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1.  Magnetic Resonance Elastography for Staging Liver Fibrosis in Non-alcoholic Fatty Liver Disease: A Diagnostic Accuracy Systematic Review and Individual Participant Data Pooled Analysis 
European radiology  2015;26(5):1431-1440.
Objectives
We conducted an individual participant data (IPD) pooled analysis on the diagnostic accuracy of magnetic resonance elastography (MRE) to detect fibrosis stage in patients with NAFLD.
Methods
Through a systematic literature search, we identified studies of MRE (at 60–62.5Hz) for staging fibrosis in patients with NAFLD, using liver biopsy as gold standard and contacted study authors for IPD. Through pooled analysis, we calculated the cluster-adjusted AUROC, sensitivity and specificity of MRE for any (≥stage 1), significant (≥stage 2) and advanced fibrosis (≥stage 3) and cirrhosis (stage 4).
Results
We included 9 studies reporting on 232 patients with NAFLD (mean age, 51±13y; 37.5% males; mean BMI, 33.5±6.7 kg/m2; interval between MRE and biopsy <1 year, 98.3%). Fibrosis stage distribution (stage 0/1/2/3/4) was 33.6%, 32.3%, 10.8%, 12.9% and 10.4%, respectively. Mean AUROC (and 95% confidence intervals) for diagnosis of any (≥stage 1), significant (≥stage 2) or advanced fibrosis (≥stage 3) and cirrhosis was 0.86 (0.82–0.90), 0.87 (0.82–0.93), 0.90 (0.84–0.94) and 0.91 (0.76–0.95), respectively. Similar diagnostic performance was observed in stratified analysis based on sex, obesity, and degree of inflammation.
Conclusions
Based on pooled IPD analysis, MRE has high diagnostic accuracy for detection of fibrosis in NAFLD, independent of BMI and degree of inflammation.
doi:10.1007/s00330-015-3949-z
PMCID: PMC5051267  PMID: 26314479
Fibrosis; non-invasive; elastography; diagnostic performance; pooled analysis; cirrhosis; biomarker
2.  Diagnostic Accuracy of Magnetic Resonance Elastography in Liver Transplant Recipients: A Pooled Analysis 
Annals of hepatology  2016;15(3):363-376.
Background and Aims
We conducted an individual participant data (IPD) pooled analysis on the diagnostic accuracy of magnetic resonance elastography (MRE) to detect fibrosis stage in liver transplant recipients.
Methods
Through a systematic literature search, we identified studies on diagnostic performance of MRE for staging liver fibrosis, using liver biopsy as gold standard. We contacted study authors for published and unpublished IPD on age, sex, body mass index, liver stiffness, fibrosis stage, degree of inflammation and interval between MRE and biopsy; from these we limited analysis to patients who had undergone liver transplantation. Through pooled analysis using nonparametric two-stage receiver-operating curve (ROC) regression models, we calculated the cluster-adjusted AUROC, sensitivity and specificity of MRE for any (≥stage 1), significant (≥stage 2) and advanced fibrosis (≥stage 3) and cirrhosis (stage 4).
Results
We included 6 cohorts (4 published and 2 unpublished series) reporting on 141 liver transplant recipients (mean age, 57 years; 75.2% male; mean BMI, 27.1 kg/m2). Fibrosis stage distribution stage 0, 1, 2, 3, or 4, was 37.6%, 23.4%, 24.8%, 12% and 2.2%, respectively. Mean AUROC values (and 95% confidence intervals) for diagnosis of any (≥stage 1), significant (≥stage 2), or advanced fibrosis (≥stage 3) and cirrhosis were 0.73 (0.66–0.81), 0.69 (0.62–0.74), 0.83 (0.61–0.88) and 0.96 (0.93–0.98), respectively. Similar diagnostic performance was observed in stratified analysis based on sex, obesity and inflammation grade.
Conclusions
In conclusion, MRE has high diagnostic accuracy for detection of advanced fibrosis in liver transplant recipients, independent of BMI and degree of inflammation.
doi:10.5604/16652681.1198808
PMCID: PMC5032623  PMID: 27049490
Fibrosis; non-invasive; elastography; diagnostic performance; pooled analysis; liver transplantation; biomarker
3.  The endoplasmic reticulum remains functionally connected by vesicular transport after its fragmentation in cells expressing Z-α1-antitrypsin 
The FASEB Journal  2016;30(12):4083-4097.
α1-Antitrypsin is a serine protease inhibitor produced in the liver that is responsible for the regulation of pulmonary inflammation. The commonest pathogenic gene mutation yields Z-α1-antitrypsin, which has a propensity to self-associate forming polymers that become trapped in inclusions of endoplasmic reticulum (ER). It is unclear whether these inclusions are connected to the main ER network in Z-α1-antitrypsin-expressing cells. Using live cell imaging, we found that despite inclusions containing an immobile matrix of polymeric α1-antitrypsin, small ER resident proteins can diffuse freely within them. Inclusions have many features to suggest they represent fragmented ER, and some are physically separated from the tubular ER network, yet we observed cargo to be transported between them in a cytosol-dependent fashion that is sensitive to N-ethylmaleimide and dependent on Sar1 and sec22B. We conclude that protein recycling occurs between ER inclusions despite their physical separation.—Dickens, J. A., Ordóñez, A., Chambers, J. E., Beckett, A. J., Patel, V., Malzer, E., Dominicus, C. S., Bradley, J., Peden, A. A., Prior, I. A., Lomas, D. A., Marciniak, S. J. The endoplasmic reticulum remains functionally connected by vesicular transport after its fragmentation in cells expressing Z-α1-antitrypsin.
