Frequency, prognostic impact, and subtype association of 8p12, 8q24, 11q13, 12p13, 17q12, and 20q13 amplifications in breast cancers

BACKGROUND: Oncogene amplification and overexpression occur in tumor cells. Amplification status may provide diagnostic and prognostic information and may lead to new treatment strategies. Chromosomal regions 8p12, 8q24, 11q13, 17q12 and 20q13 are recurrently amplified in breast cancers. METHODS: To assess the frequencies and clinical impact of amplifications, we analyzed 547 invasive breast tumors organized in a tissue microarray (TMA) by fluorescence in situ hybridization (FISH) and calculated correlations with histoclinical features and prognosis. BAC probes were designed for: (i) two 8p12 subregions centered on RAB11FIP1 and FGFR1 loci, respectively; (ii) 11q13 region centered on CCND1; (iii) 12p13 region spanning NOL1; and (iv) three 20q13 subregions centered on MYBL2, ZNF217 and AURKA, respectively. Regions 8q24 and 17q12 were analyzed with MYC and ERBB2 commercial probes, respectively. RESULTS: We observed amplification of 8p12 (amplified at RAB11FIP1 and/or FGFR1) in 22.8%, 8q24 in 6.1%, 11q13 in 19.6%, 12p13 in 4.1%, 17q12 in 9.9%, 20q13(Z )(amplified at ZNF217 only) in 9.9%, and 20q13(Co )(co-amplification of two or three 20q13 loci) in 8.5% of cases. The 8q24, 12p13, and 17q12 amplifications were correlated with high grade. The most frequent single amplifications were 8p12 (9.8%), 8q24 (3.3%) and 12p13 (3.3%), 20q13(Z )and 20q13(Co )(1.6%) regions. The 17q12 and 11q13 regions were never found amplified alone. The most frequent co-amplification was 8p12/11q13. Amplifications of 8p12 and 17q12 were associated with poor outcome. Amplification of 12p13 was associated with basal molecular subtype. CONCLUSION: Our results establish the frequencies, prognostic impacts and subtype associations of various amplifications and co-amplifications in breast cancers

Aire controls gene expression in the thymic epithelium with ordered stochasticity

Aire controls immunologic tolerance by inducing the ectopic thymic expression of many tissue-specific genes, acting broadly by removing stops on the transcriptional machinery. To better understand Aire’s specificity, we performed single-cell RNAseq and DNA methylation analysis in Aire-sufficient and -deficient medullary epithelial cells (mTECs). Each of Aire’s target genes was induced in only a minority of mTECs, independently of DNA methylation patterns, as small inter-chromosomal gene clusters activated in concert in a proportion of mTECs. These microclusters differed between individual mice, and thus suggest an organization of the DNA or of the epigenome that results from stochastic determinism, but is bookmarked and stable through mTEC divisions, ensuring more effective presentation of self-antigens, and favoring diversity of self-tolerance between individuals

Assessment of biological effect of nab-paclitaxel combined with gemcitabine, using contrast enhanced ultrasonography and elastography, in advanced pancreatic ductal carcinoma: A single-center pilot study

International audienceEUS associated with contrast-enhanced harmonic EUS (CH-EUS) and EUS elastography (EUS-E) are used in clinical practice to assess pancreatic tumor at the diagnosis. In case of pancreatic ductal adenocarcinoma (PDAC) with liver metastasis, nab-paclitaxel combined with gemcitabine is a first-line treatment option. We aimed to assess the modification of PDAC microenvironment induced by the combination of nab-paclitaxel with gemcitabine, by endoscopic ultrasonography techinics. This single center phase III study conducted between February 2015 and June 2016 included patients with pancreatic adenocarcinoma with mesurable liver metastasis and no prior cancer treatment fit for two cycles of nab-paclitaxel combined with gemcitabine. We aimed to perform EUS with CH-EUS and EUS-E of the pancreatic tumor, CT scan and contrast enhanced ultrasonogram (CE-US) of a reference liver metastasis, before and after the two cylces of chemotherapy. Primary end point was modification of vascularizaion of primary tumor and a reference liver metastasis. Secondary end points were modification of stromal content, safety profile of drug combination and tumor response rate. Sixteen patients were analyzed, but only 13 received two cycled of chemotherapy (CT) (toxicity [n = 1] or death [n = 2]). There was no statistical modification induced by CT concering vascularity of primary tumor (time to maximum intensity P = 0.24, value of maximum intensity P = 0.71, hypoechogenic aspect generated by injection of contrast enhancing agent), vascularity of a reference liver metastasis (time to maximum intensity P = 0.99, value of maximum intensity P = 0.71) and tumor elasticity (P = 0.22). Eleven patients had tumor response assessement, 6/11 (54%) had measurable disease response 4/11 (36%) with partial responses and 2/11 (18%) with stable disease. All other patients showed disease progression. No serious side effects occurred, 6/11 patients had a dose adjustment. We did not show significant modification of vascularity and elasticity but these results should be taken with caution because of important limitations

