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Flow cytometric DNA analysis using cytokeratin labeling for identification of tumor cells in carcinomas of the breast and the female genital tract.

Flow cytometric assessment of DNA-ploidy and S-phase fraction in malignant tumors is compromised by the heterogeneity of cell subpopulations derived from the malignant and surrounding connective tissue, e.g., tumor, stromal and inflammatory cells. To evaluate the effect on quality of DNA cell cycle analysis and determination of DNA ploidy, cytokeratin labeling of epithelial cells was used for tumor cell enrichment in breast, ovarian, cervical and endometrial cancer prior to DNA analysis. In a prospective study, tumor cell subpopulations of 620 malignant tumors were labeled by a FITC-conjugated cytokeratin antibody (CK 5, 6, CK18 and CK 5, 6, 8 and CK 17, respectively) prior to flow cytometric cell cycle analysis. Compared to total cell analysis, detection rate of DNA-aneuploid tumors following cytokeratin labeling was increased from 62% to 76.5% in breast cancer, from 68% to 77% in ovarian cancer, from 60% to 80% in cervical cancer and from 30% to 53% in endometrial cancer. Predominantly in DNA-diploid tumors, a significantly improved detection of S-phase fraction of the tumor cells was shown due to the elimination of contaminating nonproliferating "normal cells". S-phase fraction following tumor cell enrichment was increased by 10% (mean) following cytokeratin staining in ovarian and endometrial cancer, by 30% in breast cancer and even by 70% in cervical cancer compared to total cell analysis. Thus, diagnostic accuracy of DNA-analysis was enhanced by cytokeratin labeling of tumor cells for all tumor entities investigated.

Biomarkers, Tumor↗

Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment.

AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments. METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD) with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated, purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data. RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene. CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcinogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis.

Adolescent↗

A Japanese family with two types of muscular dystrophy: DNA analysis and the dystrophin test.

A unique Japanese family with both Fukuyama type congenital muscular dystrophy (FCMD) and Duchenne muscular dystrophy (DMD) is described. Four boys, all from the sixth generation of the same family, were afflicted with severe neuromuscular diseases beginning in early life, three of them presenting the typical phenotype of FCMD and one, that of DMD. Although DNA analysis by Southern blotting with complementary DNAs representing the whole of the dystrophin coding sequence detected neither gross deletions nor duplications, immunohistochemistry and Western blotting of the biopsied skeletal muscle with an antidystrophin monoclonal antibody (dystrophin test) showed that the approximately 400-kd dystrophin was expressed normally at the sarcoplasmic membrane of the FCMD phenotype patient but was completely absent in the DMD phenotype patient. From these results, it was presumed that two different childhood muscular dystrophies, FCMD and DMD, coexisted in this family. This unique case illustrates the efficacy of the dystrophin test in the differential diagnosis of the two diseases even when conventional means of diagnosis do not give definite answers and DNA analysis of the dystrophin gene is not informative.

Blotting, Southern↗

Effects of processing techniques on the forensic DNA analysis of human skeletal remains.

Human remains processed by forensic anthropologists may potentially be used for genetic analysis. Therefore, the condition of the deoxyribonucleic acid (DNA) in processed remains may become an issue for future analysis. Processing techniques employed by anthropologists are highly variable and scanning electron microscopy reveals significant alterations to the bone surface depending upon the technique used. Such damage to the bone indicates differences may exist in quality and quantity of DNA extracted. This study assessed how five processing procedures used by major forensic anthropology laboratories around the country affects the amounts of DNA extracted from human rib bones and the subsequent DNA analysis. The DNA was analyzed using the short tandem repeat (STR) locus CSF1PO and amelogenin. The findings indicate processing procedures used by forensic anthropologists do not adversely affect DNA analysis but prolonged exposure to heat during processing may decrease the yield of information from the DNA.

DNA↗

Quantitative DNA analysis and proliferation in breast carcinomas. A comparison between image analysis and flow cytometry.

