expression to basal expression remained constant at all cell cycle stages. The level of expression of another surface antigen (the CD1 antigen HTA-1) was not affected by the G1/S block. The results were confirmed by dot blot hybridization of poly(A)+ RNA using cDNA-specific probes. These findings suggest that the effect of IFN-alpha is continuous throughout the cell cycle but that a G1-dependent event determines the extent of class I HLA expression, and leads to a synergistic superinduction by IFN in G1/S-arrested cells.

Molecular genetics and potential gene therapy

Contemporary molecular techniques including gene cloning, DNA sequencing, and gene transfer permit precise and comprehensive analysis of genetic disorders. For example, the molecular basis of hemoglobin synthesis disorders (the thalassemias) can now be ascribed to more than 30 different specific mutations. These affect virtually all aspects of gene expression. The more recent capacity to reintroduce cloned genes into mammalian cells in a functional form has raised the prospect of gene therapy, that is, the replacement of an abnormal gene with its normal counterpart or merely the introduction of a normal gene into a cell containing a defective copy. Genetic correction of enzyme-deficiency disorders whose effects are manifest in bone-marrow-derived cells seems most likely to be amenable to "somatic" (as opposed to germ line) gene therapy. Treatment of severe combined immunodeficiency due to adenosine deaminase (ADA) deficiency may be a suitable model for this approach. This report will review the molecular genetics of ADA, the methods by which ADA gene sequences may be transferred into various cells, and goals for current and future research.

Molecular biology of the adenosine deaminase gene and messenger RNA

The human adenosine deaminase cDNA has been cloned in a lambda-vector. Contained within a sequence of over 1500 nucleotides is an open reading frame of 1089 nucleotides that encodes the amino acids of ADA. The functional ADA gene contains at least six kilobases and has at least two introns. Using in vitro translation, molecular hybridization to ADA cDNA, and S1 nuclease mapping, ADA mRNA has been characterized in lymphoblast lines from seven different ADA-deficient children. All of the lines contain substantial amounts of RNA, which hybridizes specifically to the ADA cDNA. Four of the cell lines contain translatable mRNAs with small defects such as single base substitutions that are not detectable by S1 mapping. Deficiency of ADA activity in these lines appears secondary to synthesis of structurally altered proteins containing simple amino acid substitutions. Three of the lines contain mRNAs with S1 nuclease detectable defects. Some or all of these defective mRNAs are postulated to result from anomalous RNA processing. In these cases the causes of the ADA deficiency may be more complex than simple amino acid substitutions in the protein and could include small insertions or deletions of amino acids as well as changes in the efficiency of translation of the mRNAs.

Molecular aspects of erythroenzymopathies associated with hereditary hemolytic anemia

Since the discovery of glucose 6-phosphate dehydrogenase (G6PD) and of pyruvate kinase deficiencies, erythroenzymopathies associated with hereditary hemolytic anemia have been extensively investigated. Kinetic and electrophoretic studies have shown that most, if not all, erythroenzymopathies are caused by the production of a mutant enzyme. Except for a few enzymes that are abundant in blood and tissues, it is difficult to obtain enough sample to study the functional and structural abnormalities of mutant enzymes associated with genetic disorders in man. The primary structures of only two normal red cell enzymes which can cause hereditary hemolytic anemia, phosphoglycerate kinase (PGK) and adenylate kinase, have been determined. Single amino acid substitutions of PGK variants have been found, and the identification of the exact molecular abnormalities of such variants has helped us to understand the accompanying functional abnormality. Gene cloning makes possible the identification of the DNA sequence that codes for enzyme proteins. Recently, human complementary DNA (cDNA) for aldolase, PGK, G6PD, and adenosine deaminase (ADA) have been isolated, and the nucleotide sequences for PGK and ADA determined. In the near future, human cDNA sequencing should permit identification of the gene alteration that gives rise to the mutant enzymes.

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

An approach to a selection system for adenosine-deaminase-positive (ADA+) cells and detection of rat ADA+ "revertants"

We have substituted deoxyadenosine or adenosine for hypoxanthine in the standard HAT selection system in an attempt to select for ADA-normal (ADA+) cells. ADA- human lymphoid line cells could not utilize deoxyadenosine as an alternative to hypoxanthine as a purine source (DAT) and failed to grow but were only somewhat inhibited in growth when adenosine was substituted for hypoxanthine (AAT). In contrast, ADA+ cells utilized adenosine or deoxyadenosine as efficiently as hypoxanthine as a purine source. Growth in DAT, but not in HAT, of an artificial mixture of one ADA+ human lymphoid cells in 1,000 ADA- cells resulted in enrichment of ADA+ cells to 25-86% of total cells. When we grew a rat ADA- cell line in two variations of the DAT system, we detected at least three electrophoretically different ADA+ patterns, one of which corresponded to normal rat ADA. These could represent "revertants."

Introduction of sequences encoding functional human adenosine deaminase into mouse cells using a retroviral shuttle system

A retroviral packaging system was used to generate a murine virus carrying sequences encoding human adenosine deaminase (ADA). To this end, human ADA cDNA was inserted into the retroviral shuttle vector pZIP-NeoSV(X)1. This vector provides all of the cis-acting sequences necessary for the efficient packaging and transmission of the viral genome as well as a selectable gene for G418 resistance. Transfection of this recombinant plasmid into cells that provide essential virus products (psi-2 cells) yielded cell lines that stably produced virions carrying the coding sequence of human ADA. We have used these virions to infect NIH3T3 cells, which after 48 h synthesized catalytically active human ADA. Furthermore, G418-resistant cell lines were obtained from the virus-infected NIH3T3 cells that stably produced the human ADA enzyme.

Cloning of human adenosine deaminase cDNA and expression in mouse cells

A previously isolated partial cDNA sequence encoding human adenosine deaminase (ADA) was used to probe a cDNA library prepared from human cultured cell mRNA. Clones containing a combined overlapping length of 1462 bp were isolated and sequenced. One of these was found to include the entire ADA coding region. An open reading frame consisting of 363 codons was identified, predicting a polypeptide of Mr 40762. A mammalian expression plasmid was constructed, positioning the ADA coding sequence to be under transcriptional control of the mouse metallothionein promoter. Transfection of cultured mouse L-cells with this plasmid resulted in the acute expression of human ADA enzymatic activity, as assayed by isoelectric focusing.

Development of homozygosity for chromosome 11p markers in Wilms' tumour

Somatic alterations in the genome are found in many human tumours. Chromosome rearrangements or base substitutions that activate cellular oncogenes appear to act dominantly. In contrast, recessive alleles apparently contribute to childhood retinoblastoma, as homozygosity (or hemizygosity ) for chromosome 13 is often established in tumours, by either mitotic nondisjunction or recombination. Parallels exist between retinoblastoma and childhood Wilms' tumour (WT). Retinoblastoma is often inherited and accompanied by a deletion of chromosome 13 (band q14), while WT is occasionally associated with aniridia and deletion of chromosome 11 band p13. Most Wilms' tumours are sporadic and not accompanied by these findings, although interstitial deletion of chromosome 11 in tumour, but not normal, cells has been reported. In view of these parallels, we compared constitutional and tumour DNAs from WT patients by using chromosome 11p DNA probes. We report here that although heterozygosity in constitutional DNAs was often preserved in tumour DNAs, one case developed homozygosity for chromosome 11p markers in tumour cells, implying the involvement of chromosomal events in revealing a recessive WT locus. This observation suggests the action of such general mechanisms in a tumour other than retinoblastoma.