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.

Association of Systemic Inflammation with Depressive Symptoms in Individuals with COPD.

RATIONALE: Depression is a prevalent comorbidity of chronic obstructive pulmonary disease (COPD) that, along with COPD, has been associated with inflammation. An association between inflammation and depression in COPD has not been validated in a large COPD cohort. METHODS: Individuals from the University of Pittsburgh SCCOR cohort and the COPDGene cohort with tobacco use history and airway obstruction (FEV1/FVC <0.7) were evaluated using the Beck Depression Inventory II (BDI-II) and the Hospital Anxiety and Depression Scale (HADS), respectively. Participants completed symptom-related questionnaires and plasma IL-6 measurements. T-test, Fisher's Exact tests and logistic regression were used for statistical analysis. RESULTS: The SCCOR cohort included 220 obstructed participants: 44% female and 21.4% with elevated depressive symptoms. GOLD staging distribution was predominantly stage I and II. The COPDGene cohort included 745 obstructed participants: 44% female and 13.0% with elevated depressive symptoms. GOLD distribution was predominantly stage II and III. In the SCCOR cohort, correlation between IL-6 and depressive symptoms trended toward significance (p= 0.08). Multivariable modeling adjusted for FEV1, age, gender and medical comorbidities showed a significant association (OR = 1.70, 95% CI = 1.08-2.69). IL-6 was significantly associated with elevated depressive symptoms in COPDGene in both univariate (p=0.001) and multivariable modeling (OR = 1.52, 95% CI =1.13-2.04). CONCLUSION: Elevated plasma IL-6 levels are associated with depressive symptoms in individuals with COPD independent of airflow limitation and comorbid risk factors for depression. Our results suggest that systemic inflammation may play a significant and possibly bidirectional role in depression associated with COPD.

Improving clinical disease subtyping and future events prediction through a chest CT-based deep learning approach.

PURPOSE: To develop and evaluate a deep learning (DL) approach to extract rich information from high-resolution computed tomography (HRCT) of patients with chronic obstructive pulmonary disease (COPD). METHODS: We develop a DL-based model to learn a compact representation of a subject, which is predictive of COPD physiologic severity and other outcomes. Our DL model learned: (a) to extract informative regional image features from HRCT; (b) to adaptively weight these features and form an aggregate patient representation; and finally, (c) to predict several COPD outcomes. The adaptive weights correspond to the regional lung contribution to the disease. We evaluate the model on 10 300 participants from the COPDGene cohort. RESULTS: Our model was strongly predictive of spirometric obstruction ( r 2  =  0.67) and grouped 65.4% of subjects correctly and 89.1% within one stage of their GOLD severity stage. Our model achieved an accuracy of 41.7% and 52.8% in stratifying the population-based on centrilobular (5-grade) and paraseptal (3-grade) emphysema severity score, respectively. For predicting future exacerbation, combining subjects' representations from our model with their past exacerbation histories achieved an accuracy of 80.8% (area under the ROC curve of 0.73). For all-cause mortality, in Cox regression analysis, we outperformed the BODE index improving the concordance metric (ours: 0.61 vs BODE: 0.56). CONCLUSIONS: Our model independently predicted spirometric obstruction, emphysema severity, exacerbation risk, and mortality from CT imaging alone. This method has potential applicability in both research and clinical practice.

Diagnosis and Outpatient Management of Chronic Obstructive Pulmonary Disease: A Review.

