Transcription from a gene desert in a melanoma porcine model.

The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients' care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM model. Indeed, a large region of the Sus scrofa chromosome 1 has been identified by linkage and association analyses, but the causal mechanisms have remained elusive. To deepen the analysis of this candidate region, a dedicated SNP panel was used to fine map the locus, downsizing the interval to less than 2 Mb, in a genomic region located within a large gene desert. Transcription from this locus was addressed using a tiling array strategy and further validated by RT-PCR in a large panel of tissues. Overall, the gene desert showed an extensive transcriptional landscape, notably dominated by repeated element transcription in tumor and fetal tissues. The transcription of LINE-1 and PERVs has been confirmed in skin and tumor samples from MeLiM pigs. In conclusion, although this study still does not identify a candidate mutation for melanoma occurrence or progression, it highlights a potential role of repeated element transcriptional activity in the MeLiM model.

A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination.

A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.

Analysis of Borrelia burgdorferi IgG antibodies with a combination of IgG ELISA and VlsE C6 peptide ELISA.

Enzyme-linked immunosorbent assays (ELISAs) were used to detect antibodies to the C6 peptide of the Borrelia burgdorferi VlsE protein and a selection of B. burgdorferi IgG antigens, separately and as a combination, in 355 serum specimens from blood donors and patients. Western immunoblotting was used as the reference method. The sensitivity of the combined analysis of IgG antigen and C6 peptide analysis was markedly superior to those of the separate analyses. When the C6 peptide and IgG results were concordant, the customary confirmatory Western immunoblotting assay could be omitted, thus reducing the time and cost of analysis.

Assignment of fourteen microsatellite markers to the chicken linkage map.

A large mapping population, with 874 F2 individuals, was generated by reciprocally intercrossing 2 chicken lines. A genetic map of 2,426.6 cM comprising 25 linkage groups was established based on 145 microsatellite markers. Chromosome locations were assigned for 14 previously unmapped markers. The marker ADL0132 was previously mapped to chromosome 9; however, here close linkage to the MCW0091 marker on chromosome 4 was found. With this exception, the derived linkage map was in excellent agreement with the chicken consensus map. A comparison with the chicken genome assembly (http://genome.ucsc.edu; February 2004) suggested a few minor errors in the assembly. A PCR-RFLP test was used to genotype a single nucleotide polymorphism in the melanocortin receptor 3 (MC3R) gene in the intercross, and pyrosequencing was used to map the genes for Hemopoetic Cell Kinase (HCK) and Bone Morphogenic Protein 7 (BMP7). The HCK and BMP7 genes on linkage group E32 showed significant linkage to MC3R on the distal end of linkage group E47W24, consequently joining the 2 linkage groups. A comparison between the linkage data in the current study and the physical location of markers as revealed in the chicken genome sequence assembly (February 2004) showed a 3-fold higher recombination rate on microchromosomes than on macrochromosomes.

Anaplastic thyroid carcinoma: three protocols combining doxorubicin, hyperfractionated radiotherapy and surgery.

Patients with anaplastic thyroid carcinoma can rarely be cured, but every effort should be made to prevent death due to suffocation. Between 1984 and 1999, 55 consecutive patients with anaplastic thyroid carcinoma were prospectively treated according to a combined regimen consisting of hyperfractionated radiotherapy, doxorubicin, and when feasible surgery. Radiotherapy was carried out for 5 days a week. The daily fraction until 1988 was 1.0 Gyx2 (A) and 1989-92 1.3 Gyx2 (B). Thereafter 1.6 Gyx2 (C) was administered. Radiotherapy was administered to a total target dose of 46 Gy; of which 30 Gy was administered preoperatively in the first two protocols (A and B), while the whole dose was given preoperatively in the third protocol (C). The therapy was otherwise identical. Twenty mg doxorubicin was administered intravenously weekly. Surgery was possible in 40 patients. No patient failed to complete the protocol due to toxicity. In only 13 cases (24%) was death attributed to local failure. Five patients (9%) 'had a survival' exceeding 2 years. No signs of local recurrence were seen in 33 patients (60%); 5 out of 16 patients in Protocol A, 11 out of 17 patients in Protocol B, 17 out of 22 patients in Protocol C (P=0.017). In the 40 patients undergoing additional surgery, no signs of local recurrence were seen in 5 out of 9 patients, 11 out of 14 patients and 17 out of 17 patients, respectively (P=0.005).

