Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study

Although prognostic gene expression signatures for survival in early-stage lung cancer have been proposed, for clinical application, it is critical to establish their performance across different subject populations and in different laboratories. Here we report a large, training-testing, multi-site, blinded validation study to characterize the performance of several prognostic models based on gene expression for 442 lung adenocarcinomas. The hypotheses proposed examined whether microarray measurements of gene expression either alone or combined with basic clinical covariates (stage, age, sex) could be used to predict overall survival in lung cancer subjects. Several models examined produced risk scores that substantially correlated with actual subject outcome. Most methods performed better with clinical data, supporting the combined use of clinical and molecular information when building prognostic models for early-stage lung cancer. This study also provides the largest available set of microarray data with extensive pathological and clinical annotation for lung adenocarcinomas.     

Aggregation of spores and its effect on aerodynamic behaviour

Spores of fungi and actinomycetes are often aggregated, greatly affecting their aerodynamic behaviour with significance for both plant pathology and medicine. However, apart from experimental work with inorganic particles relative to industrial hygiene and lung deposition, the effects of aggregation on aerodynamic behaviour have been little studied. The available information is reviewed and methods are suggested for the study of microbial aggregates.     

胎鼠肺泡Ⅱ型上皮细胞分离、纯化与鉴定

肺泡Ⅱ型上皮细胞（type Ⅱ alveolar epithlial cell,AEC Ⅱ）一直是肺疾病领域的研究热点和难点.AEC Ⅱ是肺泡上皮细胞的＂祖细胞＂,与肺组织生理功能密切相关.获取胎鼠AEC Ⅱ为该领域提供了良好的实验模型和基础.迄今为止,尚没有一套完善的有关AEC Ⅱ分离、纯化与鉴定的方法.文章就目前国内外AEC Ⅱ分离、纯化、鉴定的实验室方法进行综述与介绍,为肺疾病领域的研究奠定实验基础.     

Immunocytochemical study of the lung of domestic fowl and pigeon: endocrine cells and nerves

the presence of endocrine cells and nerves in the lung of 2 avian species (Gallus gallus and Columba livia domestica) has been studied by peroxidase-antiper-oxidase (PAP) and avidin-biotin complex (ABC) immunocytochemical methods at the light-microscopic level. Two immunoreactive cell-types have been identified in the epithelium of the primary and secondary bronchi of chick lung: serotonin- and bombesin-immunoreactive cells; and 3 cell-types, namely, serotonin-, bombesin- and CGRP-(calcitonin gene related peptide) immunoreactive cells, have been located in the bronchial epithelium of pigeon lung. Co-localization of 2 different immunoreactivities within the same cell has not been detected. VIP-immunoreactive nerves have been observed in different locations in chick lung.     

Comparative Subpopulation Analysis of Plasma Exosomes from Cancer Patients

Pre-selection of tumor exosomes from a total pool of circulating microvesicles is an important stage required to increase sensitivity and specificity of the developing methods for diagnostics of oncological diseases. In this study, universal proteins characterized by increased expression in plasma exosomes have been identified in patients with colorectal cancer, head and neck squamous cell carcinomas, and lung cancer. The use of antibodies against major exosomal proteins will help to develop a simple and high-performance method of affinity isolation of tumor exosomes.     

Fine needle aspiration biopsy versus sputum and bronchial material in the diagnosis of lung cancer. A comparative study of 168 patients

A group of 168 consecutive lung cancer patients in whom a definitive diagnosis of primary lung cancer was established either in a conventional cytologic specimen of sputum or bronchial material or in a specimen obtained by fine needle aspiration (FNA) biopsy was reviewed to compare the relative accuracies between the modalities of sputum and bronchial material on one hand versus FNA cytology on the other in the diagnosis of lung cancer. The patients included in the study were selected from a total of 1,093 patients who had been diagnosed and treated for lung cancer at Duke University Medical Center over the five-year period of January 1, 1980, through December 31, 1984. In 325 (29.8%) of the 1,093 patients, a definitive cancer diagnosis was established from histopathologic study alone, without any cytologic diagnoses. In 420 patients (38.4%), both histologic and cytologic material had been interpreted as being conclusively diagnostic for lung cancer. In 348 patients (31.8%), a cytologic diagnosis of lung cancer was made without a histologic confirmation. Thus, in a total of 768 (70.3%) of the 1,093 cases, a definitive cytologic diagnosis of cancer had been made. Of these 768 patients, 168 had been evaluated by both conventional respiratory cytologic methods (examination of sputum and bronchial material) and with FNA biopsy cytology. In 9 patients (5.4%), only conventional respiratory cytologic specimens were conclusively diagnostic for cancer. In 122 patients (72.6%), only the FNA biopsy specimen was diagnostic. In 37 patients (22.0%), both conventional respiratory specimens and FNA specimens yielded a definitive lung cancer diagnosis. The FNA specimen was the only positive cytologic specimen in 90.2% of large cell undifferentiated carcinomas, 79.5% of adenocarcinomas, 66.7% of small cell undifferentiated carcinomas and 58.2% of squamous cell carcinomas. In 26.5% of the patients, a diagnosis of cancer could have been established on conventional cytologic specimens, without the necessity of proceeding to percutaneous FNA biopsy. From this study, it is concluded that the techniques of conventional respiratory cytology and FNA biopsy cytology are complementary in the diagnosis of lung cancer. While the percentage of lung cancers diagnosed by FNA biopsy cytology alone is much greater than that obtained by conventional respiratory cytology alone, more than one-fourth of these cancers could be detected by the less invasive techniques of sputum collection and bronchoscopy.     