IMPORTANCE: There are 30 million adults (12%) in the United States who have chronic obstructive pulmonary disease (COPD). Chronic obstructive pulmonary disease accounts for 3.2% of all physician office visits annually and is the fourth leading cause of death (126 000 deaths per year). Most patients are diagnosed by their primary care clinicians who must address the highly variable clinical features and responses to therapy. The diagnosis and treatment of COPD is rapidly changing, so understanding recent advances is important for the delivery of optimal patient care. OBSERVATIONS: Chronic obstructive pulmonary disease is characterized by incompletely reversible expiratory airflow limitation. Spirometry is the reference standard for diagnosing and assessing the severity of COPD. All patients should be counseled about and receive preventive measures such as smoking cessation and vaccination. Treatment should be guided by the severity of lung impairment, symptoms such as dyspnea, the amount of cough and sputum production, and how often a patient experiences an exacerbation. When dyspnea limits activity or quality of life, COPD should be treated with once- or twice-daily maintenance long-acting anticholinergic and ß-agonist bronchodilators. Patients with acute exacerbations may benefit from the addition of inhaled corticosteroids, particularly those with elevated peripheral eosinophil levels. Pulmonary rehabilitation, which includes strength and endurance training and educational, nutritional, and psychosocial support, improves symptoms and exercise tolerance but is underutilized. Supplemental oxygen for patients with resting hypoxemia (defined as Spo2 <89%) improves survival. CONCLUSIONS AND RELEVANCE: Chronic obstructive pulmonary disease is a complicated disease requiring intensive treatment. Appropriate use of long-acting maintenance bronchodilators, inhaled corticosteroids, and pulmonary rehabilitation decreases symptoms, optimizes functional performance, and reduces exacerbation frequency. Supplemental oxygen in patients with resting hypoxemia prolongs life, and other advanced treatments are available based on specific patient characteristics.

Bronchoscopic device intervention in chronic obstructive pulmonary disease.

PURPOSE OF REVIEW: Chronic obstructive pulmonary disease is a heterogeneous syndrome associated with varying degrees of parenchymal emphysema and airway inflammation resulting in decreased expiratory flow, lung hyperinflation, and symptoms leading to decreased exercise tolerance and quality of life. Impairment in lung function and quality of life persists following guideline-based medical therapy, thus surgical and minimally invasive bronchoscopic approaches were developed to address this unmet need. We offer a narrative review of the available technologies. RECENT FINDINGS: Although lung volume reduction surgery has been shown to improve survival in appropriately selected patients, it is infrequently performed. Less invasive bronchoscopic procedures have thus been explored including endobronchial valves, coils, lung sealant, thermal vapor, and other airway approaches. Selection criteria including severity of physiologic and radiographic impairment, degree of lung hyperinflation, presence of intact fissures, type of symptoms, and presence of comorbidities are critical in selecting appropriate candidates. SUMMARY: Recent advances in minimally invasive approaches to lung volume reduction have offered alternatives to surgical approaches. Two endobronchial valve devices are Food and Drug Administration approved for clinical use, and investigations into alternative bronchoscopic therapies to treat both emphysema and chronic bronchitis have been performed or are currently underway. Notably, each of these treatments requires unique selection criteria and thus a personalized approach to treatment.

Clinical Implications of Having Reduced Mid Forced Expiratory Flow Rates (FEF25-75), Independently of FEV1, in Adult Patients with Asthma.

INTRODUCTION: FEF25-75 is one of the standard results provided in spirometry reports; however, in adult asthmatics there is limited information on how this physiological measure relates to clinical or biological outcomes independently of the FEV1 or the FEV1/FVC ratio. PURPOSE: To determine the association between Hankinson's percent-predicted FEF25-75 (FEF25-75%) levels with changes in healthcare utilization, respiratory symptom frequency, and biomarkers of distal airway inflammation. METHODS: In participants enrolled in the Severe Asthma Research Program 1-2, we compared outcomes across FEF25-75% quartiles. Multivariable analyses were done to avoid confounding by demographic characteristics, FEV1, and the FEV1/FVC ratio. In a sensitivity analysis, we also compared outcomes across participants with FEF25-75% below the lower limit of normal (LLN) and FEV1/FVC above LLN. RESULTS: Subjects in the lowest FEF25-75% quartile had greater rates of healthcare utilization and higher exhaled nitric oxide and sputum eosinophils. In multivariable analysis, being in the lowest FEF25-75% quartile remained significantly associated with nocturnal symptoms (OR 3.0 [95%CI 1.3-6.9]), persistent symptoms (OR 3.3 [95%CI 1-11], ICU admission for asthma (3.7 [1.3-10.8]) and blood eosinophil % (0.18 [0.07, 0.29]). In the sensitivity analysis, those with FEF25-75%

Dosimetric evaluation of the interplay effect in respiratory-gated RapidArc radiation therapy.

