Role of ethambutol and rifampicin in the treatment of Mycobacterium avium complex pulmonary disease.

BACKGROUND: A three-drug regimen (macrolide, ethambutol, and rifampicin) is recommended for the treatment of Mycobacterium avium complex pulmonary disease (MAC-PD). Although macrolide has proven efficacy, the role of ethambutol and rifampicin in patients without acquired immune deficiency syndrome is not proven with clinical studies. We aimed to clarify the roles of ethambutol and rifampicin in the treatment of MAC-PD. METHODS: Patients treated for MAC-PD between March 1st, 2009 and October 31st, 2018 were reviewed retrospectively. Rates of culture conversion, microbiological cure, treatment failure, and recurrence were compared according to the maintenance (≥6 months) of ethambutol or rifampicin with macrolide. RESULTS: Among the 237 patients, 122 (51.5%) maintained ethambutol and rifampicin with macrolide, 58 (24.5%) maintained ethambutol and macrolide, 32 (13.5%) maintained rifampicin and macrolide, and 25 (10.6%) maintained macrolide only. Culture conversion was reached for 190/237 (80.2%) patients and microbiological cure was achieved for 129/177 (72.9%) who completed the treatment. Treatment failure despite ≥12 months of treatment was observed in 66/204 (32.4%), and recurrence was identified in 16/129 (12.4%) who achieved microbiological cure. Compared with maintenance of macrolide only, maintenance of ethambutol, rifampicin or both with macrolide were associated with higher odds of culture conversion [odds ratio (OR), 95% confidence interval (CI): 18.06, 3.67-88.92; 15.82, 2.38-105.33; and 17.12, 3.93-74.60, respectively]. Higher odds of microbiological cure were associated with maintenance of both ethambutol and rifampicin with macrolide (OR, 95% CI: 5.74, 1.54-21.42) and macrolide and ethambutol (OR, 95% CI: 5.12, 1.72-15.24) but not macrolide and rifampicin. Maintenance of both ethambutol and rifampicin with macrolide was associated with lower odds of treatment failure (OR, 95% CI: 0.09, 0.01-0.53) compared with macrolide only, while maintenance of one of these with macrolide was not. Maintenance of both ethambutol and rifampicin or one of these with macrolide did not decrease the probability of recurrence when compared with macrolide only. CONCLUSIONS: Maintenance (≥6 months) of ethambutol and rifampicin with macrolide was associated with the most favorable treatment outcomes among patients with MAC-PD. Given the association between ongoing ethambutol use and microbiological cure, clinicians should maintain ethambutol unless definite adverse events develop.

Extracellular vesicle-based EGFR genotyping in bronchoalveolar lavage fluid from treatment-naive non-small cell lung cancer patients.

BACKGROUND: Extracellular vesicles (EV) have been proven to contain double-stranded DNA reflecting the mutational status of the parental tumor cells in non-small cell lung cancer (NSCLC), which can be translated into clinically useful EV-based liquid biopsy for Epidermal growth factor receptor (EGFR) genotyping using bronchoalveolar lavage fluid (BALF) obtained from tumor site. METHODS: Patients subjected for an initial lung cancer work-up underwent bronchoscopy and BALF was obtained from tumor site. After isolating EVs from BALF by ultracentrifugation, EV-derived DNA (EV DNA) was extracted for subsequent EGFR genotyping performed through peptide nucleic acid (PNA)-mediated Real-Time PCR. The sensitivity, specificity, and concordance rate of BALF EV-based EGFR genotyping were calculated in comparison to tissue genotyping. RESULTS: The average sensitivity and specificity of BALF EV-based EGFR genotyping were 76% and 87%, respectively, while the sensitivity significantly increased as the stage progressed. Especially, in stage IV, BALF EV-based EGFR typing identified all tissue-proven EGFR mutant cases (n=31) and detected 6 additional mutant cases. The concordance rate was 79% in stage I, 100% in stage II, 74% in stage III, and 92% in stage IV. As TNM stage advanced, especially in the presence of metastasis, concordance rate significantly increased (P<0.05). CONCLUSIONS: The use of BALF for the collection of EV DNA in lung cancer patients resulted in a highly accurate diagnosis. The establishment of a fast and reliable method to identify target genes using EV DNA illustrated that it can overcome the problems of low sensitivity and instability in using cell-free DNA (cfDNA).