Strategies for analysing missing item response data with an application to lung cancer

Missing data problems persist in many scientific investigations. Although various strategies for analyzing missing data have been proposed, they are mainly limited to data on continuous measurements. In this paper, we focus on implementing some of the available strategies to analyze item response data. In particular, we investigate the effects of popular missing data methods on various missing data mechanisms. We examine large sample behaviors of estimators in a simulation study that evaluates and compares their performance. We use data from a quality of life study with lung cancer patients to illustrate the utility of these methods.     

DNA Methylation Markers in Lung Cancer

Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.     

Comparison of elastolytic activity in lung lavage from current, ex- and non-smokers

Cigarette smokers have an increased risk of developing a wide variety of lung diseases compared to non-smokers, and there have been many studies of the possible biochemical changes underlying this increased susceptibility. However, although epidemiological and physiological studies have shown that in the ex-smoker, the risk of smoking-related lung diseases falls between that of current and non-smokers, the biochemical and cellular mechanisms responsible for this intermediate status have not been investigated. In the present study, therefore, the extracellular elastolytic activities in lung lavage fluid from current, ex- and non-smokers have been compared. Elastolytic enzyme activity was investigated, since it is significantly elevated in lung lavage from smokers, and because it has been implicated in the development of pulmonary emphysema. In the subjects studied, extracellular elastolytic activities in lung lavage from ex-smokers were intermediate between those from current and non-smokers. There was no correlation between the time of abstinence from smoking, or the number of pack-years smoked and the extracellular elastolytic activities in ex-smokers' lung lavage. Elastolytic activity may remain elevated in ex-smokers' lungs for a number of reasons, including the persistence of particulate matter which may activate phagocytic cells on the lung surface. The possible significance of the raised elastolytic activity remains to be fully determined.     

Prostaglandin Production by Mast Cells and the Regulation of Airway Smooth Muscle Responses

The role of mast cell activation and the generation of mediator release are important factors in determining the reactivity of lung tissue during allergic reactions and asthma. In this article, the advantages of our procedure for isolating mast cells from lung tissue over other methods are discussed. Our studies have demonstrated the importance of cross talk between mast cells and other cell types that also release mediators of bronchoconstriction during activation, thus amplifying the response. In addition, it has been found that inositol phospholipid turnover in response to various mast cell mediators is enhanced in hyperresponsive lung tissue. The consequences to the contractility of the tissue of such alterations in the cellular signaling system in lung tissue are discussed.     

Electroporation of the vasculature and the lung

Electroporation has proven to be a highly effective technique for the in vivo delivery of genes to a number of solid tissues. In most of the reported methods, DNA is injected into the target tissue and electrodes are placed directly on or in the tissue for application of the electric field. While this works well for solid tissues, there are many tissues and organs that are not amenable to such an approach. In this review I will focus on the development of electroporation protocols for two such tissues: the vasculature and the lung. Several methods for in vivo electroporation of the vasculature have been developed in recent years that deliver DNA to vessel segments from either the inside or outside of the vessel. The advantages and disadvantages of each are discussed, as are the applications for which they have been used. In more recent work, our laboratory has developed a novel method to deliver genes to the rodent lung that results in high level, uniform, gene expression throughout all cell types of the lung. Most importantly, this technique is safe, and causes no inflammatory response or alterations in normal physiology of the organs. Taken together, these studies demonstrate the utility of electroporation for gene transfer to non injectible tissues.     

Functional lung imaging with synchrotron radiation: Methods and preclinical applications

Many lung disease processes are characterized by structural and functional heterogeneity that is not directly appreciable with traditional physiological measurements. Experimental methods and lung function modeling to study regional lung function are crucial for better understanding of disease mechanisms and for targeting treatment. Synchrotron radiation offers useful properties to this end: coherence, utilized in phase-contrast imaging, and high flux and a wide energy spectrum which allow the selection of very narrow energy bands of radiation, thus allowing imaging at very specific energies. K-edge subtraction imaging (KES) has thus been developed at synchrotrons for both human and small animal imaging. The unique properties of synchrotron radiation extend X-ray computed tomography (CT) capabilities to quantitatively assess lung morphology, and also to map regional lung ventilation, perfusion, inflammation and biomechanical properties, with microscopic spatial resolution. Four-dimensional imaging, allows the investigation of the dynamics of regional lung functional parameters simultaneously with structural deformation of the lung as a function of time. This review summarizes synchrotron radiation imaging methods and overviews examples of its application in the study of disease mechanisms in preclinical animal models, as well as the potential for clinical translation both through the knowledge gained using these techniques and transfer of imaging technology to laboratory X-ray sources.     

