HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP

Human T-lymphotropic virus type 1 (HTLV-1) causes leukaemia or chronic inflammatory disease in ∼5% of infected hosts. The level of proviral expression of HTLV-1 differs significantly among infected people, even at the same proviral load (proportion of infected mononuclear cells in the circulation). A high level of expression of the HTLV-1 provirus is associated with a high proviral load and a high risk of the inflammatory disease of the central nervous system known as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). But the factors that control the rate of HTLV-1 proviral expression remain unknown. Here we show that proviral integration sites of HTLV-1 in vivo are not randomly distributed within the human genome but are associated with transcriptionally active regions. Comparison of proviral integration sites between individuals with high and low levels of proviral expression, and between provirus-expressing and provirus non-expressing cells from within an individual, demonstrated that frequent integration into transcription units was associated with an increased rate of proviral expression. An increased frequency of integration sites in transcription units in individuals with high proviral expression was also associated with the inflammatory disease HAM/TSP. By comparing the distribution of integration sites in human lymphocytes infected in short-term cell culture with those from persistent infection in vivo, we infer the action of two selective forces that shape the distribution of integration sites in vivo: positive selection for cells containing proviral integration sites in transcriptionally active regions of the genome, and negative selection against cells with proviral integration sites within transcription units

Peripheral Blood Mitochondrial DNA as a Biomarker of Cerebral Mitochondrial Dysfunction Following Traumatic Brain Injury in a Porcine Model

Background Traumatic brain injury (TBI) has been shown to activate the peripheral innate immune system and systemic inflammatory response, possibly through the central release of damage associated molecular patterns (DAMPs). Our main purpose was to gain an initial understanding of the peripheral mitochondrial response following TBI, and how this response could be utilized to determine cerebral mitochondrial bioenergetics. We hypothesized that TBI would increase peripheral whole blood relative mtDNA copy number, and that these alterations would be associated with cerebral mitochondrial bioenergetics triggered by TBI. Methodology Blood samples were obtained before, 6 h after, and 25 h after focal (controlled cortical impact injury: CCI) and diffuse (rapid non-impact rotational injury: RNR) TBI. PCR primers, unique to mtDNA, were identified by aligning segments of nuclear DNA (nDNA) to mtDNA, normalizing values to nuclear 16S rRNA, for a relative mtDNA copy number. Three unique mtDNA regions were selected, and PCR primers were designed within those regions, limited to 25-30 base pairs to further ensure sequence specificity, and measured utilizing qRT-PCR. Results Mean relative mtDNA copy numbers increased significantly at 6 and 25 hrs after following both focal and diffuse traumatic brain injury. Specifically, the mean relative mtDNA copy number from three mitochondrial-specific regions pre-injury was 0.84 ± 0.05. At 6 and 25 h after diffuse non-impact TBI, mean mtDNA copy number was significantly higher: 2.07 ± 0.19 (P \u3c 0.0001) and 2.37 ± 0.42 (P \u3c 0.001), respectively. Following focal impact TBI, relative mtDNA copy number was also significantly higher, 1.35 ± 0.12 (P \u3c 0.0001) at 25 hours. Alterations in mitochondrial respiration in the hippocampus and cortex post-TBI correlated with changes in the relative mtDNA copy number measured in peripheral blood. Conclusions Alterations in peripheral blood relative mtDNA copy numbers may be a novel biosignature of cerebral mitochondrial bioenergetics with exciting translational potential for non-invasive diagnostic and interventional studies

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

Treatment of HIV-infected individuals with antiretroviral agents selects for drug-resistant mutants, resulting in frequent treatment failures. Although the major antiretroviral resistance mutations are routinely characterized by DNA sequencing, treatment failures are still common, probably in part because undetected rare resistance mutations facilitate viral escape. Here we combined DNA bar coding and massively parallel pyrosequencing to quantify rare drug resistance mutations. Using DNA bar coding, we were able to analyze seven viral populations in parallel, overall characterizing 118 093 sequence reads of average length 103 bp. Analysis of a control HIV mixture showed that resistance mutations present as 5% of the population could be readily detected without false positive calls. In three samples of multidrug-resistant HIV populations from patients, all the drug-resistant mutations called by conventional analysis were identified, as well as four additional low abundance drug resistance mutations, some of which would be expected to influence the response to antiretroviral therapy. Methods for sensitive characterization of HIV resistance alleles have been reported, but only the pyrosequencing method allows all the positions at risk for drug resistance mutations to be interrogated deeply for many HIV populations in a single experiment

Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I–hypersensitive sites (i.e., +/− 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins

Anesthesiologists' and surgeons' perceptions about routine pre-operative testing in low risk patients: application of the Theoretical Domains Framework to identify factors that influence physicians' decisions to order pre-operative tests

