Amrik Sahota

Polymorphisms in the human apolipoprotein-J/clusterin gene: ethnic variation and distribution in Alzheimer’s disease

Abstract Apolipoprotein-J/clusterin (APOJ/CLI) shares many biological properties with apolipoprotein-Ε (APOE) including, but not limited to, avid binding with β-amyloid peptide. Thus, APOJ/CLI warrants scrutiny as a candidate Alzheimer’s disease (AD) susceptibility gene. We identified seven nucleotide sequence polymorphisms in APOJ/ CLI, two of which, in exon 7, alter the predicted amino acid sequence. The JVIIB variant is an asparagine-to-histidine substitution, which deletes a glycosylation signal at amino acid 317; the JVIIC variant is an aspartate-to-asparagine substitution, which forms a new glycosylation signal at position 328. Both of these coding variants, as well as two neutral polymorphisms in exon 2, were more frequent in African-Americans than Hispanics and were rare in Caucasians. However, no individual coding or noncoding variant was consistently associated with AD. At the population level, APOJ/CLI polymorphisms are frequent among persons of African descent, but probably do not alter susceptibility to AD.

Polymerase chain reaction amplification and sequence analysis of human mutant adenine phosphoribosyltransferase genes : the nature and frequency of errors caused by Taq DNA polymerase

Using the polymerase chain reaction (PCR) with Taq DNA polymerase, we have amplified a 2.4-kb fragment of genomic DNA containing the adenine phosphoribosyltransferase (APRT) gene from patients with APRT deficiency. Several clones from each patient were sequenced after subcloning the PCR product into M13mp18. Selected regions of the amplified fragment were also sequenced directly. This enabled us to distinguish PCR-induced errors from endogenous mutations and polymorphisms in each clone. 44 PCR errors were found in a total of 57,94 kb of DNA sequenced from 25 clones from 7 patients. All the errors were due to the PCR process and not to subcloning, as shown by sequence analysis of 5 APRT-positive clones isolated from a phage genomic library.

Evaluation of seven PCR-based assays for the analysis of microchimerism.

OBJECTIVEnThe presence of small numbers of cells of donor origin in the circulation of recipients of organ transplants (microchimerism) may correlate with immunologic tolerance. As part of our ongoing studies on microchimerism, we evaluated the utility of seven PCR-based assays for the detection of the less abundant DNA in paired mixtures (100 ng total DNA).nnnDESIGN AND METHODSnDNA samples were screened to identify pairs informative for one or more PCR assays. DNA mixtures from the informative pairs were then analyzed using at least one assay. The assays were based on the X-Y homologous region; a Y chromosome microsatellite locus; three autosomal microsatellite loci; the D1S80 minisatellite locus; and sequence specific oligonucleotide probe (SSOP) analysis of the HLA DRB1 locus.nnnRESULTSnAbout 0.1% of male DNA against a background of female DNA was detectable using primers for the X-Y homologous region, but the sensitivity was increased to 0.0001% using nested primers for the Y chromosome microsatellite marker. Analysis of the minor DNA component was difficult with the three autosomal microsatellite assays because of the presence of shadow bands. Similar problems with the D1S80 assay were resolved using more stringent PCR conditions, and the sensitivity was 0.1%. Using the DRB1 locus, we were able to detect 1% DNA in the mixed samples.nnnCONCLUSIONSnThese studies show that: (a) nested PCR for the Y chromosome is the most sensitive assay for the detection of microchimerism; (b) D1S80 is a useful marker for microchimerism; (c) additional optimization of analytical conditions is required if autosomal microsatellite markers and the SSOP assay are to be used for microchimerism analysis.

Purine and pyrimidine metabolism in man VIII

These volumes record the presentations made at the VIII International Symposium on Purine and Pyrimidine Metabolism in Manheld at Indiana University, Bloomington, USA from May 22- May 27, 1994. This was a continuation of meetings held every three years with the idea of bringing clinicians and basic scientists together, which we hope results in cross-fertilization of ideas. Some of the papers presented in this volume represent oral contributions and others are from posters, but we emphasize that both are considered of equal merit. As is obvious from a perusal of the titles of the papers there has been a shift in the focus of this meeting, which reflects a general shift in the area of purine and pyrimidine metabolism. The emphasis has definitely shifted to gene structure and molecular genetics, with the beginnings we hope of gene therapy as an important branch of this area of science. Although many of the inherited diseases discussed in this text can be treated with drugs, the major thrust in the futurewill be in gene therapy, where the gene (or cDNA) will be used to treat the patient with enzyme deficiency, particularly if the patient is young. As can be seen from the Iist of authors there is a remarkable degree of international cooperation in this area across countries and continents. We thank the many participants who have attended these symposia many times, and we welcome the large group of scientists from Eastern Europe who are attending this meeting for the first time.