A novel method to isolate and map endothelial membrane proteins from pulmonary vasculature

Vascular endothelium has attracted extensive attention due to its important role in many physiological and pathological processes. Many methods have been developed to study the components and their functions in vascular endothelium. Here we report a novel approach to investigate vascular endothelium using normal rat lungs as the model. We perfused lung vascular beds with sulfosuccinimidyl-6-(biotinamido) hexanoate, a biotin analog, to label endothelial membrane proteins. The biotinylated proteins were isolated from lung homogenate with immobilized monomeric avidin and confirmed to be highly pure endothelial membrane proteins with little contamination of intracellular proteins. These biotinylated proteins were used as immunogens for development of monoclonal antibodies. Indeed, newly generated monoclonal antibodies have revealed different expression patterns of proteins across tissues. Some proteins were found highly specifically expressed to capillary vessels of pulmonary vasculature. This method has also been proven useful for investigating vasculature of other organs, as this study explored. vascular endothelium; biotinylation; tissue specific; monoclonal antibodies     

Physiological imaging of the lung: single-photon-emission computed tomography (SPECT).

Emission tomography provides three-dimensional, quantitative images of the distribution of radiotracers used to mark physiological, metabolic, or pathological processes. Quantitative single photon emission computed tomography (SPECT) requires correction for the image-degrading effects due to photon attenuation and scatter. Phantom experiments have shown that radioactive concentrations can be assessed within some percentage of the true value when relevant corrections are applied. SPECT is widely spread, and radiotracers are available that are easy to use and comparably inexpensive. Compared with other methods, SPECT suffers from a lower spatial resolution, and the time required for image acquisition is longer than for some alternative methods. In contrast to some other methods, SPECT allows simultaneous imaging of more than one process, e.g., both regional blood flow and ventilation, for the whole lung. SPECT has been used to explore the influence of posture and clinical interventions on the spatial distribution of lung blood flow and ventilation. Lung blood flow is typically imaged using macroaggregates of albumin. Both radioactive gases and particulate aerosols labeled with radioactivity have been used for imaging of regional ventilation. However, all radiotracers are not equally suited for quantitative measurements; all have specific advantages and limitations. With SPECT, both blood flow and ventilation can be marked with radiotracers that remain fixed in the lung tissue, which allows tracer administration during conditions different from those at image registration. All SPECT methods have specific features that result from the used radiotracer, the manner in which it is administered, and how images are registered and analyzed.     

Peptides from the Variable Region of Specific Antibodies Are Shared among Lung Cancer Patients

Late diagnosis of lung cancer is still the main reason for high mortality rates in lung cancer. Lung cancer is a heterogeneous disease which induces an immune response to different tumor antigens. Several methods for searching autoantibodies have been described that are based on known purified antigen panels. The aim of our study is to find evidence that parts of the antigen-binding-domain of antibodies are shared among lung cancer patients. This was investigated by a novel approach based on sequencing antigen-binding-fragments (Fab) of immunoglobulins using proteomic techniques without the need of previously known antigen panels. From serum of 93 participants of the NELSON trial IgG was isolated and subsequently digested into Fab and Fc. Fab was purified from the digested mixture by SDS-PAGE. The Fab containing gel-bands were excised, tryptic digested and measured on a nano-LC-Orbitrap-Mass-spectrometry system. Multivariate analysis of the mass spectrometry data by linear canonical discriminant analysis combined with stepwise logistic regression resulted in a 12-antibody-peptide model which was able to distinguish lung cancer patients from controls in a high risk population with a sensitivity of 84% and specificity of 90%. With our Fab-purification combined Orbitrap-mass-spectrometry approach, we found peptides from the variable-parts of antibodies which are shared among lung cancer patients.     

