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PubMed2006

Epigenetic inactivation of tumor suppressor genes in serum of patients with cutaneous melanoma.

Small amounts of cell-free DNA circulate in both healthy and diseased human blood, while increased concentrations of DNA are present in the serum of cancer patients. Tumor-specific mutations or epigenetic modifications have predominantly been detected in tissue specimens. The purpose of this study was to investigate methylation of five different genes involved in tumor suppression and DNA repair (suppressors of cytokine signaling 1 and 2 (SOCS1, SOCS2)), Ras-association domain family protein 1A (RASSF1a), D-type p16(INK4a) cyclin-dependent kinase inhibitor (CDKN), and O6-methylguanine DNA-methyltransferase (MGMT)) in the serum of 100 patients using methylation-specific PCR. In all, 41 melanoma patients (stage I = 18; stage II = 10; stage III/IV = 13), 13 healthy controls without nevi, and 10 individuals with more than 15 nevi of >5 mm in size were investigated. For comparison, sera from patients with other skin tumors (nine basal cell cancers, five Kaposi's sarcoma), different metastasized cancers (five breast cancers, five colon cancers), and several chronic inflammatory diseases (n = 12) were also analyzed. In addition, we examined if methylation was involved in silencing transcription of these genes in 12 melanoma specimens. SOCS1, SOCS2, RASSF1a, CDKN2a, and MGMT were methylated in 75, 43, 64, 75, and 64% of melanoma samples, respectively. Of the 41 melanoma patients, 83% had one hypermethylated gene, while 66, 51, and 41% had two, three, or four hypermethylated genes, respectively. Also, 20% of these patients showed hypermethylation for all genes, while only 17% showed no methylation. Importantly, the methylation profile of the selected genes from melanoma patients was distinct from the other analyzed tumors. Transcription of SOCS1, SOCS2, CDKN2a, and RASSF1a genes was significantly reduced in fresh melanoma samples, while MGMT showed a 12-fold upregulation at the messenger ribonucleic acid level (P < 0.001). Our findings suggest that epigenetic silencing of the studied tumor suppressor genes is a common and probably important mechanism for melanoma formation. This convenient method using a simple blood sample may contribute to classification of melanoma and awaits clinical validation.

Adult↗
PubMed2006

Abnormal histone acetylase and deacetylase expression and function in lung inflammation.

Post-translational modifications in DNA and histone proteins are heritable changes that are not coded for in the DNA sequence itself but play an important role in the control of gene expression. These modifications include histone acetylation, methylation, ubiquitination, sumoylation and phosphorylation. These changes are not only critical for generating diversity of cell types during mammalian development, but are also important for maintaining the stability and integrity of the expression profiles of different cell types. Until recently, the study of human disease has focused on genetic mechanisms rather than on non-coding events. However, it is becoming increasingly clear that altered patterns of histone modifications can lead to several major pathologies. This review focuses on histone acetylation and its role in inflammatory gene expression. Interestingly, the expression and activity of enzymes that regulate this modification have been reported to be abnormal in the airways of patients with respiratory disease. Histone modifications, despite being heritable and stably maintained, are also potentially reversible and there is scope for the development of "epigenetic therapies" for disease.

Animals↗
PubMed2005

Temozolomide and cisplatin versus temozolomide in patients with advanced melanoma: a randomized phase II study of the Hellenic Cooperative Oncology Group.

PURPOSE: Temozolomide (TMZ) is an oral alkylating agent that produces methyl adducts at the 0.6 position of guanine. The methyl adducts are removed by the DNA repair enzyme AGAT. As demonstrated by in vitro studies, cisplatin (CDDP) is able to down-regulate the AGAT activity, suggesting that CDDP could enhance the antitumor activity of TMZ. We designed a randomized phase II study to evaluate and compare the activity and safety profile of the combination versus single-agent TMZ in patients with advanced melanoma. PATIENTS AND METHODS: From January 2000 to April 2002, 132 patients were enrolled on the study. Patient and tumor characteristics were well balanced between the two arms. Patients with cerebral metastases were included. Patients received TMZ 200 mg/m(2)/day orally for five consecutive days every 4 weeks or TMZ + CDDP 200 mg/m(2) daily on days 1-5 and 75 mg/m(2) of CDDP on day 1. RESULTS: Tumor responses (complete and partial responses) were seen in 16 patients (26%) in arm A and 19 patients (29%) in arm B. The median time to progression (TTP) was 3.8 months in arm A and 5.8 months in arm B. The median overall survival (OS) was 11.5 months in arm A and 12 months in arm B. The difference between treatment arms regarding objective response rates, TTP and OS were not statistically significant. Toxicity was comparable between the two arms for anemia, leukopenia, neutropenia, thrombocytopenia, fatigue, constipation and arthralgias/myalgias. There was significantly more grade 3 and 4 emesis in the combination arm. CONCLUSIONS: No clear benefit in terms of response rates, median TTP or OS was shown with the combination of TMZ + CDDP. Additionally, the combination was associated with higher incidence of grade 3 and 4 emesis.

