Somatic cell genetics of adenosine deaminase expression and severe combined immunodeficiency disease in humans

Detecting somatic mosaicism: considerations and clinical implications

Human disease is rarely a matter of all or nothing; variable expressivity is generally observed. Part of this variability is explained by somatic mosaicism, which can arise by a myriad of genetic alterations. These can take place at any stage of development, possibly leading to unusual features visible at birth, but can also occur later in life, conceivably leading to cancer. Previously, detection of somatic mosaicism was extremely challenging, as many gold standard tests lacked the necessary resolution. However, with the advances in high-throughput sequencing, mosaicism is being detected more frequently and at lower levels. This raises the issue of normal variation within each individual vs mosaicism leading to disease, and how to distinguish between the two. In this article, we will define somatic mosaicism with a brief overview of its main mechanisms in concrete clinical examples, discuss the impact of next-generation sequencing technologies in its detection, and expand on the clinical implications associated with a discovery of somatic mosaicism in the clinic.

Carrier frequency of a nonsense mutation in the adenosine deaminase (ADA) gene implies a high incidence of ADA-deficient severe combined immunodeficiency (SCID) in Somalia and a single, common haplotype indicates common ancestry

Inherited adenosine deaminase (ADA) deficiency is a rare metabolic disorder that causes immunodeficiency, varying from severe combined immunodeficiency (SCID) in the majority of cases to a less severe form in a small minority of patients. Five patients of Somali origin from four unrelated families, with severe ADA-SCID, were registered in the Greater London area. Patients and their parents were investigated for the nonsense mutation Q3X (ADA c7C>T), two missense mutations K80R (ADA c239A>G) and R142Q (ADA c425G>A), and a TAAA repeat located at the 3' end of an Alu element (AluVpA) positioned 1.1 kb upstream of the ADA transcription start site. All patients were homozygous for the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7. Among 207 Somali immigrants to Denmark, the frequency of ADA c7C>T and the maximum likelihood estimate of the frequency of the haplotype ADA-7T/ADA-239G/ADA-425G/AluVpA7 were both 0.012 (carrier frequency 2.4%). Based on the analysis of AluVpA alleles, the ADA c7C/T mutation was estimated to be approximately 7,100 years old. Approximately 1 out of 5 - 10000 Somali children will be born with ADA deficiency due to an ADA c7C/T mutation, although within certain clans the frequency may be significantly higher. ADA-SCID may be a frequent immunodeficiency disorder in Somalia, but will be underdiagnosed due to the prevailing socioeconomic and nutritional deprivation.

Exploration of replicative senescence-associated genes in human dermal fibroblasts by cDNA microarray technology

The aging process is known to be regulated by specific genes in various organisms, including yeast, the nematode C. elegans, fruitflies and mice. To explore the novel genes involved in aging process, we applied cDNA microarray technology to a replicative senescence model of human dermal fibroblasts (HDF). Eighty-four genes, including inflammatory genes, cell cycle regulatory genes, cytoskeletal genes, and metabolic genes were found to show more than two fold expressional differences in young and old fibroblasts. Furthermore, 31 genes were confirmed to be up- or down-regulated during replicative senescence by semi-quantitative RT-PCR. The overexpressions of several genes including CD36, putative lymphocyte G0/G1 switch gene (G0S2), tumor protein D52-like 1 (TPD52L1), chemokine (C-X-C motif) ligand 6, myxovirus resistant gene 1 (MX1), and the down-regulation of the immunoglobulin superfamily containing leucine-rich repeat (ISLR), neurotrimin, insulin-like growth factor 2 associated protein (IGF2A), and apoptosis-related RNA binding protein (NAPOR3) were newly identified. These results suggest that fibroblasts show the deregulation of various cellular processes, such as inflammatory response, mitosis, cell adhesion, transport, signal transduction, and metabolism during replicative senescence.

Regional localization of DPP4 (alias CD26 and ADCP2) to chromosome 2q24

A panel of microcell hybrids containing fragments of chromosome 2 was analyzed for the presence of human DPP4, the gene that codes for dipeptidyl peptidase IV (or CD26), by specific PCR amplification of a fragment of the 3' untranslated region of the gene. This analysis placed DPP4 between LCT and GAD in bands q21 to q31. The localization was confirmed by in situ hybridization using two genomic probes that each revealed a hybridization signal in band q24. We also use the recent identification of the ADA binding protein as DPPIV to propose that the gene ADCP2 should be renamed DPP4.

Characterization of adenosine deaminase from normal human epidermis and squamous cell carcinoma of the skin

We compared the characteristics of adenosine deaminases (ADs) (E.C. 3.5.4.4.) in squamous cell carcinoma and normal human epidermis. Increased specific activity (per mg protein) of AD was observed in squamous cell carcinoma compared with that of the normal epidermis. In normal human epidermis most of the AD existed as a large form (Mr 300,000-350,000, type A). Squamous cell carcinoma of the skin was characterized by a high proportion of small-form (Mr 30,000-40,000, type C) AD. The proportion of the small-form enzyme varied from tumor to tumor. Comparison of the large-form AD from squamous cell carcinoma to that from normal epidermis revealed that both enzymes were similar in relative substrate specificity, Km values for adenosine, pH optima, heat stability pattern, isoelectric point, and sensitivity to inhibition by coformycin, a tight binding inhibitor of AD. However, the low molecular weight of AD from squamous cell carcinoma was less heat stable than that from the large-molecular-weight form. Increased AD activity and the high proportion of the small form of AD might be significant features of squamous cell carcinoma of the skin.

