Predictors of Nicotine Replacement Therapy Adherence: Mixed-Methods Research With a Convergent Parallel Design

BACKGROUND

Few studies have examined the effect of baseline attitudes toward nicotine replacement therapy (NRT) on its actual adherence in a smoking cessation intervention.

PURPOSE

This study (i) examined the predictability of baseline variables (quantitative data) on NRT adherence and (ii) explored the congruence of participants' statements about NRT products (qualitative data) during counseling sessions with their baseline attitudes.

METHODS

This is a mixed-methods research study using a convergent parallel design. Participants included 74 individuals in the treatment group who received behavioral counseling and combination NRT. A Poisson regression analysis was performed to identify baseline variables predicting NRT adherence. Thematic analysis was completed with a subset of participants (n = 38) who varied in NRT attitude scores and adherence. A joint display was created to integrate quantitative and qualitative data and discover convergence.

RESULTS

Approximately 59% of the participants (41/74) used NRT continuously for ≥5 weeks. Having negative attitudes toward NRT and depressive symptoms predicted NRT adherence even after controlling for education and anxiety symptoms. Thematic analysis revealed that NRT adherence is a learning process that consists of the following three distinctive but interrelated phases: (i) information needs, (ii) comprehensive readiness, and (iii) experiential learning. Of the 38 participants, 34 (89.5%) showed convergence between baseline attitude scores and statements about NRT made during counseling sessions.

CONCLUSIONS

Individuals who have negative attitudes toward NRT are less likely to use the products in a smoking cessation intervention. Counselors should assess attitudes toward NRT at baseline and address them proactively during counseling sessions.

Machine learning models for blood pressure phenotypes combining multiple polygenic risk scores

We construct non-linear machine learning (ML) prediction models for systolic and diastolic blood pressure (SBP, DBP) using demographic and clinical variables and polygenic risk scores (PRSs). We developed a two-model ensemble, consisting of a baseline model, where prediction is based on demographic and clinical variables only, and a genetic model, where we also include PRSs. We evaluate the use of a linear versus a non-linear model at both the baseline and the genetic model levels and assess the improvement in performance when incorporating multiple PRSs. We report the ensemble model's performance as percentage variance explained (PVE) on a held-out test dataset. A non-linear baseline model improved the PVEs from 28.1% to 30.1% (SBP) and 14.3% to 17.4% (DBP) compared with a linear baseline model. Including seven PRSs in the genetic model computed based on the largest available GWAS of SBP/DBP improved the genetic model PVE from 4.8% to 5.1% (SBP) and 4.7% to 5% (DBP) compared to using a single PRS. Adding additional 14 PRSs computed based on two independent GWASs further increased the genetic model PVE to 6.3% (SBP) and 5.7% (DBP). PVE differed across self-reported race/ethnicity groups, with primarily all non-White groups benefitting from the inclusion of additional PRSs.

Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: the Framingham Heart Study

Expression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression. The present study describes an eQTM resource of CpG-transcript pairs derived from whole blood DNA methylation and RNA sequencing gene expression data in 2115 Framingham Heart Study participants. We identified 70,047 significant cis CpG-transcript pairs at p < 1E-7 where the top most significant eGenes (i.e., gene transcripts associated with a CpG) were enriched in biological pathways related to cell signaling, and for 1208 clinical traits (enrichment false discovery rate [FDR] ≤ 0.05). We also identified 246,667 significant trans CpG-transcript pairs at p < 1E-14 where the top most significant eGenes were enriched in biological pathways related to activation of the immune response, and for 1191 clinical traits (enrichment FDR ≤ 0.05). Independent and external replication of the top 1000 significant cis and trans CpG-transcript pairs was completed in the Women's Health Initiative and Jackson Heart Study cohorts. Using significant cis CpG-transcript pairs, we identified significant mediation of the association between CpG sites and cardiometabolic traits through gene expression and identified shared genetic regulation between CpGs and transcripts associated with cardiometabolic traits. In conclusion, we developed a robust and powerful resource of whole blood eQTM CpG-transcript pairs that can help inform future functional studies that seek to understand the molecular basis of disease.

Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants

Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-sequencing data in GTEx V8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased whole genome sequencing data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.

Blood Gene Expression and Immune Cell Subtypes Associated with Chronic Obstructive Pulmonary Disease Exacerbations

Rationale: Acute exacerbations of chronic obstructive pulmonary disease (AE-COPDs) are associated with a significant disease burden. Blood immune phenotyping may improve our understanding of a COPD endotype at increased risk of exacerbations. Objective: To determine the relationship between the transcriptome of circulating leukocytes and COPD exacerbations. Methods: Blood RNA sequencing data (n = 3,618) from the COPDGene (Genetic Epidemiology of COPD) study were analyzed. Blood microarray data (n = 646) from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study were used for validation. We tested the association between blood gene expression and AE-COPDs. We imputed the abundance of leukocyte subtypes and tested their association with prospective AE-COPDs. Flow cytometry was performed on blood in SPIROMICS (Subpopulations and Intermediate Outcomes in COPD Study) (n = 127), and activation markers for T cells were tested for association with prospective AE-COPDs. Measurements and Main Results: Exacerbations were reported 4,030 and 2,368 times during follow-up in COPDGene (5.3 ± 1.7 yr) and ECLIPSE (3 yr), respectively. We identified 890, 675, and 3,217 genes associated with a history of AE-COPDs, persistent exacerbations (at least one exacerbation per year), and prospective exacerbation rate, respectively. In COPDGene, the number of prospective exacerbations in patients with COPD (Global Initiative for Chronic Obstructive Lung Disease stage ⩾2) was negatively associated with circulating CD8+ T cells, CD4+ T cells, and resting natural killer cells. The negative association with naive CD4+ T cells was replicated in ECLIPSE. In the flow-cytometry study, an increase in CTLA4 on CD4+ T cells was positively associated with AE-COPDs. Conclusions: Individuals with COPD with lower circulating lymphocyte counts, particularly decreased CD4+ T cells, are more susceptible to AE-COPDs, including persistent exacerbations.

