DIANA-microT web server: elucidating microRNA functions through target prediction.

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

Gene expression profiling of breast cancer patients treated with docetaxel, doxorubicin, and cyclophosphamide within the GEPARTRIO trial: HER-2, but not topoisomerase II alpha and microtubule-associated protein tau, is highly predictive of tumor response.

Gene expression analysis in breast cancer patients undergoing neoadjuvant chemotherapy is an interesting tool for identification of gene signatures and new markers to predict tumor response. However, the detection of predictive markers strongly depends on the drugs used in the specific therapeutic setting. There is growing evidence that topoisomerase II-alpha (TOPO IIalpha) is a marker for anthracycline-, and microtubule-associated protein tau (MAPT) for taxane sensitivity. HER-2 has been described as a marker of both anthracycline and taxane sensitivity. We performed gene expression profiling of 50 patients within the GEPARTRIO study, an anthracycline and taxane neoadjuvant chemotherapy trial. Here we investigate the predictive value of TOPO IIalpha, MAPT and HER-2 mRNA expression for pathological complete response (pCR) in this setting. Interestingly, HER-2 gene expression was strongly predictive of pCR (P=0.017) as well as overall response (P=0.037) and clinical complete response (cCR, P=0.050). In contrast, for both TOPO IIalpha and MAPT no correlation with pCR was observed in our sample group.

Methylation of estrogen receptor beta promoter correlates with loss of ER-beta expression in mammary carcinoma and is an early indication marker in premalignant lesions.

The function of estrogen receptor beta (ER-beta) in mammary tissue is not completely understood. While early observations were often conflicting, more recent data suggest an important role as a tumor-suppressor gene. A decrease of ER-beta expression has been observed in ductal carcinoma in situ and invasive carcinoma as compared with benign mammary epithelial cells. The loss of ER-beta resulted in abnormal growth of mammary epithelial cells. We have previously shown that the mRNA expression of the ER-beta gene is almost totally suppressed in breast carcinomas from patients with a poor prognosis. Here we analyzed whether methylation changes in the different promoters of ER-beta are responsible for the loss of expression of the gene. A methylation assay with high specificity and sensitivity was developed, and a panel of breast tissue samples (n = 175) was characterized for methylation status. In contrast to benign breast, more than two-thirds of invasive breast cancers showed a high degree of methylation. Importantly, increased methylation was also detectable in numerous premalignant lesions. By analysis of breast tumors, previously characterized by gene-expression profiling, methylation was predominantly detected in a subgroup of patients with an unfavorable prognosis, suggesting a possible prognostic value of the ER-beta methylation status. We also investigated the structural characteristics of the two ER-beta promoters, which were both found to be closely associated with a second, downstream, localized and opposite-oriented promoter. However, we could not detect endogenous antisense RNA transcribed from these promoters, which may be involved in epigenetic gene silencing. We also failed to induce ER-beta promoter methylation by expressing siRNAs in cell lines. Interestingly, by comparing the promoter sequences of ER-beta with other genes known to be epigenetically inactivated in breast cancers, we identified a sequence motif possibly involved in promoter methylation.

Twenty years experience with abdominal aneurysmectomy. Surgical considerations and analysis of late results.

This report is concerned with presentation of overall experience with abdominal aneurysmectomy, carried out upon 500 consecutive cases during the last 20 years. Emphasis is placed upon substantially improved results of the last decade in terms of survival and late mortality thus, leading to an increased spectrum of operative indications together with justified surgical aggression in the overall management of abdominal aneurysm. Elective surgery was applied upon 385 cases whereas in the remaining 115, emergency undertaking was necessary. Mortality in elective surgery was 3%. From the group of 115 emergency operations, 70 represent formal rupture with a mortality of 32% and 35 exhibited symptomatology compatible with threatening rupture. Mortality in this particular group was 8%. There was an age ranging from 38 to 87 years, with a mean age of 62.2. A definite preponderance of the disease was noted in patients between 60 and 70 years of age (17%-29%). Risk factors including heart disease, hypertension and advanced age, were responsible for the majority of deaths occurred within 30 days. Subsequent decrease of mortality should be attributed to improvements of anesthesia, monitor equipments and other supportive measures during and immediately following the operation within modern intensive care unit. Cardiac cases were the predominant cause of late death (24%) with following cerebrovascular insufficiency (8.1%), cancer (5%) and chronic pulmonary disease (6%). No particular difference in mortality was noted among the three group of patients classified according to the 60, 70 and 80 decade of their age.(ABSTRACT TRUNCATED AT 250 WORDS)

Gene expression profiles of breast cancer obtained from core cut biopsies before neoadjuvant docetaxel, adriamycin, and cyclophoshamide chemotherapy correlate with routine prognostic markers and could be used to identify predictive signatures.

