ABSTRACT
Epigenetic silencing of tumour suppressor genes is an important mechanism involved in cell transformation and tumour progression. The Set and RING-finger-associated domain-containing protein UHRF1 might be an important link between different epigenetic pathways. Here, we report that UHRF1 is frequently overexpressed in human prostate tumours and has an important role in prostate cancer pathogenesis and progression. Analysis of human prostate cancer samples by microarrays and immunohistochemistry showed increased expression of UHRF1 in about half of the cases. Moreover, UHRF1 expression was associated with reduced overall survival after prostatectomy in patients with organ-confined prostate tumours (P < 0.0001). UHRF1 expression was negatively correlated with several tumour suppressor genes and positively with the histone methyltransferase (HMT) EZH2 both in prostate tumours and cell lines. UHRF1 knockdown reduced proliferation, clonogenic capability and anchorage-independent growth of prostate cancer cells. Depletion of UHRF1 resulted in reactivation of several tumour suppressor genes. Gene reactivation upon UHRF1 depletion was associated with changes in histone H3K9 methylation, acetylation and DNA methylation, and impaired binding of the H3K9 HMT Suv39H1 to the promoter of silenced genes. Co-immunoprecipitation experiments showed direct interaction between UHRF1 and Suv39H1. Our data support the notion that UHRF1, along with Suv39H1 and DNA methyltransferases, contributes to epigenetic gene silencing in prostate tumours. This could represent a parallel and convergent pathway to the H3K27 methylation catalyzed by EZH2 to synergistically promote inactivation of tumour suppressor genes. Deregulated expression of UHRF1 is involved in the prostate cancer pathogenesis and might represent a useful marker to distinguish indolent cancer from those at high risk of lethal progression.
Subject(s)
CCAAT-Enhancer-Binding Proteins/genetics , CCAAT-Enhancer-Binding Proteins/metabolism , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Acetylation , Cell Growth Processes/physiology , Cell Line, Tumor , DNA Methylation , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Disease Progression , Enhancer of Zeste Homolog 2 Protein , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Gene Silencing , Genes, Tumor Suppressor , HEK293 Cells , Histone Methyltransferases , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histones/genetics , Histones/metabolism , Humans , Immunoprecipitation/methods , Male , Polycomb Repressive Complex 2/genetics , Polycomb Repressive Complex 2/metabolism , Promoter Regions, Genetic , Prostatic Neoplasms/pathology , Ubiquitin-Protein LigasesABSTRACT
Non-small cell lung cancers (NSCLC), in particular adenocarcinoma, are often mixed with normal cells. Therefore, low sensitivity of direct sequencing used for K-Ras mutation analysis could be inadequate in some cases. Our study focused on the possibility to increase the detection of K-Ras mutations in cases of low tumour cellularity. Besides direct sequencing, we used wild-type hybridisation probes and peptide-nucleic-acid (PNA)-mediated PCR clamping to detect mutations at codons 12 and 13, in 114 routine consecutive NSCLC frozen surgical tumours untreated by targeted drugs. The sensitivity of the analysis without or with PNA was 10 and 1% of tumour DNA, respectively. Direct sequencing revealed K-Ras mutations in 11 out of 114 tumours (10%). Using PNA-mediated PCR clamping, 10 additional cases of K-Ras mutations were detected (21 out of 114, 18%, P<0.005), among which five in samples with low tumour cellularity. In adenocarcinoma, K-Ras mutation frequency increased from 7 out of 55 (13%) by direct sequencing to 15 out of 55 (27%) by clamped-PCR (P<0.005). K-Ras mutations detected by these sensitive techniques lost its prognostic value. In conclusion, a rapid and sensitive PCR-clamping test avoiding macro or micro dissection could be proposed in routine analysis especially for NSCLC samples with low percentage of tumour cells such as bronchial biopsies or after neoadjuvant chemotherapy.
