Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases

Background

Our group has used deep sequencing to identify viral RNA signatures in human brain specimens. We have previously used this method to detect HSV1, GBV-C, and measles virus sequence in brain tissue from deceased donors. Deep sequencing was performed on brain specimens from a cohort of patients who died with progressive forms of MS, revealing evidence of increased expression of some human endogenous retrovirus (HERV) domains.

Objectives

Identify RNA sequences and new antigens involved in the pathogenesis of MS

Methods

Deep sequencing was performed on RNA extracted from 12 progressive MS, 2 neuromyelitis optica (MS/NMO = demyelination group), 14 normal control, and 7 other neurologic disease (OND) control frozen brain specimens. The resulting single-ended 50 bp sequences (reads) were compared to a non redundant viral database representing (NRVDB) all 1.2 M viral records in GenBank. A retroviral gene catalog (RVGC) was prepared by identifying human genetic loci (GRCh37.p13) homologous to domains contained in the Gypsy 2.0 retro element database. Reads were aligned to the RVGC and human transcriptome with Bowtie2. The resulting viral hit rates (VHRs) were normalized by the number of high quality reads. The expression of human genes, including HERVs, was determined using Cufflinks. Comparisons between the groups were performed using the false discovery rate.

Results

Fifty to 131 million high quality reads per specimen were obtained. Comparison of the reads to the NRVDB suggested that the demyelination and OND specimens had higher VHRs against some retroviral sequences compared with the controls. This was confirmed by retroviral domain averaging. Gene expression analysis showed differential expression among some HERV sequences. Single read mapping revealed one envelope and one reverse transcriptase sequence record that were significantly enriched among the demyelination samples compared to the normal controls. Less restrictive (comprehensive) read mapping showed that 2 integrase, 2 core, 2 envelope, and 3 KRAB sequences that were overexpressed in the demyelination group.

Conclusions

These data demonstrate that some endogenous retroviral sequences are significantly overexpressed in these demyelination brain tissue specimens, but the magnitude of this overexpression is small. This is consistent with the concept of HERV activation as a part of the innate immune response.

Modeling birds on wires

In this paper we introduce a mathematical model to study the group dynamics of birds resting on wires. The model is agent-based and postulates attraction-repulsion forces between the interacting birds: the interactions are "topological", in the sense that they involve a given number of neighbors irrespective of their distance. The model is first mathematically analyzed and then simulated to study its main properties: we observe that the model predicts birds to be more widely spaced near the borders of each group. We compare the results from the model with experimental data, derived from the analysis of pictures of pigeons and starlings taken in New Jersey: two different image elaboration protocols allow us to establish a good agreement with the model and to quantify its main parameters. We also discuss the potential handedness of the birds, by analyzing the group organization features and the group dynamics at the arrival of new birds. Finally, we propose a more refined mathematical model that describes landing and departing birds by suitable stochastic processes.

Functional and genetic predisposition to rhinovirus lower respiratory tract infections in prematurely born infants

Term born infants are predisposed to human rhinovirus (HRV) lower respiratory tract infections (LRTI) by reduced neonatal lung function and genetic susceptibility. Our aim was to investigate whether prematurely born infants were similarly predisposed to HRV LRTIs or any other viral LRTIs. Infants born less than 36 weeks of gestational age were recruited. Prior to neonatal/maternity unit discharge, lung function (functional residual capacity by helium gas dilution and multiple breath washout, lung clearance index and compliance (C_rs), and resistance (R_rs) of the respiratory system) was assessed and DNA samples assessed for eight single nucleotide polymorphisms (SNPs) in seven genes: ADAM33, IL10, MMP16 NFκB1A,SFTPC, VDR, and NOS2A. Infants were prospectively followed until 1 year corrected age. Nasopharyngeal aspirates (NPAs) were sent whenever an infant developed a LRTI and tested for 13 viruses. One hundred and thirty-nine infants were included in the analysis. Infants who developed HRV LRTIs had reduced C_rs (1.6 versus 1.2 mL/cmH₂O/kg, p = 0.044) at 36 weeks postmenstrual age. A SNP in the gene coding for the vitamin D receptor was associated with the development of HRV LRTIs and any viral LRTIs (p = 0.02).