doi:10.1096/fj.201600430R
PMCID: PMC5102109  PMID: 27601439
ER stress; homotypic fusion; serpin; SNARE
4.  The iFly Tracking System for an Automated Locomotor and Behavioural Analysis of Drosophila melanogaster 
The use of animal models in medical research provides insights into molecular and cellular mechanisms of human disease, and helps identify and test novel therapeutic strategies. Drosophila melanogaster – the common fruit fly – is one of the most established model organisms, as its study can be performed more readily and with far less expense than for other model animal systems, such as mice, fish, or indeed primates. In the case of fruit flies, standard assays are based on the analysis of longevity and basic locomotor functions. Here we present the iFly tracking system, which enables to increase the amount of quantitative information that can be extracted from these studies, and to reduce significantly the duration and costs associated with them. The iFly system uses a single camera to simultaneously track the trajectories of up to 20 individual flies with about 100μm spatial and 33ms temporal resolution. The statistical analysis of fly movements recorded with such accuracy makes it possible to perform a rapid and fully automated quantitative analysis of locomotor changes in response to a range of different stimuli. We anticipate that the iFly method will reduce very considerably the costs and the duration of the testing of genetic and pharmacological interventions in Drosophila models, including an earlier detection of behavioural changes and a large increase in throughput compared to current longevity and locomotor assays.
doi:10.1039/c0ib00149j
PMCID: PMC5011414  PMID: 21698336
Animal models; 3D tracking; Locomotor analysis; Fly cam; Computer vision
5.  THE RELIABILITY OF MAGNETIC RESONANCE ELASTOGRAPHY USING MULTISLICE 2D SPIN-ECHO ECHO-PLANAR IMAGING (SE-EPI) AND 3D INVERSION RECONSTRUCTION FOR ASSESSING RENAL STIFFNESS 
PURPOSE
To evaluate the reliability of MRE using a spin-echo echo-planar imaging (SE-EPI) renal MRE technique in healthy volunteers
MATERIALS AND METHODS
Institutional review board approved prospective study in which all participants provided written informed consent. Sixteen healthy volunteers comprising seven males and nine females with a median age of 35 years (age range: 23 to 59 years) were included. Coronal 90-Hz and 60-Hz MRE acquisitions were performed twice within a 30-minute interval between examinations. Renal MRE reliability was assessed by i) test-retest repeatability, and ii) inter-rater agreement between two independent readers. The MRE-measured averaged renal stiffness values were evaluated using: intraclass correlation coefficient (ICC), Bland-Altman and the within-subject coefficient of variation (COV).
RESULTS
For test-retest repeatability, Bland-Altman showed a mean stiffness difference between examinations of 0.07 kPa (95% limits of agreement: −1.41, 1.54) at 90-Hz and 0.01 kPa (95% limits of agreement: −0.51, 0.53) at 60-Hz. Coefficient of repeatability was 1.47 kPa and 0.52 kPa at 90-Hz and 60-Hz, respectively. The within-subject COV was 13.6% and 7.7% at 90-Hz and 60-Hz, respectively. ICC values were 0.922 and 0.907 for test-retest repeatability and 0.998 and 0.989 for inter-rater agreement, respectively (p < 0.001).
CONCLUSION
SE-EPI renal MRE is a reliable technique
doi:10.1002/jmri.24826
PMCID: PMC4560097  PMID: 25537823
Magnetic resonance elastography; Kidneys; Diagnostic reliability
6.  A Genome-wide analysis of the response to inhaled beta2-agonists in Chronic Obstructive Pulmonary Disease 
The pharmacogenomics journal  2015;16(4):326-335.
Short-acting β2-agonist bronchodilators are the most common medications used in treating chronic obstructive pulmonary disease (COPD). Genetic variants determining bronchodilator responsiveness (BDR) in COPD have not been identified.
We performed a genome-wide association study (GWAS) of BDR in 5789 current or former smokers with COPD in one African American and four white populations. BDR was defined as the quantitative spirometric response to inhaled β2-agonists. We combined results in a meta-analysis.
In the meta-analysis, SNPs in the genes KCNK1 (P=2.02×10−7) and KCNJ2 (P=1.79×10−7) were the top associations with BDR. Among African Americans, SNPs in CDH13 were significantly associated with BDR (P=5.1×10−9). A nominal association with CDH13 was identified in a gene-based analysis in all subjects.
We identified suggestive association with BDR among COPD subjects for variants near two potassium channel genes (KCNK1 and KCNJ2). SNPs in CDH13 were significantly associated with BDR in African Americans.
doi:10.1038/tpj.2015.65
PMCID: PMC4848212  PMID: 26503814
7.  Interactions between N‐linked glycosylation and polymerisation of neuroserpin within the endoplasmic reticulum 
The Febs Journal  2015;282(23):4565-4579.