Prognostic value of histopathological response to radiotherapy and microvessel density in oral squamous cell carcinomas.

The prognostic value of histopathological response to preoperative radiotherapy (50 Gy) in radically resected oral carcinomas was studied in 39 consecutive patients. Microvessel density (MVD) was evaluated for relation to radioresponse and outcome. Resected tumour tissue was examined histopathologically and response to radiotherapy was scored according to induced morphological changes. Pretreatment biopsies were stained with antibodies to von Willebrand factor to evaluate MVD in hot-spot regions, in stromal tissue and in tumour epithelial tissue. Histopathological response to radiotherapy was highly prognostic of local failures and survival (p = 0.002), though microscopic surgical radicality was obtained. In good responders to preoperative radiotherapy, the 5-year survival rate was 68% compared with 24% in poor responders. In 12 patients with local recurrence after radical surgery, 11 had poor histopathological radiotherapy responses. In univariate analysis, a high MVD score in tumour epithelium was associated with poor clinical outcome but MVD did not correlate with histopathological radiotherapy response.

Dominant expression and distribution of oestrogen receptor beta over oestrogen receptor alpha in the human corpus luteum.

To investigate the potential importance of oestrogen as a local regulator of human corpus luteum function, the mRNA expression pattern and cellular localization of oestrogen receptors (ERs), ER-alpha and ER-beta, were studied in corpora lutea grouped according to age, where days 2-5 post-LH rise were designated as the early luteal phase, days 6-10 as mid-luteal and days 11-14 as the late luteal phase respectively. Northern blot analysis using an ER-beta probe in samples from whole ovarian tissue and isolated corpora lutea, revealed a major band at 7.5 kb and several minor bands between 4-10 kb, while no signals for ER-alpha mRNA were obtained. However, using a semi-quantitative reverse transcription-polymerase chain reaction followed by Southern blotting, ER-beta mRNA levels were found to be 63% lower (P: < 0.05, n = 39) in the mid-luteal phase compared with the early luteal phase, while ER-alpha mRNA expression showed no statistical differences between the different age groups. Using in-situ hybridization, ER-beta mRNA expression was localized to the steroidogenic luteal cells as well as perivascular cells and fibroblasts in the corpus luteum. Immunohistochemistry confirmed the localization of ER-beta protein, but no clear staining of luteal cells was found using antibodies against ER-alpha. Collectively, the findings of low to moderate expression of ER-beta mRNA and protein in the steroidogenic cells, and also in vascular endothelial cells of the corpus luteum, as opposed to diminutive amounts of ER-alpha mRNA, suggest that oestrogen activity is primarily transduced via ER-beta in the human corpus luteum.

Methods for robust clustering of epileptic EEG spikes.

We investigate algorithms for clustering of epileptic electroencephalogram (EEG) spikes. Such a method is useful prior to averaging and inverse computations since the spikes of a patient often belong to a few distinct classes. Data sets often contain outliers, which makes algorithms with robust performance desirable. We compare the fuzzy C-means (FCM) algorithm and a graph-theoretic algorithm. We give criteria for determination of the correct level of outlier contamination. The performance is then studied by aid of simulations, which show good results for a range of circumstances, for both algorithms. The graph-theoretic method gave better results than FCM for simulated signals. Also, when evaluating the methods on seven real-life data sets, the graph-theoretic method was the better method, in terms of closeness to the manual assessment by a neurophysiologist. However, there was some discrepancy between manual and automatic clustering and we suggest as an alternative method a human choice among a limited set of automatically obtained clusterings. Furthermore, we evaluate geometrically weighted feature extraction and conclude that it is useful as a supplementary dimension for clustering.

Evaluation of treatment responses in late Lyme borreliosis on the basis of antibody decrease during the follow-up period.

