Data Integration in Genetics and Genomics: Methods and Challenges

Due to rapid technological advances, various types of genomic and proteomic data with different sizes, formats, and structures have become available. Among them are gene expression, single nucleotide polymorphism, copy number variation, and protein-protein/gene-gene interactions. Each of these distinct data types provides a different, partly independent and complementary, view of the whole genome. However, understanding functions of genes, proteins, and other aspects of the genome requires more information than provided by each of the datasets. Integrating data from different sources is, therefore, an important part of current research in genomics and proteomics. Data integration also plays important roles in combining clinical, environmental, and demographic data with high-throughput genomic data. Nevertheless, the concept of data integration is not well defined in the literature and it may mean different things to different researchers. In this paper, we first propose a conceptual framework for integrating genetic, genomic, and proteomic data. The framework captures fundamental aspects of data integration and is developed taking the key steps in genetic, genomic, and proteomic data fusion. Secondly, we provide a review of some of the most commonly used current methods and approaches for combining genomic data with focus on the statistical aspects

Biological and Sociocultural Differences in Perceived Barriers to Physical Activity

BACKGROUND:Inadequate physical activity (PA) contributes to the high prevalence of overweight and obesity among U.S. adolescent girls. Barriers preventing adolescent girls from meeting PA guidelines have not been thoroughly examined. OBJECTIVES: The threefold purpose of this study was to (a) determine pubertal stage, racial/ethnic, and socioeconomic status (SES) differences in ratings of interference of barriers to PA; (b) examine relationships between perceived barriers and age, body mass index, recreational screen time, sedentary activity, and PA; and (c) identify girls\u27 top-rated perceived barriers to PA. METHODS: Girls (N = 509) from eight Midwestern U.S. schools participated. Demographic, pubertal stage, perceived barriers, and recreational screen time data were collected via surveys. Height and weight were measured. Accelerometers measured sedentary activity, moderate-to-vigorous PA (MVPA), and light plus MVPA. RESULTS: Girls of low SES reported greater interference of perceived barriers to PA than those who were not of low SES (1.16 vs. 0.97, p = .01). Girls in early/middle puberty had lower perceived barriers than those in late puberty (1.03 vs. 1.24, p \u3c .001). Girls\u27 perceived barriers were negatively related to MVPA (r = -.10, p = .03) and light plus MVPA (r = -.11, p = .02). Girls\u27 top five perceived barriers included lack of skills, hating to sweat, difficulty finding programs, being tired, and having pain. DISCUSSION: Innovative interventions, particularly focusing on skill development, are needed to assist girls in overcoming their perceived barriers to PA

Biological and Sociocultural Differences in Perceived Barriers to Physical Activity among 5th–7th Grade Urban Girls

Background: Inadequate physical activity (PA) contributes to the high prevalence of overweight and obesity among U.S. adolescent girls. Barriers preventing adolescent girls from meeting PA guidelines have not been thoroughly examined. Objectives: The threefold purpose of this study was to: (a) determine pubertal stage, racial/ethnic, and socioeconomic status (SES) differences in ratings of interference of barriers to PA; (b) examine relationships between perceived barriers and age, body mass index (BMI), recreational screen time, sedentary activity, and PA; and (c) identify girls’ top-rated perceived barriers to PA. Methods: Girls (N = 509) from eight Midwestern U.S. schools participated. Demographic, pubertal stage, perceived barriers, and recreational screen time data were collected via surveys. Height and weight were measured. Accelerometers measured sedentary activity, moderate-to-vigorous physical activity (MVPA), and light plus MVPA. Results: Girls of low SES reported greater interference of perceived barriers to PA than those who were not of low SES (1.16 vs. 0.97, p = .01). Girls in early/middle puberty had lower perceived barriers than those in late puberty (1.03 vs. 1.24, p \u3c .001). Girls’ perceived barriers were negatively related to MVPA (r = -.10, p = .03) and light plus MVPA (r = -.11, p = .02). Girls’ top five perceived barriers included lack of skills, hating to sweat, difficulty finding programs, being tired, and having pain. Discussion: Innovative interventions, particularly focusing on skill development, are needed to assist girls in overcoming their perceived barriers to PA

Effects of the Girls on the Move randomized trial on adiposity and aerobic performance (secondary outcomes) in low-income adolescent girls

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151987/1/ijpo12559_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151987/2/ijpo12559.pd

The structured health intervention for truckers (SHIFT) cluster randomised controlled trial : a mixed methods process evaluation

Funding This project was funded by the National Institute for Health Research (NIHR) Public Health Research programme (reference: NIHR PHR 15/190/42). The study was also supported by the NIHR Leicester Biomedical Research Centre which is a partnership between University Hospitals of Leicester NHS Trust, Loughborough University, and the University of Leicester. Laura Gray is supported by the National Institute for Health Research (NIHR) Applied Research Collaboration East Midlands (ARC EM). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. Funding to cover intervention costs (Fitbits, cab workout equipment) was provided by the Higher Education Innovation Fund, via the Loughborough University Enterprise Projects Group. The Colt Foundation provided funding for a PhD Studentship, awarded to Amber Guest (reference: JD/618), which covered Amber’s time and contributions to this project. None of the funding bodies had any role in study design; election, synthesis, and interpretation of data; writing of the report; or the decision to submit the manuscript for publication. Acknowledgements We gratefully acknowledge the support provided by senior Health and Safety personnel and Transport Managers at our partner logistics company in facilitating this research. We also thank all participants for taking part. We are grateful to the independent members of the Trial Steering Committee for their continued support and advice throughout the trial: Dr. Derrick Bennett, Prof Emma McIntosh, Prof Petra Wark and Mr. Paul Gardiner.Peer reviewedPublisher PD

