Aberration of genomic DNA in association with human hepatocellular carcinomas detected by 2-dimensional gel analysis

Alterations of genomic DNAs in primary hepatocellular carcinomas (HCCs) were examined by restriction landmark genomic scanning (I. Hatada et al., Proc. Natl. Acad. Sci. USA, 88: 9523-9527, 1991) which is a 2-dimensional gel analysis that allows detection of deletion, amplification, or other rearrangements of genomic DNA. Sixteen HCC samples together with their normal counterparts were tested in this manner. Each HCC sample was micromanipulated to minimize possible carryover from non-malignant cells. DNAs from HCCs and their normal counterparts were cleaved with the restriction enzyme NotI, end labeled with 32P, and size fractionated by 2-dimensional electrophoresis using HinfI as the second cleavage enzyme. The resulting spots (about 2000) in HCC samples were compared with their normal counterparts. Five spots were more intense in 10-14 of the 16 HCCs (63-88%). The intensity of several spots was reduced to about half, suggesting the loss of one of two alleles. Some of these decreases were observed frequently in different HCC samples, whereas others were sporadic. Sixty of these spots reproducibly decreased in > 2 cases, with 27 showing a decrease in > 50% of the informative cases. The highest incidence was observed in 14 of 16 samples (88%). No significant correlations were observed between these changes in spots and hepatitis B virus or hepatitis B virus infection. The use of landmarks that show a reproducible increase or decrease in intensity is discussed in conjunction with future studies of genomic alterations inherent in HCC.

Determination of S-benzyl-N-acetyl-L-cysteine by gas chromatography/mass spectrometry as a new marker of toluene exposure

We investigated by gas chromatography/mass spectrometry if S-benzyl-N-acetyl-L-cysteine (SBAC) is excreted into the urine of six printing workers and 20 sniffers after exposure to toluene. SBAC was extracted from 10 mL urine with chloroform and back extracted into 1M sodium bicarbonate. After acidfying, the sample was reextracted with ethyl acetate. The SBAC in urine was also measured by selected ion monitoring methods, using deuterium-labeled SBAC as an internal standard. An excellent linearity was obtained from 0.01 to 3.0 mg/L (r = 0.998). Urinary concentrations of SBAC were determined quantitatively in all samples from sniffers and printing workers (n = 26, 0.02-43.29 mg/L) but were not determined in the urine of persons not exposed to toluene (n = 40). The results of this experiment indicate that SBAC is excreted as a minor metabolite of toluene in human urine. The analysis of urinary SBAC is a useful tool in identifying toluene exposure.

Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification

The heme compound found in deoxyribonucleic acid (DNA) extracted from bloodstains, which is regarded as a major inhibitor of polymerase chain reaction (PCR), was characterized in comparison with alkaline and acid hematin, histidine and ammonia hemochromogens, and globin and serum albumin hemochromogens digested by proteinase K. Alkaline and acid hematin were almost completely removed by phenol/chloroform treatment and ethanol precipitation, so as not to be copurified with DNA from the specimens. Spectrophotometric results indicated that the contaminant was likely to be the product of proteinase K digestion of some heme-blood protein complex, which was not completely extracted by organic solvents and remained in the ethanol precipitates of DNA. The results of polyacrylamide gradient gel electrophoresis and intensity of the inhibition of PCR suggested that the ligand of the contaminant was a somewhat large molecule, resistant to the proteolysis by proteinase K. The addition of bovine serum albumin to the reaction mixture prevented the inhibition of PCR by the heme compounds, probably by binding to the heme. This showed that the inhibition was not due to the irreversible inactivation of the enzyme.

Different effect of thymidine kinase loss on TTP pools; comparison among human leukemia cell lines

Thymidine kinase (TK)-deficient cells were established from six human leukemia cell lines to evaluate the role of TK in maintaining intracellular TTP pools. The residual TK activities in mutant cells were less than 3% of those of wild-type strains, except for a B-lymphoid cell line, Ball-1 (8.7%). In a promyelocytic leukemia cell line (HL-60), a splenic B cell line (WI-L2) and Ball-1, a mutational loss of TK resulted in a decrease of TTP pools by 80%, 33% and 54%, respectively. On the other hand, in the T cell lines, Molt-3, Molt-4 and CEM, TTP did not show any significant differences between parent and TK-deficient cells. TK-deficient HL-60 cells had, however, comparable levels of dATP, dGTP and dCTP with wild-type cells. An analysis of growth characteristics showed that the decrease of TTP was not due to the change of the cell cycle distribution. These results indicate that TK plays a different role in maintaining TTP pools among human leukemia cell lines.

