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Showing papers by "National Jewish Health published in 2018"


Journal ArticleDOI
11 Jan 2018-Thorax
TL;DR: Smoking duration alone provides stronger risk estimates of COPD than the composite index of pack-years.
Abstract: Background Cigarette smoking is the strongest risk factor for COPD. Smoking burden is frequently measured in pack-years, but the relative contribution of cigarettes smoked per day versus duration towards the development of structural lung disease, airflow obstruction and functional outcomes is not known. Methods We analysed cross-sectional data from a large multicentre cohort (COPDGene) of current and former smokers. Primary outcome was airflow obstruction (FEV 1 /FVC); secondary outcomes included five additional measures of disease: FEV 1 , CT emphysema, CT gas trapping, functional capacity (6 min walk distance, 6MWD) and respiratory morbidity (St George’s Respiratory Questionnaire, SGRQ). Generalised linear models were estimated to compare the relative contribution of each smoking variable with the outcomes, after adjustment for age, race, sex, body mass index, CT scanner, centre, age of smoking onset and current smoking status. We also estimated adjusted means of each outcome by categories of pack-years and combined groups of categorised smoking duration and cigarettes/day, and estimated linear trends of adjusted means for each outcome by categorised cigarettes/day, smoking duration and pack-years. Results 10 187 subjects were included. For FEV 1 /FVC, standardised beta coefficient for smoking duration was greater than for cigarettes/day and pack-years (P 1 /FVC with increase in pack-years (regression coefficient β=−0.023±SE0.003; P=0.003) and duration over all ranges of smoking cigarettes/day (β=−0.041±0.004; P 1 , 6MWD and SGRQ. Conclusion Smoking duration alone provides stronger risk estimates of COPD than the composite index of pack-years. Trial registration number Post-results; NCT00608764.

84 citations


Journal ArticleDOI
TL;DR: Future research should investigate the burden of childhood asthma specifically attributable to extreme temperatures and temperature variation using advanced statistical approach, particularly in rural areas, after properly considering aeroallergens and air pollution.
Abstract: The objectives of this study are to review available information on the association between ambient temperature and childhood asthma, and to elucidate the possible underlying mechanisms of this relationship. A systematic review was conducted based on the papers retrieved from four databases, including PubMed, ProQuest, ScienceDirect, and Scopus. Papers examining the association of absolute temperature or temperature variation with childhood asthma published from 1 January 2000 to 31 December 2016 were included. Thirteen papers have quantified the effect of absolute temperature on childhood asthma, and six papers have examined the effect of intra- or inter-day temperature variation on childhood asthma. All studies were conducted in urban areas. Aeroallergen sensitizations were only considered in the analyses of one study. Discrepancy existed in the significance of the relationship between absolute temperature and childhood asthma, and also in the shape of this relationship (i.e. linear or non-linear) and whether temperature effects were lagged. Increasing evidence is suggesting non-linear relationship between absolute temperature and childhood asthma. Future research should investigate the burden of childhood asthma specifically attributable to extreme temperatures and temperature variation using advanced statistical approach, particularly in rural areas, after properly considering aeroallergens and air pollution. Projecting future burden of childhood asthma under climate change scenarios is also warranted.

47 citations


Book ChapterDOI
TL;DR: The process of isolating and expanding human and mouse airway epithelial cells, as well as differentiation of airway endothelial cells by air-liquid interface culture are described.
Abstract: Air-liquid interface culture enables airway epithelial cells to differentiate into a pseudostratified cell layer, consisting of ciliated cells, goblet/secretory cells, and basal cells (Ghio et al., Part Fibre Toxicol 10:25, 2013). This technique is critically important for in vitro studies of lung diseases such as asthma, chronic obstructive pulmonary disease, and cystic fibrosis, since differentiated airway epithelial cells are more representative of the in vivo lung environment than non-differentiated cells (Derichs et al., FASEB J 25:2325-2332, 2011; Hackett et al., Am J Respir Cell Mol Biol 45:1090-1100, 2011;Schneider et al., Am J Respir Crit Care Med 182: 332-340, 2010). Here we describe the process of isolating and expanding human and mouse airway epithelial cells, as well as differentiation of airway epithelial cells by air-liquid interface culture.