Transhiatal esophagectomy as a treatment for locally advanced adenocarcinoma of the gastroesophageal junction: postoperative and oncologic results of a single-center cohort THE for locally advanced GEJC

International audienceBackground and purpose: To report the postoperative and oncological outcomes of transhiatal esophagectomy for locally advanced cancer of the gastroesophageal junction. Methods: Medical records of 120 consecutive patients who underwent transhiatal esophagectomy for locally advanced cancer of the gastroesophageal junction with curative intent after neoadjuvant treatment between February 2006 and December 2018 at our center were reviewed. Results: All patients received either chemotherapy (46.7%) or chemoradiation (53.3%). The 90-day mortality and overall morbidity rates were 0.8% and 56.7%, respectively. Respiratory complications were the most common (30.8%). Anastomotic leakage occurred in 19 patients (15.8%), who were treated by local wound care (n = 13) or surgical drainage (n = 6). Recurrent laryngeal nerve injury occurred in 12 patients (9.9%). The median length of hospital stay was 15.5 days. The rate of R0 resection was 95.8%, and the median number of nodes removed was 17.5. Over a median follow-up of 77 months, the rate of recurrence was 40.8%, and the overall survival rates at 1, 3, and 5 years were 91%, 75%, and 65%, respectively. The median survival time was not reached. In multivariate analysis, disease stage was the only independent significant prognostic factor. Conclusions: Transhiatal esophagectomy is a safe and effective procedure with good long-term oncological outcomes for locally advanced tumors after neo-adjuvant treatment. It can be recommended for all patients with cancer of the gastroesophageal junction, regardless of the Siewert classification, tumor stage, and comorbidities

Prediction of Early Breast Cancer Metastasis from DNA Microarray Data Using High-Dimensional Cox Regression Models

Background DNA microarray studies identified gene expression signatures predictive of metastatic relapse in early breast cancer. Standard feature selection procedures applied to reduce the set of predictive genes did not take into account the correlation between genes. In this paper, we studied the performances of three high-dimensional regression methods – CoxBoost, LASSO (Least Absolute Shrinkage and Selection Operator), and Elastic net – to identify prognostic signatures in patients with early breast cancer. Methods We analyzed three public retrospective datasets, including a total of 384 patients with axillary lymph node-negative breast cancer. The Amsterdam van't Veer's training set of 78 patients was used to determine the optimal gene sets and classifiers using sensitivity thresholds resulting in misclassification of no more than 10% of the poor-prognosis group. To ensure the comparability between different methods, an automatic selection procedure was used to determine the number of genes included in each model. The van de Vijver's and Desmedt's datasets were used as validation sets to evaluate separately the prognostic performances of our classifiers. The results were compared to the original Amsterdam 70-gene classifier. Results The automatic selection procedure reduced the number of predictive genes up to a minimum of six genes. In the two validation sets, the three models (Elastic net, LASSO, and CoxBoost) led to the definition of genomic classifiers predicting the 5-year metastatic status with similar performances, with respective 59, 56, and 54% accuracy, 83, 75, and 83% sensitivity, and 53, 52, and 48% specificity in the Desmedt's dataset. In comparison, the Amsterdam 70-gene signature showed 45% accuracy, 97% sensitivity, and 34% specificity. The gene overlap and the classification concordance between the three classifiers were high. All the classifiers added significant prognostic information to that provided by the traditional prognostic factors and showed a very high overlap with respect to gene ontologies (GOs) associated with genes overexpressed in the predicted poor-prognosis vs. good-prognosis classes and centred on cell proliferation. Interestingly, all classifiers reported high sensitivity to predict the 4-year status of metastatic disease. Conclusions High-dimensional regression methods are attractive in prognostic studies because finding a small subset of genes may facilitate the transfer to the clinic, and also because they strengthen the robustness of the model by limiting the selection of false-positive predictive genes. With only six genes, the CoxBoost classifier predicted the 4-year status of metastatic disease with 93% sensitivity. Selecting a few genes related to ontologies other than cell proliferation might further improve the overall sensitivity performance

Laparoscopy is not enough: full ERAS compliance is the key to improvement of short-term outcomes after colectomy for cancer

