PUREE: accurate pan-cancer tumor purity estimation from gene expression data.

Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable.

Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma.

Angiosarcomas are rare, clinically aggressive tumors with limited treatment options and a dismal prognosis. We analyzed angiosarcomas from 68 patients, integrating information from multiomic sequencing, NanoString immuno-oncology profiling, and multiplex immunohistochemistry and immunofluorescence for tumor-infiltrating immune cells. Through whole-genome sequencing (n = 18), 50% of the cutaneous head and neck angiosarcomas exhibited higher tumor mutation burden (TMB) and UV mutational signatures; others were mutationally quiet and non-UV driven. NanoString profiling revealed 3 distinct patient clusters represented by lack (clusters 1 and 2) or enrichment (cluster 3) of immune-related signaling and immune cells. Neutrophils (CD15+), macrophages (CD68+), cytotoxic T cells (CD8+), Tregs (FOXP3+), and PD-L1+ cells were enriched in cluster 3 relative to clusters 2 and 1. Likewise, tumor inflammation signature (TIS) scores were highest in cluster 3 (7.54 vs. 6.71 vs. 5.75, respectively; P < 0.0001). Head and neck angiosarcomas were predominant in clusters 1 and 3, providing the rationale for checkpoint immunotherapy, especially in the latter subgroup with both high TMB and TIS scores. Cluster 2 was enriched for secondary angiosarcomas and exhibited higher expression of DNMT1, BRD3/4, MYC, HRAS, and PDGFRB, in keeping with the upregulation of epigenetic and oncogenic signaling pathways amenable to targeted therapies. Molecular and immunological dissection of angiosarcomas may provide insights into opportunities for precision medicine.

Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line.

Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner.

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

A Case of Tracheal Hamartoma Treated with Endoscopic Mucosal Resection / 계명의대학술지

A 77-year-old male patient was hospitalized due to dyspnea and cough. At chest auscultation, Rhonchi was heard from both lung fields. The chest computed tomography (CT) observed nodular lesions within mid-trachea. Bronchoscope observed salient mass from the membranous portion in the mid-trachea, and after taking a biopsy, it was diagnosed as hamartoma. Tracheal hamartoma is a rare benign tumor of lung. Similar way to the endoscopic mucosal resection (EMR), we did endoscopic resection of tracheal hamartoma. We report a case of tracheal hamartoma treated with Endoscopic mucosal resection via flexible bronchoscopy.

Reference equations for the six-minute walk distance in healthy korean adults, aged 22-59 years.

BACKGROUND: The six-minute walk test has been widely used in people with chronic cardiopulmonary disorders as an outcome assessment with regards to therapeutic or prognostic determinants. This study was undertaken to determine the six-minute walk distance (6MWD) in a sample of healthy Koreans and to create a reference equation. We also compared the 6MWD of our cohort with previously published equations. METHODS: Two hundred fifty-nine healthy subjects (95 males) aged 22-59 years performed two walking tests using a standardized protocol. 6MWD was defined as the greatest distance achieved from the two tests. The effect of anthropometrics on the 6MWD was also investigated. RESULTS: The average 6MWD was 598.5±57.92 m, with significantly longer distances by males (628.9±59.51 m) than females (580.9±47.80 m) (p<0.001). Age, height, weight, and body mass index were significantly correlated with 6MWD in univariate analysis. Stepwise multiple regression showed height to be single independent predictor of 6MWD (r(2)=0.205, p<0.001). The reference equations derived in Caucasian and North African populations tend to overestimate the distance walked by Korean subjects, while Asian equations underestimate it. CONCLUSION: The average 6MWD in these Korean populations was 600 m. The regression equation revealed that individual's height was the most significant predictor of distance, explaining 20.5% of the distance variance.

Detection of chromosomal breakpoints in patients with developmental delay and speech disorders.

Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7-11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).

Reference Equations for the Six-Minute Walk Distance in Healthy Korean Adults, Aged 22-59 Years / 결핵및호흡기질환

