Quantification and utility of monosialylated alpha-fetoprotein in the diagnosis of hepatocellular carcinoma with nondiagnostic serum total alpha-fetoprotein.

BACKGROUND: At concentrations <500 microg/L, serum alpha-fetoprotein (AFP) has low specificity in the diagnosis of hepatocellular carcinoma (HCC), but monosialylated AFP (msAFP) is more specific for HCC. We describe two strategies for quantitative analysis of msAFP and explore their diagnostic accuracy in cases of HCC with nondiagnostic serum total AFP concentrations. METHODS: We first used isoelectric focusing, Western blot, and densitometry (IEF-Western blot assay). We then developed a second assay, a novel glycosylation immunosorbent assay (GISA), based on the specificity of sialyltransferase and immunosorbent technology. Both assays were used to measure msAFP and msAFP percentage relative to total AFP in sera with nondiagnostic AFP concentrations from 36 patients with newly diagnosed HCC and from 18 patients with liver cirrhosis. RESULTS: The msAFP percentages and concentrations were significantly higher in the HCC patient group regardless of the quantification methods. The msAFP concentrations and msAFP percentages obtained by the two assays were highly correlated (r = 0.70 and 0.49, respectively). For discrimination of HCC with nondiagnostic serum total AFP from liver cirrhosis, the areas under the ROC curves were 0.81 (95% confidence interval, 0.70-0.92) for msAFP by IEF-Western blot assay, 0.73 (0.58-0.87) for msAFP by GISA, 0.89 (0.80-0.97) for msAFP percentage by IEF-Western blot assay, and 0.74 (0.59-0.89) for msAFP percentage by GISA. CONCLUSIONS: Both the serum concentration and percentage of msAFP are potential diagnostic markers for HCC with nondiagnostic AFP. GISA can quantify a specific glycoform of a serologic marker.

Third ventricle enlargement and lower heart rate levels in a high-risk sample.

Heart rate activity and computed tomographic measures of structural brain abnormalities were evaluated in 32 individuals with a genetic risk for schizophrenia (offspring of schizophrenic mothers). Heart rate activity was assessed in 1962 when the subjects were a mean age of 15.1 years. Diagnostic and computed tomography assessments were conducted in 1980. Compared to individuals with normal third ventricles, individuals with enlarged third ventricles evidenced significantly lower heart rate levels overall and significantly lower heart rate during rest and during the periods preceding conditioning and test for conditioning stimulus trials. These effects were independent of age, psychiatric diagnosis, and abnormalities in other brain regions. Difficulties in interpretation posed by the index of brain abnormality employed and by the 18-year time interval between the heart rate and computed tomography assessments are discussed. Together with prior evidence of a relationship between third ventricle enlargement and reduced electrodermal responsiveness in the same subjects, these findings provide a preliminary indication that enlargement of the third ventricle may involve damage to diencephalic structures involved in autonomic nervous system activity.

Direct quantitation of biotin-labeled nucleotide analogs in RNA transcripts.

We have developed a method to determine directly the number of biotinylated (Bio) nucleotide analogs incorporated into RNA transcripts. Transcripts synthesized in vitro in the presence of [alpha 32-P]CTP and varying concentrations of Bio-4-UTP were subjected to alkaline hydrolysis and the resulting 2' and 3' nucleoside monophosphates separated by reverse-phase HPLC. The amount of 32P transferred to each monophosphate was indicative of the frequency of their incorporation into the transcript. Transcripts synthesized in the presence of equimolar concentrations of Bio-4-UTP and UTP resulted in 70 out of the 125 possible UTP sites occupied by Bio-4-UMP. This study agrees with kinetic data in suggesting that T7 RNA polymerase does not significantly discriminate between the natural and the biotinylated nucleotide. Therefore, the number of biotinylated residues that are incorporated into a transcript can be controlled by varying the ratio of Bio-4-UTP to UTP in the transcription reaction. We have shown that as few as 10 Bio-4-UMP residues per 486 nucleotide transcript still results in greater than 90% binding efficiency on a streptavidin/biotin-cellulose affinity column.

Affinity chromatography of DNA labeled with chemically cleavable biotinylated nucleotide analogs.

DNA labeled with the chemically cleavable biotinylated nucleotide Bio-12-SS-dUTP was chromatographed on biotin cellulose affinity columns using either avidin or streptavidin as the affinity reagent. Although both proteins were equally effective in binding the Bio-12-SS-DNA to the affinity resin, two important differences were found. First, nonbiotinylated DNA bound to avidin, but not to streptavidin, in buffers containing 50 mM NaCl. Second, Bio-12-SS-DNA was released much more slowly from the streptavidin affinity column than from the avidin column upon washing with buffer containing dithiothreitol. This difficulty in reducing the disulfide bond of Bio-12-SS-DNA bound to streptavidin is most likely due to steric protection of the disulfide bond by the protein. This conclusion is supported by our finding that DNA labeled with another biotinylated nucleotide analog, Bio-19-SS-dUTP, is rapidly and efficiently recovered from a streptavidin column. In Bio-19-SS-DNA, the distance between the disulfide bond and the biotin group is approximately 10 A greater than that in Bio-12-SS-DNA. Therefore, Bio-19-SS-dUTP and streptavidin form the basis of an efficient affinity system for the isolation and subsequent recovery of biotinylated DNA in the presence of low ionic strength buffers.

