Influence of Biopsy Technique on Molecular Genetic Tumor Characterization in Non-Small Cell Lung Cancer—The Prospective, Randomized, Single-Blinded, Multicenter PROFILER Study Protocol

The detection of molecular alterations is crucial for the individualized treatment of advanced non-small cell lung cancer (NSCLC). Missing targetable alterations may have a major impact on patient’s progression free and overall survival. Although laboratory testing for molecular alterations has continued to improve; little is known about how biopsy technique affects the detection rate of different mutations. In the retrospective study detection rate of epidermal growth factor (EGFR) mutations in tissue extracted by bronchoscopic cryobiopsy (CB was significantly higher compared to other standard biopsy techniques. This prospective, randomized, multicenter, single blinded study evaluates the accuracy of molecular genetic characterization of NSCLC for different cell sampling techniques. Key inclusion criteria are suspected lung cancer or the suspected relapse of known NSCLC that is bronchoscopically visible. Patients will be randomized, either to have a CB or a bronchoscopic forceps biopsy (FB). If indicated, a transbronchial needle aspiration (TBNA) of suspect lymph nodes will be performed. Blood liquid biopsy will be taken before tissue biopsy. The primary endpoint is the detection rate of molecular genetic alterations in NSCLC, using CB and FB. Secondary endpoints are differences in the combined detection of molecular genetic alterations between FB and CB, TBNA and liquid biopsy. This trial plans to recruit 540 patients, with 178 evaluable patients per study cohort. A histopathological and molecular genetic evaluation will be performed by the affiliated pathology departments of the national network for genomic medicine in lung cancer (nNGM), Germany. We will compare the diagnostic value of solid tumor tissue, lymph node cells and liquid biopsy for the molecular genetic characterization of NSCLC. This reflects a real world clinical setting, with potential direct impact on both treatment and survival

Diagnostic Yield of Transbronchial Lung Cryobiopsy Compared to Transbronchial Forceps Biopsy in Patients with Sarcoidosis in a Prospective, Randomized, Multicentre Cross-Over Trial

Background: Transbronchial lung forceps biopsy (TBLF) is of limited value for the diagnosis of interstitial lung disease (ILD). However, in cases with predominantly peribronchial pathology, such as sarcoidosis, TBLF is considered to be diagnostic in most cases. The present study examines whether transbronchial lung cryobiopsy (TBLC) is superior to TBLF in terms of diagnostic yield in cases of sarcoidosis. Methods: In this post hoc analysis of a prospective, randomized, controlled, multicentre study, 359 patients with ILD requiring diagnostic bronchoscopic tissue sampling were included. TBLF and TBLC were both used for each patient in a randomized order. Histological assessment was undertaken on each biopsy and determined whether sarcoid was a consideration. Results: A histological diagnosis of sarcoidosis was established in 17 of 272 cases for which histopathology was available. In 6 out of 17 patients, compatible findings were seen with both TBLC and TBLF. In 10 patients, where the diagnosis of sarcoidosis was confirmed by TBLC, TBLF did not provide a diagnosis. In one patient, TBLF but not TBLC confirmed the diagnosis of sarcoidosis. Conclusions: In this post hoc analysis, the histological diagnosis of sarcoidosis was made significantly more often by TBLC than by TBLF. As in other idiopathic interstitial pneumonias (IIPs), the use of TBLC should be considered when sarcoidosis is suspected

Emerging roles of ATF2 and the dynamic AP1 network in cancer

Cooperation among transcription factors is central for their ability to execute specific transcriptional programmes. The AP1 complex exemplifies a network of transcription factors that function in unison under normal circumstances and during the course of tumour development and progression. This Perspective summarizes our current understanding of the changes in members of the AP1 complex and the role of ATF2 as part of this complex in tumorigenesis.Fil: Lopez Bergami, Pablo Roberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental (i); Argentina; ArgentinaFil: Lau, Eric . Burnham Institute for Medical Research; Estados UnidosFil: Ronai, Zeev . Burnham Institute for Medical Research; Estados Unido