The DNA content and proliferation in 100 invasive breast carcinomas were evaluated by computerized image analysis (IA) and flow cytometry (FCM). For DNA content, image analysis of Feulgen-stained slides of fresh tumor imprints were compared with flow cytometry of propidium iodide-stained disaggregated fresh tumor tissue. The DNA indices obtained by the two methods showed close correlation by linear regression analysis (r = 0.89, p less than .001). There were 44 (44%) diploid and 56 (56%) aneuploid tumors. There was agreement between the two methods in detection of aneuploidy in 81% of tumors. Image analysis required smaller tissue samples, permitted direct visualization and selection of tumor cells, and was more sensitive in detecting tetraploid and highly aneuploid cell populations. In contrast, flow cytometry histograms provided better resolution, and were more effective in detecting multiploid tumors and near-diploid aneuploid tumors. Aneuploidy was significantly related to various adverse prognostic parameters, namely, negative estrogen receptor, high mitotic rate, high histologic and nuclear grades. Proliferation was evaluated by measuring the FCM S phase fraction (SPF), and by image analysis quantitation of immunohistochemical staining using Ki-67 monoclonal antibody. SPF and Ki-67 count showed modest correlation (r = 0.42). Both SPF and Ki-67 count were significantly related to the mitotic rate, histologic and nuclear grades. Our results indicate that the two methods provide comparable results, but offer individual advantages and are complementary techniques in analyzing DNA ploidy and proliferation in breast carcinomas.

Adenocarcinoma, Mucinous↗

DNA analysis for antenatal diagnosis of thalassaemia and haemophilia.

Two years' experience with DNA analysis for the antenatal diagnosis of thalassaemia and haemophilia is described. The advantages of DNA testing, including a first-trimester diagnosis and greater availability, must be considered in relation to the problems that are associated with this procedure. In particular, the risk of recombination in DNA polymorphism studies should be understood and explained fully to the patient.

Amniocentesis↗

Single and multiple strain colonization in patients with Helicobacter pylori-associated gastritis: detection by macrorestriction DNA analysis.

Helicobacter pylori isolates from 18 patients were examined by macrorestriction DNA analysis to determine whether > or = 2 strains can coexist in the human stomach. Four biopsy samples from different sites in each patient's stomach were cultured, and 12-14 clones of H. pylori per patient were analyzed. DNA of 15 of the 18 isolates was digestible: 12 by NotI and 3 by NruI. Within 14 of these digestible isolates, the patterns of all clones were identical. The isolate of 1 patient showed two digestion patterns, a finding that was confirmed by arbitrary primer polymerase chain reaction. The typeable isolates of all patients, except 2 who underwent gastroscopy on the same day, differed markedly from each other. These results indicate a noticeable discrepancy between the pronounced interpatient heterogeneity and the rare intrapatient variation of H. pylori.

Base Sequence↗

[The diagnostic value of flow cytometric DNA analysis in bladder cancer--comparison with conventional cytology].

The aim of this research was to assess the clinical value of flow cytometry (FCM) compared with conventional cytology in the detection and diagnosis of bladder cancer. The practical application of FCM combined with cytology was also investigated. Seventy patients with bladder cancer and 50 without neoplastic disease of the urinary tract were studied. The exfoliated cells used for FCM-DNA analysis and cytology by the Papanicolaou technique were obtained from voided urine and subsequent bladder irrigation specimens. The false negative rates for urine cytology, irrigation cytology, urine FCM, and irrigation FCM were 36%, 38%, 14% and 13%, respectively. Corresponding false positive rates were 2%, 0%, 14%, and 18%. When the above-mentioned examinations were paired, the combination of urine cytology and urine FCM appeared to be the most acceptable way to secure a correct diagnosis. Using this combination, the false negative and false positive rates were 4%, and 16%, respectively. When three or four examinations were combined, the false negative fate could not be improved despite the fact that the false positive rate worsened. It is noteworthy that FCM-DNA analysis seems to be less reliable in patients who have inflammatory diseases of the urinary tract or a history of intravesical chemotherapy.