40 citations


Journal ArticleDOI
TL;DR: It is shown for both species that mutations at the C-terminal end of this epitope dramatically improve presentation to these T cells, suggesting that pancreas-specific posttranslational modifications of this peptide may play a role in the induction of diabetes and explain how the pathogenic T cells escape deletion in the thymus.
Abstract: A polymorphism at β57 in some major histocompatibility complex class II (MHCII) alleles of rodents and humans is associated with a high risk for developing type 1 diabetes (T1D). However, a highly diabetogenic insulin B chain epitope within the B:9-23 peptide is presented poorly by these alleles to a variety of mouse and human CD4 T cells isolated from either nonobese diabetic (NOD) mice or humans with T1D. We have shown for both species that mutations at the C-terminal end of this epitope dramatically improve presentation to these T cells. Here we present the crystal structures of these mutated peptides bound to mouse IAg7 and human HLA-DQ8 that show how the mutations function to improve T-cell activation. In both peptide binding grooves, the mutation of B:22R to E in the peptide changes a highly unfavorable side chain for the p9 pocket to an optimal one that is dependent on the β57 polymorphism, accounting for why these peptides bind much better to these MHCIIs. Furthermore, a second mutation of the adjacent B:21 (E to G) removes a side chain from the surface of the complex that is highly unfavorable for a subset of NOD mouse CD4 cells, thereby greatly enhancing their response to the complex. These results point out the similarities between the mouse and human responses to this B chain epitope in T1D and suggest there may be common posttranslational modifications at the C terminus of the peptide in vivo to create the pathogenic epitopes in both species.

30 citations


Book ChapterDOI
TL;DR: The lung parenchyma is comprised of many cells including the structurally important stromal fibroblasts, which are important in the maintenance of alveolar epithelial cells and homeostasis and disease.
Abstract: The lung parenchyma is comprised of many cells including the structurally important stromal fibroblasts. Fibroblasts function to produce extracellular matrix and are important in the maintenance of alveolar epithelial cells. To understand the role of fibroblasts both in homeostasis and disease, we isolate fibroblasts and grow them in culture. Two methods are presented here for the isolation and maintenance of mouse primary lung fibroblasts.

30 citations


Journal ArticleDOI
01 Jan 2018
TL;DR: This study provides valuable insight regarding the informational needs of IPF patients and their caregivers and it is hoped that identifying or creating sources of this information, and insuring that patients and caregivers have access to it, will improve well-being for patients with IPF and their caregiver.
Abstract: Background Idiopathic pulmonary fibrosis (IPF) is a progressive, incurable lung disease whose intrusive symptoms rob patients of their quality of life Patients with IPF rely on their caregivers for support and assistance in amounts that vary according to patients’ individual circumstances and disease severity Knowledgeable and well-informed patients and caregivers are best suited to deal with life-altering conditions like IPF Methods We conducted two hour-long focus groups with 13 patients with IPF and 4 caregivers of patients with IPF to better understand their informational needs and in what format such information should be delivered Results Patients discussed the challenges IPF creates in their daily lives They wanted information on how to live well despite having IPF, practical information on how they could remain active and travel and how they could preserve their quality of life despite living with a life-threatening disease like IPF Caregivers wanted information on the general aspects of IPF, because it would help them understand what patients were going through They also wanted specific information on how to give care to a patient with IPF, even when physical care may not be needed (as in earlier phases of the disease) Patients and caregivers both needed efficient information delivery from trustworthy sources, including the healthcare team involved in their care They considered both spoken and written information valuable, and ease of access was critical Conclusion This study provides valuable insight regarding the informational needs of IPF patients and their caregivers It is hoped that identifying or creating sources of this information, and insuring that patients and caregivers have access to it, will improve well-being for patients with IPF and their caregivers

24 citations


Book ChapterDOI
TL;DR: The cell types that contribute to lung innate immunity and inflammation are discussed and how their activities are coordinated to promote lung health is discussed.
Abstract: The nasal passages, conducting airways and gas-exchange surfaces of the lung, are constantly exposed to substances contained in the air that we breathe. While many of these suspended substances are relatively harmless, some, for example, pathogenic microbes, noxious pollutants, and aspirated gastric contents can be harmful. The innate immune system, lungs and conducting airways have evolved specialized mechanisms to protect the respiratory system not only from these harmful inhaled substances but also from the overly exuberant innate immune activation that can arise during the host response to harmful inhaled substances. Herein, we discuss the cell types that contribute to lung innate immunity and inflammation and how their activities are coordinated to promote lung health.