Adult↗
PubMed2004

Kidney gene database: a curated and integrated database of genes involved in kidney disease.

PURPOSE: We have created a curated and integrated database, the Kidney Gene Database (KGDB) (http://www.urogene.org/kgdb) that contains current information about genes or genomic loci involved in human kidney disease. MATERIALS AND METHODS: Genes that undergo molecular, genetic or epigenetic events that affect kidney function are identified through a biomedical literature search and catalogued in the database. RESULTS: Events that are currently screened for are gene amplification, mutation, deletion, polymorphism, loss of heterozygosity, DNA methylation and DNA hypomethylation. In addition, genes that are uniquely expressed in the kidney, as determined by analyzing the expressed sequence tags database and the Serial Analysis of Gene Expression database, are also included in KGDB. For each gene KGDB provides basic information about the gene product, a tissue type gene expression profile, links to protein, mRNA and genomic DNA sequence information, relevant literature citations and cross-references to other databases. CONCLUSIONS: We present KGDB, which is to our knowledge the first curated and integrated database of genes involved in human kidney disease. KGDB is free, widely accessible and easy to use, and it provides a wealth of relevant information. In addition, KGDB will be continuously updated every 6 months to include new information published in the biomedical literature or in gene expression databases. We envision that KGDB will serve as a valuable resource for scientists and clinicians.

Databases, Genetic↗
PubMed2005

Distinct gene expression profiles in adult rat brains after acute MK-801 and cocaine treatments.

Uncompetitive N-methyl-D-aspartate (NMDA) receptor antagonists have been suggested to attenuate the self-administration and rewarding effects of psychostimulants. Microarrays containing 14,500 rat cDNAs were hybridized to identify alterations in gene expression levels in rat brain regions elicited by the uncompetitive NMDA receptor antagonist MK-801 (dizocilpine, 1 mg/kg), the dopamine agonist cocaine (20 mg/kg), or combined treatment (MK-801 15 min prior to cocaine) 4 h after injections. Total genes up regulated (Z-ratio >2) in parietal cortex and nucleus accumbens were 111 and 158, respectively. Total genes down regulated (Z-ratio <2) in the same tissues were 360 and 166, respectively. These genes fell into multiple molecular function gene ontology (GO) categories, but were highly represented in catalytic activities (44% of all genes), signal transduction (14%), protein (20%), nucleotide (18%), and nucleic acid (15%) binding. In nucleus accumbens, genes up regulated by MK-801 (87 genes) did not overlap those up regulated by cocaine (46 genes). Genes down regulated by MK-801 (33 genes) consisted of 2 overlapping genes with those down regulated by cocaine (89 genes). In parietal cortex, low numbers of overlapping regulated genes were also observed. Combined treatments also indicated low numbers (0-10) of genes commonly regulated when compared with single treatments alone. In situ hybridisation studies indicated significant increases in b-ZIP transcription factors (CREM, ICER, CBP, and c-fos) elicited by MK-801 and decreases in c-fos elicited by cocaine. The results indicate independent gene expression signatures following acute MK-801 and cocaine administration that appears to be largely non-overlapping and context dependent.

Animals↗
PubMed1989

Genetic and physical mapping of a novel region close to the fragile X site on the human X chromosome.