BACKGROUND: Neoadjuvant administration of chemotherapy provides a unique opportunity to monitor response to treatment in breast cancer and assesses response exactly. Global gene expression profiling by microarrays has been used as a valuable tool for the identification of prognostic and predictive marker genes. Even though this technology is now wide spread and relatively standardized, there are only few data available which compare established parameters with expression values to determine reliability of this method. Therefore we analyzed gene expression data of pretreatment biopsies of breast cancer patients and compared them with the results of the immunohistochemical receptor expression for ER/ PR and Her-2, as well as FISH testing for HER-2 amplification. We analyzed the change of expression of these markers before and after neoadjuvant chemotherapy. Furthermore we evaluated the predictive significance of prognostic gene signatures as described by Sorlie, van't Veer and Ahr for response to neoadjuvant chemotherapy. METHODS: Pretherapeutic core biopsies were obtained from 70 patients undergoing neoadjuvant TAC chemotherapy within the GEPARTRIO-trial. Samples were characterized according to standard pathology including ER, PR and HER2 IHC and amount of cancer cells. Only biopsies with more than 80 % tumor cells were considered for further examination. RNA was isolated and expression profiling performed using Affymetrix Hg U133 Arrays (22 500 genes). GeneData's Expressionist software was used for bioinformatic analyses. RESULTS: More than two thirds of the biopsies yielded sufficient amounts (> 5 microg) of RNA for expression profiling and high quality data were obtained for 50 samples. Unsupervised clustering broadly revealed a correlation with hormone receptor status. When ER-alpha, PR and HER2 as analyzed by immunohistochemistry were compared to the corresponding mRNA data from gene chips more than 90 % concordance was observed. We could observe a switch of receptor expression for ER, PR or HER-2 from positive to negative and vice versa in 16/35 cases (45.7 %) and 5/22 cases (22.7 %) respectively. The prognostic marker sets of Sorlie, van't Veer and Ahr could not discriminate responders from non-responders in our patient group. CONCLUSIONS: Our results demonstrate that reliable expression profiles can be achieved by using limited amounts of tissue obtained during neoadjuvant chemotherapy. Microarray data capture conventional prognostic markers but might contain additional informative gene sets correlated with treatment outcome. Prognostic marker sets are not suitable to predict tumor response in the neoadjuvant setting, suggesting the necessity of class prediction methods to identify marker sets predictive for the type of therapy used.

Bronchobiliary fistula due to echinococcosis of the liver.

In Greece, which has the second highest incidence of echinococcosis in the world, there has been an overall decrease in the frequency of this disease and its complications during the past 15 years. Between 1920 and 1960, approximately 46 patients per year were operated on for echinococcosis at the Hellenic Red Cross Hospital, and 1.8% of 1037 hepatic hydatid cysts had ruptured into the bronchi. From 1960 to 1975, the number of patients requiring operation decreased to approximately 25 per year, and incidence of rupture into the bronchi declined to 1% of 288 liver cysts. The reduction has resulted from improvements in preventive medicine and surgical care and a decrease in the frequency of infected cysts. Bronchobiliary fistula is a serious complication of hydatid cyst of the liver and it must be treated surgically. A right thoracotomy or thoracoabdominal approach offers the possibility of dealing simultaneously with the hepatic cyst and the pulmonary lesions. The choice of operation depends on the findings and ranges from simple drainage of the hepatic cavity with division of the bronchobiliary communication, to resection of the lung (usually lobectomy) when a chronically infected pulmonary cavity is present. If a hydatid cyst of the liver ruptures simultaneously into the lung and the extra-hepatic biliary tree with resultant obstruction of the common bile duct, unblocking of the common duct by evacuation of cysts and debris through a laparotomy takes priority over any other surgical action. Of 3 patients with bronchobiliary fistulas treated during the past 15 years, 2 were cured by simple drainage through a transabdominal approach.

The mid-aortic dysplastic syndrome. Surgical considerations with a 2 to 18 year follow-up and selective histopathological study.

Mild-aortic dysplastic syndrome is usually presented with advanced hypertension in young individuals in association with either weak or absent femoral pulses, due to diffuse narrowing of the aorta in its mid thoraco-abdominal course. There is frequent involvement of visceral arterial branches such as renal and superior mesenteric arteries. Although the disease has been popularised by the appealing name of "abdominal coarctation", the term mid-aortic dysplastic syndrome is more appropriate. In spite of the fact that the syndrome was described almost three decades ago, its exact aetiology remains obscure and pathogenesis speculative. Surgical revascularisation remains the only therapeutic remedy, in dealing with this particular group of young hypertensive patients. The clinical presentation, angiographic assessment and long-term outcome, following reconstruction in 11 patients (mean age 24.4 years) with mid-aortic dysplastic syndrome were evaluated, in an effort to determine the effectiveness of surgery. Late follow-up, slightly exceeding 16 years (mean 5.6 years) has shown normal and relief from hypertension in practically all individuals. Furthermore, in order to elucidate at least some aspects of histopathology, studies were undertaken upon specimens from the aortic wall and the renal, carotid, lumbar and brachial arteries. The results suggested predominantly dysplastic features in the media, intima and particularly along the course of internal lamina. Aortography, using different projections, revealed variable patterns of high mid-aortic stenosis with or without associated renal artery disease. All patients were hypertensive (mean blood pressure 170 mmHg) and co-exist renal artery disease, unilateral in three and bilateral in three cases, was detected.(ABSTRACT TRUNCATED AT 250 WORDS)