BACKGROUND: The six-minute walk test has been widely used in people with chronic cardiopulmonary disorders as an outcome assessment with regards to therapeutic or prognostic determinants. This study was undertaken to determine the six-minute walk distance (6MWD) in a sample of healthy Koreans and to create a reference equation. We also compared the 6MWD of our cohort with previously published equations. METHODS: Two hundred fifty-nine healthy subjects (95 males) aged 22-59 years performed two walking tests using a standardized protocol. 6MWD was defined as the greatest distance achieved from the two tests. The effect of anthropometrics on the 6MWD was also investigated. RESULTS: The average 6MWD was 598.5+/-57.92 m, with significantly longer distances by males (628.9+/-59.51 m) than females (580.9+/-47.80 m) (p<0.001). Age, height, weight, and body mass index were significantly correlated with 6MWD in univariate analysis. Stepwise multiple regression showed height to be single independent predictor of 6MWD (r2=0.205, p<0.001). The reference equations derived in Caucasian and North African populations tend to overestimate the distance walked by Korean subjects, while Asian equations underestimate it. CONCLUSION: The average 6MWD in these Korean populations was 600 m. The regression equation revealed that individual's height was the most significant predictor of distance, explaining 20.5% of the distance variance.

Patient's perception of symptoms related to morning activity in chronic obstructive pulmonary disease: the SYMBOL Study.

BACKGROUND/AIMS: Patients with chronic obstructive pulmonary disease (COPD) experience more problematic respiratory symptoms and have more trouble performing daily activities in the morning. The aim of this study was to assess the perception of COPD symptoms related to morning activities in patients with severe airflow limitation. METHODS: Data of 133 patients with severe airflow limitation were analyzed in a prospective, non-interventional study. A clinical symptom questionnaire was completed by patients at baseline. In patients having morning symptoms, defined by at least one or more prominent or aggravating symptom during morning activities, a morning activity questionnaire was also completed at baseline and following 2 months of COPD treatment. RESULTS: The most frequently reported COPD symptom was breathlessness (90.8%). Morning symptoms were reported in 76 (57%) patients; these had more frequent and severe clinical COPD symptoms. The most frequently reported morning activity was getting out of bed (82.9%). The long acting muscarinic antagonist (odds ratio [OR], 6.971; 95% confidence interval [CI], 1.317 to 11.905) and chest tightness (OR, 0.075; 95% CI, 0.011 to 0.518) were identified as significantly related to absence of morning symptoms. There was no significant correlation between the degree of forced expiratory volume in 1 second improvement and severity score differences of all items of morning activity after 2-month treatment. CONCLUSIONS: Fifty-seven percent of COPD patients with severe airflow limitation have morning symptoms that limit their morning activities. These patients also have more prevalent and severe COPD symptoms. The results of this study therefore provide valuable information for the development of patient-reported outcomes in COPD.

Patient's Perception of Symptoms Related to Morning Activity in Chronic Obstructive Pulmonary Disease: The SYMBOL Study

BACKGROUND/AIMS: Patients with chronic obstructive pulmonary disease (COPD) experience more problematic respiratory symptoms and have more trouble performing daily activities in the morning. The aim of this study was to assess the perception of COPD symptoms related to morning activities in patients with severe airflow limitation. METHODS: Data of 133 patients with severe airflow limitation were analyzed in a prospective, non-interventional study. A clinical symptom questionnaire was completed by patients at baseline. In patients having morning symptoms, defined by at least one or more prominent or aggravating symptom during morning activities, a morning activity questionnaire was also completed at baseline and following 2 months of COPD treatment. RESULTS: The most frequently reported COPD symptom was breathlessness (90.8%). Morning symptoms were reported in 76 (57%) patients; these had more frequent and severe clinical COPD symptoms. The most frequently reported morning activity was getting out of bed (82.9%). The long acting muscarinic antagonist (odds ratio [OR], 6.971; 95% confidence interval [CI], 1.317 to 11.905) and chest tightness (OR, 0.075; 95% CI, 0.011 to 0.518) were identified as significantly related to absence of morning symptoms. There was no significant correlation between the degree of forced expiratory volume in 1 second improvement and severity score differences of all items of morning activity after 2-month treatment. CONCLUSIONS: Fifty-seven percent of COPD patients with severe airflow limitation have morning symptoms that limit their morning activities. These patients also have more prevalent and severe COPD symptoms. The results of this study therefore provide valuable information for the development of patient-reported outcomes in COPD.

Dynamic changes in the human methylome during differentiation.

DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell-type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than introns, and sharp transitions of methylation occurred at exon-intron boundaries, suggesting a role for differential methylation in transcript splicing. Developmental stage was reflected in both the level of global methylation and extent of non-CpG methylation, with hESC highest, fibroblasts intermediate, and monocytes lowest. Differentiation-associated differential methylation profiles were observed for developmentally regulated genes, including the HOX clusters, other homeobox transcription factors, and pluripotence-associated genes such as POU5F1, TCF3, and KLF4. Our results highlight the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms.