Chromosomal assignments of novel genes expressed in HL60 granulocytes

By collecting 3'-directed cDNA sequences called gene signatures (GSs) on a large scale, it is possible to make an expression profile of genes in a particular tissue, as well as discovering a number of novel genes. A total of 305 novel GSs collected from granulocytoid cells derived from HL60, a human promyelocytic leukemia cell line, by exposure to dimethyl sulfoxide were radiolabeled and used for Southern blot analyses to determine the copy number of the corresponding genes. Of these, 198 GSs identified as representing single-copy genes were then used as probes for hybridization analyses using a monochromosomal hybrid cell DNA panel. Sixty-nine of them were assigned to individual chromosomes. These results demonstrate that the chromosomal distribution of the GSs seems not to be proportional to the cytogenetic length of each chromosome.

Induction of apoptosis in childhood acute leukemia by chemotherapeutic agents: failure to detect evidence of apoptosis in vivo

This study is designed to investigate whether apoptosis occurs in vivo in pediatric patients with acute leukemia during induction therapy. When patients with common acute lymphoblastic leukemia (cALL) and acute myeloblastic leukemia (AML) were treated with prednisolone (60 mg/m2/day, p.o. or i.v.) and etoposide (150 mg/m2/day, i.v.), respectively, the blast cell counts fell to below 30% and 5%, respectively, in 1 week. However, during this cytoreduction phase, neither morphologically apoptotic cells nor fragmentation of DNA derived from peripheral blast cells were detected at any preparations. On the other hand, cALL but not AML cells spontaneously undergo apoptosis following their culture in vitro. The addition of autologous serum instead of fetal calf serum substantially prevented apoptosis from occurring spontaneously in cALL cells. When cALL and AML cells freshly obtained from patients before therapy were treated in vitro with 10 mumol/l prednisolone and 20 micrograms/ml etoposide, respectively, these cells underwent apoptosis within 6 hours, as determined by a morphological and DNA fragmentation assay. These in vivo and in vitro findings suggest that, although anticancer drugs may induce apoptosis in vivo, these apoptotic cells cannot be detected due to their rapid removal from the circulation.

Chromosomal assignment of short cDNA sequences by PCR using overlapping and tailed short primers

Overlapping primers and tailed short primers are effective agents for mapping very short cDNA sequences. By using such primers, human cDNAs as short as 32 nucleotides in length can produce PCR bands. Using these and other primers of ordinary size, 44 cDNAs were assigned to chromosomes, of which 24 were assigned to single chromosomes, and 2 were assigned to two chromosomes and two were assigned to three chromosomes, respectively. Among the 24 cDNAs, all of which matched GenBank entries, 6 cDNAs were observed to map to the same chromosomes as reported previously.

Different mode of cell death induced by calcium ionophore in human leukemia cell lines: possible role of constitutive endonuclease

The mechanism of cell death induced by calcium ionophore, A23187, was investigated in six human leukemia cell lines. Following exposure to 1 microM A23187, the myelogenous cell lines (HL-60, U-937, KG-1) underwent apoptosis within 3 h as determined by their morphology and DNA fragmentation assay. In contrast, T-lymphoblastic leukemia cell lines (Molt-4, Molt-3, CEM) revealed necrotic cell death after 24 h of incubation. However, an initial rise of intracellular free calcium concentrations and growth inhibition after treatment with A23187 were similar in the two cell types. We further showed that an endonuclease capable of mediating internucleosomal DNA fragmentation was constitutively expressed in the cytosol but not in the nuclei of the myelogenous cell lines, although this endonuclease was not detected in either the nuclei or the cytosol of the T-lymphoblastic cell lines. The activation of the endonuclease in myelogenous cells is calcium-independent and has an optimal pH of 7.5-9. It is inhibited by 1 mM zinc ion or 300 microM aurintricarboxylic acid. We propose that this constitutive endonuclease may be related to the susceptibility of myelogenous leukemia cell lines to apoptotic cell death.