PURPOSE: Volumetric modulated arc therapy (VMAT) with gating capability has had increasing adoption in many clinics in the United States. In this new technique, dose rate, gantry rotation speed, and the leaf motion speed of multileaf collimators (MLCs) are modulated dynamically during gated beam delivery to achieve highly conformal dose coverage of the target and normal tissue sparing. Compared with the traditional gated intensity-modulated radiation therapy technique, this complicated beam delivery technique may result in larger dose errors due to the intrafraction tumor motion. The purpose of this work is to evaluate the dosimetric influence of the interplay effect for the respiration-gated VMAT technique (RapidArc, Varian Medical Systems, Palo Alto, CA). Our work consisted of two parts: (1) Investigate the interplay effect for different target residual errors during gated RapidArc delivery using a one-dimensional moving phantom capable of producing stable sinusoidal movement; (2) Evaluate the dosimetric influence in ten clinical patients' treatment plans using a moving phantom driven with a patient-specific respiratory curve. METHODS: For the first part of this study, four plans were created with a spherical target for varying residual motion of 0.25, 0.5, 0.75, and 1.0 cm. Appropriate gating windows were applied for each. The dosimetric effect was evaluated using EDR2 film by comparing the gated delivery with static delivery. For the second part of the project, ten gated lung stereotactic body radiotherapy cases were selected and reoptimized to be delivered by the gated RapidArc technique. These plans were delivered to a phantom, and again the gated treatments were compared to static deliveries by the same methods. RESULTS: For regular sinusoidal motion, the dose delivered to the target was not substantially affected by the gating windows when evaluated with the gamma statistics, suggesting the interplay effect has a small role in respiratory-gated RapidArc therapy. Varied results were seen when gated therapy was performed on the patient plans that could only be attributed to differences in patient respiratory patterns. Patients whose plans had the largest percentage of pixels failing the gamma statistics exhibited irregular breathing patterns including substantial interpatient variation in depth of respiration. CONCLUSIONS: The interplay effect has a limited impact on gated RapidArc therapy when evaluated with a linear phantom. Variations in patient breathing patterns, however, are of much greater clinical significance. Caution must be taken when evaluating patients' respiratory efforts for gated arc therapy.

Gel purification of radiolabeled nucleic acids via phosphorimaging: Dip-N-Dot.

RNA and DNA oligonucleotides radiolabeled with (32)P or (33)P often require gel electrophoresis to remove undesired side and/or degradation products. Common ways to visualize these molecules after electrophoresis are by ultraviolet (UV) shadowing, which necessarily reduces the specific activity of the oligonucleotide, and by autoradiography using film, which is cumbersome and increases the cost of generating the radiolabeled molecule. A more cost-effective method is to physically inject the gel with a "Dip-N-Dot" solution of dye and radionuclide after electrophoresis but prior to phosphorimaging. The gel can be overlaid on its computer-generated image, allowing the labeled molecules to be visualized quickly.

Daily functioning and quality of life in children with sickle cell disease pain: relationship with family and neighborhood socioeconomic distress.

UNLABELLED: The aim of this study was to examine the relationship between individual/family and neighborhood socioeconomic distress, pain, and functional outcomes in children with sickle cell disease (SCD). We hypothesized that both individual economic distress as well as residence in neighborhoods of severe economic distress would predict children's level of pain-related functional disability and health-related quality of life (HRQOL). Participants (mean age, 12.14 years; 57% male, n = 56) were recruited from an outpatient hematology clinic at a Midwestern tertiary referral hospital. Questionnaires assessing pain, depression, functional disability, and HRQOL were completed by children and their caregivers. Individual socioeconomic data including parental education and family income were reported by caregivers. Neighborhood socioeconomic distress was identified using publicly available census tract data and was based on neighborhood poverty, female head of household, male unemployment, and high school dropout levels. Multivariate regression analyses revealed that individual/family socioeconomic distress was a significant predictor of children's functional disability and physical and psychosocial HRQOL. Neighborhood socioeconomic distress emerged as a significant independent predictor of physical HRQOL only, where living in a distressed neighborhood predicted diminished physical HRQOL. Findings suggest that individual socioeconomic status and neighborhood economic distress play similar but independent roles in predicting children's functional outcomes related to SCD pain. PERSPECTIVE: Little is known about the influence of either individual/family or neighborhood socioeconomic factors on pain and functioning in children with SCD. Our findings suggest that socioeconomic distress defined at both the individual level and at the neighborhood/community level are significant independent predictors of pain-related disability and HRQOL in children with SCD.

