Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer (NSCLC) risk, biological mechanisms of these variants remain largely unknown. By integrating a large-scale genotype data of 15 581 lung adenocarcinoma (AD) cases, 8350 squamous cell carcinoma (SqCC) cases, and 27 355 controls, as well as multiple transcriptome and epigenomic databases, we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants. We identified 3064 credible risk variants for NSCLC, which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites. Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific. Functional annotation and gene-based analysis implicated 894 target genes, including 274 specifics for AD and 123 for SqCC, which were overrepresented in somatic driver genes (ER = 1.95, P = 0.005). Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways, while SqCC genes were homologous recombination deficiency related. Our results illustrate the molecular basis of both well-studied and new susceptibility loci of NSCLC, providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments.
Adenocarcinoma of Lung/genetics* ; Carcinoma, Non-Small-Cell Lung/genetics* ; Carcinoma, Squamous Cell/genetics* ; Genetic Heterogeneity ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Lung Neoplasms/genetics* ; Polymorphism, Single Nucleotide

Laccases (EC 1.10.3.2), a group of multi-copper oxidases (MCOs), play multiple biological functions and widely exist in many species. Fungal laccases have been extensively studied for their industrial applications, however, there was no database specially focused on fungal laccases. To provide a comparative genomics platform for fungal laccases, we have developed a comparative genomics platform for laccases and MCOs (http://laccase.riceblast.snu.ac.kr/). Based on protein domain profiles of characterized sequences, 3,571 laccases were predicted from 690 genomes including 253 fungi. The number of putative laccases and their properties exhibited dynamic distribution across the taxonomy. A total of 505 laccases from 68 genomes were selected and subjected to phylogenetic analysis. As a result, four clades comprised of nine subclades were phylogenetically grouped by their putative functions and analyzed at the sequence level. Our work would provide a workbench for putative laccases mainly focused on the fungal kingdom as well as a new perspective in the identification and classification of putative laccases and MCOs.

Malignant gastric outlet obstruction describes a constellation of symptoms that can result as a common endpoint from a variety of primary tumours, particularly those of the upper gastrointestinal tract and pancreas. Affected patients face a dismal, undignified and rapid decline in health secondary to malnutrition, dehydration and constant nausea with associated vomiting. Palliative treatment has traditionally involved a gastrojejunostomy—a major undertaking given the functional status of these patients. More recent advances in the endoscopic placement of metal stents to relieve obstruction have clear benefits over the surgical method. We look at the factors involved in patient selection, the techniques and considerations involved in stent deployment and the potential complications associated with this method.
Dehydration ; Duodenal Neoplasms ; Endoscopy ; Gastric Outlet Obstruction ; Humans ; Malnutrition ; Methods ; Mortuary Practice ; Nausea ; Palliative Care ; Pancreas ; Patient Selection ; Stents ; Upper Gastrointestinal Tract ; Vomiting

NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes.
Biological Processes ; Computer Simulation* ; Eukaryota ; Genome ; Genome, Fungal ; Glycosylation ; Humans ; NADP ; NADPH Oxidase* ; Oomycetes ; Oxidoreductases ; Phylogeny ; Plants ; Protein Isoforms ; Reactive Oxygen Species ; Sequence Analysis*

Chronic GVHD was recognized as a complication of allogeneic hematopoietic cell transplantation more than 30 years ago, but progress has been slowed by the limited insight into the pathogenesis of the disease and the mechanisms that lead to development of immunological tolerance. Only 6 randomized phase III treatment studies have been reported. Results of retrospective studies and prospective phase II clinical trials suggested overall benefit from treatment with mycophenolate mofetil or thalidomide, but these results were not substantiated by phase III studies of initial systemic treatment for chronic GVHD. A comprehensive review of published reports showed numerous deficiencies in studies of secondary treatment for chronic GVHD. Fewer than 10% of reports documented an effort to minimize patient selection bias, used a consistent treatment regimen, or tested a formal statistical hypothesis that was based on a contemporaneous or historical benchmark. In order to enable valid comparison of the results from different studies, eligibility criteria, definitions of individual organ and overall response, and time of assessment should be standardized. Improved treatments are more likely to emerge if reviewers and journal editors hold authors to higher standards in evaluating manuscripts for publication.
Bias (Epidemiology) ; Cell Transplantation ; Mycophenolic Acid ; Patient Selection ; Publications ; Thalidomide ; Transplants

No abstract available.