International audienceBackground: The enhanced recovery after surgery (ERAS) programs and laparoscopic techniques both reduce hospital stay and postoperative morbidity in patients undergoing colorectal cancer surgery. Laparoscopic techniques are an integral part of the ERAS program. However, evidence showing that the implementation of a multimodal rehabilitation program in addition to laparoscopy for colonic cancer would improve postoperative outcomes is still lacking. This study aimed to evaluate the impact of ERAS program on postoperative outcomes after elective laparoscopic colonic cancer resection.Methods: This is a single-center observational study from a prospectively maintained database. Two groups were formed from all patients undergoing laparoscopic colonic surgery for neoplasm during a defined period before (standard group) and after introduction of an ERAS program (ERAS group). The primary endpoint was postoperative 90-day morbidity. Secondary endpoints were the total length of hospital stay, readmission rate, and compliance with ERAS protocol.Results: A total of 320 patients were included in the analyses, with 160 patients in the standard group and 160 in the ERAS group. There were no differences in the baseline characteristics between the two groups. Overall morbidity was significantly lower in the ERAS group (21.25%) than that in the standard group (34.4%; OR = 0.52 [0.31-0.85], p < 0.01). This difference was not due to the reduction in major complications. Mean total hospital stay was significantly lower in the ERAS group (5.8 days) than that in the standard group (8.2 days, p < 0.01). There were no differences in readmission rates and anastomotic complications.Conclusions: The ERAS pathway reduced the overall morbidity rates and shortened the length of hospital stay, without increasing the readmission rates. A significant reduction in nonsurgical complications was evident, whereas no significant reduction was found for surgical complications

Comparison of Variable Selection Methods for Time-to-Event Data in High-Dimensional Settings

National audienceOver the last decades, molecular signatures have become increasingly important in oncology and are opening up a new area of personalized medicine. Nevertheless, biological relevance and statistical tools necessary for the development of these signatures have been called into question in the literature. Here, we investigate six typical selection methods for high-dimensional settings and survival endpoints, including LASSO and some of its extensions, component-wise boosting, and random survival forests (RSF). A resampling algorithm based on data splitting was used on nine high-dimensional simulated datasets to assess selection stability on training sets and the intersection between selection methods. Prognostic performances were evaluated on respective validation sets. Finally, one application on a real breast cancer dataset has been proposed. The false discovery rate (FDR) was high for each selection method, and the intersection between lists of predictors was very poor. RSF selects many more variables than the other methods and thus becomes less efficient on validation sets. Due to the complex correlation structure in genomic data, stability in the selection procedure is generally poor for selected predictors, but can be improved with a higher training sample size. In a very high-dimensional setting, we recommend the LASSO-pcvl method since it outperforms other methods by reducing the number of selected genes and minimizing FDR in most scenarios. Nevertheless, this method still gives a high rate of false positives. Further work is thus necessary to propose new methods to overcome this issue where numerous predictors are present. Pluridisciplinary discussion between clinicians and statisticians is necessary to ensure both statistical and biological relevance of the predictors included in molecular signatures

Palliative endoscopic drainage of malignant stenosis of biliary confluence: Efficiency of multiple drainage approach to drain a maximum of liver segments

International audienceBackground and aim:More than 50% of the liver should be drained in case of unresectable hilar liver stenosis; however, it remains unclear if the use of several types of drainage (endoscopic retrograde cholangiography and pancreatography, percutaneous-biliary drainage, endoscopic ultrasound biliary drainage (EUS-BD)), allowing better drainage, has an impact on survival. The aim of our study was to evaluate the percentage of liver drained and its correlation on survival whatever the drainage technique used.Patients and methods:This study was a retrospective analysis of a prospective registry of patients with malignant drainage stenosis of the hilum. The quality of drainage was evaluated based on the percentage of liver segments drained, which was calculated by dividing the number of liver segments drained by the total number of liver segments. Drainage could be achieved via an endoscopic, EUS-guided or percutaneous route not associated with the procedure.Results:Sixty patients (38 men) were included from January 2015 to July 2016. The mean patient age was 69.84 years. Stenosis was classified as type II for 17 (29%) patients, type III for 20 (34%) patients, and type IV for 22 (37%) patients. Histology revealed cholangiocarcinoma for 26 (43%) patients, metastatic disease from colorectal cancer for 15 (25%) patients and another cancer for 19 (32%) patients. The median survival time was five (2.3-12.3) months.The percentage of liver segments drained had a significant prognostic impact on overall survival regardless of the technique used to drain the liver. The percentage of liver segments drained was dichotomized based on a threshold value of 80%, resulting in two groups (<80% and ≥80%). Univariate analysis of overall survival revealed that the patients with <80% of liver segments drained had significantly worse prognoses (hazard ratio (HR) = 3.25 (1.66-6.36), p < 0.001) than the patients with ≥80% of liver segments drained. This effect was confirmed in multivariate analysis (HR = 2.46 (1.16-5.23), p = 0.02).The other factor that affected survival was invasion of <50% of the liver by the tumor.A receiver operating characteristic curve was used to establish a correlation between patients receiving chemotherapy and the percentage of liver drained (area under the curve = 0.77 (0.65-0.88)).Conclusion:The survival of patients with malignant stenosis of the biliary confluence is highly correlated with the percentage of liver segments drained, regardless of the technique used

Correction to: Transhiatal esophagectomy as a treatment for locally advanced adenocarcinoma of the gastroesophageal junction: postoperative and oncologic results of a single-center cohort

No abstract availabl