Lung Imaging in COPD Part 2: Emerging Concepts

The diagnosis, prognostication, and differentiation of phenotypes of COPD can be facilitated by CT scan imaging of the chest. CT scan imaging of the chest is a prerequisite for lung volume reduction surgery and lung transplantation. Quantitative analysis can be used to evaluate extent of disease progression. Evolving imaging techniques include micro-CT scan, ultra-high-resolution and photon-counting CT scan imaging, and MRI. Potential advantages of these newer techniques include improved resolution, prediction of reversibility, and obviation of radiation exposure. This article discusses important emerging techniques in imaging patients with COPD. The clinical usefulness of these emerging techniques as they stand today are tabulated for the benefit of the practicing pulmonologist.

Clinical Features of Genetic Resilience in Chronic Obstructive Pulmonary Disease

Introduction

In the personalized risk quantification of chronic obstructive pulmonary disease (COPD), genome-wide association studies and polygenic risk scores (PRS) complement traditional risk factors, such as age and cigarette smoking. However, despite being at considerable levels of risk, some individuals do not develop COPD. Research on COPD resilience remains largely unexplored.

Methods

We applied the previously published COPD PRS to whole genome sequencing data from non-Hispanic white and African American individuals in the COPDGene study. We defined genetic resilience as individuals unaffected by COPD with a polygenic risk score above the 90 ^th percentile. We defined risk-matched case individuals as those with COPD (i.e., FEV ₁ /FVC < 0.70) and a PRS above the 90 ^th percentile. We defined low risk individuals without COPD (i.e., FEV ₁ /FVC > 0.70) as a polygenic risk score below the 10 ^th percentile. We compared genetically resilient individuals to risk-matched individuals with COPD and low risk individuals by demographics, lung function, respiratory symptoms, co-morbidities, and chest CT scan measurements. We also performed survival analyses, differential expression analysis, and matching for sensitivity analyses.

Results

We identified 211 resilient individuals without COPD, 605 genetic risk-matched individuals with COPD, and 527 low-risk individuals without COPD. Resilient individuals had higher FEV ₁ % predicted and lower percent emphysema. In contrast, resilient individuals had higher airway wall thickness compared to low-risk unaffected individuals. While there was no difference in survival between low-risk and resilient individuals, resilient individuals had higher survival compared to risk matched cases. We also identified two genes that were differentially expressed between low-risk unaffected individuals and resilient individuals.

Conclusion

Genetically resilient individuals had a reduced burden of COPD disease-related measures compared to risk-matched cases but had subtly increased measures compared to low-risk unaffected individuals. Further genetic studies will be needed to illuminate the underlying pathobiology of our observations.

Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants

Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-seq data in GTEx v8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased WGS data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.

Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis

BACKGROUND

Chronic obstructive pulmonary disease (COPD) varies significantly in symptomatic and physiologic presentation. Identifying disease subtypes from molecular data, collected from easily accessible blood samples, can help stratify patients and guide disease management and treatment.

METHODS

Blood gene expression measured by RNA-sequencing in the COPDGene Study was analyzed using a network perturbation analysis method. Each COPD sample was compared against a learned reference gene network to determine the part that is deregulated. Gene deregulation values were used to cluster the disease samples.

RESULTS

The discovery set included 617 former smokers from COPDGene. Four distinct gene network subtypes are identified with significant differences in symptoms, exercise capacity and mortality. These clusters do not necessarily correspond with the levels of lung function impairment and are independently validated in two external cohorts: 769 former smokers from COPDGene and 431 former smokers in the Multi-Ethnic Study of Atherosclerosis (MESA). Additionally, we identify several genes that are significantly deregulated across these subtypes, including DSP and GSTM1, which have been previously associated with COPD through genome-wide association study (GWAS).

CONCLUSIONS

The identified subtypes differ in mortality and in their clinical and functional characteristics, underlining the need for multi-dimensional assessment potentially supplemented by selected markers of gene expression. The subtypes were consistent across cohorts and could be used for new patient stratification and disease prognosis.

An interferon-inducible signature of airway disease from blood gene expression profiling

BACKGROUND

The molecular basis of airway remodelling in chronic obstructive pulmonary disease (COPD) remains poorly understood. We identified gene expression signatures associated with chest computed tomography (CT) scan airway measures to understand molecular pathways associated with airway disease.