The neuronal serpin neuroserpin undergoes polymerisation as a consequence of point mutations that alter its conformational stability, leading to a neurodegenerative dementia called familial encephalopathy with neuroserpin inclusion bodies (FENIB). Neuroserpin is a glycoprotein with predicted glycosylation sites at asparagines 157, 321 and 401. We used site‐directed mutagenesis, transient transfection, western blot, metabolic labelling and ELISA to probe the relationship between glycosylation, folding, polymerisation and degradation of neuroserpin in validated cell models of health and disease. Our data show that glycosylation at N157 and N321 plays an important role in maintaining the monomeric state of neuroserpin, and we propose this is the result of steric hindrance or effects on local conformational dynamics that can contribute to polymerisation. Asparagine residue 401 is not glycosylated in wild type neuroserpin and in several polymerogenic variants that cause FENIB, but partial glycosylation was observed in the G392E mutant of neuroserpin that causes severe, early‐onset dementia. Our findings indicate that N401 glycosylation reports lability of the C‐terminal end of neuroserpin in its native state. This C‐terminal lability is not required for neuroserpin polymerisation in the endoplasmic reticulum, but the additional glycan facilitates degradation of the mutant protein during proteasomal impairment. In summary, our results indicate how normal and variant‐specific N‐linked glycosylation events relate to intracellular folding, misfolding, degradation and polymerisation of neuroserpin.
doi:10.1111/febs.13517
PMCID: PMC4949553  PMID: 26367528
conformational disease; neurodegeneration; protein aggregation; serpin; serpinopathies
8.  Deficiency Mutations of Alpha-1 Antitrypsin. Effects on Folding, Function, and Polymerization 
Misfolding, polymerization, and defective secretion of functional alpha-1 antitrypsin underlies the predisposition to severe liver and lung disease in alpha-1 antitrypsin deficiency. We have identified a novel (Ala336Pro, Baghdad) deficiency variant and characterized it relative to the wild-type (M) and Glu342Lys (Z) alleles. The index case is a homozygous individual of consanguineous parentage, with levels of circulating alpha-1 antitrypsin in the moderate deficiency range, but is a biochemical phenotype that could not be classified by standard methods. The majority of the protein was present as functionally inactive polymer, and the remaining monomer was 37% active relative to the wild-type protein. These factors combined indicate an 85 to 95% functional deficiency, similar to that seen with ZZ homozygotes. Biochemical, biophysical, and computational studies further defined the molecular basis of this deficiency. These studies demonstrated that native Ala336Pro alpha-1 antitrypsin could populate the polymerogenic intermediate—and therefore polymerize—more readily than either wild-type alpha-1 antitrypsin or the Z variant. In contrast, folding was far less impaired in Ala336Pro alpha-1 antitrypsin than in the Z variant. The data are consistent with a disparate contribution by the “breach” region and “shutter” region of strand 5A to folding and polymerization mechanisms. Moreover, the findings demonstrate that, in these variants, folding efficiency does not correlate directly with the tendency to polymerize in vitro or in vivo. They therefore differentiate generalized misfolding from polymerization tendencies in missense variants of alpha-1 antitrypsin. Clinically, they further support the need to quantify loss-of-function in alpha-1 antitrypsin deficiency to individualize patient care.
doi:10.1165/rcmb.2015-0154OC
PMCID: PMC4742932  PMID: 26091018
alpha-1 antitrypsin deficiency; polymerization; mutation; unfolding; serpinopathies
9.  Genome-wide site-specific differential methylation in the blood of individuals with Klinefelter Syndrome 
Klinefelter syndrome (KS) (47 XXY) is a common sex-chromosome aneuploidy with an estimated prevalence of 1 in every 660 male births. Investigations into the associations between DNA methylation and the highly variable clinical manifestations of KS have largely focused on the supernumerary X chromosome; systematic investigations of the epigenome have been limited. We obtained genome-wide DNA methylation data from peripheral blood using the Illumina HumanMethylation450K platform in 5 KS (47 XXY), 102 male (46 XY), and 113 female (46 XX) control subjects participating in the chronic obstructive pulmonary disease (COPD) Gene Study. Empirical Bayes-mediated models were used to test for differential methylation by KS status. CpG sites with a false-discovery rate <0.05 from the first-generation HumanMethylation27K platform were further examined in an independent replication cohort of 2 KS subjects, 590 male, and 495 female controls drawn from the International COPD Genetics Network (ICGN). Differential methylation at sites throughout the genome were identified, including 86 CpG sites that were differentially methylated in KS subjects relative to both male and female controls. CpG sites annotated to the HEN1 methyltransferase homolog 1 (HENMT1), calcyclin-binding protein (CACYBP), and GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) genes were among the “KS-specific” loci that were replicated in ICGN. We therefore conclude that site-specific differential methylation exists throughout the genome in KS. The functional impact and clinical relevance of these differentially methylated loci should be explored in future studies.
doi:10.1002/mrd.22483
PMCID: PMC4439255  PMID: 25988574
[MeSH]: Klinefelter syndrome; DNA methylation; epigenomics; XXY syndrome
10.  Diagnostic Performance of Magnetic Resonance Elastography in Staging Liver Fibrosis: A Systematic Review and Meta-analysis of Individual Participant Data 
Background & Aims
Magnetic resonance elastography (MRE) is a non-invasive tool for staging liver fibrosis. We conducted a meta-analysis of individual participant data collected from published studies to assess the diagnostic accuracy of MRE and for staging liver fibrosis in patients with chronic liver diseases (CLD).