Chromosomal assignments of human genes for serine proteases trypsin, chymotrypsin B, and elastase

The genes for the serine proteases trypsin, chymotrypsin B, and elastase were chromosomally assigned in man using cDNA probes that have been isolated from a rat pancreatic cDNA library. DNA from human X rodent somatic cell hybrids was cleaved with BamHI or EcoRI and analyzed by Southern filter hybridization methods for the segregation of the genes for trypsin-1 (TRY1), chymotrypsin B (CTRB), and elastase-1 (ELA1). TRY1 was assigned to human chromosome 7q22----qter, CTRB to chromosome 16, and ELA1 to chromosome 12. Although the three genes are members of the same gene family, they are dispersed over different chromosomes.

Interleukin 2 (IL2) is assigned to human chromosome 4

The human gene for interleukin 2 (IL2) was assigned to chromosome 4 using human-mouse somatic cell hybrids and Southern filter hybridization of cell hybrid DNA. To identify IL2, a recombinant DNA probe ( pIL2 - 50A ) was used which contained a human interleukin 2 cDNA insert which hybridized to a 3.5-kb fragment in human DNA when cleaved with the restriction enzyme EcoRI.

Isolation of deoxycoformycin-resistant cells with increased levels of adenosine deaminase

Deoxycoformycin (dCF) is a specific inhibitor of adenosine deaminase (ADA). Rat hepatoma cells deficient in adenosine kinase and growing on adenosine as the sole carbon source are sensitive to the lethal action of dCF. Mutants resistant to dCF arise spontaneously with a frequency of 1.7 x 10(-6). This frequency is increased to 2.6 x 10(-5) by prior mutagenesis with ethyl methane sulfonate. Initially, dCF-resistant cell lines have 3-10 times the level of adenosine deaminase when compared to sensitive parental cells. Subsequent selection of mutants resistant to increased concentrations of dCF results in cells with a 15- to 30-fold increase in ADA levels. Quantitative immunoprecipitation tests indicate that the increase in enzyme activity in one line tested is due to an increase in the number of ADA molecules. These dCF' cell lines may serve as a model system to study the human disease state, hereditary hemolytic anemia, which is associated with increased levels of ADA.

Assignment of LIPA, associated with human acid lipase deficiency, to human chromosome 10 and comparative assignment to mouse chromosome 19

The genetics of lysosomal acid lipase (LIP) has been investigated in human-Chinese hamster and mouse-Chinese hamster somatic cell hybrids. Cellulose acetate electrophoresis of human fibroblast extracts demonstrated that LIP activity consists of three isozymes. A deficiency of LIP activity has been observed in Wolman's disease (WD), cholesterol ester storage disease (CESD), and I-cell disease (ICD); this deficiency was associated with only one LIP isozyme, LIPA. We have demonstrated concordant segregation between human LIPA and human chromosome 10 and its enzyme marker glutamate oxaloacetate transaminase-1 (GOT1) in cell hybrid clones. Previous evidence suggested the different mutations associated with WD and CESD to be in the structural gene which we assign to human chromosome 10, while a different gene, involved in the processing of LIPA, is altered in ICD. These results indicate that several types of gene products are involved in the final expression of LIPA. In mouse-Chinese hamster hybrid clones, mouse Lip-1 (homologous to human LIPA) was assigned to chromosome 19. Previously, mouse Got-1 has been assigned to chromosome 19. Thus, the LIPA-GOT1 linkage groups has remained intact during the 80 X 10(6) years of evolution that separates humans and mice.

Assignment of adenosine deaminase complexing protein (ADCP) gene(s) to human chromosome 2 in rodent-human somatic cell hybrids

The experiments reported in this paper indicate that the expression of human adenosine deaminase complexing protein (ADCP) in the human-rodent somatic cell hybrids is influenced by the state of confluency of the cells and the background rodent genome. Thus, the complement of the L-cell derived A9 or B82 mouse parent apparently prevents the expression of human ADCP in the interspecific somatic cell hybrids. In the a3, E36, or RAG hybrids the human ADCP expression was not prevented by the rodent genome and was found to be proportional to the degree of confluency of the cell in the culture as in the case of primary human fibroblasts. An analysis of human chromosomes, chromosome specific enzyme markers, and ADCP in a panel of rodent-human somatic cell hybrids optimally maintained and harvested at full confluency has shown that the expression of human ADCP in the mouse (RAG)-human as well as in the hamster (E36 or a3)-human hybrids is determined by a gene(s) in human chromosome 2 and that neither chromosome 6 nor any other of the chromosomes of man carry any gene(s) involved in the formation of human ADCP at least in the Chinese hamster-human hybrids. A series of rodent-human hybrid clones exhibiting a mitotic separation of IDH1 and MDH1 indicated that ADCP is most probably situated between corresponding loci in human chromosome 2.