Adult↗

Evaluation of the specificity of alkaline phosphatase-conjugated oligonucleotide probes for forensic DNA analysis.

Current methods of forensic DNA profiling by restriction fragment length polymorphism analysis rely on radioactive detection of DNA. The use of radioactive isotopes is complicated, expensive and requires elaborate safety precautions. Recently, non-radioactive detection methods involving the use of alkaline phosphatase-conjugated oligonucleotide probes have become available. These probes differ from most 32P-labeled probes in that they are synthetic oligonucleotides, whereas the 32P-labeled probes are purified plasmid inserts from cloned VNTR regions. Because of this difference, it is possible that the specificity of the non-isotopic probe will differ from that of the 32P-labeled probe. This study compares the specificity of the two types of probes by parallel analysis of a set of DNA samples, including a subset of relatively small alleles, at the loci D1S7, D2S44, D4S139, D10S28, and D17S26. We found that although the alkaline phosphatase detection method is slightly less sensitive than 32P detection, the AP-conjugated oligonucleotide probes tested have specificity comparable to, and are appropriate and suitable substitutes for, 32P-labeled plasmid inserts.

Alkaline Phosphatase↗

Cytomorphological grading and Feulgen DNA-analysis of metaplastic and neoplastic bronchial cells.

Quantitative determinations of nuclear DNA were made on squamous metaplastic and neoplastic cells from sputum cytology specimens. The cellular material was processed by destaining diagnostic smears, restaining by the Feulgen method and relocating the cells for measurement. Adventitious leucocytes were used as internal controls. There was good correlation between increasing degree of aneuploidy as judged from DNA values, and increasing degree of morphologic nuclear atypia. The data indicate a progressive aberration from normality of nuclear DNA content in squamous metaplastic and neoplastic cells exhibiting a progressive degree of atypia. This implies that squamous bronchial carcinoma is preceded by sequential changes of the cellular composition which may be recorded by both quantitative DNA analysis and cytology.

Adolescent↗

Demonstration of clonality, by X-linked DNA analysis, in chronic natural killer cell lymphocytosis and successful therapy with oral cyclophosphamide.

The expanded lymphocyte population in large granular lymphocyte (LGL)-leukemia carries the phenotypic characteristics of either cytotoxic T lymphocytes (CD3+,CD8+) or natural killer (NK) cells (CD3-,CD15+). In the former subset, clonality has been demonstrated by T-cell receptor gene rearrangement studies. Since NK cells do not rearrange T-cell receptor genes, the neoplastic nature of chronic NK cell lymphocytosis has not been well defined. We used X-linked DNA analysis to study the clonal nature of an expanded NK cell population in a patient with a 3-year history of relative lymphocytosis associated with anemia and neutropenia. Southern blot analysis showed no clonal T-cell receptor gene rearrangement. The majority of the circulating lymphocytes had a NK cell phenotype and demonstrated both direct NK cell-mediated cytotoxicity and antibody-dependent cellular cytotoxicity. However, the in vitro growth characteristics of these cells did not suggest that they were polyclonal expansions of normal NK cells. To determine directly the clonal origin of these cells, we performed X-linked DNA analysis. Density gradient centrifugation methods were used to isolate mononuclear cells, and NK cells were positively selected by CD16-immunoconjugated magnetic beads. The DNA of these cells was analyzed by restriction fragment length polymorphism-methylation strategy and showed a monoclonal pattern of X-chromosome inactivation while a polyclonal pattern was obtained in corresponding skin tissue. Treatment of the patient with oral cyclophosphamide resulted in complete hematologic remission. We conclude that chronic NK lymphocytosis may be clonal and responsive to immunosuppressive therapy.

Aged↗

p53 immunostaining and image cytometry DNA analysis in precancerous and cancerous squamous epithelial lesions of the larynx.