Liquid biopsy using the supernatant of a pleural effusion for EGFR genotyping in pulmonary adenocarcinoma patients: a comparison between cell-free DNA and extracellular vesicle-derived DNA.

BACKGROUND: EGFR genotyping in pulmonary adenocarcinoma patients who develop pleural effusions is mostly performed using cytology or cell block slides with low sensitivity. Liquid biopsy using the supernatant of pleural effusions may be more effective because they contain many components released by cancer cells. Extracellular vesicles (EVs) are known to carry oncogenic double-stranded DNA that is considered a notable biomarker. Here, we investigate the efficiency of liquid biopsy using cell-free DNA (cfDNA) and extracellular vesicle-derived DNA (EV-derived DNA) from the supernatant of pleural effusions for EGFR genotyping in patients with pulmonary adenocarcinoma. METHODS: Fifty pleural effusion samples from patients with pulmonary adenocarcinoma were evaluated. The supernatant, after removing the cell pellet by centrifugation, was used for liquid biopsy, and EVs were isolated from the pleural effusion by ultracentrifugation. EV-derived DNA and cfDNA were extracted separately, and EGFR genotyping was performed by the PNA clamping method. RESULTS: Among 32 patients who were EGFR-tyrosine kinase inhibitor (TKI) naïve with a known tissue EGFR genotype, liquid biopsy using EV-derived DNA from the pleural effusion supernatant showed 100% matching results with tissue EGFR genotyping in 19 EGFR mutant cases and detected three additional EGFR mutations in patients with wild-type (WT) tissue. Liquid biopsy using cfDNA from pleural effusion supernatants missed two cases of tissue-based EGFR mutations and found two additional EGFR mutation cases. In 18 patients who acquired resistance to EGFR-TKI, EGFR genotyping using EV-derived DNA from the pleural effusion supernatant detected the T790 M mutation in 13 of 18 (72.2%) patients, and this mutation was detected in 11 (61.1%) patients using cfDNA. By contrast, only three patients were found to present the T790 M mutation when using cell block or cytology slides. CONCLUSIONS: Liquid biopsy using the supernatant of pleural effusions showed significantly improved results for EGFR genotyping compared to those using conventional cell block or cytology samples. Liquid biopsy using EV-derived DNA is promising for EGFR genotyping, including T790 M detection in pulmonary adenocarcinoma patients who develop pleural effusions.

Cumulative smoking dose affects the clinical outcomes of EGFR-mutated lung adenocarcinoma patients treated with EGFR-TKIs: a retrospective study.