We report the isolation and characterization of a novel DNA marker (1A1) in Xqter in the region of the fragile X. Genetic studies in families segregating for the fragile X syndrome suggest that 1A1 lies between the disease mutation and the distal locus, DXS52. Studies in normal and fragile X families show that 1A1 is tightly linked to DXS52 (Zmax = 17.20; theta max = 0.03) and F8 (Zmax = 7.01; theta max = 0.08). Multipoint mapping of families supports the order Xcen-DXS105-FRAXA-1A1-DXS52-(F8, DXS115)-Xqter. Pulsed-field gel electrophoresis (PFGE) studies demonstrate that 1A1 defines a new region of at least 2 Mb of DNA not physically linked to DXS52 or F8, thus extending the physical map of Xq27-qter to over 4 Mb. Complex partial digestion PFGE patterns, probably due to differing degrees of methylation, are observed with 1A1 in unrelated normal and fragile-X-positive individuals, whereas other distal markers give uniform digestion profiles. Physical data suggest that 1A1 lies in a region less CpG rich than other distal markers in Xq27-qter.

Animals↗
PubMed2000

DNA repair: counteragent in mutagenesis and carcinogenesis-- accomplice in cancer therapy resistance.

DNA-reactive carcinogens and anticancer drugs induce many structurally distinct mutagenic and cytotoxic DNA lesions. The varying capability of normal and malignant cells to recognize and repair specific DNA lesions influences both cancer risk and the relative sensitivity or resistance of cancer cells towards cytotoxic agents. Using monoclonal antibody-based immunoanalytical assays, very low amounts of defined carcinogen-DNA adducts can be quantified in bulk genomic DNA, in individual genes, and in the nuclear DNA of single cells. DNA repair kinetics can, thus, be measured in a lesion-, gene-, and cell type-specific manner, and the DNA repair profiles of malignant cells can be monitored in individual patients. Even structurally very similar DNA lesions may be repaired with strongly differing efficiency. The miscoding DNA alkylation products O(6)-methylguanine and O(6)-ethylguanine, for example, differ only by one CH(2) group. These lesions are formed in DNA upon exposure to N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea, both of which induce mammary adenocarcinomas in female rats at high yield. Unrepaired O(6)-alkylguanines in DNA cause G:C-->A:T transition mutations via mispairing during DNA replication. O(6)-methylguanines are repaired at a similar slow rate in both transcriptionally active (H-ras, beta-actin) and inactive genes (IgE heavy chain; bulk DNA) of the target mammary epithelia (which express the repair protein O(6)-alkylguanine-DNA alkyltransferase (AGT) at a very low level). In contrast, O(6)-ethylguanines are repaired approximately 20 times faster than O(6)-methylguanines in both DNA strands of the transcribed genes selectively via an AGT-independent, as yet unclarified excision mechanism. Accordingly, G:C-->A:T transitions resulting from the misreplication of an O(6)-methylated guanine at the second position of codon 12 (GGA) of H-ras represent a frequent "signature" mutation in rat mammary adenocarcinomas that develop after exposure to N-methyl-N-nitrosourea. However, this mutation is not observed when these tumors are induced by N-ethyl-N-nitrosourea, due to the fast repair of O(6)-ethylguanines in the H-ras gene. The key importance of "conventional" and "conditional" gene knockout technology for resolving the intricacies of the complex network of DNA repair pathways is briefly discussed.

Adenocarcinoma↗
PubMed2003

Profile of aberrant CpG island methylation along multistep gastric carcinogenesis.