Unravelling higher order chromatin organisation through statistical analysis

Recent technological advances underpinned by high throughput sequencing have given new insights into the three-dimensional structure of mammalian genomes. Chromatin conformation assays have been the critical development in this area, particularly the Hi-C method which ascertains genome-wide patterns of intra and inter-chromosomal contacts. However many open questions remain concerning the functional relevance of such higher order structure, the extent to which it varies, and how it relates to other features of the genomic and epigenomic landscape. Current knowledge of nuclear architecture describes a hierarchical organisation ranging from small loops between individual loci, to megabase-sized self-interacting topological domains (TADs), encompassed within large multimegabase chromosome compartments. In parallel with the discovery of these strata, the ENCODE project has generated vast amounts of data through ChIP-seq, RNA-seq and other assays applied to a wide variety of cell types, forming a comprehensive bioinformatics resource. In this work we combine Hi-C datasets describing physical genomic contacts with a large and diverse array of chromatin features derived at a much finer scale in the same mammalian cell types. These features include levels of bound transcription factors, histone modifications and expression data. These data are then integrated in a statistically rigorous way, through a predictive modelling framework from the machine learning field. These studies were extended, within a collaborative project, to encompass a dataset of matched Hi-C and expression data collected over a murine neural differentiation timecourse. We compare higher order chromatin organisation across a variety of human cell types and find pervasive conservation of chromatin organisation at multiple scales. We also identify structurally variable regions between cell types, that are rich in active enhancers and contain loci of known cell-type specific function. We show that broad aspects of higher order chromatin organisation, such as nuclear compartment domains, can be accurately predicted in a variety of human cell types, using models based upon underlying chromatin features. We dissect these quantitative models and find them to be generalisable to novel cell types, presumably reflecting fundamental biological rules linking compartments with key activating and repressive signals. These models describe the strong interconnectedness between locus-level patterns of local histone modifications and bound factors, on the order of hundreds or thousands of basepairs, with much broader compartmentalisation of large, multi-megabase chromosomal regions. Finally, boundary regions are investigated in terms of chromatin features and co-localisation with other known nuclear structures, such as association with the nuclear lamina. We find boundary complexity to vary between cell types and link TAD aggregations to previously described lamina-associated domains, as well as exploring the concept of meta-boundaries that span multiple levels of organisation. Together these analyses lend quantitative evidence to a model of higher order genome organisation that is largely stable between cell types, but can selectively vary locally, based on the activation or repression of key loci

Different Prevalences of Pneumological Disease Patterns in Outpatient and Inpatient Care

Background Evaluating the focus of treatment in pneumological inpatient and outpatient care is of special interest due to its impact on physician, patient and research. This work describes differences and commonalities in the focus of treatment of current pneumological inpatient and outpatient care and discusses their impact on patient, physician and research. Methods This study compares the inpatient and outpatient sector based on the prevalence of ICD codes of a pneumological specialist clinic (5.211 cases of 2016) and the most prevalent ICD-10 codes of pneumology practices in the third quarter 2016, published by the Association of Statutory Health Insurance Physicians North Rhine (Kassenarztliche Vereinigung Nordrhein, 142.431 cases). Results Whereas the proportion of many pneumological disease patterns treated in physicians' practices and hospitals is similar, the relative frequencies of specific diseases differ considerably between the two. Treatment of allergic conditions such as allergic rhinopathy and bronchial asthma is mostly done on an outpatient basis while respiratory insufficiency and lung carcinoma constitute domains of pneumological inpatient care. Conclusion Despite many commonalities in the focus of treatment in pneumological inpatient and outpatient care, there are also substantial differences between the two. These affect medical training, the conduct of clinical studies, and in particular, patient care. In order to maintain a high level of medical care in all areas of pneumology a close exchange between inpatient and outpatient sector seems crucial. In the end, the availability of medical expertise across both sectors will benefit all: physicians, patients and medical science

First case report of a curative wedge resection in epithelial-myoepithelial carcinoma of the lung

Epithelial-myoepithelial carcinoma is a well differentiated malignant neoplasm, which originates from the salivary glands. The primary pulmonary manifestation is rare-about 30 cases have been reported worldwide. In the literature, anatomical resection has been described as the standard surgical approach. In the presented case, a wedge resection was performed, with no evidence for tumor relapse in the follow-up reevaluation after 24 months. This is the first case report of a primary pulmonary epithelial-myoepithelial carcinoma that has been treated with a non-anatomical wedge resection and lymph node dissection as a curative approach

Supplementary Material for: Decannulation/Weaning Potential and Success in Home Intensive Care

Background: The number of patients receiving home long-term ventilation has risen considerably in recent decades owing to medical advancements. Experts believe that the potential for ventilator weaning or tracheostoma removal is currently insufficiently exploited. Objective: The objective of this study was to investigate the characteristics, prognosis, and decannulation/weaning potential of patients under home intensive care. Methods: In this retrospective analysis of 607 patients on home intensive care, decannulation/weaning status and survival were documented for a 2-year period after initial assessment. At the time of hospital discharge, when clinicians had deemed the weaning process concluded, an independent expert noninvasively assessed the long-term decannulation/weaning. Comparative analyses based on specific criteria, such as ventilation and decannulation/weaning status, age, and underlying diseases, were performed. Potential predictors of survival were identified via multivariable logistic regression. Results: Eighteen percent of patients were decannulated/weaned within 2 years after hospital discharge and had better mean survival than patients not decannulated/weaned (552 vs. 420 days, p Conclusion: Successful decannulation/weaning of patients on long-term home intensive care is associated with better survival. Even in the absence of decannulation/weaning potential at the time of hospital discharge, patients may develop decannulation/weaning potential over time, which should therefore be assessed repeatedly