Methods
Through a systematic literature search of multiple databases (2003–2013), we identified studies on diagnostic performance of MRE for staging liver fibrosis in patients with CLD with native anatomy, using liver biopsy as the standard. We contacted study authors to collect data on each participant’s age, sex, body mass index (BMI), liver stiffness (measured by MRE), fibrosis stage, staging system used, degree of inflammation, etiology of CLD, and interval between MRE and biopsy. Through pooled analysis, we calculated the cluster-adjusted area under receiver-operating curve (AUROC), sensitivity, and specificity of MRE for any fibrosis (≥stage 1), significant fibrosis (≥stage 2), advanced fibrosis (≥stage 3), and cirrhosis (stage 4)
Results
We analyzed data from 12 retrospective studies, comprising 697 patients (mean age, 55±13 years; 59.4% male; mean BMI, 26.9±6.7 kg/m2; 92.1% with <1 year interval between MRE and biopsy; hepatitis C in 47.1%). Participants had fibrosis stages 0, 1, 2, 3, or 4 (19.5%, 19.4%, 15.5%, 15.9% and 29.7%, respectively). Mean AUROC values (and 95% confidence intervals) for diagnosis of any (≥stage 1), significant (≥stage 2), or advanced fibrosis (≥stage 3), and cirrhosis, were 0.84 (0.76–0.92), 0.88 (0.84–0.91), 0.93 (0.90–0.95), and 0.92 (0.90–0.94), respectively. Similar diagnostic performance was observed in stratified analysis based on sex, obesity, and etiology of CLD. The overall rate of failure of MRE was 4.3%.
Conclusion
Based on pooled analysis of data from individual participants, MRE has high accuracy for diagnosis of significant or advanced fibrosis and cirrhosis, independent of BMI and etiology of CLD. Prospective studies are warranted to better understand the diagnostic performance of MRE.
doi:10.1016/j.cgh.2014.09.046
PMCID: PMC4333001  PMID: 25305349
IPD; non-invasive; elastography; diagnostic performance; pooled analysis
11.  IREB2 and GALC Are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease 
Pulmonary hypertension is associated with advanced chronic obstructive pulmonary disease (COPD), although pulmonary vascular changes occur early in the course of the disease. Pulmonary artery (PA) enlargement (PAE) measured by computed tomography correlates with pulmonary hypertension and COPD exacerbation frequency. Genome-wide association studies of PAE in subjects with COPD have not been reported. To investigate whether genetic variants are associated with PAE within subjects with COPD, we investigated data from current and former smokers from the COPDGene Study and the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints study. The ratio of the diameter of the PA to the diameter of the aorta (A) was measured using computed tomography. PAE was defined as PA/A greater than 1. A genome-wide association study for COPD with PAE was performed using subjects with COPD without PAE (PA/A ≤ 1) as a control group. A secondary analysis used smokers with normal spirometry as a control group. Genotyping was performed on Illumina platforms. The results were summarized using fixed-effect meta-analysis. Both meta-analyses revealed a genome-wide significant locus on chromosome 15q25.1 in IREB2 (COPD with versus without PAE, rs7181486; odds ratio [OR] = 1.32; P = 2.10 × 10−8; versus smoking control subjects, rs2009746; OR = 1.42; P = 1.32 × 10−9). PAE was also associated with a region on 14q31.3 near the GALC gene (rs7140285; OR = 1.55; P = 3.75 × 10−8). Genetic variants near IREB2 and GALC likely contribute to genetic susceptibility to PAE associated with COPD. This study provides evidence for genetic heterogeneity associated with a clinically important COPD vascular subtype.
doi:10.1165/rcmb.2014-0210OC
PMCID: PMC4370263  PMID: 25101718
chronic obstructive pulmonary disease; genome-wide association; pulmonary hypertension; subtyping
12.  Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci 
Human Molecular Genetics  2014;24(4):1200-1210.
Genetic risk loci have been identified for a wide range of diseases through genome-wide association studies (GWAS), but the relevant functional mechanisms have been identified for only a small proportion of these GWAS-identified loci. By integrating results from the largest current GWAS of chronic obstructive disease (COPD) with expression quantitative trait locus (eQTL) analysis in whole blood and sputum from 121 subjects with COPD from the ECLIPSE Study, this analysis identifies loci that are simultaneously associated with COPD and the expression of nearby genes (COPD eQTLs). After integrative analysis, 19 COPD eQTLs were identified, including all four previously identified genome-wide significant loci near HHIP, FAM13A, and the 15q25 and 19q13 loci. For each COPD eQTL, fine mapping and colocalization analysis to identify causal shared eQTL and GWAS variants identified a subset of sites with moderate-to-strong evidence of harboring at least one shared variant responsible for both the eQTL and GWAS signals. Transcription factor binding site (TFBS) analysis confirms that multiple COPD eQTL lead SNPs disrupt TFBS, and enhancer enrichment analysis for loci with the strongest colocalization signals showed enrichment for blood-related cell types (CD3 and CD4+ T cells, lymphoblastoid cell lines). In summary, integrative eQTL and GWAS analysis confirms that genetic control of gene expression plays a key role in the genetic architecture of COPD and identifies specific blood-related cell types as likely participants in the functional pathway from GWAS-associated variant to disease phenotype.
doi:10.1093/hmg/ddu525
PMCID: PMC4806382  PMID: 25315895
13.  General review of magnetic resonance elastography 
World Journal of Radiology  2016;8(1):59-72.