Drivers with and without Obesity Respond Differently to a Multi-Component Health Intervention in Heavy Goods Vehicle Drivers

Funding This project was funded by the National Institute for Health Research (NIHR) Public Health Research programme (reference: NIHR PHR 15/190/42). The study was also supported by the NIHR Leicester Biomedical Research Centre which is a partnership between University Hospitals of Leicester NHS Trust, Loughborough University and the University of Leicester. Laura Gray is supported by the National Institute for Health Research (NIHR) Applied Research Collaboration East Midlands (ARC EM). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. Funding to cover the intervention costs (Fitbits and cab workout equipment) was provided by the Higher Education Innovation Fund, via the Loughborough University Enterprise Projects Group. The Colt Foundation provided funding for a PhD Studentship, awarded to Amber Guest (reference: JD/618), which covered Amber’s time and contributions to this project. The funders played no role in study design, data collection, data analysis, data interpretation or in the preparation of this manuscript.Peer reviewedPublisher PD

Combined Vorinostat and Chloroquine Inhibit Sodium Iodide Symporter Endocytosis and Enhance Radionuclide Uptake In Vivo

Purpose Patients with aggressive thyroid cancer are frequently failed by the central therapy of ablative radioiodide (RAI) uptake, due to reduced plasma membrane (PM) localization of the sodium/iodide symporter (NIS). We aimed to understand how NIS is endocytosed away from the PM of human thyroid cancer cells, and whether this was druggable in vivo.Experimental DesignInformed by analysis of endocytic gene expression in patients with aggressive thyroid cancer, we used mutagenesis, NanoBiT interaction assays, cell surface biotinylation assays, RAI uptake and NanoBRET to understand the mechanisms of NIS endocytosis in transformed cell lines and patient-derived human primary thyroid cells. Systemic drug responses were monitored via 99mTc pertechnetate gamma counting and gene expression in BALB/c mice.ResultsWe identify an acidic dipeptide within the NIS C-terminus which mediates binding to the 2 subunit of the Adaptor Protein 2 (AP2) heterotetramer. We discovered that the FDA-approved drug chloroquine modulates NIS accumulation at the PM in a functional manner that is AP2 dependent. In vivo, chloroquine treatment of BALB/c mice significantly enhanced thyroidal uptake of 99mTc pertechnetate in combination with the histone deacetylase (HDAC) inhibitor vorinostat/ SAHA, accompanied by increased thyroidal NIS mRNA. Bioinformatic analyses validated the clinical relevance of AP2 genes with disease-free survival in RAI-treated DTC, enabling construction of an AP2 gene-related risk score classifier for predicting recurrence.ConclusionsNIS internalisation is specifically druggable in vivo. Our data therefore provide new translatable potential for improving RAI therapy using FDA-approved drugs in patients with aggressive thyroid cancer.<br/

Marine Compounds Selectively Induce Apoptosis in Female Reproductive Cancer Cells but Not in Primary-Derived Human Reproductive Granulosa Cells

Anticancer properties of tyrindoleninone and 6-bromoisatin from Dicathais orbita were tested against physiologically normal primary human granulosa cells (HGC) and reproductive cancer cell lines. Tyrindoleninone reduced cancer cell viability with IC50 values of 39 µM (KGN; a tumour-derived granulosa cell line), 39 μM (JAr), and 156 μM (OVCAR-3), compared to 3516 μM in HGC. Apoptosis in HGC’s occurred after 4 h at 391 µM tyrindoleninone compared to 20 µM in KGN cells. Differences in apoptosis between HGC and KGN cells were confirmed by TUNEL, with 66 and 31% apoptotic nuclei at 4 h in KGN and HGC, respectively. These marine compounds therefore have potential for development as treatments for female reproductive cancers

Lunatic Fringe Deficiency Cooperates with the Met/Caveolin Gene Amplicon to Induce Basal-like Breast Cancer

Basal-like breast cancers (BLBC) express a luminal progenitor gene signature. Notch receptor signaling promotes luminal cell fate specification in the mammary gland, while suppressing stem cell self-renewal. Here we show that deletion of Lfng, a sugar transferase that prevents Notch activation by Jagged ligands, enhances stem/progenitor cell proliferation. Mammary-specific deletion of Lfng induces basal-like and claudin-low tumors with accumulation of Notch intracellular domain fragments, increased expression of proliferation-associated Notch targets, amplification of the Met/Caveolin locus, and elevated Met and Igf-1R signaling. Human BL breast tumors, commonly associated with JAGGED expression, elevated MET signaling, and CAVEOLIN accumulation, express low levels of LFNG. Thus, reduced LFNG expression facilitates JAG/NOTCH luminal progenitor signaling and cooperates with MET/CAVEOLIN basal-type signaling to promote BLBC