Health provider perspectives of electronic medication monitoring in outpatient asthma care: a qualitative investigation using the consolidated framework for implementation research.

OBJECTIVE: Little is known about the implementation challenges health providers might face with the use of digital health in outpatient asthma care. To qualitatively explore the experience of health providers with electronic medication monitoring (EMM) using an implementation science framework. METHODS: Using the Consolidated Framework of Implementation Research (CFIR), we conducted interviews (n = 10) exploring health providers' experience with EMM with asthma patients from 5 primary care or specialty clinics. The EMM tracked albuterol and inhaled corticosteroid (ICS) use, and health providers called parents whenever ICS adherence waned, or albuterol use increased. Interviews were audio-recorded, transcribed, and deductively analyzed using directed content analysis. RESULTS: Health providers reported the intervention's primary advantage, compared with current asthma care, was the ability to monitor medication use at-home. Most felt the intervention improved care delivery. Nurses and medical assistants described a process of phone calls and checking alerts, that had varying levels of administrative burden and complexity. Health providers felt that sustained implementation of the intervention model would require additional employees to handle the administrative and clinical workload. Half of the interviewed providers were unsure if patient needs were met by the intervention, while some cited technology syncing issues, others liked the enhanced interactions for asthma education. CONCLUSION: Health providers reported positive experiences supporting parents and children with asthma using EMM but also highlighted intervention components that needed improvement or refinement to yield successful implementation in outpatient pediatric clinics. Recommendations for enhancing the intervention for a scaled-up implementation were discussed.

Parent Experiences With Electronic Medication Monitoring in Pediatric Asthma Management: Qualitative Study.

BACKGROUND: Electronic medication monitoring (EMM) is a digital tool that can be used for tracking daily medication use. Previous studies of EMM in asthma management have been conducted in adults or have examined pediatric interventions that use EMM for less than 1 year. To understand how to improve EMM-enhanced interventions, it is necessary to explore the experiences of parents of children with asthma, recruited from outpatient practices, who completed a 12-month intervention trial. OBJECTIVE: The objective of our study was to use qualitative inquiry to answer the following questions: (1) how did using an EMM-enhanced intervention change parents'/caregivers' experiences of managing their child's asthma, and (2) what do parents recommend for improving the intervention in the future? METHODS: Parents were recruited from the intervention arm of a multicomponent health intervention enhanced by Bluetooth-enabled sensors placed on inhaler medications. Semistructured interviews were conducted with 20 parents of children aged 4-12 years with asthma. Interviews were audio-recorded, transcribed, and inductively analyzed using a constant comparative approach. RESULTS: Interview participants reflected an even mix of publicly and privately insured children and a diverse racial-ethnic demographic. Parents discussed 6 key themes related to their experience with the EMM-enhanced intervention for the management of their child's asthma: (1) compatibility with the family's lifestyle, (2) impact on asthma management, (3) impact on the child's health, (4) emotional impact of the intervention, (5) child's engagement in asthma management with the intervention, and (6) recommendations for future intervention design. Overall, parents reported that the 12-month EMM intervention was compatible with their daily lives, positively influenced their preventive and acute asthma management, and promoted their child's engagement in their own asthma management. While parents found the intervention acceptable and generally favorable, some parents identified compatibility issues for families with multiple caregivers and frustration when the technology malfunctioned. CONCLUSIONS: Parents generally viewed the intervention as a positive influence on the management of their child's asthma. However, our study also highlighted technology challenges related to having multiple caregivers, which will need to be addressed in future iterations for families. Attention must be paid to the needs of parents from low socioeconomic households, who may have more limited access to reliable internet or depend on other relatives for childcare. Understanding these family factors will help refine how a digital tool can be adopted into daily disease management of pediatric asthma.

Sensor-Based Electronic Monitoring for Asthma: A Randomized Controlled Trial.