ERCC1, XPD and RAI mRNA levels in lymphocytes are not associated with lung cancer risk in a prospective study of Danes

Low DNA-repair capacity has been associated with increased risk of several types of cancer. mRNA levels of the nucleotide excision repair genes ERCC1 and XPD have been shown to correlate with the DNA-repair capacity. Likewise, mRNA levels of several DNA-repair genes including ERCC1 have been shown to be lower in lymphocytes from patients with lung cancer and head and neck cancer compared with healthy persons. In these studies, the low DNA-repair gene expression levels could be either a risk factor for disease or a consequence of the same. In this nested case-cohort study, which to our knowledge, is the first prospective study of DNA-repair gene mRNA levels as predictors of lung cancer, we have investigated the occurrence of lung cancer in relation to the mRNA level of the two DNA-repair genes ERCC1 and XPD and the NF kappaB inhibitor RAI in blood samples prior to disease. Among 54,220 members of a Danish prospective cohort study, 265 lung cancer cases were identified and a sub-cohort comprising 272 individuals was used for comparison. The expression levels of the three adjacent genes were found to be highly inter-correlated, to be higher in women compared to men and to be lower in older individuals. The incidence rate ratios for lung cancer in association with one log-unit increase (natural logarithm) in mRNA levels were 1.12 (CI=0.89-1.41) for ERCC1, 1.00 (CI=0.83-1.21) for XPD and 1.25 (0.89-1.74) for RAI. In conclusion, this study indicated no association between mRNA expression of the DNA-repair genes ERCC1 and XPD and risk of subsequent development of lung cancer.     

Lung specific developmental expression of the Xenopus laevis surfactant protein C and B genes

Efforts to characterize the mechanisms underlying early lung development have been confounded by the absence of a model that permits study of lung development prior to the onset of endodermal differentiation. Since Xenopus laevis development occurs in an extrauterine environment, we sought to determine whether the classical molecular markers of lung development and function, surfactant protein genes, are expressed in X. laevis. Surfactant protein C (SP-C) is a specific marker for lung development, expressed early in development and exclusively in the lung. Surfactant protein B (SP-B) expression is essential for life, as its absence results in neonatal death in mice and gene mutations have been associated with neonatal respiratory failure in humans. Here, we report the cloning of the first non-mammalian SP-C and SP-B genes (termed xSP-C and xSP-B) using the Xenopus model. The processed mature translated regions of both xSP-C and xSP-B have high homology with both human and mouse genes. xSP-C and xSP-B are both expressed throughout the lung of the X. laevis swimming tadpoles soon after the initiation of lung development as assessed by RT-PCR and whole mount in situ hybridization. The temporal expression patterns of xSP-C and xSP-B are consistent with the expression patterns in mammalian models of lung development. In both the tadpole and the adult X. laevis, xSP-C and xSP-B are expressed only in lung. Knowledge of the sequence and expression pattern of these two surfactant proteins in Xenopus might allow for use of this organism to study early lung development.     

Streptococcus pneumoniae induced c-Jun-N-terminal kinase- and AP-1 -dependent IL-8 release by lung epithelial BEAS-2B cells

Background

Chronic lung diseases are a major issue in public health. A serial pulmonary assessment using imaging techniques free of ionizing radiation and which provides early information on local function impairment would therefore be a considerably important development. Magnetic resonance imaging (MRI) is a powerful tool for the static and dynamic imaging of many organs. Its application in lung imaging however, has been limited due to the low water content of the lung and the artefacts evident at air-tissue interfaces. Many attempts have been made to visualize local ventilation using the inhalation of hyperpolarized gases or gadolinium aerosol responding to MRI. None of these methods are applicable for broad clinical use as they require specific equipment.

Methods

We have shown previously that low-field MRI can be used for static imaging of the lung. Here we show that mathematical processing of data derived from serial MRI scans during the respiratory cycle produces good quality images of local ventilation without any contrast agent. A phantom study and investigations in 85 patients were performed.

Results

The phantom study proved our theoretical considerations. In 99 patient investigations good correlation (r = 0.8; p ≤ 0.001) was seen for pulmonary function tests and MR ventilation measurements. Small ventilation defects were visualized.

Conclusion

With this method, ventilation defects can be diagnosed long before any imaging or pulmonary function test will indicate disease. This surprisingly simple approach could easily be incorporated in clinical routine and may be a breakthrough for lung imaging and functional assessment.     

An Improved Method for Rapid Intubation of the Trachea in Mice

Despite some anatomical and physiological differences, mouse models continue to be an essential tool for studying human lung disease. Bleomycin toxicity is a commonly used model to study both acute lung injury and fibrosis, and multiple methods have been developed for administering bleomycin (and other toxic agents) into the lungs. However, many of these approaches, such as transtracheal instillation, have inherent drawbacks, including the need for strong anesthetics and survival surgery. This paper reports a quick, reproducible method of intratracheal intubation that involves mild inhaled anesthesia, visualization of the trachea, and the use of a surrogate spirometer to confirm exposure. As a proof of concept, 8-12 week old C57BL/6 mice were administered either 2.0 U/kg of bleomycin or an equivalent volume of PBS, and both damage and fibrotic endpoints were measured post-exposure. This procedure allows researchers to treat a large cohort of mice in a relatively short period with little expense and minimal post-procedure care.