BACKGROUND: Although lung adenocarcinoma with activating epidermal growth factor receptor (EGFR) mutations is common in never smokers, one-third of the patients are ever-smokers. We aimed to investigate the effect of cumulative smoking dose(CSD) on clinical outcomes, including progression-free survival (PFS) and overall survival (OS), in patients with EGFR-mutated lung adenocarcinoma receiving EGFR-tyrosine kinase inhibitors (TKIs). METHODS: We retrospectively analyzed 142 patients with EGFR-mutation positive advanced or recurrent lung adenocarcinoma who were administered gefitinib, erlotinib, afatinib, and osimertinib. These patients were classified based on their CSD as never smokers, light smokers (≤10 pack-years [PYs]), moderate smokers (11-30 PYs), and heavy smokers (> 30 PYs). PFS and OS were analyzed according to smoking subgroups via Kaplan-Meier curves. RESULTS: Among the 142 patients, 91 (64.1%), 12 (8.5%), 22 (15.5%), and 17 (12%) were never, light, moderate, and heavy smokers, respectively. CSD was inversely associated with median PFS in a statistically significant dose-dependent manner (11.8 months (mo), 11.0 mo, 7.4 mo, and 3.9 mo; p < 0.001). Statistically significant negative association was observed between CSD and median OS (33.6 mo, 26.3 mo, 20 mo, and 8.9 mo; p < 0.001). In the multivariate analysis adjusted for age, sex, performance status, stage, and timing of EGFR-TKIs, CSD was an independent predictive factor for disease progression (hazard ratio [HR], 4.00; 95% confidence interval [CI], 1.95-8.23; p = 0.012) and OS (HR, 3.9; 95% CI, 1.84-8.28; p < 0.001). CONCLUSION: CSD is an important predictive and prognostic factor in patients with EGFR-mutated lung adenocarcinoma, and associated smoking-related gene signatures might affect the outcomes.

A Deep Belief Network and Dempster-Shafer-Based Multiclassifier for the Pathology Stage of Prostate Cancer.

Object: Pathologic prediction of prostate cancer can be made by predicting the patient's prostate metastasis prior to surgery based on biopsy information. Because biopsy variables associated with pathology have uncertainty regarding individual patient differences, a method for classification according to these variables is needed. Method: We propose a deep belief network and Dempster-Shafer- (DBN-DS-) based multiclassifier for the pathologic prediction of prostate cancer. The DBN-DS learns prostate-specific antigen (PSA), Gleason score, and clinical T stage variable information using three DBNs. Uncertainty regarding the predicted output was removed from the DBN and combined with information from DS to make a correct decision. Result: The new method was validated on pathology data from 6342 patients with prostate cancer. The pathology stages consisted of organ-confined disease (OCD; 3892 patients) and non-organ-confined disease (NOCD; 2453 patients). The results showed that the accuracy of the proposed DBN-DS was 81.27%, which is higher than the 64.14% of the Partin table. Conclusion: The proposed DBN-DS is more effective than other methods in predicting pathology stage. The performance is high because of the linear combination using the results of pathology-related features. The proposed method may be effective in decision support for prostate cancer treatment.

Extracellular vesicle-derived DNA for performing EGFR genotyping of NSCLC patients.

Tumor cells shed an abundance of extracellular vesicles (EVs) to body fluids containing bioactive molecules including DNA, RNA, and protein. Investigations in the field of tumor-derived EVs open a new horizon in understanding cancer biology and its potential as cancer biomarkers as well as platforms for personalized medicine. This study demonstrates that successfully isolated EVs from plasma and bronchoalveolar lavage fluid (BALF) of non-small cell lung cancer (NSCLC) patients contain DNA that can be used for EGFR genotyping through liquid biopsy. In both plasma and BALF samples, liquid biopsy results using EV DNA show higher accordance with conventional tissue biopsy compared to the liquid biopsy of cfDNA. Especially, liquid biopsy with BALF EV DNA is tissue-specific and extremely sensitive compared to using cfDNA. Furthermore, use of BALF EV DNA also demonstrates higher efficiency in comparison to tissue rebiopsy for detecting p.T790 M mutation in the patients who developed resistance to EGFR-TKIs. These finding demonstrate possibility of liquid biopsy using EV DNA potentially replacing the current diagnostic methods for more accurate, cheaper, and faster results.

Implication of species change of Nontuberculous Mycobacteria during or after treatment.