Clustering-based approach for predicting motif pairs from protein interaction data.

UNLABELLED: Predicting motif pairs from a set of protein sequences based on the protein-protein interaction data is an important, but difficult computational problem. Tan et al. proposed a solution to this problem. However, the scoring function (using chi(2) testing) used in their approach is not adequate and their approach is also not scalable. It may take days to process a set of 5000 protein sequences with about 20,000 interactions. Later, Leung et al. proposed an improved scoring function and faster algorithms for solving the same problem. But, the model used in Leung et al. is complicated. The exact value of the scoring function is not easy to compute and an estimated value is used in practice. In this paper, we derive a better model to capture the significance of a given motif pair based on a clustering notion. We develop a fast heuristic algorithm to solve the problem. The algorithm is able to locate the correct motif pair in the yeast data set in about 45 minutes for 5000 protein sequences and 20,000 interactions. Moreover, we derive a lower bound result for the p-value of a motif pair in order for it to be distinguishable from random motif pairs. The lower bound result has been verified using simulated data sets. AVAILABILITY: http://alse.cs.hku.hk/motif_pair.

Prevalence and Risk Factors of Depression in Patients with Chronic Obstructive Pulmonary Disease / 결핵및호흡기질환

BACKGROUND: Due to the irreversible nature of chronic obstructive pulmonary disease (COPD), the treatment aim in patients with COPD is not to cure but to reduce the symptoms, increase lung function, and improve the quality of life. It has been suggested that depression is a common emotional disturbance in patients with COPD who are faced with a major physical impairment and embarrassing symptoms. This study evaluated the prevalence and risk factors of depression in patients with chronic obstructive pulmonary disease. METHODS: A total of 59 patients with a registered diagnosis of chronic obstructive pulmonary disease were selected. Depression was assessed using the Centers for Epidemiologic Studies Depression (CES-D) scale. The quality of life was assessed using the Korean version of the St. George's Respiratory Questionnaire. RESULTS: The prevalence of depression was 17.0%. In the correlation model, the interaction of the FEV1% over predicted value and SGRQ score(symptom, activity, impact, overall score) was statistically significant. The interaction of the FEV1% over predicted value and depression scale(CES-D) was also statistically significant. There was a positive correlation between the SGRQ scores(symptom, activity, impact, overall score) and the depression scale. CONCLUSION: The prevalence of depression in patients with chronic obstructive pulmonary disease is relatively high. The pulmonary function and the living standards were found to be significant risk factors for depression.

Chronic Obstructive Pulmonary Disease with Severe Pulmonary Hypertension: A Case Report / 영남의대학술지

Pulmonary hypertension is an increase in blood pressure in the pulmonary artery, pulmonary vein or pulmonary capillaries. Depending on the cause, pulmonary hypertension can be a severe disease with markedly decreased exercise tolerance and right-sided heart failure. Pulmonary hypertension can present as one of five different types: arterial, venous, hypoxic, thromboembolic, or miscellaneous. Chronic obstructive pulmonary disease with severe pulmonary hypertension is a rare disease. A 52-year-old man presented with a complaint of aggravating dyspnea. The mean pulmonary arterial pressure was 61.5 mmHg by Doppler echocardiogram. The patient was prescribed diuretics, digoxin, bronchodilator, sildenafil, bosentan and an oxygen supply. However, he ultimately died of cor pulmonale. Thus, diagnosis and early combination therapy are important.

A case of leptomeningeal metastasis from adenocarcinoma of the lung improved by treatment with Gefitinib / 대한내과학회지

Leptomeningeal metastasis occurs in approximately 1% of patients with non-small cell lung cancer and this is an extremely serious complication. Without treatment, the median survival of patients is 4~6 weeks. The treatment options currently available are limited and achieve only modest results. Gefitinib was recently approved for the treatment of advanced/refractory non-small cell lung cancer. In addition, there have been case reports showing activity of gefitinib against brain metastasis in non-small cell lung cancer patients. However, there is limited data on the ability of gefitinib to cross the blood-brain barrier. We report the case of a patient with leptomeningeal metastasis from adenocarcinoma of the lung that had a dramatic response to gefitinib treatment.

Finding linear motif pairs from protein interaction networks: a probabilistic approach.