BACKGROUND: Although sensor-based monitoring of daily inhaled corticosteroids (ICSs) and short-acting ß-agonist medications may improve asthma outcomes, the effectiveness of these interventions in diverse pediatric populations remains unclear. METHODS: Caregiver and child dyads were randomly assigned to receive inhaler sensors that allowed for caregiver and clinician electronic monitoring of medications. End points included Asthma Control Test scores (≥19 indicated asthma control) and asthma health care use. Caregiver quality of life (QoL) and child ICS adherence were also assessed. Multilevel models were used to estimate adjusted changes from baseline. RESULTS: Dyads were assigned to the control (n = 127) or intervention (n = 125) arms. At the end line, the mean Asthma Control Test score increased from 19.1 (SE = 0.3) to 21.8 (SE = 0.4) among the intervention and from 19.4 (SE = 0.3) to 19.9 (SE = 0.4) among the control (Δintervention-control = 2.2; SE = 0.6; P < .01). Adjusted rates of emergency department visits and hospitalizations among the intervention were significantly greater (incidence rate ratioemergency department = 2.2; SE = 0.5; P < .01; incidence rate ratiohospital = 3.4; SE = 1.4; P < .01) at endline than the control. Caregiver QoL was greater among the intervention at the endline (Δintervention-control = 0.3; SE = 0.2; P = .1) than the control. CONCLUSIONS: Findings suggest that sensor-based inhaler monitoring with clinical feedback may improve asthma control and caregiver QoL within diverse populations. Higher health care use was observed among the intervention participants relative to the control, indicating further refinement is warranted.

Parental quality of life and self-efficacy in pediatric asthma.

Objective: Self-efficacy is the personal belief that a behavior can produce a desired result; and in asthma, self-efficacy in asthma care has been related to improvements in asthma outcomes and children's quality of life. To appreciate the full burden of asthma on families, the relationship between parental self-efficacy and quality of life also needs further study. We aim to characterize this relationship.Methods: Secondary analysis of measurements of parents of children with persistent asthma (n = 252; ages 4-17 years) from a large urban area were identified from a randomized trial; the association between baseline assessments of parental quality of life, measured by the Pediatric Asthma Caregiver's Quality of Life Questionnaire (PACQLQ), and parental self-efficacy, measured through the Parental Asthma Management Self-Efficacy Scale (PAMSES), were examined through multivariable linear regression.Results: Parental self-efficacy in asthma was positively associated with quality of life among parents of racially and ethnically diverse children (p = 0.01). Confidence in using medications correctly (p = 0.03), having inhalers during a child's serious breathing problem (p = 0.02), and knowing which medications to use during a child's serious breathing problem (p = 0.04) were associated with a clinically meaningful difference in parental quality of life. Other significant factors associated with parental quality of life included Hispanic/Latino ethnicity (p < 0.01) of the child and Asthma Control Test scores (p < 0.01).Conclusion: The findings suggest that improving parental confidence on when and how to use their child's asthma medications, particularly during an asthma attack, might be clinically meaningful in enhancing parent's quality of life.

The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis.

RATIONALE: Peripheral blood biomarkers are needed to identify and determine the extent of idiopathic pulmonary fibrosis (IPF). Current physiologic and radiographic prognostic indicators diagnose IPF too late in the course of disease. We hypothesize that peripheral blood biomarkers will identify disease in its early stages, and facilitate monitoring for disease progression. METHODS: Gene expression profiles of peripheral blood RNA from 130 IPF patients were collected on Agilent microarrays. Significance analysis of microarrays (SAM) with a false discovery rate (FDR) of 1% was utilized to identify genes that were differentially-expressed in samples categorized based on percent predicted D(L)CO and FVC. MAIN MEASUREMENTS AND RESULTS: At 1% FDR, 1428 genes were differentially-expressed in mild IPF (D(L)CO >65%) compared to controls and 2790 transcripts were differentially- expressed in severe IPF (D(L)CO >35%) compared to controls. When categorized by percent predicted D(L)CO, SAM demonstrated 13 differentially-expressed transcripts between mild and severe IPF (< 5% FDR). These include CAMP, CEACAM6, CTSG, DEFA3 and A4, OLFM4, HLTF, PACSIN1, GABBR1, IGHM, and 3 unknown genes. Principal component analysis (PCA) was performed to determine outliers based on severity of disease, and demonstrated 1 mild case to be clinically misclassified as a severe case of IPF. No differentially-expressed transcripts were identified between mild and severe IPF when categorized by percent predicted FVC. CONCLUSIONS: These results demonstrate that the peripheral blood transcriptome has the potential to distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted D(L)CO, but not FVC.