22 citations


Journal ArticleDOI
TL;DR: It is reported that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells, and the T cell antigen receptor repertoire and phenotype of CD1D1−/− mice differed fromCD1d1-selected type INKT cells.
Abstract: MHC class I-like CD1 molecules have evolved to present lipid-based antigens to T cells. Differences in the antigen-binding clefts of the CD1 family members determine the conformation and size of the lipids that are presented, although the factors that shape CD1 diversity remain unclear. In mice, two homologous genes, CD1D1 and CD1D2, encode the CD1d protein, which is essential to the development and function of natural killer T (NKT) cells. However, it remains unclear whether both CD1d isoforms are equivalent in their antigen presentation capacity and functions. Here, we report that CD1d2 molecules are expressed in the thymus of some mouse strains, where they select functional type I NKT cells. Intriguingly, the T cell antigen receptor repertoire and phenotype of CD1d2-selected type I NKT cells in CD1D1−/− mice differed from CD1d1-selected type I NKT cells. The structures of CD1d2 in complex with endogenous lipids and a truncated acyl-chain analog of α-galactosylceramide revealed that its A′-pocket was restricted in size compared with CD1d1. Accordingly, CD1d2 molecules could not present glycolipid antigens with long acyl chains efficiently, favoring the presentation of short acyl chain antigens. These results indicate that the two CD1d molecules present different sets of self-antigen(s) in the mouse thymus, thereby impacting the development of invariant NKT cells.

21 citations


Posted ContentDOI
10 Jul 2018-bioRxiv
TL;DR: It is found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads, and this knowledge advances understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.
Abstract: Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the U.S. and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal versus well water, and in U.S. households as compared to European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the U.S. where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria and these hot spots generally overlapped with those regions where NTM lung disease is most prevalent. Together these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.

19 citations


Journal ArticleDOI
TL;DR: This paper proposes a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups, and identifies gene connections that are disrupted with increased disease severity and that characterize the disease evolution.
Abstract: In this paper, we propose a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups In our approach, we link graphs through a Markov random field prior This prior on network similarity provides a measure of pairwise relatedness that borrows strength only between related groups We incorporate the computational efficiency of continuous shrinkage priors, improving scalability for network estimation in cases of larger dimensionality Our model is applied to patient groups with increasing levels of chronic obstructive pulmonary disease severity, with the goal of better understanding the break down of gene pathways as the disease progresses Our approach is able to identify critical hub genes for four targeted pathways Furthermore, it identifies gene connections that are disrupted with increased disease severity and that characterize the disease evolution We also demonstrate the superior performance of our approach with respect to competing methods, using simulated data

17 citations


Journal ArticleDOI
TL;DR: Clinical data is lacking, but relatively small and early studies suggest that EPIT has an excellent safety profile, particularly compared to other methods of specific allergen immunotherapy, which is needed to prove efficacy and further demonstrate the safety profile of EPIT for food allergy.
Abstract: The food allergy epidemic of recent years has led to the search for safe and effective methods of immunotherapy for foods. Studies of epicutaneous immunotherapy (EPIT) in mice have shown promising safety and efficacy data. Murine models have also identified probable mechanisms for the development of tolerance to food allergens, including the induction of regulatory T cells. Clinical data is lacking, but relatively small and early studies among peanut and cow’s milk allergic subjects suggest that EPIT has an excellent safety profile, particularly compared to other methods of specific allergen immunotherapy. Efficacy data are also promising for peanut allergy, among younger patients (ages 4–11 years of age), suggesting that a majority of young patients will experience an increase in reaction threshold with therapy. The goal of this therapy is the protection from accidental exposures to a known food allergen. Additional clinical data is needed to prove efficacy and further demonstrate the safety profile of EPIT for food allergy, prior to approval by the Food and Drug Administration.