METHODS

In 2396 subjects in the COPDGene Study, we examined the relationship between quantitative CT airway phenotypes and blood transcriptomes to identify airway disease-specific genes and to define an airway wall thickness (AWT) gene set score. Multivariable regression analyses were performed to identify associations of the AWT score with clinical phenotypes, bronchial gene expression and genetic variants.

RESULTS

Type 1 interferon (IFN)-induced genes were consistently associated with AWT, square root wall area of a hypothetical airway with 10 mm internal perimeter (Pi10) and wall area percentage, with the strongest enrichment in AWT. A score derived from 18 genes whose expression was associated with AWT was associated with COPD-related phenotypes including reduced lung function (forced expiratory volume in 1 s percentage predicted β= -3.4; p<0.05) and increased exacerbations (incidence rate ratio 1.7; p<0.05). The AWT score was reproducibly associated with AWT in bronchial samples from 23 subjects (β=3.22; p<0.05). The blood AWT score was associated with genetic variant rs876039, an expression quantitative trait locus for IKZF1, a gene that regulates IFN signalling and is associated with inflammatory diseases.

CONCLUSIONS

A gene expression signature with IFN-stimulated genes from peripheral blood and bronchial brushings is associated with CT AWT, lung function and exacerbations. Shared genes and genetic associations suggest viral responses and/or autoimmune dysregulation as potential underlying mechanisms of airway disease in COPD.

Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

α1-anti-trypsin (A1AT), encoded by SERPINA1, is a neutrophil elastase inhibitor that controls the inflammatory response in the lung. Severe A1AT deficiency increases risk for Chronic Obstructive Pulmonary Disease (COPD), however, the role of A1AT in COPD in non-deficient individuals is not well known. We identify a 2.1-fold increase (p = 2.5x10-6) in the use of a distal poly-adenylation site in primary lung tissue RNA-seq in 82 COPD cases when compared to 64 controls and replicate this in an independent study of 376 COPD and 267 controls. This alternative polyadenylation event involves two sites, a proximal and distal site, 61 and 1683 nucleotides downstream of the A1AT stop codon. To characterize this event, we measured the distal ratio in human primary tissue short read RNA-seq data and corroborated our results with long read RNA-seq data. Integrating these results with 3' end RNA-seq and nanoluciferase reporter assay experiments we show that use of the distal site yields mRNA transcripts with over 50-fold decreased translation efficiency and A1AT expression. We identified seven RNA binding proteins using enhanced CrossLinking and ImmunoPrecipitation precipitation (eCLIP) with one or more binding sites in the SERPINA1 3' UTR. We combined these data with measurements of the distal ratio in shRNA knockdown experiments, nuclear and cytoplasmic fractionation, and chemical RNA structure probing. We identify Quaking Homolog (QKI) as a modulator of SERPINA1 mRNA translation and confirm the role of QKI in SERPINA1 translation with luciferase reporter assays. Analysis of single-cell RNA-seq showed differences in the distribution of the SERPINA1 distal ratio among hepatocytes, macrophages, αβ-Tcells and plasma cells in the liver. Alveolar Type 1,2, dendritic cells and macrophages also vary in their distal ratio in the lung. Our work reveals a complex post-transcriptional mechanism that regulates alternative polyadenylation and A1AT expression in COPD.

Emphysema Progression and Lung Function Decline Among Angiotensin Converting Enzyme Inhibitors and Angiotensin-Receptor Blockade Users in the COPDGene Cohort

BACKGROUND

Attenuation of transforming growth factor β by blocking angiotensin II has been shown to reduce emphysema in a murine model. General population studies have demonstrated that the use of angiotensin converting enzyme inhibitors (ACEis) and angiotensin-receptor blockers (ARBs) is associated with reduction of emphysema progression in former smokers and that the use of ACEis is associated with reduction of FEV₁ progression in current smokers.

RESEARCH QUESTION

Is use of ACEi and ARB associated with less progression of emphysema and FEV₁ decline among individuals with COPD or baseline emphysema?

METHODS

Former and current smokers from the Genetic Epidemiology of COPD Study who attended baseline and 5-year follow-up visits, did not change smoking status, and underwent chest CT imaging were included. Adjusted linear mixed models were used to evaluate progression of adjusted lung density (ALD), percent emphysema (%total lung volume <-950 Hounsfield units [HU]), 15th percentile of the attenuation histogram (attenuation [in HU] below which 15% of voxels are situated plus 1,000 HU), and lung function decline over 5 years between ACEi and ARB users and nonusers in those with spirometry-confirmed COPD, as well as all participants and those with baseline emphysema. Effect modification by smoking status also was investigated.

RESULTS

Over 5 years of follow-up, compared with nonusers, ACEi and ARB users with COPD showed slower ALD progression (adjusted mean difference [aMD], 1.6; 95% CI, 0.34-2.9). Slowed lung function decline was not observed based on phase 1 medication (aMD of FEV₁ % predicted, 0.83; 95% CI, -0.62 to 2.3), but was when analysis was limited to consistent ACEi and ARB users (aMD of FEV₁ % predicted, 1.9; 95% CI, 0.14-3.6). No effect modification by smoking status was found for radiographic outcomes, and the lung function effect was more pronounced in former smokers. Results were similar among participants with baseline emphysema.

INTERPRETATION

Among participants with spirometry-confirmed COPD or baseline emphysema, ACEi and ARB use was associated with slower progression of emphysema and lung function decline.