Molecular phenotypes distinguish patients with relatively stable from progressive idiopathic pulmonary fibrosis (IPF).

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic interstitial lung disease that is unresponsive to current therapy and often leads to death. However, the rate of disease progression differs among patients. We hypothesized that comparing the gene expression profiles between patients with stable disease and those in which the disease progressed rapidly will lead to biomarker discovery and contribute to the understanding of disease pathogenesis. METHODOLOGY AND PRINCIPAL FINDINGS: To begin to address this hypothesis, we applied Serial Analysis of Gene Expression (SAGE) to generate lung expression profiles from diagnostic surgical lung biopsies in 6 individuals with relatively stable (or slowly progressive) IPF and 6 individuals with progressive IPF (based on changes in DLCO and FVC over 12 months). Our results indicate that this comprehensive lung IPF SAGE transcriptome is distinct from normal lung tissue and other chronic lung diseases. To identify candidate markers of disease progression, we compared the IPF SAGE profiles in stable and progressive disease, and identified a set of 102 transcripts that were at least 5-fold up regulated and a set of 89 transcripts that were at least 5-fold down regulated in the progressive group (P-value

Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping.

BACKGROUND: The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK), a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. RESULTS: Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05) after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. CONCLUSION: The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models of complex human diseases in a mixed cell population and might be a valuable technology to determine whether environmental exposures can lead to epigenetic changes.

In utero supplementation with methyl donors enhances allergic airway disease in mice.

Asthma is a complex heritable disease that is increasing in prevalence and severity, particularly in developed countries such as the United States, where 11% of the population is affected. The contribution of environmental and genetic factors to this growing epidemic is currently not well understood. We developed the hypothesis, based on previous literature, that changes in DNA methylation resulting in aberrant gene transcription may enhance the risk of developing allergic airway disease. Our findings indicate that in mice, a maternal diet supplemented with methyl donors enhanced the severity of allergic airway disease that was inherited transgenerationally. Using a genomic approach, we discovered 82 gene-associated loci that were differentially methylated after in utero supplementation with a methyl-rich diet. These methylation changes were associated with decreased transcriptional activity and increased disease severity. Runt-related transcription factor 3 (Runx3), a gene known to negatively regulate allergic airway disease, was found to be excessively methylated, and Runx3 mRNA and protein levels were suppressed in progeny exposed in utero to a high-methylation diet. Moreover, treatment with a demethylating agent increased Runx3 gene transcription, further supporting our claim that a methyl-rich diet can affect methylation status and consequent transcriptional regulation. Our findings indicate that dietary factors can modify the heritable risk of allergic airway disease through epigenetic mechanisms during a vulnerable period of fetal development in mice.

PLXDC1 (TEM7) is identified in a genome-wide expression screen of glioblastoma endothelium.

Glioblastomas are a highly aggressive brain tumor, with one of the highest rates of new blood vessel formation. In this study we used a combined experimental and bioinformatics strategy to determine which genes were highly expressed and specific for glioblastoma endothelial cells (GBM-ECs), compared to gene expression in normal tissue and endothelium. Starting from fresh glioblastomas, several rounds of negative and positive selection were used to isolate GBM-ECs and extract total RNA. Using Serial Analysis of Gene Expression (SAGE), 116,259 transcript tags (35,833 unique tags) were sequenced. From this expression analysis, we found 87 tags that were not expressed in normal brain. Further subtraction of normal endothelium, bone marrow, white blood cell and other normal tissue transcripts resulted in just three gene transcripts, ANAPC10, PLXDC1(TEM7), and CYP27B1, that are highly specific to GBM-ECs. Immunohistochemistry with an antibody for PLXDC1 showed protein expression in GBM microvasculature, but not in the normal brain endothelium tested. Our results suggest that this study succeeded in identifying GBM-EC specific genes. The entire gene expression profile for the GBM-ECs and other tissues used in this study are available at SAGE Genie (http://cgap.nci.nih.gov/SAGE). Functionally, the protein products of the three tags most specific to GBM-ECs have been implicated in processes critical to endothelial cell proliferation and differentiation, and are potential targets for anti-angiogenesis based therapy.

Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE.

PURPOSE: To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). METHODS: Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. RESULTS: Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. CONCLUSIONS: The EyeSAGE database, combining three different gene-profiling platforms including the authors' multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions.

Genomic amplification of orthodenticle homologue 2 in medulloblastomas.

To better understand the genetic basis of medulloblastoma development, we sought genomic amplifications and deletions in these tumors using digital karyotyping in combination with expression analysis. Five medulloblastoma genomes were karyotyped by sequencing an average of 195,745 genomic DNA tags for each analysis. Tags were tallied at unique positions and mapped to the human genome to determine DNA copy numbers in high resolution along each chromosome. Genomic alterations normally associated with medulloblastomas, including MYC amplification and isochromosome 17q, were easily detected. Surprisingly, analysis of only five genomes revealed novel amplicons on chromosome 14q, one of which contained the orthodenticle homologue 2 (OTX2) homeobox gene. DNA copy number analysis showed that OTX2 had undergone genomic amplification in 2 of 11 medulloblastoma cell lines and 8 of 42 primary tumors. The three genes and a predicted open reading frame flanking OTX2 in the 14q amplicon were not amplified in at least one of the other nine amplicons, implicating OTX2 as the gene target conferring a selective advantage. The degree of OTX2 amplification ranged from 8 copies to over 50 copies of the gene. OTX2 transcript was highly and specifically expressed in medulloblastoma or developing cells. Serial analysis of gene expression of 240 different human tumors or normal tissues revealed that 96% of all 783 OTX2 transcripts sequenced were in medulloblastomas or embryonic stem cells. OTX2 functions to specify the fate of neuroectoderm in various regions of the developing brain. This developmental role is consistent with the evidence suggesting that OTX2 is a medulloblastoma oncogene.

Identification of astrocytoma associated genes including cell surface markers.

BACKGROUND: Despite intense effort the treatment options for the invasive astrocytic tumors are still limited to surgery and radiation therapy, with chemotherapy showing little or no increase in survival. The generation of Serial Analysis of Gene Expression (SAGE) profiles is expected to aid in the identification of astrocytoma-associated genes and highly expressed cell surface genes as molecular therapeutic targets. SAGE tag counts can be easily added to public expression databases and quickly disseminated to research efforts worldwide. METHODS: We generated and analyzed the SAGE transcription profiles of 25 primary grade II, III and IV astrocytomas 1. These profiles were produced as part of the Cancer Genome Anatomy Project's SAGE Genie 2, and were used in an in silico search for candidate therapeutic targets by comparing astrocytoma to normal brain transcription. Real-time PCR and immunohistochemistry were used for the validation of selected candidate target genes in 2 independent sets of primary tumors. RESULTS: A restricted set of tumor-associated genes was identified for each grade that included genes not previously associated with astrocytomas (e.g. VCAM1, SMOC1, and thymidylate synthetase), with a high percentage of cell surface genes. Two genes with available antibodies, Aquaporin 1 and Topoisomerase 2A, showed protein expression consistent with transcript level predictions. CONCLUSIONS: This survey of transcription in malignant and normal brain tissues reveals a small subset of human genes that are activated in malignant astrocytomas. In addition to providing insights into pathway biology, we have revealed and quantified expression for a significant portion of cell surface and extra-cellular astrocytoma genes.

Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes.

