Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy

Facio-Scapulo Humeral dystrophy (FSHD) is the third most common myopathy, affecting 1 amongst 10,000 individuals (FSHD1, OMIM #158900). This autosomal dominant pathology is associated in 95% of cases with genetic and epigenetic alterations in the subtelomeric region at the extremity of the long arm of chromosome 4 (q arm). A large proportion of the remaining 5% of cases carry a mutation in the SMCHD1 gene (FSHD2, OMIM #158901). Here, we explored the 3D organization of the 4q35 locus by three-dimensions DNA in situ fluorescent hybridization (3D-FISH) in primary fibroblasts isolated from patients and healthy donors. We found that D4Z4 contractions and/or SMCHD1 mutations impact the spatial organization of the 4q35 region and trigger changes in the expression of different genes. Changes in gene expression were corroborated in muscle biopsies suggesting that the modified chromatin landscape impelled a modulation in the level of expression of a number of genes across the 4q35 locus in FSHD. Using induced pluripotent stem cells (hIPSC), we further examined whether chromatin organization is inherited after reprogramming or acquired during differentiation and showed that folding of the 4q35 region is modified upon differentiation. These results together with previous findings highlight the role of the D4Z4 macrosatellite repeat in the topological organization of chromatin and further indicate that the D4Z4-dependent 3D structure induces transcriptional changes of 4q35 genes expression.

Green function, quasi-classical Langevin and Kubo-Greenwood methods in quantum thermal transport

With the advances in fabrication of materials with feature sizes at the order of nanometers, it has been possible to alter their thermal transport properties dramatically. Miniaturization of device size increases the power density in general, hence faster electronics require better thermal transport, whereas better thermoelectric applications require the opposite. Such diverse needs bring new challenges for material design. Shrinkage of length scales has also changed the experimental and theoretical methods to study thermal transport. Unsurprisingly, novel approaches have emerged to control phonon flow. Besides, ever increasing computational power is another driving force for developing new computational methods. In this review, we discuss three methods developed for computing vibrational thermal transport properties of nano-structured systems, namely Green function, quasi-classical Langevin, and Kubo-Green methods. The Green function methods are explained using both nonequilibrium expressions and the Landauer-type formula. The partitioning scheme, decimation techniques and surface Green functions are reviewed, and a simple model for reservoir Green functions is shown. The expressions for the Kubo-Greenwood method are derived, and Lanczos tridiagonalization, continued fraction and Chebyshev polynomial expansion methods are discussed. Additionally, the quasi-classical Langevin approach, which is useful for incorporating phonon-phonon and other scatterings is summarized.

Bioelectric impedance vector analysis (BIVA) in hospitalised children; predictors and associations with clinical outcomes

BACKGROUND

Clinical use of bioelectric impedance is limited by variability in hydration. Analysis of raw bioelectric impedance vectors (BIVA), resistance (R), reactance (Xc) and phase angle (PA) may be an alternative for monitoring disease progression/treatment. Clinical experience of BIVA in children is limited. We investigated predictors of BIVA and their ability to predict clinical outcomes in children with complex diagnoses.

METHODS

R, Xc and PA were measured (BODYSTAT Quadscan 4000) on admission in 108 patients (4.6-16.8 years, mean 10.0). R and Xc were indexed by height (H) and BIVA-SDS for age and sex calculated using data from healthy children. Potential predictors and clinical outcomes (greater-than-expected length-of-stay (LOS), complications) were recorded.

RESULTS

Mean R/H-SDS was significantly higher (0.99 (SD 1.32)) and PA-SDS lower (-1.22 (1.68))) than expected, with a wide range for all parameters. In multivariate models, the Strongkids risk category predicted R/H-SDS (adjusted mean for low, medium and high risk = 0.49, 1.28, 2.17, p = 0.009) and PA-SDS (adjusted mean -0.52, -1.53, -2.36, p = 0.01). BIVA-SDS were not significantly different in patients with or without adverse outcomes.

CONCLUSIONS

These complex patients had abnormal mean BIVA-SDS suggestive of reduced hydration and poor cellular health according to conventional interpretation. R/H-SDS was higher and PA-SDS lower in those classified as higher malnutrition risk by the StrongKids tool. Further investigation in specific patient groups, including those with acute fluid shifts and using disease-specific outcomes, may better define the clinical role of BIV.

Preoperative magnetic resonance imaging in predicting early continence recovery after robotic radical prostatectomy

INTRODUCTION AND AIMS

Urinary incontinence is a common complication after radical prostatectomy. The aim of our study was to describe the preoperative anatomical features using magnetic resonance imaging in order to predict early continence recovery after robotic radical prostatectomy.