TRIAL REGISTRY

ClinicalTrials.gov; No.: NCT00608764; URL: www.clinicaltrials.gov.

Age-related loss of gene-to-gene transcriptional coordination among single cells

A long-standing model holds that stochastic aberrations of transcriptional regulation play a key role in the process of ageing. While transcriptional dysregulation is observed in many cell types in the form of increased cell-to-cell variability, its generality to all cell types remains doubted. Here, we propose a new approach for analysing transcriptional regulation in single-cell RNA sequencing data by focusing on the global coordination between the genes rather than the variability of individual genes or correlations between pairs of genes. Consistently, across very different organisms and cell types, we find a decrease in the gene-to-gene transcriptional coordination in ageing cells. In addition, we find that loss of gene-to-gene transcriptional coordination is associated with high mutational load of a specific, age-related signature and with radiation-induced DNA damage. These observations suggest a general, potentially universal, stochastic attribute of transcriptional dysregulation in ageing.

Integrated transcriptomic correlation network analysis identifies COPD molecular determinants

Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called "switch genes" - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.

Turning subtypes into disease axes to improve prediction of COPD progression

Chronic obstructive pulmonary disease (COPD) is an umbrella definition encompassing multiple disease processes. COPD heterogeneity has been described as distinct subgroups of individuals (subtypes) or as continuous measures of COPD variability (disease axes). There is little consensus on whether subtypes or disease axes are preferred, and the relative value of disease axes and subtypes for predicting COPD progression is unknown. Using a propensity score approach to learn disease axes from pairs of subtypes, we demonstrate that these disease axes predict prospective forced expiratory volume in 1 s decline and emphysema progression more accurately than the subtype pairs from which they were derived.

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

BACKGROUND

Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants.

METHODS

We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance.

RESULTS

The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies.

CONCLUSIONS

Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.

Genomics and response to long-term oxygen therapy in chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, and long-term oxygen therapy has been shown to reduce mortality in COPD patients with severe hypoxemia. However, the Long-term Oxygen Treatment Trial (LOTT), a large randomized trial, found no benefit of oxygen therapy in COPD patients with moderate hypoxemia. We hypothesized that there may be differences in response to oxygen which depend on genotype or gene expression. In a genome-wide time-to-event analysis of the primary outcome of death or hospitalization in 331 subjects, 97 single nucleotide polymorphisms (SNPs) showed evidence of interaction with oxygen therapy at P < 1e-5, including 7 SNPs near arylsulfatase B (ARSB; P = 6e-6). In microarray expression profiling on 51 whole blood samples from 37 individuals, at screening and/or at 12-month follow-up, ARSB expression was associated with the primary outcome depending on oxygen treatment. The significant SNPs were conditional expression quantitative trait loci for ARSB expression. In a network analysis of genes affected by long-term oxygen, two observed clusters including 26 co-expressed genes were enriched in mitochondrial function. Using data from the observational COPDGene Study, we validated the expression of 25 of these 26 genes, plus ARSB. The effect of long-term oxygen therapy in COPD varied based on ARSB expression and genotype. ARSB has previously been shown to be associated with hypoxemia in human bronchial and colonic epithelial cells and in a mouse model. In peripheral blood, long-term oxygen treatment affected expression of mitochondrial-related genes, a biologically relevant pathway in COPD. SNPs and expression of ARSB are associated with response to long-term oxygen in COPD. The ARSB SNPs were expression quantitative trait loci depending on oxygen therapy. Genes differentially expressed by long-term oxygen were enriched in mitochondrial functions. This suggests a potential biomarker to personalize use of long-term oxygen in COPD.

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p < 8 X 10-10) pQTLs in 38 (43%) of blood proteins tested. Most pQTL SNPs were novel with low overlap to eQTL SNPs. The pQTL SNPs explained >10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10-392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group.

Genetic regulation of expression of leukotriene A4 hydrolase

In chronic inflammatory lung disorders such as chronic obstructive pulmonary disease (COPD), the concurrent organ-specific and systemic inflammatory responses lead to airway remodelling and vascular dysfunction. Although a major common risk factor for COPD, cigarette smoke alone cannot explain the progression of this disease; there is increasing evidence that genetic predisposition also plays a role in COPD susceptibility and progression. A key enzyme in chronic lung inflammation is leukotriene A4 hydrolase (LTA4H). With its aminopeptidase activity, LTA4H degrades the neutrophil chemoattractant tripeptide PGP. In this study, we used the luciferase reporter gene analysis system and quantitative trait locus analysis to explore the impact of single-nucleotide polymorphisms (SNPs) in the putative promoter region of LTA4H on LTA4H expression. We show that not only is the putative promoter of LTA4H larger than previously reported but also that SNPs in the expanded promoter region regulate expression of LTA4H both in cell-based systems and in peripheral blood samples from human subjects. These findings provide significant evidence for an active region upstream of the previously reported LTA4H promoter, which may have implications related to ongoing inflammatory processes in chronic lung disease.

