Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets.

The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. K-mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as k-mers can be used to quantify accurately gene expression in a less resource-consuming way. We present the Kmerator Suite, a set of three tools designed to extract specific k-mer signatures, quantify these k-mers into RNA-seq datasets and quickly visualize large dataset characteristics. The core tool, Kmerator, produces specific k-mers for 97% of human genes, enabling the measure of gene expression with high accuracy in simulated datasets. KmerExploR, a direct application of Kmerator, uses a set of predictor gene-specific k-mers to infer metadata including library protocol, sample features or contaminations from RNA-seq datasets. KmerExploR results are visualized through a user-friendly interface. Moreover, we demonstrate that the Kmerator Suite can be used for advanced queries targeting known or new biomarkers such as mutations, gene fusions or long non-coding RNAs for human health applications.

Sequential Emboli Detection From Ultrasound Outpatient Data.

This paper addresses the detection of emboli from signals acquired with a new miniaturized and portable transcranial Doppler ultrasound device. The use of this device enables outpatient monitoring but increases the number of artifacts. These artifacts usually come from the patient voice and motion and can be superimposed to emboli. For this reason and because of the scarcity of emboli compared to artifacts, reliably detect emboli is a challenging task. As an example, the 11809 s of signal used in this study contained 0.06 % of embolic events and 10.14 % of artifacts. Herein, we propose an automatic and sequential approach. The method is based on sequential determination of high intensity transient signals. We also define efficient features to describe emboli in the time frequency representation. On our database, the number of artifacts detected as emboli is divided by more than 10 compared to the other algorithms reported in the literature.

Joint segmentation and characterization of the dermis in 50 MHz ultrasound 2D and 3D images of the skin.

We propose a novel joint segmentation and characterization algorithm for the assessment of skin aging using 50 MHz high-frequency ultrasound images. The proposed segmentation method allows a fine determination of the envelope signal's statistics in the dermis as a function of depth. The sequence of statistical estimates obtained is then combined into a single aging score. The segmentation is based on tailored recursive non-linear filters. The epidermis and the dermis are jointly segmented with a non-parametric active contour combining a texture criterion, an epidermis indicator map and the geometric constraint of horizontal continuity. The algorithm is designed to apply to 2D and 3D images as well. We evaluated skin photo-aging on ultrasound images with an experimental study on a cohort of 76 women separated into 2 groups of different ages. Two aging scores are computed from the images: local dermal contrast and skin roughness. We show that these scores are much better at identifying the two groups (p-value ≈10-6) than the previously used MGVR indicator (p-value 0.046). Moreover, we find that a combined score more reliably evaluates skin photo-aging, with 84% success, than a scoring of the ultrasound images by 4 experts.

RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis.

RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events. We also recommend the best practices for the bioinformatics analysis and describe the experimental process for RNA validation using real-time PCR and sequencing.

Segmentation of Skin Tumors in High-Frequency 3-D Ultrasound Images.

High-frequency 3-D ultrasound imaging is an informative tool for diagnosis, surgery planning and skin lesion examination. The purpose of this article was to describe a semi-automated segmentation tool providing easy access to the extent, shape and volume of a lesion. We propose an adaptive log-likelihood level-set segmentation procedure using non-parametric estimates of the intensity distribution. The algorithm has a single parameter to control the smoothness of the contour, and we describe how a fixed value yields satisfactory segmentation results with an average Dice coefficient of D = 0.76. The algorithm is implemented on a grid, which increases the speed by a factor of 100 compared with a standard pixelwise segmentation. We compare the method with parametric methods making the hypothesis of Rayleigh or Nakagami distributed signals, and illustrate that our method has greater robustness with similar computational speed. Benchmarks are made on realistic synthetic ultrasound images and a data set of nine clinical 3-D images acquired with a 50-MHz imaging system. The proposed algorithm is suitable for use in a clinical context as a post-processing tool.

Mutation of TP53 and alteration of p14(arf) expression in EGFR- and KRAS-mutated lung adenocarcinomas.

