PMC:4156421 / 7138-19876 JSON TXT

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PubTator4TogoVar

{"project":"PubTator4TogoVar","denotations":[{"id":"27636","span":{"begin":8617,"end":8627},"obj":"SNP"},{"id":"27675","span":{"begin":11100,"end":11110},"obj":"SNP"},{"id":"27676","span":{"begin":10865,"end":10875},"obj":"SNP"},{"id":"27649","span":{"begin":8919,"end":8929},"obj":"SNP"},{"id":"27652","span":{"begin":8996,"end":9006},"obj":"SNP"},{"id":"27653","span":{"begin":9074,"end":9085},"obj":"SNP"},{"id":"27667","span":{"begin":10590,"end":10600},"obj":"SNP"},{"id":"27669","span":{"begin":10122,"end":10132},"obj":"SNP"}],"attributes":[{"id":"A27636","pred":"resolved_to","subj":"27636","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27675","pred":"resolved_to","subj":"27675","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27676","pred":"resolved_to","subj":"27676","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27649","pred":"resolved_to","subj":"27649","obj":"tmVar:rs4727443;VariantGroup:6;RS#:4727443"},{"id":"A27652","pred":"resolved_to","subj":"27652","obj":"tmVar:rs1981997;VariantGroup:25;CorrespondingGene:4137;RS#:1981997;CorrespondingSpecies:9606"},{"id":"A27653","pred":"resolved_to","subj":"27653","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27667","pred":"resolved_to","subj":"27667","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27669","pred":"resolved_to","subj":"27669","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"Results\n\nClinical history\nThe patient was a 61 year-old man of European-American ancestry without significant prior medical history who enjoyed good health until approximately eight months before he expired, when he developed flu-like symptoms marked by progressive dry cough and dyspnea. He first sought medical attention when, two months later, he presented with lower extremity edema. Pulmonary artery catheterization at that time revealed severe pulmonary artery hypertension and other changes consistent with cor pulmonale. Subsequently, he developed atrial flutter requiring cardioversion and increasing dependence on supplemental oxygen. X-ray computed tomography (CT) of the chest revealed changes consistent with chronic pulmonary fibrosis, comprised of severe dilation of the main pulmonary artery, diffuse basilar ground-glass opacities, and subpleural reticular opacities. The patient had no known family history of pulmonary diseases. He was married and a father. He worked as a truck driver and was previously employed in a chemical manufacturing facility. There was no known history of asbestos exposure. He kept a pet bird as a younger adult. He had not resided in regions associated with endemic fungal disease. Substance abuse was confined to a 32 pack-year history of smoking.\nThe patient's symptoms worsened despite treatment consisting of diuretics, corticosteroids, and sildenafil. Approximately two months prior to death, he was transferred to our institution for evaluation for lung transplant. Imaging studies and routine clinical laboratory analysis revealed no evidence for thromboembolism, infection, connective tissue disease, or underlying immunodeficiency. During this interval, it became increasingly difficult to maintain adequate oxygenation. Radiographic chest imaging showed progressive lobar consolidation. As hypoxia worsened, mental status deteriorated. His family requested that care be limited to comfort measures, and he died shortly afterward. Lung tissue was not obtained for diagnosis prior to death.\n\nGross anatomic findings\nThe lungs exhibited smooth pleural surfaces, and sectioning revealed diffuse consolidation, without evidence of accentuated subpleural fibrosis and honeycomb patterns of airspace enlargement. The pulmonary vessels showed focal intimal thickening and plaque formation, consistent with pulmonary hypertension, but no evidence of recent or remote thromboemboli. The hilum and mediastinum contained enlarged, reactive-appearing lymph nodes. The heart was also enlarged, and all chambers were hypertrophic. The right ventricle demonstrated marked muscular hypertrophy, and had a wall thickness that equaled the left ventricle, consistent with cor pulmonale. There was no significant atherosclerotic coronary artery disease, valvular disease, or evidence of myocardial infarction.