Book ChapterDOI
TL;DR: How to identify pulmonary MPs using flow cytometry and how to isolate them via cell sorting are described and will be important to understanding their role in maintaining homeostasis and during the development of disease.
Abstract: There is a diverse population of mononuclear phagocytes (MPs) in the lungs, comprised of macrophages, dendritic cells (DCs), and monocytes. The existence of these various cell types suggests that there is a clear division of labor and delicate balance between the MPs under steady-state and inflammatory conditions. Here we describe how to identify pulmonary MPs using flow cytometry and how to isolate them via cell sorting. In steady-state conditions, murine lungs contain a uniform population of alveolar macrophages (AMs), three distinct interstitial macrophage (IM) populations, three DC subtypes, and a small number of tissue-trafficking monocytes. During an inflammatory response, the monocyte population is more abundant and complex since it acquires either macrophage-like or DC-like features. All in all, studying how these cell types interact with each other, structural cells, and other leukocytes within the environment will be important to understanding their role in maintaining homeostasis and during the development of disease.

Journal ArticleDOI
13 Feb 2018-Thorax
TL;DR: A single-nucleotide polymorphism in the mucin 5B (MUC5B) gene promoter is associated with pulmonary fibrosis and interstitial features on chest CT but may also have beneficial effects.
Abstract: A single-nucleotide polymorphism (rs35705950) in the mucin 5B (MUC5B) gene promoter is associated with pulmonary fibrosis and interstitial features on chest CT but may also have beneficial effects In non-Hispanic whites in the COPDGene cohort with interstitial features (n=454), the MUC5B promoter polymorphism was associated with a 61% lower odds of a prospectively reported acute respiratory disease event (P=0001), a longer time-to-first event (HR=057; P=0006) and 40% fewer events (P=0016) The MUC5B promoter polymorphism may have a beneficial effect on the risk of acute respiratory disease events in smokers with interstitial CT features

Book ChapterDOI
TL;DR: The generation of a differentiated mucociliary human airway epithelium is described using an in vitro air-liquid interface (ALI) culture model system and methods to stimulate this culture model with IL-13 and harvest cells and biomolecules to interrogate cellular and molecular aspects of theAirway epithelialIL-13 response are described.
Abstract: The airway epithelium lines the respiratory tract and provides the primary protective barrier against inhalational insults including toxic environmental substances and microorganisms. The airway epithelium also plays a critical role in regulating airway immune responses. The airway epithelial response to the type 2 cytokine, interleukin-13 (IL-13), is critical to airway inflammation, mucus production, and airway hyperresponsiveness present in asthma. Relevant primary cell models of the human airway epithelium are needed to investigate the biology of IL-13-mediated airway epithelial effects. Here, we describe the generation of a differentiated mucociliary human airway epithelium using an in vitro air-liquid interface (ALI) culture model system. We also describe methods to stimulate this culture model with IL-13 and harvest cells and biomolecules to interrogate cellular and molecular aspects of the airway epithelial IL-13 response.

Book ChapterDOI
TL;DR: Methods for the isolation of mouse and rat ATII cells are presented, which are important for gas exchange and fluid and ion transport and for understanding the biology of these cells.
Abstract: The gas exchange surface of the lungs is lined by an epithelium consisting of alveolar type (AT) I and ATII cells. ATII cells function to produce surfactant, play a role in host defense and fluid and ion transport, and serve as progenitors. ATI cells are important for gas exchange and fluid and ion transport. Our understanding of the biology of these cells depends on the investigation of isolated cells. Here, we present methods for the isolation of mouse and rat ATII cells.