COPD subtypes identified by network-based clustering of blood gene expression

One of the most common smoking-related diseases, chronic obstructive pulmonary disease (COPD), results from a dysregulated, multi-tissue inflammatory response to cigarette smoke. We hypothesized that systemic inflammatory signals in genome-wide blood gene expression can identify clinically important COPD-related disease subtypes, and we leveraged pre-existing gene interaction networks to guide unsupervised clustering of blood microarray expression data. Using network-informed non-negative matrix factorization, we analyzed genome-wide blood gene expression from 229 former smokers in the ECLIPSE Study, and we identified novel, clinically relevant molecular subtypes of COPD. These network-informed clusters were more stable and more strongly associated with measures of lung structure and function than clusters derived from a network-naïve approach, and they were associated with subtype-specific enrichment for inflammatory and protein catabolic pathways. These clusters were successfully reproduced in an independent sample of 135 smokers from the COPDGene Study.

Comparison of metaiodobenzylguanidine scintigraphy with positron emission tomography in the diagnostic work-up of pheochromocytoma and paraganglioma: a systematic review

AIM

The aim of this paper was to systematically review published data about the comparison of radiolabelled metaiodobenzylguanidine (MIBG) scintigraphy and positron emission tomography (PET) with different radiopharmaceuticals in patients with pheochromocytoma and paraganglioma (Pheo/PGL).

METHODS

A comprehensive literature search of studies published in PubMed/MEDLINE and Embase databases through September 2012 and regarding MIBG scintigraphy and PET imaging with different radiopharmaceuticals in patients with Pheo/PGL was carried out.

RESULTS

Twenty-eight studies comprising 852 patients who underwent both MIBG scintigraphy and PET or PET/CT with different radiopharmaceuticals were included and discussed. Three studies evaluated carbon-11-hydroxyephedrine ([11C]HED) as PET radiopharmaceutical, nine studies fluorine-18-dopamine ([18F]DA), eight studies fluorine-18-dihydroxyphenylalanine ([18F]DOPA), twelve studies fluorine-18-fluorodeoxyglucose ([18F]FDG) and five studies gallium-68-somatostatin analogues.

CONCLUSIONS

Despite the heterogeneity of the studies included in the analysis, it can be concluded that the diagnostic performance of PET with various agents is clearly superior to that of MIBG scintigraphy in patients with Pheo/PGL, mainly for familial, extra-adrenal and metastatic diseases; however, MIBG maintains a unique role in selecting patients suitable for 131I-MBG therapy. Further larger prospective studies comparing MIBG and different PET tracers in patients with Pheo/PGL as well as a cost-effectiveness analysis of the two techniques are needed.

A qualitative study of stakeholder views of the conditions for and outcomes of successful clinical networks

Background

Clinical networks have been established to improve health outcomes and processes of care by implementing a range of innovations and undertaking projects based on perceived local need. Limited research exists on the necessary conditions required to bring about successful network outcomes and what characterises network success from the perspective of those involved in network initiatives. This qualitative study identified stakeholder views on i) the conditions for effective clinical networks; and ii) desirable outcomes of successful clinical networks.

Methods

Twenty-seven participants were interviewed using face-to-face audio-recorded semi-structured interviews. Transcribed data were coded and analysed to generate themes relating to the study aims.

Results

Five key factors represented as sub-themes were identified as important conditions for the establishment of successful clinical networks under the main theme of effective network structure, organisation and governance. These were: building relationships; effective leadership; strategic evidence-based workplans; adequate resources; and ability to implement and evaluate network initiatives. Two major themes encapsulated views on desirable outcomes of successful clinical networks: connecting and engaging which represented the outcomes of interdisciplinary and consumer collaboration and, partnerships with state health and local health services, and changing the landscape of care, which represented the importance of outcomes associated with improving services, care and patient health outcomes and implementing evidence-based practice.

Conclusions

This study provides new knowledge on the conditions needed to establish successful clinical networks and on desirable outcomes arising from network projects and initiatives that are considered to be valuable by those working in or associated with clinical networks. This provides health services with information on what needs to be in place for successful networks and on the types of outcomes that can be considered for assessing network effectiveness.

An unusual case of adrenal metastasis from colorectal cancer: computed tomography and fluorine 18-fluoro-deoxy-glucose positron emission tomography-computed tomography features and literature review

Incidentally discovered adrenal masses are a common diagnostic problem. While computed tomography (CT) and magnetic resonance (MR) imaging can adequately characterize most benign or malignant adrenal masses, in some cases the results are indeterminate. We report and discuss a case of an adrenal metastasis with misleading clinical and CT features, in which an abnormal metabolic uptake detected through fluorine 18-fluoro-deoxy-glucose positron emission tomography (¹⁸F-FDG PET)-CT raised the suspicion of adrenal metastasis relatively early compared with apparently normal results on repeated follow-up CT examinations.

CYP2D6 testing to predict response to tamoxifen in women with breast cancer: Pharmacogenomic

Tamoxifen, a selective estrogen receptor modulator, is the standard of care for premenopausal women with estrogen or progesterone receptor-positive breast cancer and a valid option for treating post-menopausal women. However, a substantial number of tamoxifen-treated patients relapse following surgical resection, while others remain disease-free for many years. It appears that the primary effectors of tamoxifen activity are its active metabolites, rather than tamoxifen itself. Cytochrome P450 (CYP) enzymes, CYP2D6 in particular, play a major role in the metabolism of tamoxifen to active metabolites. More than 75 germline CYP2D6 variants have been identified.