The stomach is one of the organs whose epithelial cells frequently undergo aberrant methylation of CpG islands. To date, several reports on the methylation of various genes in gastric cancer (GC) have been published. However, most of these studies have focused on cancer tissues or a single gene only and gave no information about the methylation status of specific genes in the premalignant stages or the concurrent methylation of other genes in specific lesions. We attempted to investigate methylation of multiple genes in a large sample collection of GC (n = 80), gastric adenoma (GA) (n = 79), intestinal metaplasia (IM) (n = 57), and chronic gastritis (CG) (n = 74). We determined the methylation frequency of 12 genes, including APC, COX-2, DAP-kinase, E-cadherin, GSTP1, hMLH1, MGMT, p16, p14, RASSF1A, THBS1, and TIMP3, by methylation-specific PCR. Five different classes of methylation behaviors were found: (a). genes methylated in GC only (GSTP1 and RASSF1A), (b). genes showing low methylation frequency (<12%) in CG, IM, and gastric adenoma (GA) but significantly higher methylation frequency in GC (COX-2, hMLH1, p16), (c). a gene with low and similar methylation frequency (8.8-21.3%) in four-step lesions (MGMT), (d). genes with high and similar methylation frequency (53-85%) in four-step lesions (APC and E-cadherin), and (e). genes showing an increasing tendency with or without fluctuation of the methylation frequency along the progression (DAP-kinase, p14, THBS1, and TIMP-3). The average number of methylated genes was 2.7, 3.6, 3.4, and 5.2 per 12 tested genes in CG, IM, GA, and GC, respectively. Aberrant methylation at multiple loci in the same lesions suggests an overall deregulation of the methylation control, which occurs early in multistep gastric carcinogenesis. Our results suggest that tumor-suppressor genes show a gene-type specific methylation profile along the multistep carcinogenesis and that aberrant CpG island methylation tend to accumulate along the multistep carcinogenesis.

Adenoma↗
PubMed1996

Growth regulation by peroxisome proliferators: opposing activities in early and late G1.

Peroxisome proliferators (PPs) are a diverse group of nongenotoxic rodent liver carcinogens. One potential mechanism for the carcinogenicity of PPs is epigenetic modulation of growth-regulatory signal transduction pathways. We investigated the effects of PPs on growth-regulatory gene expression and cell proliferation in immortalized mouse liver cells, comparing PPs with other growth regulators and tumor promoters of known activity. The PPs Wy-14643, mono-ethylhexyl phthalate, clofibrate, and ciprofibrate ethyl-ester were found to be potent inducers of immediate-early gene expression (including c-fos, c-jun, junB, egr-1, NUP475, and to a lesser extent fosB, JE, and KC, with maximal expression seen 1 h after treatment of serum-deprived quiescent cells. The gene induction was potently inhibited by protein kinase inhibitor H7 [1-(5-isoquinolinesulfonyl)-2-methylpiperazine dihydrochloride] but not by H8 [N-¿2-(methyl-amino)ethyl¿-5-isoquinolinesulfonamide dihydrochloride], indomethacin, or nordihydroguaiaretic acid. Compared with other growth regulators, the profile of PP-induced gene expression was most similar to that induced by arachidonic acid and eicosatetraynoic acid. The induction of immediate-early gene expression by PPs was followed by enhanced progression into S phase (DNA synthesis) when quiescent cells were treated with the PPs for only 1 h, washed, and then incubated without PPs. However, no stimulation of DNA synthesis was seen when the PPs were continually present. Furthermore, the PPs inhibited serum-induced DNA synthesis, even when they were added 6 h after serum stimulation (in late G1). Dehydroepiandrosterone-sulfate, a unique PP in being a steroid, had no detectable effect on immediate-early gene expression, did not stimulate DNA synthesis when applied for only 1 h, but did inhibit serum-induced DNA synthesis. Thapsigargin and A23187 mimicked this mitoinhibitory activity of PPs, suggesting that calcium mobilization by PPs might be involved. Our results demonstrate that PPs can modulate cell proliferation either by a stimulatory activity that functions in early G1, associated with activation of immediate-early gene expression, or by an inhibitory activity that functions in late G1; both activities could potentially play a role in tumor promotion by PPs.

Animals↗
PubMed2004

Diversity Arrays Technology (DArT) for whole-genome profiling of barley.

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised approximately 385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.

Chromosome Mapping↗
PubMed2005

Expression profiling of rat femur revealed suppression of bone formation genes by treatment with alendronate and estrogen but not raloxifene.