BACKGROUND: Squamous epithelial cancer can develop from progressive epithelial changes connoted dysplasias. Histopathologic evaluation/grading of these lesions is difficult and gives poor information concerning the risk for progression to cancer. Squamous cell carcinoma of the head and neck (SCCHN) frequently show p53 alteration and DNA-ploidy aberration. Could these markers be used as indicators for malignancy risk in the larynx? METHODS: Immunohistochemical staining (IHC), with the CM-1 antibody against p53, and image cytometry (ICM) DNA analysis were performed in 60 lesions from 12 patients--and 21 controls--who were initially seen with laryngeal lesions prior to cancer in situ (cis) or invasive cancer diagnosis at the same site. RESULTS: All but one of the invasive cancers, and 77% of the lesions which preceded cancer or cancer in situ, showed positive p53 immunostaining, as compared with only 10% of the controls. All but one of the invasive cancer lesions, and 77% of the precancerous lesions, showed aberrant DNA-ploidy results, whereas all controls were diploid. When DNA and p53 analysis were combined, only one of the lesions preceding cis or invasive cancer was negative. CONCLUSIONS: Both p53 immunoreactivity and DNA-ploidy aberration appear to be early events in the multistep process of squamous epithelial carcinogenesis. Immunohistochemical staining p53 analysis and ICM DNA analysis does increase the diagnostic sensitivity for cancerous and true precancerous lesions in the larynx.

Adult↗

Visible diode lasers can be used for flow cytometric immunofluorescence and DNA analysis.

This report describes a feasibility study concerning the use of a visible diode laser for two important fluorescence applications in a flow cytometer. With a 3 mW 635 nm diode laser, we performed immunofluorescence measurements using the fluorophore allophycocyanin (APC). We have measured CD8 positive lymphocytes with a two-step labeling procedure and the resulting histograms showed good separation between the negative cells and the dim and the bright fluorescent subpopulations. As a second fluorescence application, we chose DNA analysis with the recently developed DNA/RNA stains TOTO-3 and TO-PRO-3. In our setup TO-PRO-3 yielded the best results with a CV of 3.4%. Our results indicate that a few milliwatts of 635 nm light from a visible diode laser is sufficient to do single color immunofluorescence measurements with allophycocyanin and DNA analysis with TO-PRO-3. The major advantages of using a diode laser in a flow cytometer are the small size, the low price, the high efficiency, and the long lifetime.

DNA↗

Factors influencing survival after resection of pancreatic cancer. A DNA analysis and a histomorphologic study.

BACKGROUND: The influence of DNA content on prognosis in stomach cancer has been investigated rarely, and the results are controversial. METHOD: The prognostic relevance of the DNA content and histomorphologic parameters was evaluated in 41 patients after resection of pancreatic cancer. RESULTS: In the univariate analysis, the DNA content, tumor size, lymph node status, tumor stage, nuclear grade, and type of resection had a statistically significant influence on the prognosis. No association was found between the DNA content and the histomorphologic features. Apart from the operative procedure, the DNA content was the strongest indicator of prognosis in the multivariate analysis. CONCLUSIONS: Further investigations are necessary to find out if DNA analysis can be performed preoperatively on material obtained by fine-needle aspiration.

Cell Nucleus↗

DNA analysis in patients with lissencephaly type I and other cortical dysplasias.

DNA markers YNZ22.1, YNH37.3, 144D6, and VAW508 were studied in five patients with the Miller-Dieker syndrome, 17 patients with the isolated lissencephaly sequence, one patient with a non-classified lissencephaly, and nine patients with an atypical cortical dysplasia. All patients had normal chromosomes except for a deletion 17p13.3 in one of the five Miller-Dieker patients. The five Miller-Dieker patients showed deletions of markers YNZ22.1 and YNH37.3 in contrast to the other patients tested. In one patient, the deletion was in the maternally contributed chromosome. Prenatal diagnosis by DNA analysis allowed exclusion of the recurrence of Miller-Dieker syndrome in a subsequent pregnancy.

Brain↗

Prognostic significance of flow-DNA analysis and cell surface isoantigens in carcinoma of bilharzial bladder.