Subject(s)
Carcinoma, Non-Small-Cell Lung/genetics , Genes, ras , Lung Neoplasms/genetics , Mutation , Peptide Nucleic Acids/genetics , Polymerase Chain Reaction/methods , Proto-Oncogene Proteins/genetics , ras Proteins/genetics , Aged , ErbB Receptors/antagonists & inhibitors , Female , Humans , Male , Middle Aged , Nucleic Acid Hybridization , Proto-Oncogene Proteins p21(ras) , Sensitivity and SpecificityABSTRACT
The epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) erlotinib improves survival of lung cancer as second- or third-line therapy. However, after an initial response, most patients will recur, particularly within the central nervous system. The present study reports the case of a 27-yr-old nonsmoking male presenting with a metastatic lung adenocarcinoma with EGFR exon 19 deletion, associated with sensitivity to EGFR-TKI. Gefitinib, followed by chemotherapy and finally erlotinib resulted in prolonged disease control, until multiple liver metastases were detected. After stopping EGFR-TKI, brain metastases with carcinomatous meningitis were diagnosed. A secondary T790M mutation, associated with resistance to EGFR-TKI, was found on the liver biopsy but not in the cerebrospinal fluid. Erlotinib was reintroduced and allowed a quick neurological improvement, even though the extra-cranial disease remained resistant to erlotinib. The present report underscores the interest of molecular monitoring in lung cancer. Persistent cerebral tyrosine kinase inhibitor sensitivity should be considered in patients presenting with an early central nervous system relapse after stopping epidermal growth factor receptor tyrosine kinase inhibitor, even with a T790M-resistant mutation in noncerebral metastases. Questions remain concerning the selection of sub-clones during epidermal growth factor receptor tyrosine kinase inhibitor therapy, which could differ according to metastatic sites, especially in the central nervous system.
Subject(s)
Adenocarcinoma/pathology , Adenocarcinoma/therapy , Central Nervous System Neoplasms/secondary , Central Nervous System Neoplasms/therapy , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/metabolism , Lung Neoplasms/pathology , Lung Neoplasms/therapy , Adult , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Drug Resistance, Neoplasm , Erlotinib Hydrochloride , Gefitinib , Humans , Liver Neoplasms/secondary , Liver Neoplasms/therapy , Male , Neoplasm Metastasis , Quinazolines/administration & dosage , Recurrence , Treatment OutcomeABSTRACT
The French Cancer Plan 2003-2007 has made translational research central to its research programme, to ensure the care-research continuum and the quickest application possible for the most recent discoveries, for the patients' benefit. This is a new field of research, still little-known or ill-understood. A working group, composed of physicians and researchers from academic research and industrial research, sought to define translational research in cancerology and define the issues at stake in it. Translational research needs to develop in close connection with the patients in order to enable a bi-directional flow of knowledge from cognitive research toward medical applications and from observations made on patients toward cognitive research. Placed under the aegis of the French National Cancer Institute and Leem Research, the group has put forth a strategy for implementing translational research in cancerology in France to make it attractive, competitive and efficient and to foster the development of public-private partnerships.
Subject(s)
Biomedical Research/organization & administration , Diffusion of Innovation , Neoplasms/therapy , Biomedical Research/standards , France , Humans , Interdisciplinary Communication , Models, Animal , Neoplasms/genetics , Patient Participation/methodsABSTRACT
Evaluation of the role of clonal heterogeneity in colon tumour sensitivity/resistance to drugs and/or in conferring metastatic potential requires an adequate experimental model in which the tumour cells maintain the initial genetic alterations and intra-tumoral heterogeneity through maintenance of the genetic clones present in the initial tumour. Therefore, we xenografted subcutaneously into nude mice seven human colonic tumours (from stages B1 to D) that showed chromosome instability and transplanted them sequentially for up to 14 passages. Maintenance after xenografting of the genetic alterations present in the initial tumours was scored by allelotype studies targeting 45 loci localized on 18 chromosomes. We show that xenografting does not alter the genetic or the histological profiles of the tumours even after 14 passages. Screening of the entire genome of one tumour by comparative genome hybridization also showed overall stability of the alterations between the initial and the xenografted tumour. In addition, intra-tumoral heterogeneity was maintained over time, suggesting that no clonal selection occurred in the nude mice. The observation that some loci showed partial allelic imbalance in the initial tumour but loss of heterozygosity after the first passage in nude mice when all the normal cells were lost may allow identification of interesting genetic defects that could be involved in tumour expansion. Thus, sequential xenografts of colon tumours will provide a powerful model for further study of tumour clonality and for the identification of genetic profiles responsible for differential resistance to therapeutic treatments. Our data also suggest that tumour expansion can result from alterations in several distinct genetic pathways.