The pharmacological preservation of bone in the ovariectomized rat by estrogen, selective estrogen receptor modulators (SERMs), and bisphosphonates has been well described. However, comprehensive molecular analysis of the effects of these pharmacologically diverse antiresorptive agents on gene expression in bone has not been performed. This study used DNA microarrays to analyze RNA from the proximal femur metaphysis of sham and ovariectomized vehicle-treated rats, and ovariectomized rats treated for 35 days with maximally efficacious doses of 17-alpha ethinyl estradiol, the benzothiophene SERM, raloxifene, the benzopyran SERM, (S)-3-(4-hydroxyphenyl)-4-methyl-2-[4-[2-(1-piperidinyl)ethoxy]phenyl]-2H-1-benzopyran-7-ol (EM652), and the aminobisphosphonate, alendronate. Ovariectomy resulted in 644 significant probe set changes relative to sham control rats (p < 0.05), whereas E2, raloxifene, EM652, and alendronate regulated 613, 765, 652, and 737 probe sets, respectively, relative to ovariectomized control rats. An intersection of these data sets yielded 334 unique genes that were altered after ovariectomy and additionally changed by one or more antiresorptive treatment. Clustering analysis showed that the transcript profile was distinctly different for each pharmaceutical agent and that raloxifene maintained more genes at sham levels than any other treatment. In addition, E2 and alendronate suppressed a cluster of genes associated with bone formation activity below that of sham, whereas raloxifene had little effect on these genes. These data indicate stronger suppressive effects of E2 and alendronate on bone formation activity and that ovariectomy plus raloxifene resembles sham more closely than ovariectomized animals treated with E2, EM652, or alendronate.

Alendronate↗
PubMed1995

The pharmacological profile of the vesicular monoamine transporter resembles that of multidrug transporters.

Vesicular neurotransmitter transporters function in synaptic vesicles and other subcellular organelles and they were thought to be involved only in neurotransmitter storage. Several findings have led us to test novel aspects of their function. Cells expressing a c-DNA coding for one of the rat monoamine transporters (VMAT1) become resistant to the neurotoxin N-methyl-4-phenylpyridinium (MPP+) [Liu et al. (1992) Cell, 70, 539-551]. The basis of the resistance is the VMAT1-mediated transport and sequestration of the toxin into subcellular compartments. In addition, the deduced sequence of VMAT1 predicts a protein that shows a distinct homology to a class of bacterial drug resistance transporters (TEXANs) that share some substrates with mammalian multidrug resistance transporters (MDR) such as the P-glycoprotein. These findings induced us to test whether compounds that are typically transported by MDR interact also with vesicular transporters. The use of [3H]reserpine binding to determine drug interactions with VMAT allowed assessment of the ability of various drugs to bind to the substrate site of the transporter. Cytotoxic compounds such as ethidium, isometamidium, tetraphenylphosphonium, rhodamine, tacrine and doxorubicin, interact specifically with vesicular monoamine transporters. Verapamil, a calcium channel blocker, is also a competitive inhibitor of transport. In the case of rhodamine, fluorescence measurements in digitonin-permeabilized cells demonstrated ATP-dependent VMAT-mediated transport. The results imply that even though the bacterial and vesicular transporters are structurally different from the P-glycoprotein, they share a similar substrate range. These findings suggest a novel possible way of protection from the effects of toxic compounds by removal to subcellular compartments.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2005

Aberrant CpG island methylation in early-onset sporadic gastric carcinoma.

PURPOSE: Gastric carcinoma more commonly affects older patients, and it is thought that cases of early-onset gastric carcinoma may develop with a different molecular profile different from that of carcinoma occurring at a later age. We assayed the methylation status and genetic changes in genes associated with the APC-beta-catenin axis and the mismatch repair system in relatively early-onset gastric carcinoma samples to determine their association with gastric carcinogenesis. METHODS: Tumor and normal tissue DNA samples were obtained from 40 patients with early-onset (< 50 y) gastric carcinomas and assayed for APC and CTNNB1 mutations, microsatellite instability, and methylation of the promoters of the hMLH1, TIMP3, THBS1, DAP- K, GSTP1 , APC, and MINT2. RESULTS: Promoter methylation at these seven loci ranged from 12.5 to 62%, with 38/40 tumors (95%) showing promoter methylation at more than one locus. The CpG island methylation phenotype (CIMP) was classified as high in 16 tumors (40%), low in 22 tumors (55%), and negative in 2 tumors (5%). Two concurrent missense mutations (E1685G, R1763L) in the APC mutation cluster region were detected in two tumors, nine tumors showed loss of APC heterozygosity (LOH), and two showed both LOH and promoter methylation. CONCLUSIONS: Our results indicate that, unlike in colorectal carcinoma, APC and CTNNB1 mutations do not appear to be highly implicated in early-onset gastric carcinogenesis. In contrast, our data show that promoter methylation is a prevalent phenomenon in early-onset gastric carcinoma and may be related to gastric carcinogenesis.