BACKGROUND: In lung adenocarcinoma, inactivation of the tumor suppressor p53 may abrogate a safeguard mechanism preventing the development of tumors with activating mutations in EGFR or KRAS. To assess this hypothesis, we analyzed TP53 mutations and downregulation of p14(arf), a negative regulator of p53 activated by oncogenic signals, in a retrospective series of 96 patients with primary adenocarcinoma of the lung. PATIENTS AND METHODS: Mutations in TP53 (exons 4-9), KRAS (exon 1), and EGFR (exons 18-21) were identified by direct sequencing of DNA from formalin-fixed, paraffin-embedded resected tumors. Expression of p14(arf) was semiquantitatively evaluated by immunohistochemical analysis. RESULTS: TP53, KRAS, and EGFR mutations were detected in 42 of 93 (45.2%), 15 of 95 (15.8%), and 31 of 90 (34.4%) cases, respectively. Low p14(arf) expression was observed in 19 of 91 cases (20.9%). Disruption of the p53/p14(arf) pathway (defined as TP53 mutation or decreased p14(arf) expression, or both) was observed in 18 of 31 EGFR-mutated (58.1%) tumors and in 9 of 13 KRAS-mutated (69.2%) tumors. CONCLUSION: Inactivation of the p53/p14(arf) pathway is common but not systematic in EGFR- or KRAS-mutated lung adenocarcinomas. Our work highlights the need to better investigate the association between EGFR and KRAS mutations and alterations in tumor suppressor pathways.

Unusual growth rate during cystic echinococcosis.

Cystic echinococcosis is a world wild zoonosis caused by Echinococcus granulosus, leading to hepatic and lung cysts with a usually slight growth rate. We report the case of an 82year-old Algerian woman with hepatic and lung cystic echinococcosis with a 10-fold size increase in 6months.

Completion pneumonectomy in patients with cancer: postoperative survival and mortality factors.

OBJECTIVE: To describe postoperative complications and long-term outcomes of completion pneumonectomy and highlight prognostic factors. METHOD: We retrospectively reviewed the records of 46 patients (38 men, 8 women) who underwent completion pneumonectomy for lung cancer between 1995 and 2009 in one of two thoracic surgery departments. Most were current or former smokers (n = 41; 89%) and did not undergo chemotherapy (n = 38; 83%) or radiotherapy (83%) before surgery. RESULTS: Complications after surgery were respiratory failure (n = 11; 24.4%), bronchopleural fistula (n = 6; 13%, with no side preference), and empyema (n = 6; 13%). Blood transfusion was necessary for 43% of the cases (n = 20). The day 90 death rate was 15.2% (n = 7). Postoperative staging showed mostly limited disease. Ten patients (21.7%) underwent operation for a second primary cancer, 25 for local recurrence (54.3%), five for microscopically incomplete resection, and six for other reasons. Median overall survival after completion surgery was 30 months (median follow-up: 46.5 months). Among the 15 living patients (33%), 11 are free of disease (24%). In a Cox regression model, factors negatively influencing overall survival were: age older than 65 years (odds ratio [OR] = 2.47; p = 0.012), current smoker status (OR = 2.285; p = 0.033), postoperative pulmonary (OR = 5.144; p = 0.004), cardiac (OR = 3.404; p = 0.033), or parietal wound complications (OR = 5.439; p = 0.016). CONCLUSION: Despite its increased postoperative complications and mortality compared with standard pneumonectomy, completion pneumonectomy offers encouraging long-term results. Five main factors seem predictive of shorter overall survival.

Bronchial mucous gland adenoma revealed following acute pneumonia.

A 54-year old male, current smoker, was admitted to the emergency unit with lingular pneumonia. The follow-up chest CT and bronchoscopy showed an airway-blocking intrabronchial tumour. After surgical resection, pathological examination established the diagnosis of a bronchial mucous gland adenoma. The bronchial mucous gland adenoma is an extremely rare and benign lung tumour. It is composed of mucus-containing acini lined with cuboidal cells without pleomorphism. Total surgical resection is usually required for complete diagnosis and treatment. The main differential diagnoses are a low-grade mucoepidermoid carcinoma and a mucinous cystadenoma of the lung. This case highlights the importance of a complete lung workup after acute pneumonia in patients with a history of smoking, including the CT scan and bronchoscopy.

Is pneumonectomy after induction chemotherapy for non-small cell lung cancer a reasonable procedure? A multicenter retrospective study of 228 cases.