Subject(s)
Chromosomal Instability , Colonic Neoplasms/genetics , Genetic Heterogeneity , Allelic Imbalance , Animals , Cell Transformation, Neoplastic/genetics , Colonic Neoplasms/pathology , DNA, Neoplasm/genetics , Disease Models, Animal , Humans , Loss of Heterozygosity , Mice , Mice, Nude , Neoplasm Transplantation , Nucleic Acid Hybridization/methods , Transplantation, HeterologousABSTRACT
Fibroblast growth factors (FGF), hepatocyte growth factor (HGF) and their receptors, FGFR and c-Met, are essential components of the regulatory networks between the epithelium and mesenchyme in embryonic lung, but their respective roles in tumour growth are not clear. We performed allelotyping at loci containing the candidate genes FGFR-1-2-3-4, FGF-1-2-7-10, c-Met and HGF in 36 non-small cell lung cancer (NSCLC) (20 squamous-cell carcinomas (SQC) and 16 adenocarcinomas (ADC)), by surrounding each locus with two microsatellites (MS), as close as possible to the genes of interest. Unexpectedly, SQC and ADC were frequently altered at all of these loci, and SQC showed more simultaneously altered loci. In ADC, alterations at the 15q13-22 locus (FGF7 candidate gene) were significantly more frequent. Thus, these loci showed different patterns of molecular alterations between SQC and ADC. Finally, alterations at loci containing FGFR and HGF candidate genes were inversely correlated to the lymph node status in SQC and ADC, respectively.
Subject(s)
Allelic Imbalance/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Lung Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Cluster Analysis , Disease Progression , Female , Fibroblast Growth Factors/genetics , Hepatocyte Growth Factor/genetics , Humans , Male , Middle Aged , Prospective Studies , Proto-Oncogene Proteins c-met/genetics , Receptors, Fibroblast Growth Factor/geneticsABSTRACT
ICBP90 (Inverted CCAAT box Binding Protein of 90 kDa) is a recently identified nuclear protein that binds to one of the inverted CCAAT boxes of the topoisomerase IIalpha (TopoIIalpha) gene promoter. Here, we show that ICBP90 shares structural homology with several other proteins, including Np95, the human and mouse NIRF, suggesting the emergence of a new family of nuclear proteins. Towards elucidating the functions of this family, we analysed the expression of ICBP90 in various cancer or noncancer cell lines and in normal or breast carcinoma tissues. We found that cancer cell lines express higher levels of ICBP90 and TopoIIalpha than noncancer cell lines. By using cell-cycle phase-blocking drugs, we show that in primary cultured human lung fibroblasts, ICBP90 expression peaks at late G1 and during G2/M phases. In contrast, cancer cell lines such as HeLa, Jurkat and A549 show constant ICBP90 expression throughout the entire cell cycle. The effect of overexpression of E2F-1 is more efficient on ICBP90 and TopoIIalpha expression in noncancer cells (IMR90, WI38) than in cancer cells (U2OS, SaOs). Together, these results show that ICBP90 expression is altered in cancer cell lines and is upregulated by E2F-1 overexpression with an efficiency depending on the cancer status of the cell line.