RNA-directed construction of structurally complex and active ligase ribozymes through recombination.

RNA-directed recombination can be used to catalyze a disproportionation reaction among small RNA substrates to create new combinations of sequences. But the accommodation of secondary and tertiary structural constraints in the substrates by recombinase ribozymes has not been explored. Here, we show that the Azoarcus group I intron can recombine oligoribonucleotides to construct class I ligase ribozymes, which are catalytically active upon synthesis. The substrate oligonucleotides, ranging in size from 58 to 104 nucleotides (nt), along with the 152-nt ligase ribozymes they reconstitute, can contain significant amounts of secondary structure. However, substrate recognition by the Azoarcus ribozyme depends on the existence of a single accessible CAU triplet for effective recombination. A biphasic temperature reaction profile was designed such that the sequential recombination/ligation events could take place in a thermocycler without human intervention. A temperature-dependent pH shift of the reaction buffer contributes to the success of the net reaction. When the substrate for the ligase ribozyme is introduced into the reaction mixture, as much as 11% can be observed being converted to product by the recombined ligase in the same reaction vessel. Recombination followed by ligation can also occur under isothermal conditions at 37 degrees C. Tertiary structure formation of the ligase upon construction can provide some protection from cleavage by the Azoarcus ribozyme when compared to the constituent substrates. These data suggest that RNA-directed recombination can, in fact, articulate complex ribozymes, and that there are logical rules that can guide the optimal placement of the CAU recognition sequence.

Expanded divalent metal-ion tolerance of evolved ligase ribozymes.

Class I ligases are artificial ribozymes that catalyze the joining of two single-stranded RNAs. These ribozymes are between 120 and 160 nucleotides in length, making them intermediate in size for catalytic RNAs. Previous characterization of the b1-207 ribozyme suggests that it behaves similar to larger ribozymes in terms of divalent metal-ion dependence. This molecule displays a strong preference for magnesium for catalysis, and is inactive in any other metal except manganese, which actually inhibits its operation in magnesium. Here, we sought to examine the metal-ion usages of two ligases that were obtained through continuous evolution in vitro from the b1-207 sequence framework. We found an expanded catalytic range for the E(100)(#3) and B(16)(#19) ribozymes, as they are both catalytically active in calcium and strontium, and less inhibited by manganese. Though not selected for activity in these salts, the evolved ribozymes exhibit several adaptations to in vitro catalysis, and their ability to accommodate metals other than magnesium can be viewed as an example of a molecular exaptation.

Generalized RNA-directed recombination of RNA.

RNA strand exchange through phosphor-nucleotidyl transfer reactions is an intrinsic chemistry promoted by group I intron ribozymes. We show here that Tetrahymena and Azoarcus ribozymes can promote RNA oligonucleotide recombination in either two-pot or one-pot schemes. These ribozymes bind one oligonucleotide, cleave following a guide sequence, transfer the 3' portion of the oligo to their own 3' end, bind a second oligo, and catalyze another transfer reaction to generate recombinant oligos. Recombination is most effective with the Azoarcus ribozyme in a single reaction vessel in which over 75% of the second oligo can be rapidly converted to recombinant product. The Azoarcus ribozyme can also create a new functional RNA, a hammerhead ribozyme, which can be constructed via recombination and then immediately promote its own catalysis in a homogeneous milieu, mimicking events in a prebiotic soup.