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Genomic DNA Probes (genomic + dna_probe)
Selected AbstractsHomozygous deletions within the 11q13 cervical cancer tumor-suppressor locus in radiation-induced, neoplastically transformed human hybrid cellsGENES, CHROMOSOMES AND CANCER, Issue 4 2004Marc S. Mendonca Studies on nontumorigenic and tumorigenic human cell hybrids derived from the fusion of HeLa (a cervical cancer cell line) with GM00077 (a normal skin fibroblast cell line) have demonstrated "functional" tumor-suppressor activity on chromosome 11. It has been shown that several of the neoplastically transformed radiation-induced hybrid cells called GIMs (gamma ray induced mutants), isolated from the nontumorigenic CGL1 cells, have lost one copy of the fibroblast chromosome 11. We hypothesized, therefore, that the remaining copy of the gene might be mutated in the cytogenetically intact copy of fibroblast chromosome 11. Because a cervical cancer tumor suppressor locus has been localized to chromosome band 11q13, we performed deletion-mapping analysis of eight different GIMs using a total of 32 different polymorphic and microsatellite markers on the long arm (q arm) of chromosome 11. Four irradiated, nontumorigenic hybrid cell lines, called CONs, were also analyzed. Allelic deletion was ascertained by the loss of a fibroblast allele in the hybrid cell lines. The analysis confirmed the loss of a fibroblast chromosome 11 in five of the GIMs. Further, homozygous deletion (complete loss) of chromosome band 11q13 band sequences, including that of D11S913, was observed in two of the GIMs. Detailed mapping with genomic sequences localized the homozygous deletion to a 5.7-kb interval between EST AW167735 and EST F05086. Southern blot hybridization using genomic DNA probes from the D11S913 locus confirmed the existence of homozygous deletion in the two GIM cell lines. Additionally, PCR analysis showed a reduction in signal intensity for a marker mapped 31 kb centromeric of D11S913 in four other GIMs. Finally, Northern blot hybridization with the genomic probes revealed the presence of a novel >15-kb transcript in six of the GIMs. These transcripts were not observed in the nontumorigenic hybrid cell lines. Because the chromosome 11q13 band deletions in the tumorigenic hybrid cell lines overlapped with the minimal deletion in cervical cancer, the data suggest that the same gene may be involved in the development of cervical cancer and in radiation-induced carcinogenesis. We propose that a gene localized in proximity to the homozygous deletion is the candidate tumor-suppressor gene. © 2004 Wiley-Liss, Inc. [source] Interleukin-1 gene polymorphism and periodontal statusJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 5 2001A case-control study Abstract Objectives: This case-control study examined polymorphisms at the interleukin-1 gene in relation to periodontal status, subgingival bacteria and systemic antibodies to periodontal microbiota. Methods: 132 periodontitis patients were age- and gender-matched with 73 periodontally intact controls. Full-mouth clinical assessments of the periodontal tissues were performed. Subgingival plaque samples (2440 in total) were analyzed by genomic DNA probes, and serum IgG antibodies to periodontal microbiota were assessed by an immunoassay. Polymorphisms in the IL-1A gene at position +4845 and the IL-1B gene at position +3953 were studied by PCR. A composite positive genotype was defined as at least one rare (#2) allele present at each locus. Results: No skewed distribution of the composite genotype was observed between cases and controls (45.2% vs 41.7%). In cases, both the composite genotype and the number of #2 alleles were positively correlated with the severity of attachment loss. No relationship between genotype and subgingival microbial profiles was observed. Genotype positive patients revealed both overall lower serum antibody levels and specific titers against selected bacteria. Conclusions: The composite genotype failed to distinguish between periodontitis patients and controls but correlated in patients with the severity of the disease and the antibody responses to periodontal microbiota. Zusammenfassung Grundlagen: Diese Fall-kontrollierte Studie prüfte die Polymorphismen am Interleukin-1 Gen in Beziehung zum parodontalen Status, subgingivalen Bakterien und systemischen Antikörpern zu parodontalen Mikroorganismen. Methoden: 132 Parodontitis-Patienten wurden nach Alter und Geschlecht mit 73 parodontal gesunden Kontrollen gemischt. Eine vollständige klinische Überprüfung des parodontalen Gewebes wurde durchgeführt. Subgingivale Plaqueproben (insgesamt 2440) wurden mit Genom DNA Testen analysiert, und die Serum IgG Antikörper zu parodontalen Bakterien wurden mit einem Immunoassay bestimmt. Die Polymorphismen am IL-1A Gen an den Stellen +4845 und am IL-1B Gen an der Positon +3953 wurden mittels PCR überprüft. Ein zusammengefaßter positiver Genotyp wurde so definiert, daß mindestens ein seltenes Allel (#2) an jeder Position vorhanden war. Ergebnisse: Es wurde keine schiefe Verteilung der zusammengefaßten Genotypen zwischen den Probanden und den Kontrollen (45.2% versus 41.7%) beobachtet. Bei den Probanden waren sowohl der zusammengefaßte Genotyp als auch die Anzahl der #2 Allele positiv mit dem Ausmaß des Stützgewebeverlustes korreliert. Zwischen den Genotypen und den subgingivalen Bakterienprofilen wurden keine Beziehungen gefunden. Genotyp positive Patienten zeigten sowohl allgemein niedrigere Serumantikörperlevel als auch spezifischen Titer gegen die selektierten Bakterien. Zusammenfassung: Der zusammengefaßte Genotyp untereschied sich nicht zwischen den Parodontitis-Patienten und den Kontrollen, aber korrelierte bei den Patienten mit der Schwere der Erkrankung und der Antikörperantwort auf parodontalen Bakterien. Résumé Cette étude a examiné les polymorphismes du gène Interleukine-1 (IL-1) en relation avec l'état parodontal, les bactéries sous-gingivales et les anticorps systémiques aux bactéries parodontales. 