Subject(s)
CCAAT-Enhancer-Binding Proteins/biosynthesis , Cell Cycle Proteins , Cell Transformation, Neoplastic , DNA-Binding Proteins , Gene Expression Regulation, Neoplastic , Neoplasms/genetics , Transcription Factors/pharmacology , Breast Neoplasms/genetics , Breast Neoplasms/physiopathology , CCAAT-Enhancer-Binding Proteins/chemistry , Cell Cycle , E2F Transcription Factors , E2F1 Transcription Factor , Humans , Immunohistochemistry , Neoplasms/physiopathology , Transcription Factors/biosynthesis , Tumor Cells, Cultured , Ubiquitin-Protein Ligases , Up-RegulationABSTRACT
At present, the only recognised prognostic factor for primary osteosarcoma is the histological response to preoperative chemotherapy. Our study was designed to identify new diagnostic markers that could eventually have a prognostic value. A total of 54 patients under 20 years of age with primary osteosarcomas were studied while under treatment by the French Society of Paediatric Oncology OS 94 protocol. Paired normal and biopsy samples were collected. In addition, surgical resection specimens, following preoperative chemotherapy, were obtained in 13 cases. After genomic DNA extraction, an allelotyping analysis targeting microsatellites linked to Rb and p53 genes, and 9p21, 7q31 and 5q21 regions was performed. In all, 94% of the samples at diagnosis showed allelic imbalance and the biopsies were highly rearranged except for the microsatellite targeting 7q31. The same panel was highly informative at surgical resection. Microsatellites investigating Rb, p53 and the 9p21 region were particularly altered without a significant correlation with prognosis. On the other hand, the alteration of the 7q31 locus at diagnosis was significantly correlated with a worse prognosis and a new frequently altered locus, 5q21, was described. In conclusion, this panel allowed us to characterise paediatric osteosarcomas. Correlation of prognosis with the altered 7q31 region could be a useful tool and further studies are required to confirm the importance of 5q21.
Subject(s)
Bone Neoplasms/genetics , Osteosarcoma/genetics , Adolescent , Adult , Biopsy , Bone Neoplasms/drug therapy , Child , Child, Preschool , Female , Genotype , Humans , Male , Microsatellite Repeats , Osteosarcoma/drug therapy , PrognosisABSTRACT
Topoisomerase genes were analyzed at both DNA and RNA levels in 25 cases of newly diagnosed childhood acute lymphoblastic leukemia (ALL). The results of molecular analysis were compared to risk group classification of children in order to identify molecular characteristics associated with response to therapy. At diagnosis, allelic imbalance at topo-isomerase IIalpha (TOP2A) gene locus was found in 75% of informative cases whereas topoisomerase I and IIbeta gene loci are altered in none or only one case, respectively. By semi-quantitative Polymerase chain reaction, we found a 2.5 to 8-fold TOP2A gene amplification in 72% of the children, which was correlated to gene overexpression in every case. These results show that TOP2A gene amplification is a frequent event in ALL at diagnosis. Interestingly, we also identified a small population of children that do not present TOP2A gene amplification or gene overexpression and who are significantly associated with very high risk classified patients showing glucocorticoid resistance. In conclusion, characterization of TOP2A gene status in childhood ALL at diagnosis provides useful complementary information for risk assessment.
Subject(s)
DNA Topoisomerases, Type II/genetics , DNA Topoisomerases/genetics , Gene Dosage , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Allelic Imbalance , Antigens, Neoplasm , Child , Child, Preschool , DNA Topoisomerases, Type I/genetics , DNA-Binding Proteins , Drug Resistance, Neoplasm , Female , Gene Amplification , Glucocorticoids/therapeutic use , Humans , Infant , Male , Microsatellite Repeats , Poly-ADP-Ribose Binding Proteins , Polymerase Chain Reaction , Precursor Cell Lymphoblastic Leukemia-Lymphoma/enzymology , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Risk AssessmentABSTRACT
The 43 kDa ATPase domain of Thermus thermophilus gyrase B was overproduced in Escherichia coli and a three-step purification protocol yielded large quantities of highly purified enzyme which remained stable for weeks. Crystals of the 43 kDa domain in complex with novobiocin, one of the most potent inhibitors of bacterial topoisomerases, were obtained. Crystals obtained in the presence of PEG 8000 do not diffract, but a different crystal form was obtained using sodium formate as a precipitating agent. The plate-shaped crystals, which were less than 10 microm in thickness, could be cryocooled directly from the mother liquor and a full diffraction data set was collected to 2.3 A allowing the determination of the first structure of a gyrase B 43K domain in complex with a coumarin.