Synthesis and characterization of biotin-labeled nucleotide analogs.

Two biotin-labeled nucleotide analogs, Bio-4-dUTP and Bio-12-SS-dUPT, were synthesized by a modification of the procedure described by Langer et al. (1981). Deoxyuridine 5'-triphosphate was first mercurated at the 5-C and subsequently reacted with allylamine to form 5-(3-amino)allyldeoxyuridine 5'-triphosphate (AA-dUTP). AA-dUTP was purified and reacted with either N-hydroxysuccinimide-activated biotin to form Bio-4-dUTP, or with N-hydroxysuccinimide-activated 2-(biotinamido)ethyl-1,3'-dithiopropionate to form Bio-12-SS-dUTP. Bio-12-SS-dUTP is a chemically cleavable biotinylated nucleotide analog containing a disulfide bond in the 12-atom linker arm joining biotin to the pyrimidine base. Both biotinylated nucleotide analogs were purified either by ion-exchange chromatography or by ion-pair reverse-phase HPLC. Bio-4-dUTP was identified by (i) its unique absorbance spectrum, (ii) its coelution with 3H-Bio-4-dUTP during reverse-phase HPLC, and (iii) its ability to bind to avidin agarose. As a functional assay for both the synthesis and purification of the biotinylated nucleotide analogs, each nucleotide was incorporated into DNA by nick-translation. The nick-translated DNA was shown to contain biotinylated nucleotides by its ability to bind to biotin-cellulose affinity columns following incubation with soluble avidin. DNA nick-translated in the presence of Bio-12-SS-dUTP was recovered from the biotin-cellulose column following incubation in buffer containing 50 mM dithiothreitol. The susceptibility of the disulfide bond in the linker arm of Bio-12-SS-dUTP to cleavage by dithiothreitol was shown to be unaffected by the presence of avidin bound to the biotin group.

Reconstitution of nucleosomes containing dinitrophenylated histones.

Histone octamers of purified monomer nucleosomes were labelled with [3H]dinitrofluorobenzene. Authentic 11 S nucleosomes were reconstituted in vitro from a mixture of [3H]dinitrophenylated histones and excess unlabelled monomer nucleosomes. The reconstituted nucleosomes were found to contain [3H]dinitrophenylated histones H2a and H2b but not [3H]dinitrophenylated histones H3 and H4. Approx. 83% of [3H]dinitrophenylated nucleosomes were immunoprecipitable with anti-dinitrophenyl immunoglobulin and Staphylococcus aureus. These results demonstrate that histones H2a and H2b contain dinitrofluorobenzene-reactive groups that can be modified without destroying their ability to participate in nucleosome formation in vitro.

Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease.

Replicating simian virus 40 (SV40) chromosomes were found to be similar to other eukaryotic chromosomes in that the rate and extent of micrococcal nuclease (MNase) digestion were greater with replicating than with nonreplicating mature SV40 chromatin. MNase digestion of replicating SV40 chromosomes, pulse labeled in either intact cells or nuclear extracts, resulted in the rapid release of nascent DNA as essentially bare fragments of duplex DNA (3-7S) that had an average length of 120 base pairs and were degraded during the course of the reaction. In addition, nucleosomal monomers, equivalent in size to those from mature chromosomes, were released. On the other hand, MNase digestion of uniformly labeled mature SV40 chromosomes resulted in the release of only nucleosomal monomers and oligomers. The small nascent DNA fragments released from replicating chromosomes represented prenucleosomal DNA (PN-DNA) from the region of replication forks that encompasses the actual sites of DNA synthesis and includes Okazaki fragments. Predigestion of replicating SV40 chromosomes with both Escherichia coli exonuclease III (3'-5') and bacteriophage T7 gene 6 exonuclease (5'-3') resulted in complete degradation of PN-DNA. This result, together with the observation that isolated PN-DNA annealed equally well to both strands of SV40 restriction fragments, demonstrated that PN-DNA originates from both sides of replication forks. Over 90% of isolated Okazaki fragments annealed only to the retrograde DNA template. The characteristics of isolated PN-DNA were assessed by examining its sensitivity to MNase and single strand specific S1 endonuclease, sedimentation behavior before and after deproteinization, buoyant density in CsCl after formaldehyde treatment, and size on agarose gels. In addition, it was observed that MNase digestion of purified SV40 DNA also resulted in the release of a transient intermediate similar in size to PN-DNA, indicating that a DNA-protein complex is not required to account for the appearance of PN-DNA. These and other data provide a model of replicating chromosomes in which DNA synthesis occurs on a region of replication forks that is free of nucleosomes and is designated as prenucleosomal DNA.