An expression profile of active genes in human lung

An expression profile of genes active in the human lung was obtained by collecting 797 partial sequences from a 3'-directed cDNA library. Three genes were found to produce mRNA each of which comprised more than 1% of total mRNA. These three have been identified as genes for pulmonary surfactant apoprotein (PSP-A), Clara cells 10-kDa secretory protein, and HLA-E heavy chain. In the remaining 745 clones, 221 were composed of 89 species that occurred recurrently, and 524 clones appeared only once. Because the 3'-directed cDNA library faithfully represents the mRNA population in the source tissue, these numbers represent the relative activities of the gene expression. Altogether 437 gene species were novel, and 179 gene species were identified in GenBank. A significant portion of these genes encode proteins found in secretory proteins, cell surface proteins, and components in the protein synthesis machinery, representing the function of the lung.

An expression profile of active genes in human colonic mucosa

An expression profile of genes active in the human colonic mucosa was obtained by collecting 959 partial sequences from a 3'-directed cDNA library. Seven genes were found to produce mRNA each of which comprised more than 1% of total mRNA. Four of these genes are novel, and are likely to be uniquely expressed in the colonic mucosa, and the other three have been identified as genes for fatty acid binding protein, immunoglobulin lambda chain, and carcinoma-associated antigen GA733-2. In the remaining 952 clones, 310 were composed of 118 species occurred recurrently but less than 1%, and 533 clones appeared only once. Because the 3'-directed cDNA library faithfully represents the mRNA population in the source tissue, these numbers represent the relative activities of the gene expression. Altogether 156 gene species were identified in GenBank, and a significant portion of these genes encode proteins found in Golgi apparatus and lysosomes, chromosome-encoded mitochondrial proteins, cell surface proteins, and components in the protein synthesis machinery. The types and proportions of genes identified is consistent with the known major activities of the colonic mucosa such as mucous protein production, energy-dependent water absorption, and rapid cell proliferation and turnover.

Transactivating function of integrated hepatitis B virus

HBV DNAs are often found in integrated forms in human hepatocellular carcinoma (HCC). Discovery of a transactivation function coded by a limited region of the HBV genome has promoted us to survey our collection of HBV integrants with flanking cellular sequences, asking whether they might exhibit a transactivation function. In transient cotransfection assays using the HepG2 cell line, six out of the twelve integrants showed transactivation effects on the expression of cellular genes such as c-fos. These results strongly demonstrate that the transactivating effects of integrated HBV DNA are widely distributed, and some of these effects might be correlated to hepatocarcinogenesis.

cDNA analyses in the human genome project

The ultimate goal of the human genome project is to decode all the genetic information carried in the genome. Towards this goal, the physical structure of the genome, as well as the functional aspects of the genome, must be understood. We initiated a cDNA project to collect the 'expression profiles' of all human genes, a database with which to describe which genes are expressed, and to what extent, in any given human cell at a particular time. Single-cycle sequencing of randomly selected members from a 3'-directed cDNA library is most appropriate for this purpose: the sequence data serve as a 'gene signature' to identify the expressing gene, and the frequency of appearance of the gene signature reflects the activity of the gene. The compiled data, which usually cover some 1000 sequencing results per sample, are referred to as an 'expression profile.' We applied this analysis to HepG2 (a cell line derived from a hepatocellular carcinoma), liver cells and lung cells. The expression profiles shed some light upon the unique features of gene expression in the cell or tissue tested. A comparison of the expression profiles among different cells has allowed active genes to be classified as housekeepers or those with cell-specific functions. A significant fraction of the abundantly expressed genes include those that are unique to the cell. In addition, the resulting collection of thousands of gene signatures is a useful source of probes for mapping and for isolating full-size cDNAs.

Aphidicolin potentiates apoptosis induced by arabinosyl nucleosides in human myeloid leukemia cell lines

We investigated the effect of aphidicolin, an inhibitor of DNA polymerase alpha and delta, on the induction of apoptosis by arabinosyl nucleosides in a human promyelocytic leukemia cell line, HL-60. Pretreatment of HL-60 cells with aphidicolin (2 microM) significantly increased the number of morphologically apoptotic cells induced by 1-beta-D arabinofuranosylcytosine (ara-C) during 4 hr of incubation. This is consistent with the appearance of DNA fragmentation as determined quantitatively by diphenylamine or by agarose gel electrophoresis. The inhibition of cell growth on day 3 after drug exposure was correlated with the degree of apoptosis: Such synergistic interaction between aphidicolin and ara-C has also been observed in other human myeloid leukemia cell lines, U937 and KG-1. In addition, the induction of apoptosis by 9-beta-D arabinofuranosyladenine or 9-beta-D arabinofuranosylguanine is augmented by aphidicolin.