Over 1.4 million transcript tags expressed in 20 different human medulloblastomas were counted using serial analysis of gene expression. Digital gene expression profiles in the medulloblastoma were compared to multiple regions of the normal human brain, revealing 30 transcripts with high expression in multiple tumors and little or no expression in the normal cerebellum and other adult and pediatric brain regions. Using independent medulloblastoma samples and normal tissue, real-time PCR verified eight of nine selected genes as candidate tumor-associated antigens. Differential protein expression for CD24, prolactin and Topo2A was further confirmed by immunohistochemical analysis using medulloblastoma and normal brain sections and a tissue microarray. The genes highly expressed in the medulloblastoma include PRAME, a cancer-testis antigen and potential targets for immunotherapy.

Rearrangements and increased expression of cyclin D1 (CCND1) in neuroblastoma.

Cyclin D1 regulates G1 cell cycle progression by controlling the phosphorylation of the retinoblastoma protein. This pathway is frequently deregulated in many malignancies. In neuroblastoma, however, no consistent G1 cell cycle checkpoint aberrations have been found. We examined the possible deregulation of cyclin D1 (CCND1) in this tumor. mRNA expression profiles of neuroblastoma generated by SAGE (Serial Analysis of Gene Expression) revealed a high expression of CCND1 in a subset of neuroblastoma cell lines and tumors. The CCND1 expression level can be 0.3% of the total cellular mRNA. Northern blot analysis of CCND1 expression showed a relative overexpression in 16 of 23 neuroblastoma cell lines and 10 of 15 tumor samples. In the majority of cases, the high CCND1 mRNA levels also led to high CCND1 protein levels. In the search for mechanisms causing this relative overexpression, we screened for amplifications and rearrangements of CCND1. Five amplifications were found in 202 neuroblastoma tumors and cell lines. Analysis of the 3'-UTR of CCND1 showed a rearrangement in 1 of 96 tumors. These clonal aberrations of CCND1 together with the high expression suggest a role for deregulated CCND1 activity in neuroblastoma tumorigenesis.

An anatomy of normal and malignant gene expression.

A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP) uses serial analysis of gene expression (SAGE). Over 5 million transcript tags from more than 100 human cell types have been assembled. To enhance the utility of this data, the CGAP SAGE project created SAGE Genie, a web site for the analysis and presentation of SAGE data (http://cgap.nci.nih.gov/SAGE). SAGE Genie provides an automatic link between gene names and SAGE transcript levels, accounting for alternative transcription and many potential errors. These informatics advances provide a rapid and intuitive view of transcript expression in the human body or brain, displayed on the SAGE Anatomic Viewer. We report here an easily accessible view of nearly any gene's expression in a wide variety of malignant and normal tissues.

The N-myc and c-myc downstream pathways include the chromosome 17q genes nm23-H1 and nm23-H2.

Gain of chromosome 17q material is the most frequent genetic abnormality in neuroblastomas. The common region of gain is at least 375 cR large, which has precluded the identification of genes with a role in neuroblastoma pathogenesis. Neuroblastoma also frequently show amplification of the N-myc oncogene, which correlates closely with 17q gain. Both events are strong predictors of unfavorable prognosis. To identify genes that are part of the N-myc downstream pathway, we constructed SAGE libraries of an N-myc transfected and a control cell line. This identified the chromosome 17q genes nm23-H1 and nm23-H2 as being 6-10 times induced in the N-myc expressing cells. Northern and Western blot analysis confirmed this up-regulation. Time-course experiment shows that both genes are induced within 4 h after N-myc is switched on. Furthermore, we demonstrate also that c-myc can up-regulate nm23-H1 and nm23-H2 expression. Neuroblastoma tumor and cell line panels reveal a striking correlation between N-myc amplification and mRNA and protein expression of both nm23 genes. We show that the nm23 genes are located at the edge of the common region of chromosome 17q gain previously described in neuroblastoma cell lines. Our findings suggest that nm23-H1 and nm23-H2 expression is increased by 17q gain in neuroblastoma and can be further up-regulated by myc overexpression. These observations suggest a major role for nm23-H1 and nm23-H2 in tumorigenesis of unfavorable neuroblastomas.