INTRODUCTION: Pneumonectomy (PN) after induction chemotherapy (CT) for non-small cell lung cancer is controversial because high-mortality rates are still reported. METHODS: This multicenter retrospective study included all patients treated by induction CT then PN between January 1993 and April 2006 in four General and Thoracic Surgery Departments. Postoperative mortality and morbidity and long-term outcomes were studied. RESULTS: The study considered 228 patients. Doublets with cisplatin and vinorelbine or gemcitabine were used in 66% of cases. pTNM stages (World Health Organization, 1997) were 0 (2%), I (16%), II (25%), IIIA (29%), IIIB (16%), and IV (12%). The postoperative morbidity rate was 37% (84 of 228 patients). The independent risk factors identified for postoperative morbidity were chronic obstructive pulmonary disease, more than four cycles of induction CT or an association of cisplatin, and an old cytotoxic molecule, extended PN, and extended anesthesia time. Postoperative mortality rates were 5.3% at 30 days (12 of 228 patients) and 9.2% at 90 days (21 of 228 patients). The independent risk factors identified for operative mortality were chronic obstructive pulmonary disease, manual suture of the stump, and pTNM stage higher than IIIA. The 90-day mortality rates were 10.3% (12 of 117) for right PN and 8.2% (9 of 111) for left PN (p = 0.65). The overall survival (OS) rates were 68% at 1 year, 39% at 3 years, and 32% at 5 years. CONCLUSIONS: Induction CT was not found to compromise short- or long-term outcomes after PN in non-small cell lung cancer. The right or left PN performed by experienced surgeons after induction CT seems to be a reasonable procedure in case of tumor local extension.

Dendritic cells infiltrating human non-small cell lung cancer are blocked at immature stage.

The efficacy of immune response to control human cancer remains controversial. It is particularly debated whether and to what extent the capacity of tumor-infiltrating dendritic cells (DC) to drive immunization can be turned off by transformed cells, leading to tumor-specific tolerance rather than immunization. To address this issue, we have characterized the DC isolated from human non-small cell lung cancer (NSCLC). These biopsy specimens contained CD11c(high) myeloid DC (mDC), but also CD11c(-) plasmacytoid DC (pDC) and a third DC subset expressing intermediate level of CD11c. Compared with peripheral blood, CD11c(high) tumor-infiltrating DC (TIDC) displayed a "semi-mature" phenotype, and TLR4 or TLR8 stimulation drove them to mature partially and to secrete limited amounts of cytokines. In contrast, most tumor-infiltrating pDC were immature but underwent partial maturation after TLR7 activation, whereas TLR9 ligation triggered low secretion of IFN-alpha. CD11c(int) mDC represented approximately 25% of total DC in tumoral and peritumoral tissues and expressed low levels of costimulatory molecules contrasting with high levels of the immunoinhibitory molecule B7-H1. Finally, the poor APC function of total TIDC even after TLR stimulation and the migratory response of both tumor-infiltrating mDC and pDC toward CCL21 and SDF-1 in vitro suggested their ability to compromise the tumor-specific immune response in draining lymph nodes in vivo. Further studies will be required to establish the specific role of the three TIDC subsets in tumor immunity and to draw conclusions for the design of therapeutic strategies.

Preoperative chemotherapy does not increase complications after nonsmall cell lung cancer resection.

BACKGROUND: Neoadjuvant chemotherapy before resection of nonsmall cell lung cancer seems to increase survival, mainly in the early stage. Risks of postoperative complications after chemotherapy and surgery remain controversial. Here we review our experience with patients treated in one thoracic surgery center. METHODS: Patients undergoing resection for nonsmall cell lung cancer after induction chemotherapy between January 1993 and March 2002 were reviewed. Data collected included age, sex, preoperative forced expiratory volume in 1 second (FEV1), hemoglobin, and arterial oxygen pressure tension (PaO2), postoperative complications, and global survival. The main objectives were postoperative mortality and morbidity. Postoperative mortality and morbidity were defined as complications or deaths occurring within 30 days after surgery. Predictive morbidity factors were identified by univariate and multivariate analysis and overall survival by the Kaplan-Meier method. RESULTS: In all, 114 patients were reviewed. Different induction chemotherapies were used, mainly cisplatin with vinorelbine or gemicitabine. Postoperative mortality was 2 of 114, 1 of 27 after pneumonectomy, and there were no deaths after lobectomy. Complications occurred in 29% of patients (33 of 114), usually infectious pneumonia and anemia requiring transfusion. Preoperative FEV1, hemoglobin, and PaO2 are not associated with morbidity in univariate or multivariate analysis. CONCLUSIONS: Preoperative chemotherapy does not increase postoperative mortality and morbidity after nonsmall cell lung cancer surgery, performed exclusively by thoracic surgeons.