BACKGROUND: Co-existence or subsequent isolation of multiple nontuberculous mycobacteria (NTM) species in same patient has been reported. However, clinical significance of these observations is unclear. The aim of this study was to determine clinical implications of changes of NTM species during or after treatment in patients with NTM lung disease. METHODS: Patients with NTM lung disease, who experienced changes of NTM species during treatment or within 2 years of treatment completion between January 1, 2009 and December 31, 2015, were included in the analysis. Demographic, clinical, microbiological, and radiographic data were reviewed and analyzed. RESULTS: During the study period, 473 patients were newly diagnosed with NTM lung disease. Treatment was started in 164 patients (34.6%). Among these 164 patients, 16 experienced changes of NTM species during or within 2 years of treatment completion. Seven showed changes from M. avium complex (MAC) to M. abscessus subspecies abscessus (MAA) and five patients displayed changes from M. abscessus subspecies massiliense (MAM) to MAC. With isolation of new NTM species, 6 out of 7 patients with change from MAC to MAA reported worsening of symptoms, whereas none of the five patients with change from MAM to MAC reported worsening of symptoms. All MAA isolated during or after treatment for MAC lung diseases showed inducible resistance to clarithromycin. CONCLUSIONS: Change of NTM species may occur during or after treatment for NTM lung disease. Especially, changes from MAC to MAA is accompanied by symptomatic and radiographic worsening as well as inducible resistance to clarithromycin.

A Performance Comparison on the Machine Learning Classifiers in Predictive Pathology Staging of Prostate Cancer.

This study objectives to investigate a range of Partin table and several machine learning methods for pathological stage prediction and assess them with respect to their predictive model performance based on Koreans data. The data was used SPCDB and gathered records from 944 patients treated with tertiary hospital. Partin table has low accuracy (65.68%) when applied on SPCDB dataset for comparison on patients with OCD NOCD conditions. SVM (75%) represents a promising alternative to Partin table from which pathology staging can benefit.

Clinical features of lung adenocarcinomas with epidermal growth factor receptor mutations and miliary disseminated carcinomatosis.

BACKGROUND: We have occasionally encountered advanced lung cancer patients with disseminated carcinomatosis throughout the body and/or within the lung. This study investigated the clinical characteristics and outcomes of advanced lung adenocarcinoma patients with miliary disseminated carcinomatosis. METHODS: Patients with adenocarcinomas harboring epidermal growth factor receptor (EGFR) mutations who presented with miliary disseminated carcinomatosis (either intrapulmonary or distant site) were enrolled in the study. Clinical characteristics, treatment responses, and survival outcomes were collected from medical records. RESULTS: The most frequent EGFR mutation was an in-frame deletion in exon 19 (n = 44, 68.8%). Arginine substitution of leucine 858 in exon 21 and alanine substitution of glycine 719 in exon 18 were detected in 19 patients (29.7%) and one patient (1.6%), respectively. Patients with miliary disseminated carcinomatosis tended to be female and non-smokers. They expressed the E19 deletion more frequently than patients without miliary dissemination and had shorter progression-free survival times in response to EGFR tyrosine kinase inhibitors (9.7 vs. 12.8 months, P = 0.003) and poorer overall survival (15.9 vs. 29.0 months, P = 0.077). Multivariate analyses revealed that metabolic tumor volume correlated with shorter overall survival time. CONCLUSIONS: Our data indicate that lung adenocarcinoma patients with miliary dissemination have relatively shorter survival times than those without miliary dissemination. The poor prognosis of patients with miliary dissemination may reflect a high tumor burden, as represented by metabolic tumor volume.

Sudden hearing loss due to internal auditory canal metastasis of Her2-positive gastric cancer: A case report.

Internal auditory canal (IAC) metastasis due to leptomeningeal carcinomatosis (LMC) from gastric cancer (GC) has rarely been reported. Early manifestation of symptoms, such as hearing loss, vertigo and facial paralysis, in cases of IAC metastasis due to LMC may facilitate the early detection of brain metastasis. To the best of our knowledge, the present study is the first to report IAC metastasis due to LMC in human epidermal growth factor receptor 2 (Her2)-positive GC. This study reports a case of an Her2-positive GC patient with LMC including IAC metastasis, who presented with acute sensorineural hearing loss, ipsilateral facial paralysis and vertigo during trastuzumab containing chemotherapy. The current study also discusses the early diagnosis and management of this complicated condition, demonstrating that clinical suspicion is key for a prompt diagnosis and proper management of LMC including IAC metastasis in Her2-positive GC.

Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil.

The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.

Bilateral Ovarian Metastases from ALK Rearranged Non-Small Cell Lung Cancer.

Anaplastic lymphoma kinase (ALK) rearrangement, is a kind of driver mutation, accounts for 3%-5% of non-small cell lung cancer (NSCLC). NSCLC patients harboring ALK fusion genes have distinct clinical features and good response to ALK inhibitors. Metastasis from lung cancer to the ovary has rarely been known. We report a case of a 54-year-old woman with bilateral ovarian metastases from ALK rearranged NSCLC. She underwent bilateral salpingo-oophorectomy for ovary masses, which were progressed after cytotoxic chemotherapy although primary lung mass was decreased. Histopathological examination of the ovary tumor showed characteristic adenocarcinoma patterns of the lung and ALK rearrangement.

Effect of calcination temperature on the photocatalytic properties of electrospun TiO2 nanofibers.

In this study, TiO2 nanofibers with a high aspect ratio and a large specific surface area were synthesized using the electrospinning technique, and the effect of calcination temperature on their crystal structure, diameter, specific surface area and photocatalytic activity was systematically investigated. The electrospun, as-prepared PVP/TTIP nanofibers were several tens of micrometers in length with a diameter of 74 nm. TiO2 nanofibers with an average diameter of 50 nm were prepared after calcination at various temperatures. The calcination temperature significantly influenced the photocatalytic and material properties of TiO2 including grain size and specific surface area. When compared to other nanostructured TiO2 materials, such as commercial TiO2 nanoparticles (P25, Degussa), the TiO2 nanofibers exhibited greater photocatalytic activity for the degradation of acetaldehyde and ammonia.

Passive air monitoring of PCBs and PCNs across East Asia: a comprehensive congener evaluation for source characterization.

A comprehensive congener specific evaluation of polychlorinated biphenyls (PCBs) and polychlorinated naphthalenes (PCNs) in the atmosphere was conducted across East Asia in spring 2008, applying polyurethane foam (PUF) disk passive air sampler (PAS) as monitoring device. Mean concentrations derived for Japan, China and Korea were 184 ± 24, 1100 ± 118, and 156 ± 20 pg m(-3) for ∑(202) PCBs, and 9.5 ± 1.5, 61 ± 6, and 16 ± 2.4 pg m(-3) for ∑(63) PCNs, respectively. Relative to reported data from 2004, the present results suggest that air PCBs concentrations have not changed much in Japan and Korea, while it has increased by one order of magnitude in China. From principal component analysis, combustion emerged highly culpable in contemporary emissions of both PCBs and PCNs across the East Asian sub-region. Another factor derived as important to air PCBs was re-emissions/volatilization. Signals from PCBs formulations were also picked, but their general importance was virtually consigned to the re-emissions/volatilization tendencies. On the contrary, counterpart PCNs formulations did not appear to contribute much to air PCNs.

Molecular proteomics imaging of tumor interfaces by mass spectrometry.

The specific molecular profiles of ovarian cancer interface zones (IZ), the region between tumors and normal tissues, were evaluated using a new method involving matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS). We analyzed three ovarian serous carcinomas using MALDI-IMS. Principal component analysis (PCA) was used to evaluate the quality of tissue spatial features based on MALDI-IMS, and for analysis of large data sets of MALDI-IMS. Two-dimensional gel electrophoresis and fluorescence microscopy were used to verify interface-specific proteins. Unique profiles were identified for the tumors, the normal zone, and the IZ. Through MALDI analysis, two interface-specific proteins, plastin 2 and peroxiredoxin 1 (PRDX 1), were identified as differentially regulated between zones. Fluorescence microscopy revealed high expression levels of plastin 2 and PRDX 1 along the IZ of ovarian tumors. This comparative proteomics study using tissue MALDI-IMS suggested that the IZ is different from the adjacent tumor and normal zones, and that plastin 2 and PRDX 1 may be interface markers specific to ovarian tumors.