Book ChapterDOI
TL;DR: The latest protocol to generate mucociliary epithelial cultures knocked out for a specific gene from donor-isolated primary human basal airway epithelial cells is detailed, providing an excellent primary cell model system with which to characterize the function of genes involved in airway dysfunction and disease.
Abstract: The adaptation of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated endonuclease 9 (CRISPR-Cas9) machinery from prokaryotic organisms has resulted in a gene editing system that is highly versatile, easily constructed, and can be leveraged to generate human cells knocked out (KO) for a specific gene. While standard transfection techniques can be used for the introduction of CRISPR-Cas9 expression cassettes to many cell types, delivery by this method is not efficient in many primary cell types, including primary human airway epithelial cells (AECs). More efficient delivery in AECs can be achieved through lentiviral-mediated transduction, allowing the CRISPR-Cas9 system to be integrated into the genome of the cell, resulting in stable expression of the nuclease machinery and increasing editing rates. In parallel, advancements have been made in the culture, expansion, selection, and differentiation of AECs, which allow the robust generation of a bulk edited AEC population from transduced cells. Applying these methods, we detail here our latest protocol to generate mucociliary epithelial cultures knocked out for a specific gene from donor-isolated primary human basal airway epithelial cells. This protocol includes methods to: (1) design and generate lentivirus which targets a specific gene for KO with CRISPR-Cas9 machinery, (2) efficiently transduce AECs, (3) culture and select for a bulk edited AEC population, (4) molecularly screen AECs for Cas9 cutting and specific sequence edits, and (5) further expand and differentiate edited cells to a mucociliary airway epithelial culture. The AEC knockouts generated using this protocol provide an excellent primary cell model system with which to characterize the function of genes involved in airway dysfunction and disease.

Book ChapterDOI
TL;DR: This chapter highlights how to extract IMs from the lung using three different digestion enzymes: elastase, collagenase D, and Liberase TM, which was the most effective at IM extraction, particularly IM3.
Abstract: Interstitial macrophages (IMs) are present in multiple organs. Although there is limited knowledge of the unique functional role IM subtypes play, macrophages, in general, are known for their contribution in homeostatic tissue maintenance and inflammation such as clearing pathogens and debris and secreting inflammatory mediators and growth factors. IM subtypes have been identified in the heart, skin, and gut, and more recently we identified three distinct IMs in the lung. IMs express on their surface high levels of MerTK, CD64, and CD11b, with differences in CD11c, CD206, and MHC II expression, and referred to the three pulmonary IM subtypes as IM1 (CD11cloCD206+MHCIIlo), IM2 (CD11cloCD206+MHCIIhi), and IM3 (CD11chiCD206loMHCIIhi). In this chapter, we highlight how to extract IMs from the lung using three different digestion enzymes: elastase, collagenase D, and Liberase TM. Of these three commonly used enzymes, Liberase TM was the most effective at IM extraction, particularly IM3. Furthermore, alternative staining strategies to identify IMs were examined, which included CD64, MerTK, F4/80, and Tim4. Thus, future studies highlighting the functional role of IM subtypes will help further our understanding of how tissue homeostasis is maintained and inflammatory conditions are induced and resolved.

Book ChapterDOI
TL;DR: This chapter describes an array-based protocol for identifying methylated DNA regions, and discusses protocols for DNA quantification, bisulfite conversion, library preparation, and chip assembly, and presents an overview of current methods for the analysis of methylation data.
Abstract: DNA methylation is a key factor in epigenetic regulation, and contributes to the pathogenesis of many diseases, including various forms of cancers, and epigenetic events such X inactivation, cellular differentiation and proliferation, and embryonic development. The most conserved epigenetic modification in plants, animals, and fungi is 5-methylcytosine (5mC), which has been well characterized across a diverse range of species. Many technologies have been developed to measure modifications in methylation with respect to biological processes, and the most common method, long considered a gold standard for identifying regions of methylation, is bisulfite conversion. In this technique, DNA is treated with bisulfite, which converts cytosine residues to uracil, but does not affect cytosine residues that have been methylated, such as 5-methylcytosines. Following bisulfite conversion, the only cytosine residues remaining in the DNA, therefore, are those that have been methylated. Subsequent sequencing can then distinguish between unmethylated cytosines, which are displayed as thymines in the resulting amplified sequence of the sense strand, and 5-methylcytosines, which are displayed as cytosines in the resulting amplified sequence of the sense strand, at the single nucleotide level. In this chapter, we describe an array-based protocol for identifying methylated DNA regions. We discuss protocols for DNA quantification, bisulfite conversion, library preparation, and chip assembly, and present an overview of current methods for the analysis of methylation data.