Subject(s)
DNA Gyrase/chemistry , Thermus thermophilus/enzymology , Adenosine Triphosphatases/chemistry , Crystallization , Crystallography, X-Ray , DNA Gyrase/genetics , DNA Gyrase/isolation & purification , Macromolecular Substances , Molecular Weight , Novobiocin/chemistry , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Thermus thermophilus/geneticsABSTRACT
OBJECTIVE: To investigate the relationship between number and location of allelic imbalances (AI) and local tumor progression according to Astler-Coller classification. SUMMARY BACKGROUND DATA: Spontaneous errors in DNA replication (i.e., allelic imbalance or microsatellite instability) have been suggested to play an important role in carcinomatous transformation as reflecting alterations of gene function. METHODS: One hundred two consecutive patients with colorectal carcinoma undergoing surgical resection were included in this study. Patients were distributed according to the Astler-Coller classification as stages A (n = 7), B1 (n = 15), B2 (n = 24), C (n = 31), and D (n = 25). Fluorescent polymerase chain reaction was performed on frozen tumor, normal colon mucosa, and blood DNA at 35 microsatellite markers. Allelic imbalance frequency was compared with tumor staging. RESULTS: The percentage of AI was significantly higher in stage D than in A/B1 and B2. In addition, the percentage of AI was significantly higher in 10 synchronous colorectal liver metastases than in stage A/B1 and B2 tumors. However, the allelotyping revealed a subgroup of A/B1 tumors with a high AI frequency. Statistical analysis showed that the presence of AI at microsatellites D1S305, D2S138, D3S1282, D17S790, and D22S928 presented a significantly positive correlation with stages. CONCLUSION: The frequency of AI significantly correlates with tumor progression of colorectal cancer. Primary tumors with synchronous colorectal liver metastases showed a higher percentage of AI, suggesting that a frequency of AI greater than 35% with this selection of markers indicates a high risk of local progression and of development of metastases.
Subject(s)
Allelic Imbalance , Colorectal Neoplasms/genetics , Liver Neoplasms/secondary , Adult , Aged , Aged, 80 and over , Colorectal Neoplasms/pathology , Disease Progression , Female , Gene Frequency , Humans , Male , Microsatellite Repeats/genetics , Middle Aged , Polymerase Chain Reaction , PrognosisABSTRACT
Structural studies of biomolecules using nuclear magnetic resonance (NMR) rely on the availability of samples enriched in (13)C and (15)N isotopes. While (13)C/(15)N-labeled proteins are generally obtained by overexpression in transformed Escherichia coli cells cultured in the presence of an expensive mixture of labeled precursors, those of the photoautotrophic cyanobacterium Anabaena sp. PCC 7120 can be uniformly labeled by growing them in medium containing Na(15)NO(3) and NaH(13)CO(3) as the sole nitrogen and carbon sources. We report here a novel vector-host system suitable for the efficient preparation of uniformly (13)C/(15)N-labeled proteins in Anabaena sp. PCC 7120. The 24-kDa N-terminal domain of the E. coli gyrase B subunit, used as a test protein, was cloned into the pRL25C shuttle vector under the control of the tac promoter. The transformed Anabaena cells were grown in the presence of the labeled mineral salts and culture conditions were optimized to obtain over 90% of (13)C and (15)N enrichment in the constitutively expressed 24-kDa polypeptide. The yield of purified 24-kDa protein after dual isotope labeling under anaerobic conditions was similar to that obtained with E. coli cells bearing a comparable expression vector and cultured in parallel in a commercially available labeling medium. Furthermore, as probed by NMR spectroscopy and mass spectrometry, the 24-kDa N-terminal domain expressed in Anabaena was identical to the E. coli sample, demonstrating that it was of sufficient quality for 3D-structure determination. Because the Anabaena system was far more advantageous taking into consideration the expense for the labels that were necessary, these results indicate that Anabaena sp. PCC 7120 is an economic alternative for the (13)C/(15)N-labeling of soluble recombinant proteins destined for structural studies.