Prospective study of microchimerism in transplant recipients

Background. We evaluated peripheral blood microchimerism in 48 consecutive organ transplant recipients (35 kidneys, ten livers, one kidney–liver, one kidney–pancreatic islet, one kidney–pancreas) up to 12 months post‐transplantation. Patients were categorized according to the presence or absence of rejection episodes, and the patterns of microchimerism in the two groups were then compared.Methods. DNA was extracted from donor, pre‐transplant, and post‐transplant peripheral blood samples. Several polymerase chain reaction (PCR)‐based assays were developed for the detection of microchimerism. Assay sensitivities ranged from 0.0001 to 3%.Results. Microchimerism was detected only in sex‐mismatched cases (male donors and female recipients) using nested PCR for a Y‐chromosome marker. There were ten such cases (six kidneys, two livers, and two combined organ transplants). In patients without rejection (n=7), there was a peak of donor‐DNA at 1–3 wk post‐transplantation followed by a second peak between 3 wk and 4 months. In patients with biopsy‐proven rejection (n=3), the peaks were absent and the levels of microchimerism were extremely low (<0.001%). Microchimerism levels declined in all 10 patients and were barely detectable 1 yr post‐transplantation. Microchimerism was not detected in the remaining 38 patients despite using a battery of sensitive PCR‐based assays.Conclusions. In our study, microchimerism was detected using the Y‐chromosome PCR assay only and the level of donor‐DNA in a given patient varied over time. This study highlights the difficulties in establishing a correlation between microchimerism and transplant tolerance.

Analysis of germline and in vivo somatic mutations in the human adenine phosphoribosyltransferase gene: Mutational hot spots at the intron 4 splice donor site and at codon 87

We have characterized 18 germline and 10 in vivo somatic mutations in the human adenine phosphoribosyltransferase (APRT) gene. Both germline and in vivo somatic mutations were clustered at the intron 4 splice donor site and at codon 87. In vitro somatic mutations in human APRT do not appear to show this clustering. These findings suggest that the spectrum of germline mutations in APRT may be similar to that incurred by somatic cells in vivo, but different from that seen in cultured cells. Thus, in vivo, rather than in vitro, somatic mutations in this gene may be more representative of mutational events occurring in the germline.

Mutational Basis of Adenine Phosphoribosyltransferase Deficiency

The mutational basis of APRT deficiency was studied in non-Japanese and Japanese patients. Fifteen different mutations have been identified altogether. Of these 4 were common, 6 were located in exon 3, and two at the exon 4-intron 4 junction. The common mutations were a missense mutation in exon 3 (asp65----val) and a T insertion at the exon 4-intron 4 junction in non-Japanese patients, a nonsense mutation in exon 3 (trp98----end) in Type I Japanese patients, and an exon 5 missense mutation (met136----thr) in Type II patients. The other mutations in Type I patients consisted mainly of single base changes and small deletions.

Purification and characterization of adenine phosphoribosyltransferase from Saccharomyces cerevisiae.

Adenine phosphoribosyltransferase (APRT) from Saccharomyces cerevisiae was purified approximately 1500-fold. The enzyme catalyzes the Mg-dependent condensation of adenine and 5-phosphoribosylpyrophosphate (PRPP) to yield AMP. The purification procedure included anion exchange chromatography, chromatofocusing and gel filtration. Elution of the enzyme from the chromatofocusing column indicated a pI value of 4.7. The molecular mass for the native enzyme was 50 kDa; however, upon electrophoresis under denaturing conditions two bands of apparent molecular mass of 29 and 20 kDa were observed. We have previously reported the presence of two separate coding sequences for APRT, APT1 and APT2 in S. cerevisiae. The appearance of two bands under denaturing conditions suggests that, unlike other APRTs, this enzyme could form heterodimers. This may be the basis for substrate specificity differences between this enzyme and other APRTs. Substrate kinetics and product inhibition patterns are consistent with a ping-pong mechanism. The Km for adenine and PRPP were 6 microM and 15 microM, respectively and the Vmax was 15 micromol/min. These kinetic constants are comparable to the constants of APRT from other organisms.

The association between Apo E genotype and depressive symptoms in elderly African-American subjects.

In this study of 138 elderly subjects (112 without and 26 with dementia) obtained from a community sample of elderly African-American subjects, there were no significant differences in mean Geriatric Depression Scale scores by Apo E epsilon 4 status for dementia or nondementia subjects. Three subjects received a diagnosis of major depressive disorder. None of these subjects were Apo E epsilon 4-positive. These results do not support an association between depressive symptoms and Apo E allele status in this elderly African-American population.

Identification of a splice mutation at the adenine phosphoribosyltransferase locus in a German family

SummaryWe examined the molecular basis of adenine phosphoribosyltransferase (APRT) deficiency in homozygous-deficient, identical twin brothers who were born to non-consanguineous German parents. DNA was isolated from blood, and the APRT gene was amplified by PCR, subcloned into M13, and sequenced completely. A single T insertion between bases 1831–1832 or 1832–1833 was identified. This alters the consensus sequence at the exon 4 — intron 4 splice donor site and leads to aberrant splicing. The same mutation has been described previously in two affected brothers from Belgium, and the Indianapolis group has also identified it in two other, unrelated Caucasian patients. Thus, this mutation may be a common cause of APRT deficiency in the Caucasian population.