Adaptor Proteins, Signal Transducing↗
PubMed1977

Gibberellic Acid enhancement of DNA turnover in barley aleurone cells.

When imbibed, deembryonated halfseeds from barley (Hordeum vulgare L., var. Himalaya) are incubated in buffer, the DNA content of the aleurone layer increases 25 to 40% over a 24-hour period. In contrast, the DNA of isolated aleurone layers declines by 20% over the same time period. Gibberellic acid (GA) causes a reduction in DNA levels in both halfseed aleurone layers and isolated aleurone layers. GA also increases the specific radioactivity of [(3)H]thymidine-labeled halfseed aleurone layer DNA during the first 12 hours of treatment. Pulse-chase studies demonstrated that the newly synthesized DNA is metabolically labile.The buoyant density on CsCl density gradients of hormone-treated aleurone DNA is identical with that of DNA extracted from whole seedlings. After density-labeling halfseed DNA with 5-bromodeoxyuridine, a bimodal absorption profile is obtained in neutral CsCl. The light band (1.70 g/ml) corresponds to unsubstituted DNA, while the heavy band (1.725-1.74 g/ml) corresponds to a hybrid density-labeled species. GA increases the relative amount of the heavy (hybrid) peak in halfseed aleurone layer DNA, further suggesting that the hormone enhances semiconservative replication in halfseeds.DNA methylation was also demonstrated. Over 60% of the radioactivity from [(3)H-Me]methionine is incorporated into 5-methylcytosine. GA has no effect on the percentage distribution of label among the bases.It was concluded that GA enhances the rate of DNA degradation and DNA synthesis (turnover) in halfseeds, but primarily DNA degradation in isolated aleurone layers. Incorporation by isolated aleurone layers is due to DNA repair. Semiconservative replication apparently plays no physiological role in the hormone response, since both isolated aleurone layers and gamma-irradiated halfseeds respond normally. The hypothesis was advanced that endoreduplication and DNA degradation are means by which the seed stores and mobilizes deoxyribonucleotides for the embryo during germination.

Journal Article↗
PubMed2003

Genomic p16 abnormalities in the progression of chronic myeloid leukemia into blast crisis: a sequential study in 42 patients.

OBJECTIVE: The molecular abnormalities involved in the progression of chronic myeloid leukemia (CML) are poorly understood. Genetic alterations of the INK4A/ARF locus have been implicated in the lymphoid blast crisis (BC), but sequential studies are not available. The aim of this study was to contribute to a better knowledge of the status of such locus in the different phases of CML and to analyze the prognostic significance of its inactivation. MATERIALS AND METHODS: Sequential assessment by quantitative real-time polymerase chain reaction (PCR) and conventional semiquantitative PCR of p16 exon 2 deletions was performed in 42 CML patients in whom paired DNA samples from the chronic phase and the BC were available. Samples of 10 healthy donors and 30 patients with nonleukemic myeloproliferative syndromes served as controls. The methylation status of the promoter region of the p16 gene was also studied by methylation-specific PCR. RESULTS: The concordance rate between the two PCR techniques was 97.8% (87/89). By real-time PCR, homozygous p16 deletions were found in 6 of 21 patients (29%) with lymphoid BC, whereas they were not observed in chronic-phase CML nor in 21 myeloid BC patients. Hypermethylation of the p16 gene was not detected in any of the lymphoid BC. No specific clinical profile was associated with homozygous p16 deletions. Therapeutic response and survival did not significantly differ in p16-deleted and p16 germline lymphoid BC patients. CONCLUSION: P16 gene deletions are detected in a substantial proportion of lymphoid BC of CML by quantitative real-time PCR analysis, but this is not associated with any clinico-hematological feature other than lymphoid phenotype and does not influence the patients' outcome. Such technique is simple and reliable to assess the p16 gene status.

Adult↗
PubMed2005

Distinct hypermethylation profile of primary breast cancer is associated with sentinel lymph node metastasis.