Neural network-based analysis of thiol proteomics data in identifying potential selenium targets.

Generation of a monomethylated selenium metabolite is critical for the anticancer activity of selenium. Because of its strong nucleophilicity, the metabolite can react directly with protein thiols to cause redox modification. Here, we report a neural network-based analysis to identify potential selenium targets. A reactive thiol specific reagent, BIAM, was used to monitor thiol proteome changes on 2D gel. We constructed a dynamic model and evaluated the relative importance of proteins mediating the cellular responses to selenium. Information from this study will provide new clues to unravel mechanisms of anticancer action of selenium. High impact selenium targets could also serve as biomarkers to gauge the efficacy of selenium chemoprevention.

Proteasomal ATPase-associated factor 1 negatively regulates proteasome activity by interacting with proteasomal ATPases.

The 26S proteasome, composed of the 20S core and the 19S regulatory complex, plays a central role in ubiquitin-dependent proteolysis by catalyzing degradation of polyubiquitinated proteins. In a search for proteins involved in regulation of the proteasome, we affinity purified the 19S regulatory complex from HeLa cells and identified a novel protein of 43 kDa in size as an associated protein. Immunoprecipitation analyses suggested that this protein specifically interacted with the proteasomal ATPases. Hence the protein was named proteasomal ATPase-associated factor 1 (PAAF1). Immunoaffinity purification of PAAF1 confirmed its interaction with the 19S regulatory complex and further showed that the 19S regulatory complex bound with PAAF1 was not stably associated with the 20S core. Overexpression of PAAF1 in HeLa cells decreased the level of the 20S core associated with the 19S complex in a dose-dependent fashion, suggesting that PAAF1 binding to proteasomal ATPases inhibited the assembly of the 26S proteasome. Proteasomal degradation assays using reporters based on green fluorescent protein revealed that overexpression of PAAF1 inhibited the proteasome activity in vivo. Furthermore, the suppression of PAAF1 expression that is mediated by small inhibitory RNA enhanced the proteasome activity. These results suggest that PAAF1 functions as a negative regulator of the proteasome by controlling the assembly/disassembly of the proteasome.

Mass spectrometric analysis of tumor necrosis factor receptor-associated factor 1 ubiquitination mediated by cellular inhibitor of apoptosis 2.

Signaling complexes formed on tumor necrosis factor receptor 2 (TNF-R2) contain adaptor proteins TNF-R-associated factors (TRAFs) 1 and 2, and cellular inhibitors of apoptosis (cIAPs) 1 and 2 which function as regulators of programmed cell death. TRAF2, cIAP1 and cIAP2 all have RING finger domains known to possess E3 ubiquitin ligase activity, implying that ubiquitination may play an important role in the TNF signaling pathway. In this report, we have shown that cIAP2 specifically mediated ubiquitination and proteasome-dependent degradation of TRAF1. To identify the sites for cIAP2-mediated ubiquitination of TRAF1, we used high pressure liquid chromatography coupled with tandem mass spectrometry. Lys185 and Lys193 of TRAF1 were found to be modified with ubiquitin chains. Mutation of Lys185 and Lys193 to Arg almost completely blocked cIAP2-mediated ubiquitination of TRAF1, indicating that they are the major, if not the only, sites of TRAF1 ubiquitination. Our data suggest that cIAP2 may regulate the turnover of TRAF1 by adding polyubiquitin chains on Lys185 or Lys193 following its recruitment to TNF-R signaling complexes.