Flow cytometric DNA analysis and ABO(H) cell surface antigen expression were studied in 46 patients with cystectomies for carcinoma of bilharzial bladder. The most significant prognostic indicators were the DNA index and the status of the pelvic lymph nodes at operation. Diploid tumors were associated with a low metastatic potential (7.7%) and a better five-year survival (54%) in contrast to aneuploid cases that had a higher metastatic potential (45.5%) and a low five-year survival (21%). The ABO(H) isoantigen status did not correlate with pathologic parameters or the clinical course of these invasive bilharzial bladder tumors as was previously reported.

ABO Blood-Group System↗

Evaluation of breast carcinoma chemosensitivity by flow cytometric DNA analysis and computer assisted image analysis.

Flow cytometric (FCM) DNA and S-Phase (S%) analyses were compared to computerized image analysis (SAMBA 2005) in 27 breast carcinomas (T3, N0-N1, M0) treated by 3 cycles of preoperative Adriamycin, vincristine, cyclophosphamide, methotrexate, 5-fluorouracil (AVCMF) chemotherapy (CT). Twelve carcinomas had shown objective regression and 15 no regression. Samples studied were obtained by sequential fine-needle cytopunctures. Comparing DNA profiles obtained by both methods before and after the first cycle, it appears that tumors can be divided into 3 groups. In the first group (10 cases), no changes were observed after the first cycle of CT. These tumors before treatment had either single DNA peak without cells in S% and G2M or a major peak with a small S% and G2M peak. The second group (9 cases) showed some changes in DNA profiles with an increased G2M peak but no additional values; these tumors before treatment had a small S% and a G2M peak. In the third group (8 cases), before treatment, all were non-diploid with high S% and high G2M. After the first cycle, all showed obvious changes in DNA profiles with a decrease of the G0/G1 peak and an increased S% and G2M with dispersed additional values along the scale in (G2M) x 2 and (G2M) x 4 regions. When changes were compared to tumor regression in the 1st and 2nd groups, 1/10 and 3/9 cases, respectively, were evaluated as objective regression. In the third group, all had objective regression (p less than 0.001). In most cases, a good correlation was observed with both methods.(ABSTRACT TRUNCATED AT 250 WORDS)

Antineoplastic Combined Chemotherapy Protocols↗

Analysis of trimethylpsoralen photoreactivity to Z-DNA provides a general in vivo assay for Z-DNA: analysis of the hypersensitivity of (GT)n B-Z junctions.

We have described an exonuclease III/photoreversal procedure to map, with base pair resolution, the bases which have photoreacted with 4,5',8-trimethylpsoralen (Me3-psoralen) forming either monoadducts or interstrand cross-links in DNA (20). This assay allows quantitation of relative rates of Me3-psoralen photobinding to bases in DNA at levels as low as one cross-link per 8,000 base pairs. This assay should be useful for a wide variety of applications of Me3-psoralen photobinding to DNA. Here, we demonstrate the applicability of the Me3-psoralen exo III assay for analysis of the conformation of the Z forming sequences (GT)12ATGT and GAATTC(TG)6TA(TG)6. We have shown previously that Me3-psoralen forms crosslinks in the 5'TA within the (CG)6TA(CG)6 sequence when it exists in the B conformation but not when it exists in the Z conformation (34). More recently we have confirmed this result with the exo III assay and have shown at least a hundred fold increase in Me3-psoralen photoreactivity at the 5'AT sequence within the EcoR I sites (GAATTC) which presumably represent B-Z junctions flanking (CG)6TA(CG)6 (20). Here we demonstrate both the characteristic decrease in psoralen photobinding to 5'TAs within (GT)12ATGT and (TG)6TA(TG)6 and the hyperreactivity of B-Z junctions. These characteristic properties of Me3-psoralen photobinding provide an assay for Z-DNA that is applicable in vivo. The general applicability of this approach for assaying Z-DNA in vivo is discussed.

Biotechnology↗