\n\nMicroscopic findings\nHistologic examination of lung tissue revealed diffuse fibrous thickening of alveolar septae (Figure 1, Figure S1). Changes were relatively uniform throughout the lung. Dense bundles of collagen and scant mononuclear inflammatory cell infiltrates existed within thickened septae. Focally, apical subpleural regions exhibited increased fibrosis and remodeling, with associated airspace enlargement. To further characterize the histologic changes and classify this patient's pulmonary fibrosis, we processed an additional 10 blocks of tissue from representative sections of all lobes of the right and left lung. The pattern of injury was uniform throughout the lungs, showing diffuse fibrocellular thickening of the vast majority of alveolar septae. One section from the right middle lobe contained changes of microscopic honeycombing in an area of subpleural fibrosis, where small cysts lined by respiratory epithelium are present and contain mucous and neutrophils (Figure S1). Microscopic honeycombing has been reported in NSIP and other lung diseases, and to our knowledge this entity is not specific for UIP [23], [24]. The temporal uniformity of the process, and clinical presentation are most compatible with a pathologic diagnosis of the fibrosing variant of nonspecific interstitial pneumonia (NSIP), in contrast to the initial diagnosis of IPF [25]. Some of the pulmonary arteries demonstrated fibrous intimal thickening, and the myocardium showed myocyte hypertrophy. Alveolar hemosiderin-laden macrophages were present within lung sections and most likely reflect pulmonary hemorrhage secondary to pulmonary hypertension. Finally, pathological sections revealed an acute bronchopneumonia, consistent with terminal bronchopneumonia most likely due to aspiration. Lymph nodes showed only nonspecific reactive changes.\nFigure 1 Histological demonstration of the NSIP pattern of IPF in the patient's lungs. Microscopic examination of the lungs.\n(A) 40×; (B) 400×. Note uniform fibrotic thickening of the alveolar septae and type II pneumocyte hypertrophy. There was no histologic evidence of sarcoidosis, hypersensitivity pneumonitis, organizing pneumonia, or diffuse alveolar damage.\n\nGenome sequencing\nWe performed whole genome sequencing, yielding 1.14 billion read pairs resulting in 52× median coverage across the mappable genome (3.1 Gb) and 44× median coverage across the exome (36.6 Mb). A total of 3.2 million single nucleotide variants (SNVs) were identified across the genome, with a Ti:Tv of 2.12 [19]. A total of 29,646 SNVs altering protein-coding were observed, of which 146 were not seen in dbSNP v137. Additionally, 305 novel coding indels not reported in dbSNP v137, were also identified.\n\nMendelian disorders\nMutations in several genes have been reported to segregate with familial forms of IPF (Table 1). We searched the patient's genome for rare variants (minor allele frequency (MAF)\u003c0.01) in protein-coding regions within this set of genes. We did not identify rare variants predicted to alter protein sequence or splicing in these genes, although we did find 3 rare synonymous codon substitutions in each of TERT, encoding a component of telomerase; DSP, producing desmoplakin, a component of desmosomes; and DPP9, the product of which is a serine protease. While synonymous changes in protein coding regions are increasingly reported to influence heritable susceptibility to disease [26], the significance of these variants remains uncertain. DNA sequence analysis software also detected coding variants in MUC2, but upon further scrutiny we interpreted them as artifacts attributable to DNA alignment errors due to sequence similarity among mucin gene family members [13], [27].\nTable 1 Genes previously associated with familial IPF.\nGene Mutation Reference\nABCA3 c.839G\u003eA/p.R280H [40]\nc.863G\u003eA/p.R288K [40]\nc.2891G\u003eA/p.G964D [41]\nc.8784A\u003eG/p.S1262G [40]\nMICA Alleles distinguished by multiple variants [42]\nSFTPA1 Alleles distinguished by multiple variants [43]\nSFTPA2 c.593T\u003eC/p.F198S [44]\nc.692G\u003eT/p.G231V [44]\nSFTPC c.116T\u003eC/p.V39A [45]\nc.211A\u003eG/p.M71V [40]\nc.218T\u003eC/p.I73T [40], [46], [47]\nc.298G\u003eA/p.G100S [48]\nc.325-1G\u003eA/IVS3-1 [45]\nc.434+1G\u003eC/IVS4+1 [49]\nc.435+2T\u003eC/IVS4+2 [40]\nc.424delC/p.H142fs [45]\nc.435G\u003eC/p.Q145H [45]\nc.563T\u003eC/p.L188P [45]\nc.563T\u003eA/p.L188Q [50]\nc.566G\u003eA/p.C189Y [45]\nc.581T\u003eA/p.L194P [45]\nTERT c.97C\u003eT/P33S [51]\nc.164T\u003eA/L55Q [52]\nc.277+1G\u003eA/IVS1+1 [52]\nc.334delC/p.112fs [52]\nc.430G\u003eA/V144M [51]\nc.1456C\u003eT/R486C [51]\nc.1892G\u003eA/p.R631Q [53]\nc.2240delT/V747fs [51]\nc.2594G\u003eA/R865H [51], [53]\nc.2648T\u003eG/p.F883C [53]\nc.2712-2A\u003eC/IVS9-2 [52]\nc.3329C\u003eT/p.T1110M [52]\nc.3346_3522del/E1116fs [51]\nTERC r.98g\u003ea [52]\nr.37a\u003eg [51]\nr.52_86del (also described as r.53_87del) [54]\n\nGWAS variants\nWe next cross-referenced the patient's genome with SNPs previously implicated in IPF by GWAS (Table S1). The patient was heterozygous for six variants influencing susceptibility to IPF (Table 2). Two of the six are associated with elevated risk for IPF. One of these variants (Figure 2), rs35705950, is located within the promoter region of MUC5B and has a strong association with both familial and sporadic IPF, with odds ratio (OR) estimates ranging from 2.4–6.8 for heterozygote carriers. The presence of one other variant located on chromosome 7 also increases risk for IPF [13]. Four of the six variants are associated with reduced susceptibility to IPF and include SNPs in OBFC1, a gene involved in telomere maintenance, MAPT, the gene from which the microtubule-associated protein tau is produced [13], as well as the Toll interacting protein, TOLLIP, and signal peptidase, SPPL2C [10].