The purpose of this study was to identify a serological marker of successful treatment as distinct from treatment failure in late Lyme borreliosis. Consecutive serum samples from 68 treated patients with late Lyme borreliosis were analyzed during a 1-2 year follow-up period after the start of treatment. End-point enzyme immunoassay titres of IgG1, IgG2, IgG3, and combined IgG1+3 subclasses against a sonicate antigen of Borrelia burgdorferi were determined and compared to the IgG antibody response against Borrelia burgdorferi flagella. Individual half-lives of the antibody levels were calculated for each patient. The half-life values were compared to the patients' clinical outcome in order to find a serological marker of remaining disease activity or relapse. The levels of combined IgG1+3 subclass antibodies against the sonicate antigen and the individual levels of IgG1, IgG2, and IgG3 antibodies did not change significantly after treatment. In contrast, antibodies to flagella decreased markedly after successful treatment, with a half-life of 112+/-92 days (arithmetic mean value +/- SD). This was significantly shorter than the half-life after unsuccessful treatment (271+/-151 days), (P<0.0001). The decrease was observed mainly in IgG1 and IgG4 responses to flagella, less so for IgG2 or IgG3. The results suggest that a rapid decrease in flagella antibodies can serve as a marker for a successful treatment of Lyme borreliosis.

Distinct expression of gelatinase A [matrix metalloproteinase (MMP)-2], collagenase-3 (MMP-13), membrane type MMP 1 (MMP-14), and tissue inhibitor of MMPs type 1 mediated by physiological signals during formation and regression of the rat corpus luteum.

The corpus luteum (CL) is a transient endocrine organ that secretes progesterone to support pregnancy. The CL is formed from an ovulated follicle in a process that involves extensive angiogenesis and tissue remodeling. If fertilization does not occur or implantation is unsuccessful, the CL will undergo regression, which involves extensive tissue degradation. Extracellular proteases, such as serine proteases and matrix metalloproteinases (MMPs), are thought to play important roles in both the formation and regression of the CL. In this study, we have examined the physiological regulation pattern and cellular distribution of messenger RNAs coding for gelatinase A (MMP-2), collagenase-3 (MMP-13), membrane type MMP 1 (MT1-MMP, MMP-14), and the major MMP inhibitor, tissue inhibitor of MMPs type 1 (TIMP-1) in the CL of adult pseudopregnant (psp) rat. Northern blot and in situ hybridization analyses revealed that gelatinase A messenger RNA was mainly expressed during luteal development, indicating that gelatinase A may be associated with the neovascularization and tissue remodeling that takes place during CL formation. Collagenase-3 had a separate expression pattern and was only expressed in the regressing CL, suggesting that this MMP may be related with luteal regression. MT1-MMP that in vitro can activate progelatinase A and procollagenase-3 was constitutively expressed during the formation, function, and regression of the CL and may therefore be involved in the activation of these MMPs. TIMP-1 was induced during both the formation and regression of the CL, suggesting that this inhibitor modulates MMP activity during these processes. To test whether the induction of collagenase-3 and TIMP-1 is coupled with luteal regression, we prolonged the luteal phase by performing hysterectomies, and induced premature luteal regression by treating the pseudopregnant rats with a PGF2alpha analog, cloprostenol. In both treatments, collagenase-3 and TIMP-1 were induced only after the serum level of progesterone had decreased, suggesting that collagenase-3 and TIMP-1 are induced by physiological signals, which initiate functional luteolysis to play a role in tissue degradation during structural luteolysis. In conclusion, our data suggest that gelatinase A, collagenase-3, and MT1-MMP may have separate functions during the CL life span: gelatinase A mainly takes part in CL formation, whereas collagenase-3 mainly takes part in luteal regression; MT1-MMP is constitutively expressed during the CL life span and may therefore serve as an in vivo activator of both gelatinase A and collagenase-3. TIMP-1 is up-regulated both during the formation and regression of the CL and may therefore regulate MMP activity during both processes.

Vaccination against Lyme borreliosis.