132 patients avec parodontite d'âge et de sexe similaires aux 73 contrôles sans problèmes parodontaux ont été recrutés. Les analyses clinique des tissus parodontaux de toute la bouche ont été effectuées. Des échantillons de plaque dentaire sous-gingivale (2220 au total) ont été analysés par des sondes ADN génomiques et des anticorps IgG sériques aux bactéries parodontales ont été analysés par immuno-essais. Les polymorphismes de IL-1A à la position +4845 et de IL-1B à la position +3953 ont étéétudiés par une réaction de la chaîne polymérase (PCR). Un génotype composite positif était défini comme un rare (#2) allèle présent à chaque endroit. Aucune répartition spéciale du génotype composite n'a été observée entre les cas et les contrôles (45.2% versus 42%). Chez les personnes présentant des cas tant le génotype composite que le nombre d'allèle #2 étaient en relation positive avec la sévérité de la perte d'attache. Aucune relation entre le génotype et les profils microbient sous-gingivaux n'a été mise en évidence. Les patients positifs aux génotypes possédaient des niveaux d'anticorps sériques et des titres spécifiques inférieurs contre des bactéries sélectionnées. Le génotype composite ne permet pas la distinction entre les patients avec parodontite et les contrôles, mais est en corrélation chez les patients avec la sévérité de la maladie et les résponses de l'anticorps à la flore parodontale. [source] Microbial composition of supra- and subgingival plaque in subjects with adult periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 10 2000Laurie Ann Ximénez-Fyvie Abstract Background, aims: The purpose of the present study was to compare and relate the microbial composition of supra and subgingival plaque in 23 adult periodontitis subjects (mean age 51±14 years). Methods: A total of 1,170 samples of supra and subgingival plaque were collected from the mesial aspect of every tooth (up to 28 supra and 28 subgingival samples) from each subject and evaluated for the presence and levels of 40 bacterial taxa using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments including dichotomous measures of gingival redness, bleeding on probing, plaque accumulation and suppuration, as well as duplicate measures of pocket depth and attachment level, were made at 6 sites per tooth. The counts (levels), % DNA probe count (proportion) and % of sites colonized (prevalence) of each species in supra and separately in subgingival plaque were computed for each subject. Significance of differences between supra and subgingival plaque for each species was sought using the Wilcoxon signed ranks test and adjusted for multiple comparisons. Results: All 40 taxa were detected in both supra and subgingival plaque. Actinomyces species were the most prevalent taxa in both habitats. 75 to 100% of supra and 62 to 100% of subgingival sites were colonized by at least one of the 5 Actinomyces species. Supragingival samples exhibited significantly higher counts of Actinomyces naeslundii genospecies 1, Actinomyces israelii, Actinomyces odontolyticus, Neisseria mucosa, Streptococcus gordonii, Capnocytophaga ochracea and Capnocytophaga sputigena when compared with mean counts in subgingival samples taken from the same tooth surfaces. Subgingival plaque samples presented significantly higher counts of Prevotella nigrescens, Prevotella intermedia, Bacteroides forsythus and Porphyromonas gingivalis. Subgingival samples exhibited a significantly higher proportion of "red" and "orange complex" species, while supragingival plaque exhibited higher proportions of "green" and "purple" complex species as well as Actinomyces species. Suspected periodontal pathogens could be detected in supragingival plaque from sites where subgingival samples were negative for the same species. Conclusions: The data indicate that supragingival plaque can harbor putative periodontal pathogens, suggesting a possible rôle of this environment as a reservoir of such species for the spread or reinfection of subgingival sites. [source] Effect of khat chewing on 14 selected periodontal bacteria in sub- and supragingival plaque of a young male populationMOLECULAR ORAL MICROBIOLOGY, Issue 3 2005N. N. Al-Hebshi Background/aims:, The habit of chewing khat (Catha edulis) for its amphetamine-like effects is highly prevalent in Yemen and east Africa, and has expanded to Western countries. The purpose of this study was to estimate and compare the prevalence and levels of 14 periodontal bacteria in gingival plaque of khat chewers and khat nonchewers, as well as of khat chewing sides and khat nonchewing sides. Methods:, A total of 408 sub- and supragingival plaque samples were collected from 51 young males (29 khat chewers and 22 khat nonchewers; age range 19,28 years) and analyzed using whole genomic DNA probes and checkerboard DNA,DNA