Book ChapterDOI
TL;DR: This chapter provides an overview of human lung anatomy focused on the airways, the ultrastructure or parenchyma of the lung, the pulmonary vasculature, the innervation of the lungs, and the pulmonary lymphatic system.
Abstract: The lungs are a complex organ that fulfill multiple life-sustaining roles including transfer of oxygen and carbon dioxide between the ambient environment and the bloodstream, host defense, and immune homeostasis. As in any biological system, an understanding of the underlying anatomy is prerequisite for successful experimental design and appropriate interpretation of data, regardless of the precise experimental model or procedure in use. This chapter provides an overview of human lung anatomy focused on the airways, the ultrastructure or parenchyma of the lung, the pulmonary vasculature, the innervation of the lungs, and the pulmonary lymphatic system. We will also discuss notable anatomic differences between mouse and human lungs.

Book ChapterDOI
TL;DR: This chapter provides a brief overview of the CRISPR-Cas9 technology and describes a general methodology applicable to human airway biology research.
Abstract: The CRISPR-Cas9 technology is a powerful tool that enables site-specific genome modification (gene editing) and is increasingly used in research to generate gene knockout or knock-in in a variety of cells and organisms. This chapter provides a brief overview of this technology and describes a general methodology applicable to human airway biology research.

Book ChapterDOI
TL;DR: This chapter describes a quick protocol for miRNA extraction, reverse transcription, qPCR, and data analysis for measuring relative gene expression and is now also widely used to assess miRNA abundance.
Abstract: MicroRNAs are small noncoding RNAs that function to regulate gene expression. In general, miRNAs are posttranscriptional regulators that imperfectly bind to the 3'untranslated region (3'UTR) of target mRNAs bearing complementary sequences, and target more than half of all protein-coding genes in the human genome. The dysregulation of miRNA expression and activity has been linked with numerous diseases, including cancer, cardiovascular diseases, neurodegenerative disorders, and diabetes. To better understand the relationship between miRNAs and human disease, a variety of techniques have been used to measure and validate miRNA expression in many cells, tissues, body fluids, and organs. For many years, quantitative polymerase chain reaction (qPCR) has been the gold standard for measuring relative gene expression, and is now also widely used to assess miRNA abundance. In this chapter, we describe a quick protocol for miRNA extraction, reverse transcription, qPCR, and data analysis.

Book ChapterDOI
TL;DR: Methods for establishing mouse models of respiratory syncytial virus (RSV) and H1N1 influenza A virus infection are described and their potential impact is discussed.
Abstract: Viral respiratory tract infections are common in both children and adults. Mouse models of viral infection enable the characterization of host immune factors that protect against or promote virus infection; thus, mouse models are essential for interrogation of potential therapeutic targets. Moreover, they serve as critical models for the development of novel vaccine strategies. In this chapter, we describe methods for establishing mouse models of respiratory syncytial virus (RSV) and H1N1 influenza A virus infection. Protocols are provided for viral culture and expansion, plaque-forming assays for viral quantification, and infection of mice. Alternate modifications to the models are also described, and their potential impact is discussed.

Book ChapterDOI
TL;DR: This chapter discusses how the transition from family-based studies to population comparison association studies led to a critical loss of information with respect to genetic etiology and inheritance, and posit that the combination of linkage analysis, association testing, and high throughput sequencing provides a powerful approach for identifying disease-causing genes.
Abstract: For many years, family-based studies using linkage analysis represented the primary approach for identifying disease genes. This strategy is responsible for the identification of the greatest number of genes proven to cause human disease. However, technical advancements in next generation sequencing and high throughput genotyping, coupled with the apparent simplicity of association testing, led to the rejection of family-based studies and of linkage analysis. At present, genetic association methods, using case-control comparisons, have become the exclusive approach for detecting disease-related genes, particularly those underlying common, complex diseases. In this chapter, we present a historical overview of linkage analysis, including a description of how the approach works, as well as its strengths and weaknesses. We discuss how the transition from family-based studies to population comparison association studies led to a critical loss of information with respect to genetic etiology and inheritance, and we present historical and contemporary examples of linkage analysis "success stories" in identifying genes contributing to the development of human disease. Currently, linkage analysis is re-emerging as a useful approach for identifying disease genes, determining genetic parameters, and resolving genetic heterogeneity. We posit that the combination of linkage analysis, association testing, and high throughput sequencing provides a powerful approach for identifying disease-causing genes.