Subject(s)
Carbon Isotopes , Cloning, Molecular/methods , Cyanobacteria/genetics , DNA Gyrase/biosynthesis , Nitrogen Isotopes , Nuclear Magnetic Resonance, Biomolecular/methods , Carbon Isotopes/economics , Carbon Isotopes/metabolism , DNA Gyrase/chemistry , Escherichia coli Proteins , Nitrogen Isotopes/economics , Nitrogen Isotopes/metabolism , Protein Structure, Tertiary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Transformation, BacterialABSTRACT
We have recently identified a novel CCAAT box binding protein (ICBP90) involved in the regulation of topoisomerase IIalpha gene expression. We have observed that it is expressed in non-tumoral proliferating human lung fibroblast cells whereas in HeLa cells, a tumoral cell line, ICBP90 was still present even when cells were at confluence. In the present study, we have determined the ICBP90 gene structure by screening of a human placenta genomic library and PCR analysis. We report that the ICBP90 gene spans about 35.8 kb and contains six coding exons named A to F. In the 5' upstream sequence of the region containing the coding exons, two additional exons (I and II) were found. Additionally, an internal splicing site was found in exon A. A promoter region, including three putative Sp1 binding sites between exons I and A, was identified by transient transfection. Northern blot analysis of several cancer cell lines revealed the existence of two ICBP90 mRNA species of 5.1 and 4.3 kb that are transcribed from the gene. The relative amounts of these mRNAs depended on the cell type. In MOLT-4 cells and Burkitt's lymphoma Raji cells, the 4.3 kb or the 5.1 kb transcripts were mainly observed, respectively. In other cell lines, such as HL-60 cells, chronic myelogenous leukaemia K-562, lung carcinoma A549, HeLa or colorectal SW480, both 4.3 and 5.1 kb forms of ICBP90 mRNA could be detected. Interestingly, western blot analysis showed several ICBP90 protein bands in HeLa but only a single band in MOLT-4 cell extracts. Taken together our results are consistent with the ICBP90 gene exhibiting alternative splicing and promoter usage in a cell-specific manner.
Subject(s)
CCAAT-Enhancer-Binding Proteins/genetics , DNA Topoisomerases, Type II/genetics , Genes/genetics , Isoenzymes/genetics , Alternative Splicing , Animals , Antigens, Neoplasm , Base Sequence , Blotting, Northern , COS Cells , Chloramphenicol O-Acetyltransferase/genetics , Chloramphenicol O-Acetyltransferase/metabolism , Chromosome Mapping , Chromosomes, Human, Pair 19/genetics , DNA/chemistry , DNA/genetics , DNA/isolation & purification , DNA-Binding Proteins , Exons , Gene Expression , Gene Expression Regulation, Enzymologic , HL-60 Cells , Humans , In Situ Hybridization, Fluorescence , Introns , K562 Cells , Molecular Sequence Data , Promoter Regions, Genetic/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Sequence Analysis, DNA , Tumor Cells, Cultured , Ubiquitin-Protein LigasesABSTRACT
Alterations at microsatellite DNA markers in cells exfoliated in urine have been correlated to the presence of bladder cancer. To check the feasibility of such noninvasive analysis to routinely diagnose bladder cancers, we have developed a highly sensitive method using fluorescent PCR to search for DNA microsatellite alterations in urine sediment compared with a blood paired sample. One hundred eighty-three patients were included in our study. This population comprised 103 bladder cancers (64 pTa stages), the complement representing controls and other benign or malignant diseases. Results of the analysis at 17 loci in a blinded study were compared with cystoscopy and/or pathology. The high reproducibility of this technique and the analysis of 26 control patients allowed us to determine for each microsatellite a cutoff characterizing a significant allelic imbalance. For bladder cancer detection, the overall sensitivity of the test was 84%. Using this procedure, we identified alterations in 81%, 84%, 91%, and 100% of pTa, pT1, pT2, and >pT2 stages, respectively. This corresponds to 79%, 82%, and 96% sensitivity for grades I, II, and III, respectively. Interestingly, for routine purposes, we observed an overall sensitivity of 80% (76% for pTa stages) when only the eight most rearranged microsatellites were considered. In conclusion, the noninvasive feature combined with the rapidity of this fluorescent and highly sensitive technique for the detection of early stages provides us with a useful help for the diagnosis of bladder cancer.