Background Routine pre-operative tests for anesthesia management are often ordered by both anesthesiologists and surgeons for healthy patients undergoing low-risk surgery. The Theoretical Domains Framework (TDF) was developed to investigate determinants of behaviour and identify potential behaviour change interventions. In this study, the TDF is used to explore anaesthesiologists’ and surgeons’ perceptions of ordering routine tests for healthy patients undergoing low-risk surgery. Conclusion We identified key factors that anesthesiologists and surgeons believe influence whether they order pre-operative tests routinely for anesthesia management for a healthy adults undergoing low-risk surgery. These beliefs identify potential individual, team, and organisation targets for behaviour change interventions to reduce unnecessary routine test ordering. Methods Sixteen clinicians (eleven anesthesiologists and five surgeons) throughout Ontario were recruited. An interview guide based on the TDF was developed to identify beliefs about preoperative testing practices. Content analysis of physicians’ statements into the relevant theoretical domains was performed. Specific beliefs were identified by grouping similar utterances of the interview participants. Relevant domains were identified by noting the frequencies of the beliefs reported, presence of conflicting beliefs, and perceived influence on the performance of the behaviour under investigation. Results Seven of the twelve domains were identified as likely relevant to changing clinicians’ behaviour about pre-operative test ordering for anesthesia management. Key beliefs were identified within these domains including: conflicting comments about who was responsible for the test-ordering (Social/professional role and identity); inability to cancel tests ordered by fellow physicians (Beliefs about capabilities and social influences); and the problem with tests being completed before the anesthesiologists see the patient (Beliefs about capabilities and Environmental context and resources). Often, tests were ordered by an anesthesiologist based on who may be the attending anesthesiologist on the day of surgery while surgeons ordered tests they thought anesthesiologists may need (Social influences). There were also conflicting comments about the potential consequences associated with reducing testing, from negative (delay or cancel patients’ surgeries), to indifference (little or no change in patient outcomes), to positive (save money, avoid unnecessary investigations) (Beliefs about consequences). Further, while most agreed that they are motivated to reduce ordering unnecessary tests (Motivation and goals), there was still a report of a gap between their motivation and practice (Behavioural regulation)

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer

Gene transfer has been used to correct inherited immunodeficiencies, but in several patients integration of therapeutic retroviral vectors activated proto-oncogenes and caused leukemia. Here, we describe improved methods for characterizing integration site populations from gene transfer studies using DNA bar coding and pyrosequencing. We characterized 160 232 integration site sequences in 28 tissue samples from eight mice, where Rag1 or Artemis deficiencies were corrected by introducing the missing gene with gamma-retroviral or lentiviral vectors. The integration sites were characterized for their genomic distributions, including proximity to proto-oncogenes. Several mice harbored abnormal lymphoproliferations following therapy—in these cases, comparison of the location and frequency of isolation of integration sites across multiple tissues helped clarify the contribution of specific proviruses to the adverse events. We also took advantage of the large number of pyrosequencing reads to show that recovery of integration sites can be highly biased by the use of restriction enzyme cleavage of genomic DNA, which is a limitation in all widely used methods, but describe improved approaches that take advantage of the power of pyrosequencing to overcome this problem. The methods described here should allow integration site populations from human gene therapy to be deeply characterized with spatial and temporal resolution

De novo mutations in histone modifying genes in congenital heart disease

Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births1. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. By analysis of exome sequencing of parent-offspring trios, we compared the incidence of de novo mutations in 362 severe CHD cases and 264 controls. CHD cases showed a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging mutations. Similar odds ratios were seen across major classes of severe CHD. We found a marked excess of de novo mutations in genes involved in production, removal or reading of H3K4 methylation (H3K4me), or ubiquitination of H2BK120, which is required for H3K4 methylation2–4. There were also two de novo mutations in SMAD2; SMAD2 signaling in the embryonic left-right organizer induces demethylation of H3K27me5. H3K4me and H3K27me mark `poised' promoters and enhancers that regulate expression of key developmental genes6. These findings implicate de novo point mutations in several hundred genes that collectively contribute to ~10% of severe CHD

The QICKD study protocol: a cluster randomised trial to compare quality improvement interventions to lower systolic BP in chronic kidney disease (CKD) in primary care

BACKGROUND: Chronic kidney disease (CKD) is a relatively newly recognised but common long-term condition affecting 5 to 10% of the population. Effective management of CKD, with emphasis on strict blood pressure (BP) control, reduces cardiovascular risk and slows the progression of CKD. There is currently an unprecedented rise in referral to specialist renal services, which are often located in tertiary centres, inconvenient for patients, and wasteful of resources. National and international CKD guidelines include quality targets for primary care. However, there have been no rigorous evaluations of strategies to implement these guidelines. This study aims to test whether quality improvement interventions improve primary care management of elevated BP in CKD, reduce cardiovascular risk, and slow renal disease progression DESIGN: Cluster randomised controlled trial (CRT) METHODS: This three-armed CRT compares two well-established quality improvement interventions with usual practice. The two interventions comprise: provision of clinical practice guidelines with prompts and audit-based education. The study population will be all individuals with CKD from general practices in eight localities across England. Randomisation will take place at the level of the general practices. The intended sample (three arms of 25 practices) powers the study to detect a 3 mmHg difference in systolic BP between the different quality improvement interventions. An additional 10 practices per arm will receive a questionnaire to measure any change in confidence in managing CKD. Follow up will take place over two years. Outcomes will be measured using anonymised routinely collected data extracted from practice computer systems. Our primary outcome measure will be reduction of systolic BP in people with CKD and hypertension at two years. Secondary outcomes will include biomedical outcomes and markers of quality, including practitioner confidence in managing CKD. A small group of practices (n = 4) will take part in an in-depth process evaluation. We will use time series data to examine the natural history of CKD in the community. Finally, we will conduct an economic evaluation based on a comparison of the cost effectiveness of each intervention. CLINICAL TRIALS REGISTRATION: ISRCTN56023731. ClinicalTrials.gov identifier

Data Mashups in R

How do you use R to import, manage, visualize, and analyze real-world data? With this short, hands-on tutorial, you learn how to collect online data, massage it into a reasonable form, and work with it using R facilities to interact with web servers, parse HTML and XML, and more. Rather than use canned sample data, you'll plot and analyze current home foreclosure auctions in Philadelphia. This practical mashup exercise shows you how to access spatial data in several formats locally and over the Web to produce a map of home foreclosures. It's an excellent way to explore how the R environmen