Lyme borreliosis is a worldwide family of tick-borne infections caused by the spirochete Borrelia burgdorferi sensu lato. It is the most common tick-borne human infection in the Western world. There are several subgroups of the spirochete. Two monovalent vaccines against this infection have been presented in the USA, both of which use the borrelial outer surface protein A (OspA) as antigen. The first of these vaccines has been released for general use. A European polyvalent vaccine using the antigen OspC is undergoing clinical trial in the Aland Islands in Finland. Lately, another antigen group, decorin-binding proteins (Dbp), has been considered for immunization purposes. A European vaccine must be effective against several subgroups of the borrelia spirochete, and this complicates the situation compared with that in the USA, where one spirochete subspecies dominates the scene.

Carcinoma of the hypopharynx: analysis of incidence and survival in Sweden over a 30-year period.

BACKGROUND: The aim of the study was to analyze whether there were any changes in incidence and prognosis of hypopharyngeal carcinomas diagnosed between 1960 and 1989 in Sweden. METHODS: Data of primary hypopharyngeal malignant tumors reported to the Swedish Cancer Registry were collected. The total number of cases was 2012, 1396 men and 616 women, and the end of follow-up was December 31, 1992. RESULTS: For women, a significant decrease in the age-standardized incidence (ASI) was seen, with an average decrease of 2% per year (p < .001), which was most evident in rural counties. The male patients, on the contrary, showed a significant increase of about 1.5% per year (p < .001); the metropolitan areas had an ASI about twice that of more-rural areas. The 2- and 5-year overall survival was poor, only 25% and 13%, respectively. For women aged <60 years, no difference in survival between the different 10-year periods was seen, but survival for men of corresponding ages improved significantly (p < .01) during the last decade, to reach a survival similar to that in women. For patients aged > or = 60 years, no difference in survival between the different periods or between sexes was seen. CONCLUSION: The increased incidence in hypopharyngeal cancer in men is similar to that observed for oral and pharyngeal cancer in many European countries during this period. The disappearance of Plummer-Vinson syndrome may explain the decreased incidence among women. The treatment results in hypopharyngeal cancer are still very poor, and improvements of the therapeutic methods are needed.

p53 mutation, but not p53 overexpression, correlates with survival in head and neck squamous cell carcinoma.

Survival in squamous cell carcinoma of the head and neck (HNSCC) was compared with overexpression and mutation of the p53 gene. Archival tissue from 77 tumours was analysed for protein expression using immunohistochemistry (IHC) with the monoclonal antibody Do-7, and for the presence of mutation in exons 5-8 using single-stranded conformation polymorphism (SSCP), followed by DNA sequencing in SSCP-positive cases. p53 expression was scored as high (>70% nuclei stained) in 25 (32%) tumours, as intermediate (10-70% nuclei stained) in 19 (25%) tumours and as low (<10% nuclei stained) in 33 (43%) tumours. Twelve (18%) tumours exhibited gene mutation (ten missense and two nonsense mutations) and an additional five tumours contained changes that could not result in amino acid substitution or protein truncation. There was no correlation between gene expression and mutation, mutations being equally frequent in tumours with either high (4/25), intermediate (4/19) or low protein expression (4/33). Fifty-eight patients were eligible for survival analysis. There was a strong correlation between p53 mutation and cause-specific survival; median survival among mutated cases was 12.5 months compared with >160 months among non-mutated patients (P < 0.005). There was no correlation between p53 overexpression and survival. The results suggest that p53 mutation status is an important prognostic factor in HNSCC, and that IHC analysis of protein overexpression is an inadequate measure of gene mutation in these tumours.

Coordinated and cell-specific regulation of membrane type matrix metalloproteinase 1 (MT1-MMP) and its substrate matrix metalloproteinase 2 (MMP-2) by physiological signals during follicular development and ovulation.