Subject(s)
DNA, Neoplasm/urine , Microsatellite Repeats , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/urine , Adolescent , Adult , Aged , Aged, 80 and over , Alleles , Cystoscopy , DNA, Neoplasm/genetics , Evaluation Studies as Topic , Female , Humans , Male , Middle Aged , Neoplasm Staging , Reproducibility of Results , Sensitivity and Specificity , Urinary Bladder Neoplasms/pathologyABSTRACT
BACKGROUND: Several studies of colorectal cancer have shown an association between the number and type of genomic defects and the stage of disease. A subset of colorectal tumours are due to inactivation of DNA mismatch repair genes and these tumours exhibit microsatellite instability. The aim of the present study was to compare and contrast the genomic defects present in both the primary and metastatic stages of the disease using microsatellite probes. METHODS: Modifications of the allelic profiles of 25 microsatellite regions were studied in a total of 85 colorectal tumours using fluorescent polymerase chain reaction (PCR) technology and subsequent direct analysis on an automatic sequencer. This approach was used because it allows the study of microsatellite instability and allelic imbalance. Stepwise logistic regression analysis was used to develop a model to predict whether the tumour was primary or secondary from the percentage of allelic imbalance. Subsequently, a group of 17 patients with primary colorectal tumours was analysed prospectively to test the proposed model. RESULTS: Six of 39 primary tumours showed microsatellite instability compared to 0 of 29 liver metastases (P = 0.03). Primary tumours showed significantly less allelic imbalance than liver metastases (P < 0.001). Three probes (d18s53, d9s158 and d10s191) were selected for use in a model to classify a tumour as primary or secondary on the basis of the degree of allelic imbalance. When tested prospectively this model had a specificity of 82%. CONCLUSIONS: The present study demonstrates the potential importance of using microsatellite probes both as a diagnostic tool and as a research technique to investigate the mechanisms of tumour progression. An important clinical finding is that none of the colorectal liver metastases showed microsatellite instability (0 of 29). This analysis also confirmed other work that has shown a direct relationship between the degree of allelic imbalance and the stage of disease.
Subject(s)
Alleles , Base Pair Mismatch/genetics , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , DNA Repair/genetics , Gene Silencing , Liver Neoplasms/secondary , Microsatellite Repeats/genetics , Colorectal Neoplasms/classification , Humans , Logistic Models , Neoplasm Staging , Polymerase Chain Reaction , Predictive Value of Tests , Prospective Studies , Reproducibility of Results , Sensitivity and SpecificityABSTRACT
DNA-gyrase exhibits an unusual ATP-binding site that is formed as a result of gyrase B subunit dimerization, a structural transition that is also essential for DNA capture during the topoisomerization cycle. Previous structural studies on Escherichia coli DNA-gyrase B revealed that dimerization is the result of a polypeptidic exchange involving the N-terminal 14 amino acids. To provide experimental data that dimerization is critical for ATPase activity and enzyme turnover, we generated mutants with reduced dimerization by mutating the two most conserved residues of the GyrB N-terminal arm (Tyr-5 and Ile-10 residues). Our data demonstrate that the hydrophobic Ile-10 residue plays an important role in enzyme dimerization and the nucleotide-protein contact mediated by Tyr-5 side chain residue helps the dimerization process. Analysis of ATPase activities of mutant proteins provides evidence that dimerization enhances the ATP-hydrolysis turnover. The structure of the Y5S mutant of the N-terminal 43-kDa fragment of E. coli DNA GyrB subunit indicates that Tyr-5 residue provides a scaffold for the ATP-hydrolysis center. We describe a channel formed at the dimer interface that provides a structural mechanism to allow reactive water molecules to access the gamma-phosphate group of the bound ATP molecule. Together, these results demonstrate that dimerization strongly contributes to the folding and stability of the catalytic site for ATP hydrolysis. A role for the essential Mg(2+) ion for the orientation of the phosphate groups of the bound nucleotide inside the reactive pocket was also uncovered by superposition of the 5'-adenylyl beta-gamma-imidodiphosphate (ADPNP) wild-type structure to the salt-free ADPNP structure.