Structure of chromatin at deoxyribonucleic acid replication forks: location of the first nucleosomes on newly synthesized simian virus 40 deoxyribonucleic acid.

Exonucleases specific for either 3' ends (Escherichia coli exonuclease III) or 5' ends (bacteriophage T7 gene 6 exonuclease) of nascent DNA chains have been used to determine the number of nucleotides from the actual sites of DNA synthesis to the first nucleosome on each arm of replication forks in simian virus 40 (SV40) chromosomes labeled with [3H]thymidine in whole cells. Whereas each enzyme excised all of the nascent [3H]DNA from purified replicating SV40 DNA, only a fraction of the [3H]DNA was excised from purified replicating SV40 chromosomes. The latter result was attributable to the inability of either exonuclease to digest nucleosomal DNA in native replicating SV40 chromosomes, as demonstrated by the following observations: (i) digestion with either exonuclease did not reduce the amount of newly synthesized nucleosomal DNA released by micrococcal nuclease during a subsequent digestion period; (ii) in briefly labeled molecules, as much as 40% of the [3H]DNA was excised from long nascent DNA chains; (iii) the fraction of [3H]DNA excised by exonuclease III was reduced in proportion to the actual length of the radiolabeled DNA; (iv) the effects of the two exonucleases were additive, consistent with each enzyme trimming only the 3' or 5' ends of nascent DNA chains without continued excision through to the opposite end. When the fraction of nascent [3H]DNA excised from replicating SV40 DNA by exonuclease III was compared with the fraction of [32P]DNA simultaneously excised from an SV40 DNA restriction fragment, the actual length of nascent [3H]DNA was calculated. From this number, the fraction of [3H]DNA excised from replicating SV40 chromosomes was converted into the number of nucleotides. Accordingly, the average distance from either 3' or 5' ends of long nascent DNA chains to the first nucleosome on either arm of replication forks was found to be 125 nucleotides. Furthermore, each exonuclease excised about 80% of the radiolabel in Okazaki fragments, suggesting that less than one-fifth of the Okazaki fragments were contained in nucleosomes. On the basis of these and other results, a model for eukaryotic replication forks is presented in which nucleosomes appear rapidly on both the forward and retrograde arms, about 125 and 300 nucleotides, respectively, from the actual site of DNA synthesis. In addition, it is proposed that Okazaki fragments are initiated on nonnucleosomal DNA and then assembled into nucleosomes, generally after ligation to the 5' ends of long nascent DNA chains is completed.

Measurement of proviral genes in uninfected and avian myeloblastosis virus-infected cells by hybridization with 3H-labeled complementary DNA probe excess.

Viral RNA (vRNA) from avian myeloblastosis virus or DNA from virus-infected and uninfected cells was hybridized with [3H]DNA complementary to viral RNA ([3H]cDNA) under conditions of [3H]cDNA excess. When [3H]cDNA was used to drive the hybridization reaction with vRNA, a rate constant of 33.2 liters/mol-s was obtained. The same rate constant was obtained when vRNA excess was used as the driver. The specific activities of the [3H]DNA probe, estimated from kinetic measurements of the hybridization reaction and from the amount of [3H]cDNA in hybrid form at equilibrium, were 9.1 and 8.6 cpm/pg, respectively. DNA isolated from uninfected cells contained five or six copies of proviral DNA per cell genome. DNA isolated from erythrocytes infected with avian myeloblastosis virus had an additional five or six viral genes added to the cell genome, and the virus-infected target cell (myeloblasts) contained about 15 additional copies of proviral DNA per cell. The use of excess [3H]cDNA probe is an easy and accurate method to quantify the frequency of proviral DNA sequences in cell DNA and to measure a small amount (40 to 200 pg) of vRNA. Probe excess hybridization offers a number of advantages over other procedures and these are discussed.

Analysis of subunit organization in chicken erythrocyte chromatin.

Micrococcal nuclease digestion of intact chicken erythrocyte nuclei is shown to result in the formation of core nucleoprotein particles containing about 140 base pairs of DNA. These core particles, which are almost entirely devoid of histones f1 and f2c, are derived from transient nucleoprotein particles containing an average of approximately 180 base pairs of DNA. Oligomers of these latter particles may be isolated after brief nuclease digestion. The time course of digestion of these oligomers demonstrates the existence of "spacer" regions of more accessible DNA between core particles. Redigestion of purified monomer core nucleoprotein particles gives rise to both single-strand and double-strand DNA fragment patterns similar to those resulting from digestions of chromatin in situ. This observation indicates that the core particles we isolate are representative of nucleoprotein structures existing within the nucleus.