A test predicting lack of response to tamoxifen could supplement information used by clinicians and patients in treatment decision-making. For example, physicians and patients may opt to switch to an alternative therapy upfront.

A compendium of genome-wide associations for cancer: critical synopsis and reappraisal

Since 2007, genome-wide association (GWA) studies have identified numerous well-supported, novel genetic risk loci for common cancers; however, there are concerns that this technology is reaching its limits. We provide an overview of GWA-identified genetic associations with solid tumors. We simulated the distribution of population risk alleles for colorectal, prostate, testicular, and thyroid cancers based on genetic variants identified in GWA studies. We also evaluated whether statistical power to detect typical genetic effects could be improved with studies performing GWA analyses of all available samples rather than multistage designs. Fifty-six eligible articles yielded 92 eligible associations between cancer phenotypes and genetic variants with a median per-allele odds ratio (OR) of 1.22 (interquartile range = 1.15-1.36). Half of the associations pertained to prostate, colorectal, or breast cancer. Individuals at the upper quartile of simulated risk had only 2.1- to 4.2-fold higher relative risk than those in the lower quartile. Comprehensive evaluation of currently available samples with GWA platforms would yield few additional variants with per-allele OR = 1.4, but many more variants with OR = 1.2 could be detected; statistical power to detect weak associations (OR = 1.07) would still be negligible. The GWA approach is effective in identifying common genetic variants with moderate effect; however, identifying loci with very small effects and rare variants will require major new efforts. At present, the utility of GWA-identified risk loci in risk stratification for cancer is limited.

Pharyngocutaneous fistula onset after total laryngectomy: scintigraphic analysis

Pharyngocutaneous fistula is the most common non-fatal complication following total laryngectomy. To start oral feeding and exclude the presence of a pharyngocutaneous fistula, a subjective test and instrumental assessments using videofluoroscopy, have been described. The aim of this study was to evaluate the effectiveness of oral-pharyngo-oesophageal scintigraphy as an objective and non-invasive tool to establish presence, site and dimensions of the fistula. Observations were performed on 3 male patients, mean age 65 years, who underwent total laryngectomy and mono or bilateral neck dissection after failure of radiotherapy in 2 cases and of conservative laryngeal surgery in the third case, complicated by post-operative pharyngocutaneous fistula. Oral-pharyngo-oesophageal scintigraphy dynamic study with sequential images were obtained during the swallowing phases. In case 1, the test showed a wide pharyngocutaneous fistula the internal orifice of which was at the level of the base of the tongue: on the scintigraphic images, the radiomarked water bolus, from the fistulous orifice, descended along the stoma walls and only a small part reached the oesophagus. In the other two patients, the pharyngocutaneous fistula was small and the internal fistulous orifice was detected in the lower part of T-suture line. In conclusion, scintigraphy offered the possibility to precisely identify presence of pharyngocutaneous fistula and location of its internal orifice and to monitor its spontaneous closure. Therefore, important information could be obtained regarding the suture line status and the possibility of deciding whether to remove the nasogastric tube or to leave it in place. Finally, these data showed that oral-pharyngo-oesophageal scintigraphy could be performed in the early post-operative period to optimize starting safe oral feeding.

Clinical significance of focal and diffuse thyroid diseases identified by 18F-fluorodeoxyglucose positron emission tomography

(18)F-Fluorodeoxyglucose positron emission tomography (FDG-PET) thyroid incidentalomas are defined abnormal FDG uptake in the thyroid gland found at PET scan performed as part of a staging protocol and follow-up of patients with various kinds of malignancies. In the present study we report two cases of FDG PET thyroid incidentalomas, and review the literature with regard to the meaning of this new category of thyroid "disease". Since the advent of whole body FDG PET scan, a relatively high incidence of cases of thyroid FDG uptake has been reported as an incidental finding as in one of our patient. Focal uptake was found to be more likely associated to a malignant lesion, while a diffuse thyroid uptake to a benign thyroid disease. However, differential diagnosis is difficult, and reported data in literature are somewhat discordant. A focal thyroid uptake of FDG incidentally discovered at PET scan cannot be invariably considered a malignant thyroid nodule, however a prompt and complete work-up including laboratory examinations, ultrasonography and fine needle aspiration cytology, should be obtained to exclude a thyroid carcinoma. On the other hand, patients with a PET finding of diffuse FDG uptake can be considered at low risk of malignancy, being more likely associated to chronic thyroiditis or diffuse thyroid autonomy.

Evaluation of the surgical completeness after total thyroidectomy for differentiated thyroid carcinoma

BACKGROUND

To quantify the rate of patients without thyroid remnants, to identify predictive factors for the absence of residual thyroid tissue and to evaluate number, site, size and function of thyroid remnants after total thyroidectomy for differentiated thyroid carcinoma (DTC).

METHODS

Thousand one hundred and seventy-eight patients who underwent total thyroidectomy for DTC were evaluated; 343 patients with lymph node or distant metastases and 115 patients with detectable thyroglobulin autoantibodies (TgAb) were excluded. (131)I ablative treatment (RAI) without preliminary diagnostic (131)I whole body scans (DxWBS), and 24-h (131)I quantitative neck uptake (RAIU test) and thyroglobulin (Tg) off L-T4 evaluation were performed in the remaining 720 pts. In 252 patients a 99mTc-pertechnetate pre-operative thyroid scan (99mTc-scan) was used for comparison with (131)I neck scans after RAI to evaluate site of thyroid remnants. Only patients with thyroid remnants were evaluated for successful ablation 6-10 months after RAI.