Subject(s)
Adenosine Triphosphatases/metabolism , DNA Topoisomerases, Type II/metabolism , Escherichia coli/enzymology , Adenosine Triphosphatases/chemistry , Adenosine Triphosphate/metabolism , Binding Sites , Catalytic Domain , Crystallography, X-Ray , DNA Gyrase , DNA Topoisomerases, Type II/chemistry , Dimerization , Enzyme Activation , Hydrolysis , Isoleucine/metabolism , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Protein Conformation , Tyrosine/metabolismABSTRACT
The one-hybrid system with an inverted CCAAT box as the DNA target sequence was used to identify proteins acting on key DNA sequences of the promoter of the topoisomerase IIalpha gene. Screening of cDNA libraries from the leukemia Jurkat cell line and from the adult human thymus resulted in the isolation of a novel protein of 793 amino acids (89,758 Da). This protein has in vitro CCAAT binding properties and has been called ICBP90. Adult thymus, fetal thymus, fetal liver, and bone marrow, known as active tissues in terms of cell proliferation, are the tissues richest in ICBP90 mRNA. In contrast, highly differentiated tissues and cells such as the central nervous system and peripheral leukocytes are free of ICBP90 mRNA. Western blotting experiments showed a simultaneous expression of topoisomerase IIalpha and ICBP90 in proliferating human lung fibroblasts. Simultaneous expression of both proteins has also been observed in HeLa cells, but in both proliferating and confluent cells. Overexpression of ICBP90 in COS-1-transfected cells induced an enhanced expression of endogenous topoisomerase IIalpha. Immunohistochemistry experiments showed that topoisomerase IIalpha and ICBP90 were coexpressed in proliferating areas of paraffin-embedded human appendix tissues and in high-grade breast carcinoma tissues. We have identified ICBP90, which is a novel CCAAT binding protein, and our results suggest that it may be involved in topoisomerase IIalpha expression. ICBP90 may also be useful as a new proliferation marker for cancer tissues.
Subject(s)
DNA Topoisomerases, Type II , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/isolation & purification , Isoenzymes/metabolism , Adult , Amino Acid Sequence , Animals , Antigens, Neoplasm , Appendix/metabolism , Breast Neoplasms/metabolism , CCAAT-Enhancer-Binding Proteins , COS Cells/metabolism , DNA Topoisomerases, Type II/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/physiology , Fetus , Fibroblasts/metabolism , Gene Library , HeLa Cells/metabolism , Humans , Isoenzymes/genetics , Jurkat Cells/metabolism , Molecular Sequence Data , Molecular Weight , Nuclear Proteins/isolation & purification , Thymus Gland/chemistryABSTRACT
DNA gyrase is an essential enzyme that regulates the DNA topology in bacteria. It belongs to the type II DNA topoisomerase family and is responsible for the introduction of negative supercoils into DNA at the expense of hydrolysis of ATP molecules. The aim of the present work was to study the contribution of I10, one of the most important residues responsible for the stabilization of GyrB dimer and involved in the ATP-binding step, in the ATP-hydrolysis reaction and in the DNA supercoiling mechanism. We constructed MBP-tagged GyrB mutants I10G and Delta4-14. Our results demonstrate that both mutations severely affect the DNA-dependent ATPase activity and DNA supercoiling. Mutation of Y5 residue involved in the formation of ATPase catalytic site (Y5G mutant) had only little effect on the DNA-dependent ATPase activity and DNA supercoiling. Interestingly, the DNA-relaxation activity of MBP-GyrB mutants and wild type was completely inhibited by ATP. Binding of ADPNP to MBP-tagged mutants was significantly decreased. ADPNP had no effect on DNA-relaxation activity of MBP-tagged mutants but was able to inhibit MBP-tagged wild type enzyme. Our results demonstrate that GyrB N-terminal arm, and specially I10 residue is essential for ATP binding/hydrolysis efficiency and DNA transfer through DNA gyrase.