Book ChapterDOI
01 Jan 2018
TL;DR: The history, development, and institution of the lung allocation score (LAS), developed in the spirit of the important ethical principles in transplantation of utility and justice, and the ongoing evolution of the LAS are explored.
Abstract: This chapter reviews the history, development, and institution of the lung allocation score (LAS) in the United States Lung transplantation can be a lifesaving therapy for patients suffering with end-stage lung diseases for which there are no remaining therapeutic options available Unfortunately, there remains an imbalance between the number of patients in need of this therapy and the availability of suitable donor organs for transplantation The LAS was developed in the spirit of the important ethical principles in transplantation of utility and justice More specifically, the objective of the LAS is to decrease waitlist time (and thus risk for waitlist mortality) and to allocate organs based upon medical urgency so as to balance predicted urgency with predicted benefit The institution of the LAS for the allocation of suitable donor lungs to appropriate candidates on May 4, 2005, literally changed the landscape of lung transplantation overnight This chapter also explores the ongoing evolution of the LAS as advancements continue to be made in medical therapies and technologies available for the support and management of end-stage lung diseases

Book ChapterDOI
TL;DR: This chapter describes a method to measure the in vitro bactericidal activity of isolated neutrophils as the endpoint of converging innate immune functions.
Abstract: The best-known role of neutrophils is control of pathogen growth. Neutrophils contain and kill pathogens through a variety of antimicrobial activities. Regardless of the mechanism, the ability to kill pathogens is a vital outcome. This chapter describes a method to measure the in vitro bactericidal activity of isolated neutrophils as the endpoint of converging innate immune functions.

Journal ArticleDOI
TL;DR: Patients who did versus did not respond to a communication technology outreach were described and compared to find a higher asthma medication ratio (AMR), defined as the ratio of asthma controller medications to total controller medications plus inhaled beta-agonists.
Abstract: Evidence suggests that communication technology applications can improve treatment adherence.1 However, a recent Cochrane Review concluded insufficient evidence exists to determine the effects of automated communication on managing chronic conditions such as asthma.2 Because not all patients are receptive to communication technology interventions, defining factors associated with non-response to electronic outreach can inform tailoring future interventions to increase effectiveness. As part of a pragmatic trial targeting asthma patients with too frequent refills of inhaled beta-agonists (“overfill”),3 the objective of this work was to describe and compare patients who did versus did not respond to a communication technology outreach. A higher asthma medication ratio (AMR), defined as the ratio of asthma controller medications (numerator, e.g., inhaled corticosteroids) to total controller medications plus inhaled beta-agonists (denominator), is associated with better asthma outcomes.4 We hypothesized that patients who did not respond to outreach would have a lower AMR than patients who did respond.

Book ChapterDOI
TL;DR: The ability of this approach to identify transposase integration in both IL-4- and IFN-γ-expressing CD4+ T cells isolated directly from the lung and lymph nodes after helminth infection is investigated.
Abstract: Although conventional methods such as MNase-seq, DNase-seq, and ChIP-seq have been used effectively to assess chromatin and locus accessibility at the genome level, these techniques generally require large numbers of input cells. As such, much of what we understand in terms of epigenetic regulation and locus accessibility in CD4+ T cell subsets comes from in vitro culture systems, which allow for the production of large numbers of polarized T cells. However, obtaining such numbers directly ex vivo from tissues of individual mice is difficult. Here we describe a method combining cytokine reporter mice and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify genome wide locus accessibility in a small number of cytokine-expressing CD4+ T cells. This method takes you from cell isolation to library generation and quality control to query. Because the Il4 and Ifng loci are reciprocally regulated in polarized CD4+ T cell subsets (Th1 vs. Th2), we investigated the ability of this approach to identify transposase integration in both IL-4- and IFN-γ-expressing CD4+ T cells isolated directly from the lung and lymph nodes after helminth infection.