Role of protein kinase C in neutrophil survival enhanced by granulocyte colony-stimulating factor

Recombinant human granulocyte colony-stimulating factor (rhG-CSF) (10 ng/mL) prolonged human neutrophil survival in culture by at least 36 hours. The addition of H-series compounds at concentrations that are considered to inhibit both protein kinase C (PKC) and cyclic adenylate monophosphate (cAMP)-dependent protein kinase (PKA) counteracted the effect of rhG-CSF. Concomitantly, the inhibition of nucleosomal DNA fragmentation by rhG-CSF was canceled. At lower concentrations, presumably capable of inhibiting only PKA, however, the compounds exhibited marginal effects on rhG-CSF-mediated increase of cell survival. These PKC inhibitors did not influence the priming effect of rhG-CSF significantly, as determined by O2- production stimulated by N-formyl-L-methionyl-L-leucyl phenylalanine (fMLP). Our results suggest that PKC plays an important role in the mechanism by which rhG-CSF promotes neutrophil survival, in striking contrast with the priming effect elicited by rhG-CSF.

Intravenous injection of adenosine triphosphate for assessing sinus node dysfunction in patients with sick sinus syndrome

The clinical value of rapid intravenous injection of adenosine triphosphate (ATP, Adephos Kowa # L3, CAS 56-65-5) for assessing sinus node function was examined in 5 patients with sick sinus syndrome (SSS) and 6 normal controls. All patients with SSS showed cardiac pauses longer than 3 s on a 24-h Holter ECG monitoring. First, after prophylactic insertion of a temporary pacemaker in the right ventricle, overdrive suppression test was conducted using the standard technique, and sinus node recovery time (SNRT) was observed to evaluate the sinus node function. Then, 10 min later, 10 mg of ATP was rapidly injected intravenously, and body surface and intracavitary ECG were continuously recorded until the basal state was regained. The rapid injection of ATP resulted in a slight inhibition of sinus node automaticity in normal subjects, but marked inhibition was in patients with SSS associated with suppression of AV conduction. The longest post ATP atrial cycle (AA interval in the intracavitary ECG showed a close inverse relationship with SNRT corrected for basal sinus length (CSNRT), according to the following formula: longest AA interval (ms) = 3.32 x CSRT (ms) +254.4 (r = 0.91, p < 0.001). The results suggest that rapid intravenous injection is a useful tool for the diagnosis of SSS.

Identification of new genes by systematic analysis of cDNAs and database construction

The large-scale collection of partial cDNA sequences is becoming a powerful tool in biology. Similarity or motif searches in DNA databases using these partial cDNA sequences have facilitated the discovery of new genes of interest. By collecting and registering large numbers of partial sequences with a well designed non-biased cDNA library, an expression profile of active genes in a particular tissue can be obtained. Tissue-specific or stage-specific genes can be discovered by comparing the profiles from different tissues or from a tissue at different stages of development, respectively. The compilation of such expression profiles enables genes to be mapped to the tissue(s) where they are actively transcribed. The large-scale collation of gene sequences actively expressed in the body into databases complements efforts directed towards the structural analysis of the genome, with the ultimate aim of decoding all the genetic information carried in the human genome. This cDNA strategy is also being widely applied to organisms other than man.

Two-dimensional gel electrophoretograms of human chromosome specific restriction DNA fragments

Human genomic DNA can be scanned by a two-dimensional gel electrophoresis of NotI cleaved, end-labelled DNA. This method, called Restriction Landmark Genome Scanning (RLGS) method yields about 2000 landmark spots in such a two-dimensional gel electrophoresis. To assign these spots to chromosomes, DNA from flow-sorted chromosome 3 (7.7 x 10(5) copies) and chromosome 4 (6.7 x 10(5) copies) were subjected to the same analysis. Ninety seven and 122 spots, respectively, were obtained in the electrophoretograms among which 16 spots were common to other chromosomes, and the others were unique to each chromosome. A method has been devised to assign these spots to the whole genomic profile. The ability to assign each spot to a chromosome will render this new mapping technology extremely useful, in which one can detect physical aberrations occurring in chromosomes, or it can be used as an auxiliary method in physical mapping of the human genome.