Magnetic resonance elastography (MRE) is an innovative imaging technique for the non-invasive quantification of the biomechanical properties of soft tissues via the direct visualization of propagating shear waves in vivo using a modified phase-contrast magnetic resonance imaging (MRI) sequence. Fundamentally, MRE employs the same physical property that physicians utilize when performing manual palpation - that healthy and diseased tissues can be differentiated on the basis of widely differing mechanical stiffness. By performing “virtual palpation”, MRE is able to provide information that is beyond the capabilities of conventional morphologic imaging modalities. In an era of increasing adoption of multi-parametric imaging approaches for solving complex problems, MRE can be seamlessly incorporated into a standard MRI examination to provide a rapid, reliable and comprehensive imaging evaluation at a single patient appointment. Originally described by the Mayo Clinic in 1995, the technique represents the most accurate non-invasive method for the detection and staging of liver fibrosis and is currently performed in more than 100 centers worldwide. In this general review, the mechanical properties of soft tissues, principles of MRE, clinical applications of MRE in the liver and beyond, and limitations and future directions of this discipline -are discussed. Selected diagrams and images are provided for illustration.
doi:10.4329/wjr.v8.i1.59
PMCID: PMC4731349  PMID: 26834944
Magnetic resonance elastography; Elasticity imaging techniques; Liver disease; Fibrosis; Emerging applications
14.  Dissecting genetics for chronic mucus hypersecretion in smokers with and without COPD 
Background
Smoking is a notorious risk factor for chronic mucus hypersecretion (CMH). CMH frequently occurs in Chronic Obstructive Pulmonary Disease (COPD). The question arises whether the same single nucleotide polymorphisms (SNPs) are related to CMH in smokers with and without COPD.
Methods
We performed two genome wide association studies on CMH under an additive genetic model in male heavy smokers (≥20 pack-years) with COPD (n=849, 39.9% CMH) and without COPD (n=1,348, 25.4% CMH), followed by replication and meta-analysis in comparable populations, and assessment of the functional relevance of significantly associated SNPs.
Results
GWA analysis on CMH in COPD and non-COPD yielded no genome wide significance after replication. In COPD, our top SNP (rs10461985, p=5.43×10−5) was located in the GDNF-antisense gene that is functionally associated with the GDNF gene. Expression of GDNF in bronchial biopsies of COPD patients was significantly associated with CMH (p=0.007). In non-COPD, 4 SNPs had a p-value <10−5 in the meta-analysis, including a SNP (rs4863687) in the MAML3 gene, the T-allele showing modest association with CMH (p=7.57×10−6, OR=1.48) and with significantly increased MAML3 expression in lung tissue (p=2.59×10−12).
Conclusions
Our data suggest the potential for differential genetic backgrounds of CMH in individuals with and without COPD.
doi:10.1183/09031936.00093314
PMCID: PMC4498483  PMID: 25234806
15.  A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry 
BMC Genetics  2015;16:138.
Background
Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed a genome-wide association study (GWAS) in 9919 current and former smokers in the COPDGene study (6659 non-Hispanic Whites [NHW] and 3260 African Americans [AA]) to identify associations with spirometric measures (post-bronchodilator FEV1 and FEV1/FVC). We also conducted meta-analysis of FEV1 and FEV1/FVC GWAS in the COPDGene, ECLIPSE, and GenKOLS cohorts (total n = 13,532).
Results
Among NHW in the COPDGene cohort, both measures of pulmonary function were significantly associated with SNPs at the 15q25 locus [containing CHRNA3/5, AGPHD1, IREB2, CHRNB4] (lowest p-value = 2.17 × 10−11), and FEV1/FVC was associated with a genomic region on chromosome 4 [upstream of HHIP] (lowest p-value = 5.94 × 10−10); both regions have been previously associated with COPD. For the meta-analysis, in addition to confirming associations to the regions near CHRNA3/5 and HHIP, genome-wide significant associations were identified for FEV1 on chromosome 1 [TGFB2] (p-value = 8.99 × 10−9), 9 [DBH] (p-value = 9.69 × 10−9) and 19 [CYP2A6/7] (p-value = 3.49 × 10−8) and for FEV1/FVC on chromosome 1 [TGFB2] (p-value = 8.99 × 10−9), 4 [FAM13A] (p-value = 3.88 × 10−12), 11 [MMP3/12] (p-value = 3.29 × 10−10) and 14 [RIN3] (p-value = 5.64 × 10−9).
Conclusions
In a large genome-wide association study of lung function in smokers, we found genome-wide significant associations at several previously described loci with lung function or COPD. We additionally identified a novel genome-wide significant locus with FEV1 on chromosome 9 [DBH] in a meta-analysis of three study populations.