MATERIAL AND METHODS

72 patients who underwent robotic radical prostatectomy were prospectively analysed. EPIC questionnaire (1, 6 and 12 mo) and first self-reported continence were used to assess functional outcomes. Membranous urethral length (MUL) and MUL-prostate axis angle (aMULP) were assessed preoperatively on T2 weighted sagittal images.

RESULTS

Continence rate was 67.2%, 92.6% and 95.2% at 1, 6 and 12 months, respectively. Early continence was achieved in patients with the lower aMULP. At 1 month, average aMULP in continent patients was 107.21° (IC 95% 90.3-124.6) vs. 118.5° (IC 95% 117.7-134) in incontinent ones (P=.014). At 6 month differences in aMULP among groups were found: 114.24° (IC 95% 104.6-123.9) in continents vs. 142° (IC 95% 126.5-157.6) in incontinents (P=0.015). At 12 month, continent group showed a significantly higher preoperative aMULP. aMULP was revealed as the only independent predictor of urinary continence at 6 mo in multivariate analysis, OR 0.007 (IC 95% 0.002-0.012), P=0.012.

CONCLUSIONS

Preoperative anatomical parameters assessment prior surgery can help to identified those patients will achieve early continence recovery and it supports therapeutic decisions making.

Abstract P5-03-02: Pre-clinical investigation of PP2A inhibitor LB-100 in overcoming and preventing lapatinib resistance in HER2-positive breast cancer

Background: HER2-positive breast cancer (BC) accounts for approximately 15% of all BC. HER2-targeted therapies, such as trastuzumab and lapatinib, have significantly improved the outcome for these patients. However, HER2-targeted therapy resistance is a common clinical issue. We have previously shown that protein phosphatase 2A (PP2A) plays a role in mediating acquired lapatinib resistance in HER2-positive BC and that response to lapatinib is enhancedin vitroby the lab-grade PP2A inhibitor, okadaic acid. The aim of this study was to examine the in vitro and in vivo efficacy of LB-100, a PP2A inhibitor that has completed phase I clinical testing (NCT01837667), in models of HER2-positive BC with acquired resistance to lapatinib.

Methods: HER2-positiveSKBR3 and HCC1954 BC cell lines were treated with 250 nM or 1 μM lapatinib, respectively, for 6 months to generate lapatinib-resistant SKBR3-L and HCC1954-L cell lines. In vitro sensitivity to lapatinib and LB-100 was assessed by 2D acid phosphatase assay. Combination index (CI) values were generated to identify synergistic combinations. Propidium iodide staining was used to determine cell cycle arrest and apoptosis. In order to examine the in vivo efficacy of LB-100, HCC1954-L cells were implanted into the mammary fat pad of BALB/c nude mice and treated with vehicle, lapatinib, LB-100, or lapatinib plus LB-100. To examine the prevention of the development of lapatinib resistance, SKBR3 and HCC1954 cells were treated twice weekly with lapatinib, LB-100 or the combination and stained with crystal violet when confluent.

Results: SKBR3-L and HCC1954-L cells were resistant to lapatinib at clinically relevant concentrations (IC50values = 2.37 ± 0.58 μM and 1.67 ± 0.34 μM). This represents a 46- and 5.2-fold decrease in lapatinib sensitivity. LB-100 had a greater anti-proliferative effect in the lapatinib-resistant SKBR3-L and HCC1954-L cell lines compared to their respective parental cell lines (IC50values = 2.12 ± 0.2 μM v 5.38 ± 0.6 μM, and 2.31 ± 0.19 μM v 5.32 ± 0.82 μM, respectively). LB-100 overcame lapatinib resistance in both models, as lapatinib plus LB-100 was synergistic in both cell lines (CI values = 0.56 ± 0.13 and 0.68 ±0.26). LB-100 caused cell death through the induction of apoptosis in SKBR3- L (p = 0.019) and HCC1954-L (p = 0.046) and the addition of lapatinib to LB-100 increased apoptotic induction in HCC1954-L cells (p=0.046).Lapatinib plus LB-100 was well tolerated in vivo. The HCC1954-L cell line maintained resistance to lapatinib in vivo and the combination of lapatinib and LB-100 significantly reduced HCC1954-L tumour volume compared to all other treatment arms (p = 0.0006). Interestingly, in vitro short-term resistance assays showed that the addition of LB-100 to lapatinib could also block the emergence of lapatinib resistance in both parental SKBR3 and HCC1954 cell lines.