CONCLUSION

Prematurely born infants may have both a functional and genetic predisposition to HRV LRTIs. What is Known: • Term born infants are predisposed to rhinovirus lower respiratory tract (HRV LRTIs) infection by reduced neonatal lung function. • Term born infants requiring hospitalisation due to HRV bronchiolitis were more likely to have single nucleotide polymorphism (SNP) in the IL-10 gene. What is New: • Prematurely born infants who developed a HRV LRTI had lower C _rs before maternity unit discharge. • A SNP in the gene coding for the vitamin D receptor was associated with the development of HRV LRTIs and overall respiratory viral LRTIs in prematurely born infants.

Management of paediatric otogenic cerebral venous sinus thrombosis: a systematic review

BACKGROUND

Otogenic paediatric cerebral venous sinus thrombosis (CVST) is rare but has potential clinical sequelae. Its management has long been debated mainly concerning the role of surgery and the use of anticoagulant therapy.

OBJECTIVE OF REVIEW

To review the current literature and examine the medical and surgical management of paediatric otogenic CVST and its clinical and radiological outcome.

TYPE OF REVIEW

Systematic review.

SEARCH STRATEGY

The electronic databases (MEDLINE, EMBASE, Cochrane) were searched from inception to November 2014 using text words 'cerebral venous sinus thrombosis OR cerebral venous thrombosis OR lateral sinus thrombosis OR sigmoid sinus thrombosis' AND 'otogenic OR mastoiditis OR otitis media' AND 'children OR paediatric OR pediatric'.

EVALUATION METHOD

Inclusion criteria were applied by two reviewers and data extraction was carried out. The type of otological surgery (conservative versus extensive) and the use of anticoagulants with their clinical and radiological outcomes were tabulated.

RESULTS

Thirty-six studies (15 case reports and 21 case series) were included with a total of 190 patients. A total of 92.1% of patients underwent otological surgery, and 69.5% had conservative surgery and 30.5% extensive otological surgery. Anticoagulants were used in 59%. A total of 79.2% of patients were reported to have had a good clinical outcome. Within this group, 56% had conservative surgery and anticoagulants. Follow-up scans were documented in 61.6% of patients and complete recanalisation was observed in 51%. Complete recanalisation was observed in 47% of those who had been anticoagulated and 55% of those who received no anticoagulation.

CONCLUSIONS

Conservative otological surgery with the combination of anticoagulation was the most common treatment modality found in the group of patients with good clinical outcome. However, given the current low level of evidence, a multicentre collaborative study is needed to help establish the optimum surgical approach and the role of anticoagulation in managing paediatric otogenic CVST.

Pharmacist Intervention in Risk Reduction Study in High-Risk Cardiac Patients: The Effect of 2 Methods of Pharmacist Training

Objective:

To assess the effect of intensive vs conventional training on pharmacist-suggested implementation of cardiac risk reduction efforts in community practice.

Methods:

Sixty-one volunteer pharmacists from 40 pharmacies were randomized to 1 of 2 educational groups: intensive or conventional training in cardiac risk reduction. With training complete, pharmacists identified and approached patients at high risk for coronary artery disease (CAD) at their practice sites to participate in the program. After a patient interview, pharmacists documented the relevant CAD risk factors and medication history, and then faxed this information, along with risk reduction recommendations, to the primary care physician. Patients were then encouraged to book a medical appointment for further assessment and treatment, if warranted. Follow-up occurred at 4, 16, and 24 weeks to determine if any pharmacist-suggested risk reduction measures had been implemented. Pharmacists were reimbursed $30 per patient accrued.

Results:

A total of 217 patients were enrolled in the study, and of those, 216 had follow-up data available for analysis. No significant differences were observed between the groups with respect to mean number of patients enrolled per pharmacist (4.3 vs 2.7) and the proportion of pharmacists completing at least 1 patient (17/27 vs 14/34). Feedback from pharmacists on program delivery indicated no significant difference in satisfaction with the training provided. The recommendations forwarded by pharmacists of the intensive group (35.8%) received greater acceptance by physicians than those in the conventional group (23.8%).

Conclusion:

Although results are preliminary, intensive training for pharmacists was more likely to result in improvements in cardiovascular risk reduction therapy than when conventional training was used.

Pharmacist Intervention in Risk Reduction Study: High-Risk Cardiac Patients

Objectives:

Although there are guidelines for managing patients at high vascular risk, many people remain undertreated. This community-based study was designed to 1) measure the ability of the pharmacist—physician collaboration to affect a broad array of drug-related endpoints and 2) to compare 2 methods of training community pharmacists to collaborate with physicians on cardiac patient care. This paper focuses on the first outcome, and a companion paper will address the second outcome.