Electronic supplementary material
The online version of this article (doi:10.1186/s12863-015-0299-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12863-015-0299-4
PMCID: PMC4668640  PMID: 26634245
Chronic obstructive pulmonary disease; DBH; FEV1; FEV1/FVC; Genome-wide association study; Spirometry
16.  Renal impairment in cirrhosis unrelated to hepatorenal syndrome 
Regardless of etiology, the development of renal impairment in patients with cirrhosis generally leads to poor outcomes. Although hepatorenal syndrome represents the most serious complication of cirrhosis and is associated with a prognosis of weeks to months, this review focuses on other prerenal, intrinsic and postrenal causes of impairment, and acute kidney injury. The article also presents a simplified diagnostic algorithm for clinical workup for renal impairment in patients with cirrhosis.
Renal impairment is common in liver disease and may occur as a consequence of the pathophysiological changes that underpin cirrhosis or secondary to a pre-existing unrelated insult. Nevertheless, the onset of renal impairment often portends a worsening prognosis. Hepatorenal syndrome remains one of the most recognized and reported causes of renal impairment in cirrhosis. However, other causes of renal impairment occur and can be classified into prerenal, intrinsic or postrenal, which are the subjects of the present review.
PMCID: PMC4467485  PMID: 25874649
Acute kidney injury; Cirrhosis; Intrinsic renal impairment; Postrenal impairment; Prerenal impairment
17.  Common Genetic Variants Associated with Resting Oxygenation in Chronic Obstructive Pulmonary Disease 
Hypoxemia is a major complication of chronic obstructive pulmonary disease (COPD) that correlates with disease prognosis. Identifying genetic variants associated with oxygenation may provide clues for deciphering the heterogeneity in prognosis among patients with COPD. However, previous genetic studies have been restricted to investigating COPD candidate genes for association with hypoxemia. To report results from the first genome-wide association study (GWAS) of resting oxygen saturation (as measured by pulse oximetry [Spo2]) in subjects with COPD, we performed a GWAS of Spo2 in two large, well characterized COPD populations: COPDGene, including both the non-Hispanic white (NHW) and African American (AA) groups, and Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE). We identified several suggestive loci (P < 1 × 10−5) associated with Spo2 in COPDGene in the NHW (n = 2810) and ECLIPSE (n = 1758) groups, and two loci on chromosomes 14 and 15 in the AA group (n = 820) from COPDGene achieving a level of genome-wide significance (P < 5 × 10−8). The chromosome 14 single-nucleotide polymorphism, rs6576132, located in an intergenic region, was nominally replicated (P < 0.05) in the NHW group from COPDGene. The chromosome 15 single-nucleotide polymorphisms were rare in subjects of European ancestry, so the results could not be replicated. The chromosome 15 region contains several genes, including TICRR and KIF7, and is proximal to RHCG (Rh family C glyocoprotein gene). We have identified two loci associated with resting oxygen saturation in AA subjects with COPD, and several suggestive regions in subjects of European descent with COPD. Our study highlights the importance of investigating the genetics of complex traits in different racial groups.
doi:10.1165/rcmb.2014-0135OC
PMCID: PMC4224086  PMID: 24825563
chronic obstructive pulmonary disease; hypoxemia; pulse oximetry; genome-wide association study; oxygen saturation
18.  An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1-antitrypsin upon ligand binding 
Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whereas ion mobility (IM)-MS can report on conformational behavior of specific states. We used IM-MS to study a conformationally labile protein (α1-antitrypsin) that undergoes pathological polymerization in the context of point mutations. The folded, native state of the Z-variant remains highly polymerogenic in physiological conditions despite only minor thermodynamic destabilization relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z α1-antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behavior in detail by studying the effects of peptide binding on α1-antitrypsin conformation and dynamics. IM-MS is, therefore, an ideal platform for the screening of compounds that result in therapeutically beneficial kinetic stabilization of native α1-antitrypsin. Our findings are confirmed with high-resolution X-ray crystallographic and nuclear magnetic resonance spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue-specific level. IM-MS methods, therefore, have great potential for further study of biologically relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterization of ligand interactions of therapeutic interest.
PDB Code(s): 4PYW
doi:10.1002/pro.2706
PMCID: PMC4534181  PMID: 26011795
ion mobility mass spectrometry; protein dynamics; drug discovery; α1-antitrypsin; protein unfolding; mass spectrometry/methods; nuclear magnetic resonance; biomolecular; X-ray crystallography
20.  An antibody raised against a pathogenic serpin variant induces mutant-like behaviour in the wild-type protein 
Biochemical Journal  2015;468(Pt 1):99-108.
A monoclonal antibody (mAb) that binds to a transient intermediate may act as a catalyst for the corresponding reaction; here we show this principle can extend on a macro molecular scale to the induction of mutant-like oligomerization in a wild-type protein. Using the common pathogenic E342K (Z) variant of α1-antitrypsin as antigen–whose native state is susceptible to the formation of a proto-oligomeric intermediate–we have produced a mAb (5E3) that increases the rate of oligomerization of the wild-type (M) variant. Employing ELISA, gel shift, thermal stability and FRET time-course experiments, we show that mAb5E3 does not bind to the native state of α1-antitrypsin, but recognizes a cryptic epitope in the vicinity of the post-helix A loop and strand 4C that is revealed upon transition to the polymerization intermediate, and which persists in the ensuing oligomer. This epitope is not shared by loop-inserted monomeric conformations. We show the increased amenity to polymerization by either the pathogenic E342K mutation or the binding of mAb5E3 occurs without affecting the energetic barrier to polymerization. As mAb5E3 also does not alter the relative stability of the monomer to intermediate, it acts in a manner similar to the E342K mutant, by facilitating the conformational interchange between these two states.