Specific expression of the pancreatic-secretory-trypsin-inhibitor (PSTI) gene in hepatocellular carcinoma

Twenty hepatocellular carcinomas (HCC) were analyzed by Northern blotting to test the expression of pancreatic secretory trypsin inhibitor (PSTI). This gene was expressed in all HCCs, but not in other tumors, including mammary, thyroid, pulmonary and ovarian cancers. Some gastric and colonic cancers weakly expressed PSTI. Among cell lines examined in a similar manner, PSTI was expressed in all of 4 derived from hepatoma. On the other hand, among 15 cell lines derived from cancers other than hepatoma, only 3, derived from pancreatic, colonic and gastric cancers, weakly expressed PSTI. A CAT assay using a deletion set of the 5' region from the cloned PSTI gene has shown that in hepatoma cell lines, the expression of this gene is dependent on the presence of 2 regulatory regions that include an IL-6 responsive elements and an AP-I-binding site. However, in non-hepatoma cell lines, the 2 regulatory regions are not necessary for expression. The blood level of PSTI in 27 patients with HCC was significantly increased, and it was positively correlated with tumor size, suggesting that specific expression of PSTI in HCC causes this effect and that elevated blood level of PSTI without inflammation indicates the presence of HCC.

Molecular biology and life science

Molecular biology has made the transition from phase 1, dealing with prokaryotic genes and DNA, to phase 2, dealing with genes of eukaryotic multicellular organisms. This transition came about because of the DNA technology that has evolved since the early 1970s. Now we are at the beginning of the transition to phase 3, through the emerging human genome project. The background of the development of this project, its current state, and its possible impact on the life sciences is briefly outlined and discussed.

Detection and measurement of S-benzyl-N-acetylcysteine in urine of toluene sniffers using capillary gas chromatography

We examined the urinary excretion of S-benzyl-N-acetylcysteine (SBAC) of toluene sniffers using capillary gas chromatography. SBAC was extracted from 10 ml urine with chloroform and backextracted into 1 M sodium bicarbonate solution. After acidification, the aqueous solution was reextracted with ethyl acetate, and then derivatized to its methyl ester (ME). The peak appearing in the gas chromatogram was identified as SBAC-ME by mass spectrometry. The calibration curve was constructed by plotting the peak height ratio of SBAC-ME and internal standard (S-phenethyl-N-acetylcysteine)-ME against analyte concentration using 10 ml toluene unexposed urine. It showed good linearity over the range of 0.05-3.0 mg/l (r = 0.99). We have applied this technique to urine samples from toluene sniffers. SBAC was detected in all urinary samples of sniffers (n = 30, 0.11-47.13 mg/l), but not at all in the urine of toluene unexposed subjects (n = 60). These results prove that SBAC is also formed from toluene by human metabolism, and detection of SBAC is considered a useful marker for inhalation of toluene.

[Basic study of CA125 measurement using a newly developed "SD-8729" IRMA kit]

"SD-8729" is a one-step IRMA kit employing OC125 antibody as 125I-labeled tracer and M-11 antibody as an immunoadsorbent. Higher bound-radioactivity to beads was observed with shorter incubation time than that of a currently used CA125 IRMA kit which employed OC125 antibody both as 125I-labeled ligand and immunoadsorbent attached to beads. Almost identical CA125 values were obtained by using two kits. The antigenic nature recognized by the M-11 antibody seems substantially different from those of 130-22 or 145-9 antibodies recognizing CA130 antigen.

Analysis of hprt gene mutation following anti-cancer treatment in pediatric patients with acute leukemia

We evaluated the genotoxic effect of cancer therapy on somatic cell mutation by isolating 6-thioguanine-resistant mutants in peripheral lymphocytes. The study population comprised 45 children with acute lymphoblastic leukemia (ALL), 13 children with acute myelogenous leukemia (AML) and 28 age-matched healthy controls. The geometric mean mutant frequency for ALL patients was 7.8 x 10(-6), which was significantly higher than that for AML patients (1.7 x 10(-6)) or for healthy controls (1.1 x 10(-6)). Fifteen patients with ALL showed a high mutant frequency above 10 x 10(-6), although 10 of them had completed their treatment at least 24 months earlier. Moreover, repeated measurements of mutant frequency at intervals of 12 or more months revealed that the values were very stable. Structural hypoxanthine-guanine phosphoribosyl transferase (hprt) gene alterations, as determined by Southern blot analysis, were seen in 23% (12/52) of mutant clones derived from ALL patients, but not in those from the controls. These results suggest that intensive anti-cancer therapy of children may produce persistent somatic mutations, which could be related to the appearance of second neoplasms.