Book ChapterDOI
01 Jan 2018
TL;DR: The prevalence of common sleep problems in adults with cancer and key terms are described and barriers to behavioral change and strategies to assist the cancer patient and family to self-manage sleep problems are identified.
Abstract: Sleep disturbances are reported in up to 60% of patients with cancers of many types and stages. Impaired sleep has an array of detrimental effects on the health of individuals with cancer and their family caregivers, with significant societal costs. Cancer-related sleep disturbances can also affect health-related quality of life by way of persistent fatigue and altered mood. Chronic sleep loss may lead to poor adherence to cancer treatments and higher morbidity and mortality. Sleep disturbances can range from perceived or actual alterations in usual sleep patterns to diagnosed sleep disorders meeting precise diagnostic criteria. New onset or worsening of sleep disturbances are common and disabling problems for those with cancer before treatment, during treatments such as chemotherapy and radiation therapy, and after completion of treatments. Cancer pathology, treatments, and symptoms such as pain and hot flashes, disruption of daily activity and circadian rhythms, and unhealthy sleep habits contribute to acute and chronic sleep disturbances. In this chapter, we describe the prevalence of common sleep problems in adults with cancer and define key terms. This chapter also provides information about biological and behavioral conceptual models of sleep and guidelines for the assessment and management of sleep disturbances. Emphasis is given to the latest non-pharmacological evidence-based treatments. We discuss the importance of provider awareness of sleep problems and patient education. Finally, we identify barriers to behavioral change and strategies to assist the cancer patient and family to self-manage sleep problems.

Posted ContentDOI
20 Aug 2018-bioRxiv
TL;DR: This paper proposes the variant-Set Mixed Model Association Tests (SMMAT) for continuous and binary traits using the generalized linear mixed model framework and shows that all the proposed SMMAT tests correctly control type I error rates for both continuous andbinary traits in the presence of population structure and relatedness.
Abstract: With advances in Whole Genome Sequencing (WGS) technology, more advanced statistical methods for testing genetic association with rare variants are being developed. Methods in which variants are grouped for analysis are also known as variant-set, gene-based, and aggregate unit tests. The burden test and Sequence Kernel Association Test (SKAT) are two widely used variant-set tests, which were originally developed for samples of unrelated individuals and later have been extended to family data with known pedigree structures. However, computationally-efficient and powerful variant-set tests are needed to make analyses tractable in large-scale WGS studies with complex study samples. In this paper, we propose the variant-Set Mixed Model Association Tests (SMMAT) for continuous and binary traits using the generalized linear mixed model framework. These tests can be applied to large-scale WGS studies involving samples with population structure and relatedness, such as in the National Heart, Lung, and Blood Institute9s Trans-Omics for Precision Medicine (TOPMed) program. SMMAT tests share the same null model for different variant sets, and a virtue of this null model, which includes covariates only, is that it needs to be only fit once for all tests in each genome-wide analysis. Simulation studies show that all the proposed SMMAT tests correctly control type I error rates for both continuous and binary traits in the presence of population structure and relatedness. We also illustrate our tests in a real data example of analysis of plasma fibrinogen levels in the TOPMed program (n = 23,763), using the Analysis Commons, a cloud-based computing platform.

Book ChapterDOI
TL;DR: A protocol is described for in vivo detection of IL-4-expressing Tfh cells in an explanted popliteal lymph node by multi-photon microscopy to better understand the role of these cells during the GC response.
Abstract: The generation of class-switched, high-affinity, antibody-producing B cells plays a critical role in the establishment of type 2 immunity to intestinal helminths as well as in the pathogenesis of allergy and asthma. The generation of these high-affinity, antibody-producing B cells occurs in germinal centers (GC) and relies on interactions with follicular dendritic cells (FDCs) and T follicular helper (Tfh) cells. One critical mediator produced by Tfh cells in GCs is interleukin-4 (IL-4). Tfh-derived IL-4 drives class switching to type 2 antibody isotypes IgE and IgG1 and is required for high-affinity IgG1 production. In vivo detection of IL-4-expressing Tfh cells is required to better understand the role of these cells during the GC response. Detection of IL-4-expressing cells has been greatly improved by the generation of the IL-44get reporter mice, which read out IL-4 expression as green fluorescent protein (GFP). Much has been learned from these mice with regard to type 2 immunity using flow cytometry and immunohistochemistry. However, these methods do not allow the study of cellular behavior and interactions in real time. In contrast, multi-photon microscopy allows for deep tissue imaging and tracking of multiple cell types in intact tissues over time. Here, we describe a protocol for in vivo detection of IL-4-expressing Tfh cells in an explanted popliteal lymph node by multi-photon microscopy. The dynamics of Tfh cell motility and their interactions with FDC networks in the GCs were analyzed.