We show that a monoclonal antibody can act as a ‘molecular template’ in aberrant protein oligomerization, and the transient intermediate of α1-antitrypsin, a key to the molecular mechanism of disease pathogenesis, expresses a cryptic epitope also present in the oligomer.
doi:10.1042/BJ20141569
PMCID: PMC4422257  PMID: 25738741
aggregation; antibody; α1-antitrypsin; polymerization; protein stability; AF488, Alexa Fluor 488 dye; AF594, Alexa Fluor 594 dye; AT, α1-antitrypsin; ER, endoplasmic reticulum; H/D exchange, hydrogen/deuterium exchange; HRP, horseradish peroxidase; mAb, monoclonal antibody; PBS, phosphate-buffered saline
21.  Emergence of a Stage-Dependent Human Liver Disease Signature with Directed Differentiation of Alpha-1 Antitrypsin-Deficient iPS Cells 
Stem Cell Reports  2015;4(5):873-885.
Summary
Induced pluripotent stem cells (iPSCs) provide an inexhaustible source of cells for modeling disease and testing drugs. Here we develop a bioinformatic approach to detect differences between the genomic programs of iPSCs derived from diseased versus normal human cohorts as they emerge during in vitro directed differentiation. Using iPSCs generated from a cohort carrying mutations (PiZZ) in the gene responsible for alpha-1 antitrypsin (AAT) deficiency, we find that the global transcriptomes of PiZZ iPSCs diverge from normal controls upon differentiation to hepatic cells. Expression of 135 genes distinguishes PiZZ iPSC-hepatic cells, providing potential clues to liver disease pathogenesis. The disease-specific cells display intracellular accumulation of mutant AAT protein, resulting in increased autophagic flux. Furthermore, we detect beneficial responses to the drug carbamazepine, which further augments autophagic flux, but adverse responses to known hepatotoxic drugs. Our findings support the utility of iPSCs as tools for drug development or prediction of toxicity.
Graphical Abstract
Highlights
•Patient iPSC-hepatic cells model disease features that normalize with gene editing•Disease-specific transcriptomic signature emerges only upon hepatic differentiation•Patient iPSC-hepatic cells are used to test response to drugs or toxicity in vitro
In this report, Kotton and colleagues examine the global transcriptomic and epigenomic programs of iPSCs derived from diseased (AAT-deficient PiZZ) or normal human cohorts during directed differentiation. The PiZZ transcriptome diverges from controls upon reaching hepatic stage, when AAT is first expressed, providing potential clues to liver disease pathogenesis. PiZZ iPSC-hepatic cells model key liver disease features and demonstrate both therapeutic drug responsiveness and sensitivity to toxic agents.
doi:10.1016/j.stemcr.2015.02.021
PMCID: PMC4437473  PMID: 25843048
22.  Myxomaviral Anti-Inflammatory Serpin Reduces Myeloid-Derived Suppressor Cells and Human Pancreatic Cancer Cell Growth in Mice 
Modification of the tumor microenvironment by inflammatory cells represents a newly recognized driving force in cancer with critical roles in tumor invasion, growth, angiogenesis, and metastasis. Increased thrombolytic cascade serine proteases, specifically urokinase-type plasminogen activator and its receptor, correlate with inflammatory cell migration, pancreatic cancer growth, invasion and unfavorable outcomes. Inflammation in pancreatic cancer is linked with myeloid-derived suppressor cell (MDSC) activity and cancer progression. Myxomavirus is a complex DNA virus encoding highly potent immune modulators. Serp-1 and M-T7 are two such secreted anti-inflammatory myxomaviral proteins. Serp-1 inhibits uPA, plasmin and coagulation factor X while M-T7 inhibits C, CC, and CXC chemokines. We have explored the potential use of these viral proteins for treatment of a range of human cancer isolates engrafted in severe combined immunodeficient (SCID) mice. Engrafted tumors were treated with either Serp-1, neuroserpin, a related mammalian serpin that inhibits thrombolytic proteases, or M-T7. Serp-1 and neuroserpin inhibited growth of the pancreatic cancer cell line Hs766t (P=0.03 and P=0.01, respectively) at 4 weeks after implantation. Serp-1 also inhibited growth of a second pancreatic cancer cell line MIA PaCa-2 in mice (P=0.02). Growth of the human breast cancer line MDA231 was not inhibited by Serp-1. M-T7, in contrast, did not alter growth of any of the cancer cell lines tested after implant into SCID mice. Serpin inhibition of pancreatic tumor growth was associated with a significant decrease in splenocyte MDSC counts by flow cytometry (P=0.009), without detected change in other splenocyte subpopulations. Serp-1 and NSP treatment also significantly reduced macrophage infiltration in tumors (P=0.001). In summary two anti-inflammatory serpins reduced inflammatory macrophage invasion and pancreatic tumor cell growth, suggesting potential therapeutic efficacy.
doi:10.4172/1948-5956.1000219
PMCID: PMC4367486  PMID: 25798214
Serpin; Serp-1; Pancreatic cancer; Myeloid-derived suppressor cell; Tumor-associated macrophage
23.  A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity 
The FASEB Journal  2015;29(6):2667-2678.
Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.—Ordóñez, A., Pérez, J., Tan, L., Dickens, J. A., Motamedi-Shad, N., Irving, J. A., Haq, I., Ekeowa, U., Marciniak, S. J., Miranda, E., Lomas, D. A. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity.
doi:10.1096/fj.14-267351
PMCID: PMC4548814  PMID: 25757566
monoclonal antibody; scFv intrabody; serpin polymer; liver disease
24.  Quantitative Computed Tomography Measures of Pectoralis Muscle Area and Disease Severity in Chronic Obstructive Pulmonary Disease. A Cross-Sectional Study 
Rationale: Muscle wasting in chronic obstructive pulmonary disease (COPD) is associated with a poor prognosis and is not readily assessed by measures of body mass index (BMI). BMI does not discriminate between relative proportions of adipose tissue and lean muscle and may be insensitive to early pathologic changes in body composition. Computed tomography (CT)–based assessments of the pectoralis muscles may provide insight into the clinical significance of skeletal muscles in smokers.
Objectives: We hypothesized that objective assessment of the pectoralis muscle area on chest CT scans provides information that is clinically relevant and independent of BMI.
Methods: Data from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) Study (n = 73) were used to assess the relationship between pectoralis muscle area and fat-free mass. We then used data in a subset (n = 966) of a larger cohort, the COPDGene (COPD Genetic Epidemiology) Study, to explore the relationship between pectoralis muscle area and COPD-related traits.
Measurements and Main Results: We first investigated the correlation between pectoralis muscle area and fat-free mass, using data from a subset of participants in the ECLIPSE Study. We then further investigated pectoralis muscle area in COPDGene Study participants and found that higher pectoralis muscle area values were associated with greater height, male sex, and younger age. On subsequent clinical correlation, compared with BMI, pectoralis muscle area was more significantly associated with COPD-related traits, including spirometric measures, dyspnea, and 6-minute-walk distance (6MWD). For example, on average, each 10-cm2 increase in pectoralis muscle area was associated with a 0.8-unit decrease in the BODE (Body mass index, Obstruction, Dyspnea, Exercise) index (95% confidence interval, –1.0 to –0.6; P < 0.001). Furthermore, statistically significant associations between pectoralis muscle area and COPD-related traits remained even after adjustment for BMI.
Conclusions: CT-derived pectoralis muscle area provides relevant indices of COPD morbidity that may be more predictive of important COPD-related traits than BMI. However, the relationship with clinically relevant outcomes such as hospitalization and death requires additional investigation. Pectoralis muscle area is a convenient measure that can be collected in the clinical setting in addition to BMI.
doi:10.1513/AnnalsATS.201307-229OC
PMCID: PMC4028743  PMID: 24558953
COPD; wasting; pectoral muscle area; imaging
25.  Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis 
The Lancet. Respiratory medicine  2014;2(3):214-225.
Background
The genetic risk factors for susceptibility to chronic obstructive pulmonary disease (COPD) are still largely unknown. Additional genetic variants are likely to be identified by genome-wide association studies in larger cohorts or specific subgroups.
Methods
Genome-wide association analysis in COPDGene (non-Hispanic whites and African-Americans) was combined with existing data from the ECLIPSE, NETT/NAS, and GenKOLS (Norway) studies. Analyses were performed both using all moderate-to-severe cases and the subset of severe cases. Top loci not previously described as genome-wide significant were genotyped in the ICGN study, and results combined in a joint meta-analysis.
Findings
Analysis of a total of 6,633 moderate-to-severe cases and 5,704 controls confirmed association at three known loci: CHRNA3/CHRNA5/IREB2, FAM13A, and HHIP (10−12 < P < 10−14), and also showed significant evidence of association at a novel locus near RIN3 (overall P, including ICGN = 5•4×10−9). In the severe COPD analysis (n=3,497), the effects at two of three previously described loci were significantly stronger; we also identified two additional loci previously reported to affect gene expression of MMP12 and TGFB2 (overall P = 2•6x10−9 and 8•3×10−9). RIN3 and TGFB2 expression levels were reduced in a set of Lung Tissue Research Consortium COPD lung tissue samples compared with controls.
Interpretation
In a genome-wide study of COPD, we confirmed associations at three known loci and found additional genome-wide significant associations with moderate-to-severe COPD near RIN3 and with severe COPD near MMP12 and TGFB2. Genetic variants, apart from alpha-1 antitrypsin deficiency, increase the risk of COPD. Our analysis of severe COPD suggests additional genetic variants may be identified by focusing on this subgroup.
Funding
National Heart, Lung, and Blood Institute; the COPD Foundation through contributions from AstraZeneca, Boehringer Ingelheim, Novartis, and Sepracor; GlaxoSmithKline; Centers for Medicare and Medicaid Services; Agency for Healthcare Research and Quality; US Department of Veterans Affairs.
doi:10.1016/S2213-2600(14)70002-5
PMCID: PMC4176924  PMID: 24621683

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