Conclusions: This study indicates that LB-100 has in vitro and in vivo efficacy against lapatinib-resistant HER2-positive BC cell line models and justifies further investigation into its potential to circumvent or prevent lapatinib resistance in HER2-positive BC.

Citation Format: Conlon N, McDermott M, Browne B, Roche S, O'Neill F, Meiller J, Browne A, Eustace A, Collins DM, O'Donovan N, Crown J. Pre-clinical investigation of PP2A inhibitor LB-100 in overcoming and preventing lapatinib resistance in HER2-positive breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-03-02.

Sample Pooling and Inflammation Linked to the False Selection of Biomarkers for Neurodegenerative Diseases in Top-Down Proteomics: A Pilot Study

Proteomic technologies have been recently adapted to the new field of clinical proteomics. The origin of errors and biases has been well-identified in the pre-analytical steps, leading to the measurement of clinical analytes. One possible source of inadequacy in clinical proteomics is linked to sample pooling. This practice is usually related to low sample availability, variability, experiment time/cost. In this study, we first asked whether sample pooling in top–down proteomics is suitable to obtain a relevant biological average. Our second objective was to identify inflammatory biomarkers of outlier samples in our population of Creutzfeldt-Jakob disease patients. Our results demonstrated that, in a proteomics study, sample pooling as well as the inflammation status was an important source of errors: missed detection of biomarkers and false identification of others. Pooled samples were not equivalent to the average of biological values. In addition, this procedure reduced the statistical value of the identified biomarkers due to a stabilization of their standard deviation and rendered outlier samples difficult to detect. We identified serum amyloid A as a candidate biomarker of outlier samples. The presence of this protein, which could be explained by inflammatory processes, induced major modifications in the sample profiles.

[Which ovarian stimulation to which women: The polycystic ovary syndrome (PCOS)]

Polycystic ovarian syndrome (PCOS) is a frequent pathology in the young woman, linking infertility to a metabolic disease. Initial support will include a plan (in the case of overweight or obesity) to lose at least 5 to 10% of the weight. Subsequently, clomiphene citrate is the first treatment for ovulation induction with pregnancy rates of 40 to 80% after 6 cycles. If there is resistance to clomiphene citrate, the choice will be between the ovarian drilling (50-60% of pregnancy in the year following, including the half spontaneous) or ovarian stimulation with gonadotropins. The risk of ovarian stimulation in these women is hyperstimulation and multiple pregnancies. We also discuss the place of the GnRH pulsatile administration, insulin-sensitizers, in vitro fertilization and in vitro maturation in these women. Once infertility support, these women should be long-term followed because of the neoplasic and cardiovascular risks they present.

Construction and feasibility study of the SOFMER Activity Score (SAS), a new assessment of physical and cognitive activity

OBJECTIVES

For hospitalizations in rehabilitation centers (RCs) in France, the quantification of healthcare givers' activity is based on the dependency of the patients, defined as a total or partial inability to perform activities required for daily living without help. The tools currently used to quantify dependency are not sufficiently precise. Here we describe the construction of a new tool, the SOFMER Activity Score (SAS scoring), which allows for a good description of the level of activity of patients hospitalized in RCs, and a feasibility study of the tool.

METHODS

After a study group proposed the first version of the SAS, the validity of its content was studied by the Delphi consensus method: 26 physicians or healthcare professionals known for their expertise in PMR responded to the first round. The feasibility study was prospective and involved multi-site professionals. Data related to the SAS determined by a multidisciplinary team were collected and compared to the Activité de la Vie Quotidienne (AVQ) scale, which is administered to all patients and included in medical and administrative data.

RESULTS

We included 81 patients in the feasibility study. The mean (SD) time to obtain the SAS was 4.5 (3.3) min. For 97.5% of scorings, the participating professionals judged that the SAS was compatible or fairly compatible with clinical practice. The internal structure of the SAS scale seemed better than that of the AVQ scale, for which the present study confirmed a floor effect for all items.

CONCLUSIONS

The SAS allows for measuring the level of physical and cognitive activity of a patient hospitalized in an RC. If validation studies for the SAS, exploring its reliability, construct validity or criterion validity, confirm the tool's good metrological qualities, the SAS will allow for a good quantification of the burden of care.

Barriers to the treatment of childhood tuberculous infection and tuberculosis disease: a qualitative study

SETTING

In 2012, Peru's National TB Program (NTP) reported approximately 2400 incident cases of tuberculosis (TB) disease in children aged <15 years. Peru's TB burden is concentrated in the Lima metropolitan area, particularly in poor districts such as El Agustino and La Victoria, where this study was conducted.