hybridization. Clinical parameters were recorded for all teeth at six sites per tooth. Results:,Streptococcus intermedius and Veillonella parvula were significantly more prevalent in the subgingival plaque of chewers, which also showed significantly higher levels of V. parvula and Eikenella corrodens. Similar results were found for the subgingival plaque of the chewing sides compared to the nonchewing sides. However, there was a significantly higher prevalence and higher levels of Tannerella forsythia in the subgingival plaque of the nonchewing sides. No significant differences were observed for the supragingival plaque between the two study groups. There was a significantly lower prevalence of Capnocytophaga gingivalis and Fusobacterium nucleatum in the khat chewing sides, and higher levels of V. parvula and Actinomyces israelii. Conclusion:, The data suggest that khat chewing induces a microbial profile that is not incompatible with gingival health. [source] Cyclin D1 Amplification and p16(MTS1/CDK4I) Deletion Correlate With Poor Prognosis in Head and Neck Tumors,THE LARYNGOSCOPE, Issue 3 2002Ali Namazie MD Abstract Objectives/Hypothesis Cyclin D1, a cell cycle regulator localized to chromosome 11q13, is amplified in several human tumors including head and neck squamous cell carcinoma (HNSCC). Amplification and/or overexpression of cyclin D1 have been correlated to a poor prognosis. Deletion of the p16 gene, localized to 9p21, has also been observed in a significant proportion of HNSCC. The p16 gene regulates cyclin D1-CDK4 activity and prevents retinoblastoma tumor suppressor gene phosphorylation, thereby downregulating cellular proliferation. Detection of cyclin D1 amplification and p16 deletion using a simple and sensitive method will be valuable for the development of effective treatment modalities for head and neck cancer. Study Design We have used fluorescence in situ hybridization (FISH) to study cyclin D1 amplification and p16 gene deletion in head and neck tumors. Both single- and dual-color FISH were performed. Methods Paraffin-embedded tissues from 103 patients with HNSCC were analyzed using genomic DNA probes for cyclin D1 and p16. Dual-color FISH was performed with chromosome 11 or 9 centromeric probes as a control. Twenty-eight of these samples were analyzed for p16 expression by immunohistochemistry. Results Cyclin D1 amplification was observed in 30% (31/103) of patients, and p16 deletion in 52% (54/103). Lack of p16 expression was observed in 64% (18/28) of patients. There was a good correlation between the deletion of p16 sequences and the loss of p16 expression (P = .008). Amplification of cyclin D1 had a statistically significant association with recurrence, distant metastasis, and survival at 36 months. There was a significant association between p16 deletion and the development of distant metastases. Cyclin D1 amplification and p16 deletion together correlated with recurrence, distant metastasis, and survival. Conclusions We demonstrate that FISH is a simple and sensitive method for detecting cyclin D1 amplification and p16 deletion in head and neck cancer. Our results suggest that these two genetic aberrations together portend a poorer outcome than either of the abnormalities alone in head and neck cancer. [source] Fluorescence in situ hybridization for detecting genomic alterations of cyclin D1 and p16 in oral squamous cell carcinomasCANCER, Issue 10 2007Narikazu Uzawa DDS Abstract BACKGROUND Cyclin D1 (CCND1) and p16 alterations have been detected in oral squamous cell carcinomas (SCCs), suggesting that abnormalities of these genes may play an important role in the genesis or progression of oral SCCs and serve as independent prognostic indicators. The detection of CCND1 and p16 aberrations using a simple and sensitive method would be valuable for the development of effective treatment modalities for oral cancer. The objective of the current study was to determine whether CCND1 numerical aberrations and p16 deletions in oral SCCs detected by fluorescence in situ hybridization (FISH) have any impact on clinical outcome. METHODS Using genomic DNA probes for CCND1 and p16, FISH was performed on specimens that were obtained by fine-needle aspiration (FNA) from 57 primary oral SCCs. RESULTS The CCND1 numerical aberration was observed in 28 of 57 patients (49%) with oral SCCs and was associated significantly with reduced disease-free survival (P = .0004) and overall survival (P = .0179). Conversely, p16 deletion was detected in 22 of 57 patients (39%). The disease-free and overall survival rates for patients with p16 deletion were lower than those among patients without the p16 deletion, although the difference just failed to reach statistical significance (P = .0516 and P = .1878, respectively). The p16 deletion in the presence of the CCND1 numerical aberration conferred significantly worse disease-free survival (P = .0002) and overall survival (P = .0153). CONCLUSIONS Although the CCND1 numerical aberration was a good predictor of aggressive tumors, recurrence, and poor prognosis in patients with oral SCCs, the authors were able to identify subgroups of patients that had early disease recurrence and a poor prognosis more efficiently by assessment of p16 deletion in addition to CCND1 genetic status using FISH on FNA biopsy samples compared with the analysis of either alteration alone. Cancer 2007. © 2007 American Cancer Society. [source] | ||||||||||