RESULTS

Post-treatment whole body scan (TxWBS) demonstrated lack of thyroid remnants in 50/720 patients and the best predictive factors for the absence of residual thyroid tissue were RAIU <1% and undetectable Tg off L-T4. Thyroid remnants were present in 670/720 patients. In 252 patients with (99m)Tc-scan, 617 sites of functioning thyroid tissue were found: 381 within and 236 outside the thyroid bed. Complete successful ablation was achieved in 610/670 patients with thyroid remnants.

CONCLUSIONS

This study confirms that most patients (93.1%) have thyroid remnant after total thyroidectomy for DTC. Most thyroid remnants were contralateral to tumour site and were even observed outside thyroid bed. However, a real total thyroidectomy, demonstrated by negative TxWBS, RAIU <1% and undetectable Tg off L-T4, was achieved in 6.9% of patients.

Prevalence of home artificial nutrition in Italy in 2005: A survey by the Italian Society for Parenteral and Enteral Nutrition (SINPE)

AIM

To determine the prevalence (cases per million inhabitants) of home artificial nutrition (HAN), enteral (HEN) and parenteral (HPN), in Italy, grouped according to administrative regions, patient age and primary disease, and to analyze the impact both of the presence of an HAN regional regulation and of demographic characteristics.

METHODS

In April 2005, the Regional Coordinators of the Italian Society for Parenteral and Enteral Nutrition (SINPE) recorded all the ongoing cases of HAN using a structured questionnaire and were asked to estimate the representativeness of the collected sample with respect to the total expected HAN.

RESULTS

A total of 6955 cases of HAN (93.5% adults, 6.5% pediatric patients < or = 18 years) were recorded in 16 of the 20 Italian regions (80% of the Italian population; sample representativeness 78%). HAN prevalence 152.6 (83.9% HEN, 16.1% HPN); the HAN range among the regions was: prevalence 28.1-519.8; oncological disease 13.8-75.7%, neurological disease 15.5-79.9%, intestinal failure 1.3-14.0%. An HAN regulation was present in 11 regions. A positive association (P=0.012) was found between the number of years since the regulation was issued and the HAN prevalence, and also between the % neurological patients and the population density (P=0.130) and the % inhabitants > or = 75 years (P=0.040).

CONCLUSIONS

The need for HAN regards a great number of patients throughout the country; there are substantial differences between the regions with respect to both the prevalence and the use of HAN in various disease categories. A specific regulation may favor the development of HAN.

Calcitriol plus hydrochlorothiazide prevents transient post-thyroidectomy hypocalcemia

BACKGROUND

The aim of our double-blinded randomized prospective placebo-controlled study was to test if a week long pre-treatment with hypercalcemic drugs may prevent transient post-thyroidectomy hypocalcemia and reduce hospital stay.

METHODS

Forty-two patients undergoing total thyroidectomy were randomized into two groups. Group 1: 22 patients treated with calcitriol 1.5 mcg/die plus hydrochlorothiazide; Group 2: 20 patients only treated with placebo (mineral integrates) as control group. Calcium and PTHi serum levels were assayed baseline and the days before and after thyroidectomy.

RESULTS

Baseline calcium and PTHi did not differ between the two groups. Pre-surgery calcemia significantly increased in group 1 (p<0.05) while PTHi significantly decreased (p<0.05). Post-surgery calcemia and PTHi further significantly decreased in both groups, hypocalcemia (<2.10 mmol/l) occurring in 1 out of 22 patients in group 1 without symptoms and in 10 out of 20 in controls (20% developing symptoms) (p<0.01). The hospital stay resulted significantly shorter in group 1 (2.4+/-0.6 days) in respect to the control group (3.6+/-1.4 days, p<0.05).

CONCLUSION

The administration of calcitriol plus hydrochlorothiazide is able to prevent transient post-thyroidectomy hypocalcemia and to reduce hospital stay.

Prevalence of HCV antibodies in autoimmune thyroid disease

BACKGROUND AND OBJECTIVES

Auto-immune thyroid disease (AITD) has often been reported during interferon-alpha therapy for chronic viral C hepatitis (HCV) or other diseases. Recently, a high AITD prevalence has been reported in HCV independently on alpha-interferon therapy. The aim of our study is to investigate the possible relationship between AITD and HCV and HBV virus infections, and their influence on the thyroid function.

MATERIAL AND METHODS

We prospectively studied 112 patients with AITD (94 women and 18 men; mean age: 49.8 +/- 14.9 yrs) and 88 patients with non-toxic goitre (NTG) (73 women and 15 men; mean age: 50.2 +/- 13.5 yrs) as controls. In all patients HCV antibodies, HBsAg and anti-HBs antibodies, TSH, FT3 and FT4 serum levels, circulating anti-thyroid-peroxidase antibodies (TPO-Ab) and anti-thyroglobulin antibodies (TG-Ab) were measured.