OBJECTIVE

To identify barriers to the treatment of childhood tuberculous infection and TB disease in Lima from the perspective of front-line providers and patients' families.

DESIGN

We conducted 10 semi-structured focus groups with 53 purposefully sampled primary care providers, community health workers, and parents/guardians of pediatric TB patients. We also completed nine in-depth interviews with National TB Program administrators and pulmonologists specializing in TB. Two authors performed inductive thematic analysis and identified emerging themes.

RESULTS

Four main treatment barriers emerged from the data: 1) dosing errors, 2) time- and labor-intensive preparation and administration of medications, 3) provider concern that isoniazid preventive therapy (IPT) generates isoniazid resistance, and 4) poor adherence to IPT.

CONCLUSION

Our findings highlight the urgent need for child-friendly formulations, provider and parent/guardian education about IPT, and strategies to promote adherence to IPT, including support and supervision by health workers and/or regimens with fewer doses.

Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection

In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.

Influenza vaccine effectiveness among healthcare workers in comparison to hospitalized patients: A 2004-2009 case-test, negative-control, prospective study

The objective of this study was to calculate Vaccine Effectiveness (VE) in healthcare workers (HCW) and to compare VE between patients and HCW. A case-control investigation based on the prospective study was conducted between 2004 and 2009 in a teaching hospital. All HCW with influenza-like illness (ILI) from participating units (n = 24) were included, and vaccination status was characterized by interview. A total of 150 HCW presented ILI; 130 (87%) were female, 27 (18%) were positive for influenza, and 42 (28%) were vaccinated. Adjusted VE was 89% (95% CI 39 to 98). Among patients, adjusted VE was 42% (95% CI -39 to 76). The difference of VE (VEhcw - VEpat) was 46.15% (95% CI 2.41 to 144). The VE ratio (VEhcw / VEpat) was 2.09 (95% CI -1.60 to 134.17). Influenza VE differed between HCW and patients when the flu season was taken into account. This finding confirms the major impact of host determinants on influenza VE.

How to Improve the Social Utility Value of Geographic Information Systems for French Local Governments? A Delphi Study

Today, geographic information technologies (GITs) stand out as the unavoidable answers to the French local governments' new stakes. Yet, an important discrepancy has been noticed between the utility levels (in the qualitative sense) and the theoretical intrinsic potential of these technologies. The social utility value of GIT seems quite low compared with the quantitative level at which they are diffused. The authors focus on the ‘determination of value’, by considering the obstacles to the development of a spatial data infrastructure in the French context. From the results of a Delphi study, the authors bring to the fore the fact that the institutional and organisational barriers 0ack of a clear policy in matters of access and dissemination; cost of public data; absence of fully operational norms and standards; failure to raise the awareness of the potential users as a whole; etc) more than technical difficulties, are the prime causes of this phenomenon. Through this analysis, the authors emphasise the need to organise a French national spatial data infrastructure, strongly linked with most of the local initiatives developed by the local governments.

Computerised Tomographic Angiography (CTA) in extremity trauma - A level one hospital experience

INTRODUCTION

The aim of this study was to audit the use of Computerised Tomographic Angiography (CTA) in assessing extremity vascular injuries at our institution and to compare it to international standards. The primary aim was to assess the number of CTAs performed and the indications for doing them. The secondary aim was to look at CTA results and clinical findings and to correlate the two.

METHOD

This is a retrospective review of all patients aged 13 years and older who had CTA performed for suspected extremity vascular injuries due to blunt trauma or gunshot injuries, who presented from January 2012 to December 2012.

RESULTS

Two hundred and eighty five (285) CTAs were performed in 2012 and 137 met our inclusion criteria. Eleven cases were excluded due to insufficient data, leaving a total of 126 cases suitable for analysis. Eighty three patients (66%) had a normal CTA. The indications for CTA were as follows: decreased pulse in 46 patients (42%), absent pulse in 19 patients (17%), presumed knee dislocation in 18 patients (16%), injuries in the proximity of large vessels in 12 patients (11%), haematoma in 8 patients (7%), bleeding in 5 patients (4%) and an abnormal Doppler in 2 patients (2%). When comparing pulse examination to CTA results, the clinical assessment of pulses had a sensitivity of 74.4%, specificity of 53.7%, positive predictive value (PPV) of 45.7% and a negative predictive value (NPV) of 80%.

CONCLUSION

Incorrect indications are being used when ordering a CTA in extremity vascular trauma. Clinical examination is suboptimal and not a reliable indicator of vascular injury in our setting, leading to a lower threshold for ordering a CTA.