\nFigure 2 Integrated Genomics Viewer (IGV) screenshot of the rs35705950 variant.\nTable 2 Variants associated with IPF that were also seen in this individual. Allele frequencies accessed 4/16/2014.\nNearest Gene SNP ID Chromosome Position Variant Type Minor Allele Major Allele Patient Genotype MAF (1000 Genomes) OR Reference\nAZGP1 (AZGP1P1 pseudogene) rs4727443 7 99593346 intergenic A C C/A 0.411 1.3A 1.11B [13]\nMAPT rs1981997 17 44056767 intronic A G A/G 0.117 0.71A 0.67B [13]\nMUC5B rs35705950 11 1241221 promoter T G T/G 0.052 2.4–6.8 [10]–[14], [16]\nOBFC1 rs11191865 10 105672842 intronic G A A/G 0.584 0.8A 0.87B [13]\nTOLLIP rs5743890 11 1325829 Intronic C T C/T 0.0702 0.61 [10]\nSPPL2C rs17690703 17 43925297 Intronic T C C/T 0.1543 0.7 [10]\nA Discovery and Breplicate GWAS.\n\nAnalysis of variants in the vicinity of rs35705950 (MUC5B)\nThe availability of whole genome sequence allowed us to explore whether the MUC5B promoter variant contributes to increased risk for IPF, as opposed to alternatively serving only as a marker in linkage disequilibrium (LD) with other causative variant(s) in the same region (Figure 3a, Figure S2). For this analysis we used a recently described approach, Combined Annotation-Dependent Depletion scoring system (CADD) [21], which estimates the relative pathogenicity of variants based on a variety of predicted functional effects. We first used HapMap data for individuals of European ancestry to define LD in the vicinity (1 Mb in either direction) of rs35705950. The highest scoring SNV out of 2,284 in the region, a nonsense variant within MUC6 (C-score = 42) failed manual validation, due to likely misalignment, and no other SNVs had C-scores above 23. The full table of variants and scores is provided as Table S2. We also investigated the region between the MUC5AC gene and the MUC5B start site for rare variants (AF\u003c2%) that overlap with regions that may possibly influence expression (Figure 3b). Only one SNP, rs35705950, overlapped with both DNAse hypersensitivity and transcription factor binding regions.\nFigure 3 Sequencing coverage and variant distribution within the MUC5B locus.\n(A) Sequence coverage of the MUC5B gene. (B) Rare variants neighboring the MUC5B promoter variant rs35705950. Variant track is colored by allele frequency (blue: AF\u003c2%, red: AF\u003c5%, black: AF\u003c10%). No other rare variants in this region overlap with putative transcription factor binding sites, consistent with the hypothesis that the rs35705950 is causative of MUC5B dysregulation. Plots were generated using the UCSC genome browser (http://www.genome.ucsc.edu).\n\nRare coding variants\nTo assess genes not previously associated with IPF but potentially relevant to observed pathology, we filtered variants for rare protein-altering SNVs. With a MAF threshold of 0.01, we identified 1,291 novel or rare coding SNVs. A subset of 57 coding variants at nucleotide positions demonstrating significant interspecies conservation (conScoreGERP \u003e5.75) were delineated (Table S3). GeneCards (http://genecards.org) and literature searches were consulted to determine the function, associated disease, and expression profile of each of these variants. Few of these variants are known to be expressed in lung or specifically in diseased lung tissue from patients with IPF [28]; however, this does not rule out their contribution to disease as the expression profile may be incomplete, the gene's effect on the lung may be indirectly mediated through exogenous inflammatory pathways, or the deleterious effects of the genes may arise from abnormal expression. We compared our list of novel variants to a previously published set of genes that are differentially expressed between IPF patients and controls [28]. Twenty-nine/146 of the novel variants are included in this set. Three are nonsense variants: NCKAP5 and SLC25A25, which were underexpressed in IPF patients, and MNS1/TEX9, which was overexpressed in IPF patients. Other coding variants for genes in this list have previously been associated with different inherited disorders, but none seem pertinent to the patient's illness."}

PubTatorOnTogoVar

PMC:4156421 / 7138-19876 JSONTXT

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PubTator4TogoVar

PubTatorOnTogoVar

PMC:4156421 / 7138-19876 JSON TXT