In the ovary, extensive tissue remodeling is required during both follicular development and the break down of the follicular wall at the time of ovulation. Extracellular proteases such as serine proteases and matrix metalloproteinases (MMPs) are thought to play pivotal roles in these processes. In this paper, we have used in situ hybridization to study the regulation and distribution of mRNA coding for MMP-2 (gelatinase A) and its cell surface activator membrane-type MMP1 (MT1-MMP) during gonadotropin induced ovulation in the rat. In ovaries of untreated immature (23 day old) rats, the levels of MT1-MMP and MMP-2 mRNA were low. MMP-2 mRNA was found in theca-interstitial cells while MT1-MMP mRNA was found in both granulosa and theca-interstitial cells and both messages were induced after stimulation with PMSG. After an ovulatory dose of hCG, the expression of MT1-MMP was dramatically down regulated in the granulosa cell layers of large preovulatory follicles but the expression remained and appeared to be up regulated together with MMP-2 in the theca-interstitial cells surrounding the large preovulatory follicles. The expression kinetics and tissue distribution supports the notion that MT1-MMP may have dual functions in the ovary. Initially MT1-MMP may act as a matrix degrading protease inside the follicle during follicular development and later, just prior to ovulation, as an activator of proMMP-2 in theca-interstitial cells surrounding preovulatory follicles.

IgG seroprevalence of Lyme borreliosis in the population of the Aland Islands in Finland.

This is a study of people living in Aland, a group of islands in the Baltic Sea between Finland and Sweden. 500 blood donors and 3,248 health service clients who did not have Lyme borreliosis were examined for Borrelia burgdorferi IgG antibodies. The method used was an ELISA containing a selection of diagnostic antigens to a Borrelia burgdorferi PKo strain. It was found that the distribution according to sex, age and titre values was identical in the 2 groups, which were therefore treated as one. 19.7% of all the sera was positive. The prevalence in men was 23.6%, and in women 16.7%. The prevalence rises with age, the highest prevalence being seen in men (44.7%) and women (37.0%) over 70 y of age. The data show that the Aland islands are strongly endemic for Lyme borreliosis compared with international levels of infection.

Categorization of interictal epileptiform potentials using a graph-theoretic method.

OBJECTIVES: In patients with epileptic seizures, localization of the source of interictal epileptiform activity is of interest. For correct source localization, a favorable signal to noise ratio is important, and to achieve this, averaging of several epileptiform potentials is often necessary. Before averaging, a careful categorization of epileptiform potentials with different potential distributions is crucial. The aim of this study was to investigate whether a a hierarchic, graph-theoretic algorithm could be used for this categorization. METHODS: In 4 patients, 50-100 sharp waves with different surface distributions were categorized independently with the algorithm, and by visual inspection of the traces. As an independent evaluation of the algorithm, a dipole reconstruction was performed for each sharp wave, and the dipole results for the sharp waves from the different automatically obtained categories were compared. RESULTS: All patients showed a high degree of correspondence between the results of the automatic analysis and the visual estimation. There were clear differences in dipole results between the sharp waves of the different categories obtained from the automatic categorization. CONCLUSION: The results indicate that the graph-theoretic categorization algorithm provides a reliable clustering of interictal epileptiform potentials, and that the method may become a useful tool in the pre-averaging categorization of interictal epileptiform potentials prior to source localization.

Distribution of non-diploid flow-cytometric DNA indices and their relation to the nodal metastasis in squamous cell carcinomas of the head and neck.

Squamous cell carcinomas of the head and neck (HNSCC) evolve from diploid epithelial cells of the mucosa. At the time of diagnosis about two thirds of clinically diagnosed HNSCC are non-diploid according to flow-cytometric (FCM) analysis, indicating that during tumour progression there must be an acquisition and accumulation of chromosomal aberrations. At diagnosis one third to one half of HNSCC have clinically positive neck nodes. The objective of the present study was to see whether the progression to a metastatic phenotype is reflected in the distribution of FCM DNA ploidy in node-negative and node-positive HNSCC. The series comprised 200 patients with HNSCC. Tumour samples were obtained from diagnostic biopsies or primary surgery. A multistep preparation method and propidium iodide staining of nuclear DNA content was used for FCM. One hundred and forty one (71%) of the tumours were non-diploid. Only two tumours were hypodiploid (DNA index 0.73 and 0.93, respectively). Ten of the tumours exhibited two non-diploid stem cell lines. The frequency of non-diploidy in node-negative tumours was 65% and in node-positive ones about 80%. The frequency distribution of non-diploid DNA indices clustered in the hypotetraploid region (with a modal value of 1.71-1.74) and did not differ between node-negative and node-positive tumours. The hypothesis that the disposition to metastasis is reflected in the frequency distribution of non-diploid DNA indices could thus not be verified.