Spin Hall Effect and Origins of Nonlocal Resistance in Adatom-Decorated Graphene

Recent experiments reporting an unexpectedly large spin Hall effect (SHE) in graphene decorated with adatoms have raised a fierce controversy. We apply numerically exact Kubo and Landauer-Büttiker formulas to realistic models of gold-decorated disordered graphene (including adatom clustering) to obtain the spin Hall conductivity and spin Hall angle, as well as the nonlocal resistance as a quantity accessible to experiments. Large spin Hall angles of ∼0.1 are obtained at zero temperature, but their dependence on adatom clustering differs from the predictions of semiclassical transport theories. Furthermore, we find multiple background contributions to the nonlocal resistance, some of which are unrelated to the SHE or any other spin-dependent origin, as well as a strong suppression of the SHE at room temperature. This motivates us to design a multiterminal graphene geometry which suppresses these background contributions and could, therefore, quantify the upper limit for spin-current generation in two-dimensional materials.

Segregation between SMCHD1 mutation, D4Z4 hypomethylation and Facio-Scapulo-Humeral Dystrophy: a case report

Background

The main form of Facio-Scapulo-Humeral muscular Dystrophy is linked to copy number reduction of the 4q D4Z4 macrosatellite (FSHD1). In 5 % of cases, FSHD phenotype appears in the absence of D4Z4 reduction (FSHD2). In 70-80 % of these patients, variants of the SMCHD1 gene segregate with 4qA haplotypes and D4Z4 hypomethylation.

Case presentation

We report a family presenting with neuromuscular symptoms reminiscent of FSHD but without D4Z4 copy reduction. We characterized the 4q35 region using molecular combing, searched for mutation in the SMCHD1 gene and determined D4Z4 methylation level by sodium bisulfite sequencing. We further investigated the impact of the SMCHD1 mutation at the protein level and on the NMD-dependent degradation of transcript.

In muscle, we observe moderate but significant reduction in D4Z4 methylation, not correlated with DUX4-fl expression. Exome sequencing revealed a heterozygous insertion of 7 bp in exon 37 of the SMCHD1 gene producing a loss of frame with premature stop codon 4 amino acids after the insertion (c.4614-4615insTATAATA). Both wild-type and mutated transcripts are detected.

Conclusion

The truncated protein is absent and the full-length protein level is similar in patients and controls indicating that in this family, FSHD is not associated with SMCHD1 haploinsufficiency.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-016-0328-9) contains supplementary material, which is available to authorized users.

Reduced bone volumetric density and weak correlation between infection and bone markers in cystic fibrosis adult patients

In our current adult CF population, low BMD prevalence was only 20 %, lower than that historically described. We found a mild increase of serum RANK-L levels, independent from the bone resorption level. The increased fracture risk in CF may be explained by a lower tibial cortical thickness and total vBMD.

INTRODUCTION

Bone disease is now well described in cystic fibrosis (CF) adult patients. CF bone disease is multifactorial but many studies suggested the crucial role of inflammation. The objectives of this study were, in a current adult CF population, to assess the prevalence of bone disease, to examine its relationship with infections and inflammation, and to characterize the bone microarchitecture using high resolution peripheral scanner (HR-pQCT).

METHODS

Fifty-six patients (52 % men, 26 ± 7 years) were assessed in clinically stable period, during a respiratory infection, and finally 14 days after the end of antibiotic therapy. At each time points, we performed a clinical evaluation, lung function tests, and biochemical tests. Absorptiometry and dorso-lumbar radiographs were also performed. A subgroup of 40 CF patients (63 % men, 29 ± 6 years) underwent bone microarchitecture assessment and was age- and gender-matched with 80 healthy controls.

RESULTS

Among the 56 CF patients, the prevalence of low areal BMD (T-score < -2 at any site), was 20 % (95 % CI: [10.2 %; 32.4 %]). After infections, serum RANK-L (+24 %, p = 0.08) and OPG (+13 %, p = 0.04) were increased with a stable ratio. Microarchitectural differences were mostly observed at the distal tibia, with lower total and cortical vBMD and trabecular thickness (respectively -9.9, -3.0, and -5 %, p < 0.05) in CF patients compared to controls, after adjustment for age, gender, weight, and height.

CONCLUSIONS

In this study, bone disease among adult CF patients was less severe than that previously described with only 20 % of CF patients with low BMD. We found a mild increase of biological marker levels and an impaired volumetric density of the tibia that may explain the increased fracture risk in CF population.