RESULTS

HCV antibodies were positive in 11.6% of AITD patients (13/112) and in 2.3% of controls (2/88) (P < 0.05), the prevalence of HCV in the controls being similar to the expected value in the general population (about 2%). HBsAg and anti-HBs were found only in 2.6% of AITD patients (3/112) and 1.1% of controls (1/88) (P = NS), according to the expected value in the general population (about 2.5%). No difference in thyroid function was observed between positive and negative HCV subgroups.

CONCLUSION

A significant association between HCV infection and AITD was found. This finding confirms that HCV, but not HBV, could be one of the environmental factors responsible for the breakdown of immunological tolerance. Therefore detection of TPO-Ab and TG-Ab in all HCV patients, independently of IFN therapy, is suggested and the utility of a screening for HCV in all AITD patients is stressed.

Cognitive dysfunction in patients with obstructive sleep apnea (OSA): partial reversibility after continuous positive airway pressure (CPAP)

The aims of this study were to assess cognitive function in obstructive sleep apnea (OSA) patients and to evaluate the effect of short- and long-term treatment with continuous positive airway pressure treatment (CPAP). A battery of neuropsychological tests, the Epworth Sleepiness Scale (ESS), and the Beck Inventory Scale were administered to 23 patients with severe OSA (age: 56.5+/-6.13; AHI: 54.9+/-13.37) and to 23 age- and education-matched controls. The OSA patients were evaluated in a baseline condition and in two follow-up treatment sessions (after 15 days and 4 months of CPAP, respectively). At baseline, OSA patients had a significant impairment, compared to controls, in tests of sustained attention, visuospatial learning, executive function, motor performance, and constructional abilities. The longitudinal evaluation showed that after a 15-days CPAP treatment attentive, visuospatial learning, and motor performances returned to normal levels. A 4-months CPAP treatment did not result in any further improvement in cognitive tests. Performance on tests evaluating executive functions and constructional abilities was not affected by short- and long-term treatment with CPAP. The findings of this study confirm the hypothesis of partial reversibility of cognitive dysfunction in OSA patients after CPAP.

A comparison among different inversion methods for multi-exponential NMR relaxation data

The inversion of data to be represented by sums or continuous distributions of exponentials is done by different algorithms and compared. The published CONTIN program presents a chosen solution with an appropriate amount of detail. An in-house program EXDISTR allows operative choice of various constraints in order to show the consequences in quality of fit of allowing various features such as extra maxima or minima. Another in-house program based on the system theory approach, IDENT, treats the data as the output samples of a linear, time-invariant, autonomous dynamic system.

Rapid separation of CD4+ and CD19+ lymphocyte populations from human peripheral blood by a magnetic activated cell sorter (MACS)

Rapid purification of human lymphocyte subpopulations is an essential step in order to elucidate their interactions and/or contributions in various disease states. Cell purification using a Magnetic Activated Cell Sorter (MACS) is a relatively new technology which has been shown to be rapid and yield highly purified populations of cells. This report describes both a simple one-step positive selection method using the MACS to purify either human CD4+ or CD19+ lymphocytes from PBMC and a sequential separation of both CD4+ and CD19+ cell populations. These methods can separate the cell populations in approximately 4 h with yields > 90% and purity of 97 +/- 3% for CD4+ T cells and 92 +/- 5% for CD19+ B cells. In functional studies, purified CD19+ B cells secreted 13- and 24-fold more IgM and IgG, respectively, than the CD19- cell fraction in 10 day B cell stimulation assays. Purification of the two cell types did not cause any significant activation as shown by proliferation. Both cell types, however, were able to proliferate upon stimulation with interleukin-2.

Improved treatment results for lymphoblastic lymphoma in adolescents and adults using a doxorubicin-based (APO) protocol

A multi-drug chemotherapy (APO) protocol incorporating doxorubicin was used to treat 12 patients (median age 19 years) with lymphoblastic lymphoma. The APO protocol consisted of intensive induction and consolidation phases, prophylactic CNS treatment, and 24 months of maintenance therapy. Eleven patients had an anterior mediastinal mass, while T cell markers were found on the lymphoma cells in eight of the nine cases tested. Two patients had initial CNS involvement, with one also having bone marrow replacement. Complete remission was obtained in all patients, with no deaths due to treatment toxicity. There have been four relapses, one in the patient with initial CNS and leukemic disease, two in abdominal sites, and in the mediastinum in one patient. With a median follow-up time of 30 months from diagnosis, 67% of patients remain alive in first remission. These results indicate that the APO protocol provides a highly effective approach to the management of this high grade lymphoma in adolescents and adults.

The neurotoxicity of high-dose cytosine arabinoside is age-related

Fifteen patients with acute myeloid leukaemia were given a total of 17 courses of high-dose cytosine arabinoside (Ara-C). The median age of the patients was 37 years. Four patients developed severe irreversible neurotoxicity, three developed mild to moderate, reversible neurotoxicity, whereas eight patients had no toxicity. Of five patients over the age of 55 years given high dose Ara-C, four developed severe, irreversible neurotoxicity, but there were no severe episodes in nine patients aged 55 years or less. (P less than 0.01). At a dose of 3 g/m2 given intravenously every 12 hours for 3 days, three cases of severe irreversible neurotoxicity were noted in elderly patients. Neurotoxicity at this total dose has previously been considered unusual. Administration of high dose Ara-C at total doses of 18 g/m2 and over carries a risk of severe irreversible cerebellar toxicity that increases with age.