Methods:

We used a before-and-after design to assess pharmacists' ability to affect drug-related endpoints. We identified patients by various methods, one of which was medication profiles. Those providing consent were educated on risk factor modification and encouraged to consult their physicians. Pharmacists subsequently faxed the details of their assessments to the primary care physician, along with suggestions for therapy changes. Our outcome measure was the proportion of patients who achieved a composite of either a dose increase or a new target medication as a result of pharmacist recommendations during the study.

Results:

A total of 61 pharmacists recruited 217 patients, and of these, follow-up was completed on 216. Of the patients for whom a pharmacist made a suggestion, pharmacologic risk reduction therapy was initiated or enhanced in 53.7%.

Conclusion:

This community pharmacist—based program improved utilization of the therapies known to decrease vascular risk in patients considered high risk.

Recall of Dental Pain and Anxiety in a Cohort of Oral Surgery Patients

Dental patients generally recall more pain than they originally report, with ratings of pain related to state anxiety and dental fear, but the role of depression in recall of dental pain remains uncertain. This study examined the relative contributions of different variables in explaining dental pain recalled after tooth extraction. Patients presenting for tooth extraction, prior to extraction, rated their current dental pain and state anxiety, prediction of pain and state anxiety during extraction, depression, and dental fear. Immediately postprocedure and then 1 mo later, patients rated their pain and state anxiety during extraction. Hierarchical linear regression equations were used to explain variance in recalled pain and state anxiety. In addition, patients were divided into high and low dental fear and depression groups and compared on ratings of pain and state anxiety across time. In a final sample of 157 patients, the most important predictors of recalled pain were pain reported during extraction (β = .53) and recalled state anxiety (β = .52). Dental fear and depression had a significant interaction: only when patients reported less depression did those patients who reported more dental fear also report more pain than patients who reported less dental fear (P < 0.05, ω(2) = .07). Patients who reported more depression entered the dental operatory reporting more pain, but all patients generally reported less pain during extraction than they predicted or recalled. Memory of state anxiety and pain reported during tooth extraction, not depression or state anxiety at the time of extraction, were critical factors in memory of the pain associated with the procedure. At higher levels of depression, patients higher and lower in dental fear did not differ in report of pain. Future studies are needed to further clarify interactions of depression and dental fear over time.

Abstract P5-13-01: Transcript analysis of PI3K and immune-related genes and gene signatures in the pre- and post-treatment samples from the window of opportunity study of anastrozole and anastrozole with pictilisib (GDC-0941) in patients with HR-positive early breast cancer (OPPORTUNE study)

Background: The OPPORTUNE Study randomized postmenopausal patients (pts) to receive 2-week preoperative treatment with anastrozole (ANA) plus pictilisib ("ANA+PIC" arm) or ANA alone. Patients had newly diagnosed, operable, ER+, HER2- invasive breast cancer of ≥1 cm size. The primary outcome at interim analysis (n=70) revealed that the addition of PIC significantly increased the anti-proliferative response to ANA as measured by reduction in Ki67 immunohistochemistry (IHC). Multivariate analyses suggested benefit of PIC for patients with luminal B disease (Schmid et al. SABCS 2014).

Methods: RNA expression analysis of ∼800 breast cancer-related genes was performed on patients analyzed at the interim analysis, including 14 (ANA) and 20 (ANA+PIC) patients with matched pre- and post- treatment paired tumour samples using the nCounter platform (NanoString). Differential expression of individual genes by arm was assessed using paired and moderated t-tests and statistical significance assessed through false discovery rate (FDR). Ingenuity Pathway Analysis (IPA) of differentially expressed transcripts identified pathways of relevance. Protein expression was analyzed by reverse protein array ( RPPA) in pre- and post-treatment samples.