Finding motif pairs from a set of protein sequences based on the protein-protein interaction data is a challenging computational problem. Existing effective approaches usually rely on additional information such as some prior knowledge on protein groupings based on protein domains. In reality, this kind of knowledge is not always available. Novel approaches without using this knowledge is much desirable. Recently, Tan et al. proposed such an approach. However, there are two problems with their approach. The scoring function (using chi(2) testing) used in their approach is not adequate. Random motif pairs may have higher scores than the correct ones. Their approach is also not scalable. It may take days to process a set of 5000 protein sequences with about 20,000 interactions. In this paper, our contribution is two-fold. We first introduce a new scoring method, which is shown to be more accurate than the chi-score used in Tan et al. Then, we present two efficient algorithms, one exact algorithm and a heuristic version of it, to solve the problem of finding motif pairs. Based on experiments on real datasets, we show that our algorithms are efficient and can accurately locate the motif pairs. We have also evaluated the sensitivity and efficiency of our heuristics algorithm using simulated datasets, the results show that the algorithm is very efficient with reasonably high sensitivity.

A Case of Varicella Pneumonia Associated with Chickenpox in Immunocompetent Patient / 영남의대학술지

Varicella is a contagious infection in childhood disease typically affecting children aged 2-8 years and usually follows benign outcome. In the adult, clinical presentation is more severe and more commonly associated with complications. Varicella pneumonia, although rare, is a potentially life-threatening complication that should be suspected in any adult with varicella and respiratory symptoms. We report a case of varicella pneumonia in immunocompetent patient. The characteristic radiographic findings consisted of diffuse scattered coarse nodular infiltrations, less than 1cm sized, with ground glass opacity and consolidation in both lung fields. The patients was started on intravenous acyclovir. The chest radiograph performed 2 weeks later showed complete resolution of the pulmonary lesions.

The Effect of Repeated Education using a Computerized Scoring System for the Proper Use of Inhalation Medicine / 결핵및호흡기질환

BACKGROUND: The best way of delivering drugs for the treatment of asthma and chronic obstructive pulmonary disease (COPD) is via the inhaled route of administration. However, many patients use inhaler devices incorrectly. To augment the proper use of inhalation medicine and to improve knowledge of the disease and compliance, we have developed a "Computerized Respiratory Service Program" and applied the use of this program to educate patients. METHODS: Prospectively, this study was performed in 164 patients with asthma or COPD prescribed with inhaled medication. When inhalation medication was first prescribed, education using a drug model was conducted two times and thereafter every month. In addition, education using a drug model was conducted and the ability of the patient to use inhalation medicine properly was evaluated. RESULTS: A total of 164 patients participated in the sessions more than two times and received education. Fifty-seven patients participated in three sesions. After the patients received education one time, the ability of these patients to use an inhaler had an average score of 20.6. After the patients received education two times, the average score was 21.9. After the patients received education three times, the average score was 22.3, a further increase. The compliance of using the inhaler was 70.1% at the second session and increased to 81.8% at the third session. CONCLUSION: Feedback education using the "Computerized Respiratory Service Program" will increase the ability of the patient to use an inhaler and consistent education can maintain patient compliance with inhaler use.

Global map of growth-regulated gene expression in Burkholderia pseudomallei, the causative agent of melioidosis.

Many microbial pathogens express specific virulence traits at distinct growth phases. To understand the molecular pathways linking bacterial growth to pathogenicity, we have characterized the growth transcriptome of Burkholderia pseudomallei, the causative agent of melioidosis. Using a fine-scale sampling approach, we found approximately 17% of all B. pseudomallei genes displaying regulated expression during growth in rich medium, occurring as broad waves of functionally coherent gene expression tightly associated with distinct growth phases and transition points. We observed regulation of virulence genes across all growth phases and identified serC as a potentially new virulence factor by virtue of its coexpression with other early-phase virulence genes. serC-disrupted B. pseudomallei strains were serine auxotrophs and in mouse infection assays exhibited a dramatic attenuation of virulence compared to wild-type B. pseudomallei. Immunization of mice with serC-disrupted B. pseudomallei also conferred protection against subsequent challenges with different wild-type B. pseudomallei strains. At a genomic level, early-phase genes were preferentially localized on chromosome 1, while stationary-phase genes were significantly biased towards chromosome 2. We detected a significant level of chromosomally clustered gene expression, allowing us to predict approximately 100 potential operons in the B. pseudomallei genome. We computationally and experimentally validated these operons by showing that genes in these regions are preferentially transcribed in the same 5'-->3' direction, possess significantly shorter intergenic lengths than the overall genome, and are expressed as a common mRNA transcript. The availability of this transcriptome map provides an important resource for understanding the transcriptional architecture of B. pseudomallei.

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Using de novo motif discovery algorithms, we defined the cis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference-mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.