PURPOSE: Gene promoter region hypermethylation is a significant event in primary breast cancer. However, its impact on tumor progression and potential predictive implications remain relatively unknown. EXPERIMENTAL DESIGN: We conducted hypermethylation profiling of 151 primary breast tumors with association to known prognostic factors in breast cancer using methylation-specific PCR for six known tumor suppressor and related genes: RASSF1A, APC, TWIST, CDH1, GSTP1, and RAR-beta2. Furthermore, correlation with sentinel lymph node (SLN) tumor status was assessed as it represents the earliest stage of metastasis that is readily detected. Hypermethylation for any one gene was identified in 147 (97%) of 151 primary breast tumors. The most frequently hypermethylated gene was RASSF1A (81%). RESULTS: Hypermethylation of the CDH1 was significantly associated with primary breast tumors demonstrating lymphovascular invasion (P = 0.008), infiltrating ductal histology (P = 0.03), and negative for the estrogen receptor (P = 0.005), whereas RASSF1A and RAR-beta2 gene hypermethylation were significantly more common in estrogen receptor-positive (P < 0.001) and human epidermal growth factor receptor 2-positive (P < 0.001) tumors, respectively. In multivariate analysis, hypermethylation of GSTP1 and/or RAR-beta2 was significantly associated with patients having macroscopic SLN metastasis compared with those with microscopic or no sentinel node metastasis (odds ratio, 4.59; 95% confidence interval, 2.02-10.4; P < 0.001). In paired SLN metastasis, CDH1 was the most frequently methylated gene (90%) and provides evidence in patients corroborating its role in the clinical development of metastasis. CONCLUSION: Hypermethylation profiling of primary breast tumors is significantly associated with known pathologic prognostic factors and may have additional clinical and pathologic utility for assessing patient prognosis and predicting early regional metastasis.

Adult↗
PubMed1993

Thermodynamic characterization of daunomycin-DNA interactions: comparison of complete binding profiles for a series of DNA host duplexes.

Using a combination of spectroscopic and calorimetric techniques, we have determined complete thermodynamic binding profiles (delta G degree, delta H degree, and delta S degree) for the complexation of daunomycin to a series of 10 polymeric DNA duplexes. We find the resulting drug binding data to be sensitive to the base composition and sequence of the host duplex, with the binding free energies ranging from -7.5 to -10.8 kcal/mol of bound drug and the binding enthalpies ranging from +4.11 to -10.76 kcal/mol of bound drug at 25 degrees C. The smaller range in the free energy term reflects the impact of large enthalpy-entropy compensations. We observe that the three synthetic duplexes which exhibit the highest daunomycin binding affinities all contain GC (or IC) base pairs as part of alternating purine/pyrimidine sequence motifs, with these high binding affinities being strongly enthalpy driven at 25 degrees C. Specific comparisons between the binding profiles for daunomycin complexation with select pairs of host duplexes lead to the following observations: (1) The presence or absence of a major-groove methyl group does not alter daunomycin binding thermodynamics. (2) The presence or absence of a minor-groove amino group does alter daunomycin binding thermodynamics. (3) Duplexes with different base compositions but identical minor-groove functionality exhibit similar daunomycin binding thermodynamics. (4) Homopolymeric duplexes composed of either AT or AU base pairs, but not GC base pairs, exhibit large enthalpy-entropy compensations in their daunomycin binding profiles. We propose interpretations of these and other features of our thermodynamic data in terms of specific daunomycin-DNA interactions deduced from available structural data.

Base Composition↗
PubMed2005

Lack of F8 mRNA: a novel mechanism leading to hemophilia A.

Hemophilia A (HA) is caused by partial or total deficiency of F8 protein activity. In a small group, about 1.8% of patients with HA, no mutation is found in the F8 gene. Among this group, we report here on one patient with severe HA in whom no mRNA of the F8 gene was detected. Using 2 common polymorphisms in F8 exon 14, we were able to show that the same allele shared by the patient, his mother, and his sister was not detected by reverse transcription-polymerase chain reaction (RT-PCR) from total blood mRNA. Skewed X-chromosome inactivation in both the mother and the sister was excluded by studying the methylation profile of the androgen receptor gene (HUMARA locus). These findings strongly suggest that the cause of HA in this patient is either absence or rapid degradation of the F8 mRNA, which points to a novel mechanism leading to HA.

Adolescent↗