Results: In an unsupervised analysis, down-regulation of genes associated with ER signaling was observed in patients who received single-agent ANA and ANA+PIC, which included genes that regulate the cell cycle, cell death, survival, growth and proliferation and known ER target genes (e.g., PGR, GREB1). In addition, transcripts related to growth factor signaling pathway appeared to be specifically modulated in the ANA+PIC arm, possibly via the upregulation of the expression of RTK ligands. There were no clear changes in PI3K-related phosphoproteins (e.g., AKT, S6, 4E-BP1) in the post-treatment samples by RPPA. However, known PI3K-regulated genes, IRS2 and PIK3IP1, were upregulated in the post-treatment samples and a composite PI3K gene expression signature score (O'Brien et al. 2010) was reduced in both study arms following treatment. This PI3K signature was associated with pre-treatment luminal B status (n=27) and, consistent with this finding, the baseline PI3K gene signature score in the ANA arm, but not the ANA+PIC arm, was inversely associated with the decrease in post treatment Ki67. The tumor immune microenvironment was analyzed though the use of composite gene sets. In our initial observations, analysis of pre- and post-treatment samples showed that 2-week treatment with ANA resulted in a modest increase in transcripts associated with multiple immune signatures, which was further enhanced by the addition of PIC.

Conclusions: Gene expression analysis of pre- and post-treatment samples in the OPPORTUNE study demonstrates on-target inhibition of ER and PI3K signaling networks. The analysis of additional paired samples is in progress to further assess if 2-weeks of treatment with a regimen containing an AI in patients with early breast cancer impacts the tumor immune microenvironment.

Citation Format: Schmid P, Pinder SE, Bundred N, Wheatley D, Macaskill J, Zammit C, Hu J, Price R, Shia A, Lim L, Parker P, Molinero L, Yu J, O'Brien C, Wilson T, Savage H, Derynck M, Lackner MR, Amler L, Purushotham A, Thompson A, Gendreau S. Transcript analysis of PI3K and immune-related genes and gene signatures in the pre- and post-treatment samples from the window of opportunity study of anastrozole and anastrozole with pictilisib (GDC-0941) in patients with HR-positive early breast cancer (OPPORTUNE study). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-13-01.

Super-aperture metrology: overcoming a fundamental limit in imaging smooth highly curved surfaces

The imaging of smooth, highly curved or tilted surfaces is widely recognized as one of the most challenging and unsolved problems in optical imaging and metrology today. The reason is that even when such surfaces are imaged using high aperture microscope objectives the steepness of the features causes the light to be reflected in such a way that it is not captured by the lens. This is true even in the limiting case of unity numerical aperture since the illuminating light may also be reflected in the forward direction. In order to overcome this fundamental problem we have developed a method whereby such specimens are covered with a readily removable organic fluorescent film thereby creating an isotropic scattering surface. We show that we are readily able to detect slopes with angles close 90° using a 0.75 NA objective--an 82% improvement over the theoretical aperture limit. Issues of variation in film thickness deposition are shown to be readily accommodated. This approach may be used with other fluorophore materials, organic or inorganic, since there is no need for biocompatibility in this application.

Viral lower respiratory tract infections and preterm infants' healthcare utilisation

The aim of this study was to determine whether respiratory syncytial virus (RSV) and other viral lower respiratory tract infections (LRTI) in prematurely born infants were associated with similar effects on healthcare utilisation and related cost of care in the second compared to the first year after birth. Thirteen infants who had RSV LRTIs (RSV), 21 who had other viral LRTIs (other viral) and 25 had no viral LRTIs (no LRTI) were prospectively followed. Nasopharyngeal aspirates were collected whenever an infant had an LRTI regardless of whether it was in the hospital or in the community. Healthcare utilisation and the health-related cost of care were determined. Only the RSV group compared to the no LRTI group had higher overall respiratory costs in both year 1 (mean, £3,917 versus £24; p < 0.041) and year 2 (mean, £1,164 versus £61; p = 0.012). Only the RSV group required respiratory admissions; the RSV admission rate in year 2 was 3.4 % (number needed to treat 59).

CONCLUSION

RSV LRTIs are associated with increased healthcare utilisation and cost of care in the first and second year; nevertheless, if prophylaxis is to be cost-effective in the second year, a high risk group needs to be identified.

Meeting the needs of parents after a stillbirth or neonatal death

The death of a child around the time of birth is one of the most profoundly distressing events any parent will experience. These deaths are not uncommon, but are often hidden, along with the grief of mothers, fathers and families. Social stigma and negative attitudes are inextricably linked to underreporting of babies’ deaths in low- and middle-income countries. A failure to recognise the value of these lost lives leads to disenfranchised grief and diminished preventive efforts to reduce stillbirth and neonatal deaths. Acknowledging these deaths to bring them ‘out of the shadows’17 and compassionate, respectful care for parents suffering perinatal loss, irrespective of country or resources, are critical to addressing the totality of the burden of this public health problem.