Detection of Germline Mutations in Breast Cancer Patients with Clinical Features of Hereditary Cancer Syndrome Using a Multi-Gene Panel Test

Purpose

Hereditary cancer syndrome means that inherited genetic mutations can increase a person's risk of developing cancer. We assessed the frequency of germline mutations using an next-generation sequencing (NGS)–based multiple-gene panel containing 64 cancer-predisposing genes in Korean breast cancer patients with clinical features of hereditary breast and ovarian cancer syndrome (HBOC).

Materials and Methods

A total of 64 genes associated with hereditary cancer syndrome were selected for development of an NGS-based multi-gene panel. Targeted sequencing using the multi-gene panel was performed to identify germline mutations in 496 breast cancer patients with clinical features of HBOC who underwent breast cancer surgery between January 2002 and December 2017.

Results

Of 496 patients, 95 patients (19.2%) were found to have 48 deleterious germline mutations in 16 cancer susceptibility genes. The deleterious mutations were found in 39 of 250 patients (15.6%) who had breast cancer and another primary cancer, 38 of 169 patients (22.5%) who had a family history of breast cancer (≥ 2 relatives), 16 of 57 patients (28.1%) who had bilateral breast cancer, and 29 of 84 patients (34.5%) who were diagnosed with breast cancer at younger than 40 years of age. Of the 95 patients with deleterious mutations, 60 patients (63.2%) had BRCA1/2 mutations and 38 patients (40.0%) had non-BRCA1/2 mutations. We detected two novel deleterious mutations in BRCA2 and MLH1.

Conclusion

NGS-based multiple-gene panel testing improved the detection rates of deleterious mutations and provided a cost-effective cancer risk assessment.

Genomic Characteristics of Triple-Negative Breast Cancer Nominate Molecular Subtypes That Predict Chemotherapy Response

The heterogeneity of triple-negative breast cancer (TNBC) poses difficulties for suitable treatment and leads to poor outcome. This study aimed to define a consensus molecular subtype (CMS) of TNBC and thus elucidate genomic characteristics and relevant therapy. We integrated the expression profiles of 957 TNBC samples from published datasets. We identified genomic characteristics of subtype by exploring the pathway activity, microenvironment, and clinical relevance. In addition, drug response (DR) scores (n = 181) were computationally investigated using chemical perturbation gene signatures and validated in our own patient with TNBC (n = 38) who received chemotherapy and organoid biobank data (n = 64). Subsequently, cooperative functions with drugs were also explored. Finally, we classified TNBC into four CMSs: stem-like; mesenchymal-like; immunomodulatory; luminal-androgen receptor. CMSs also elucidated distinct tumor-associated microenvironment and pathway activities. Furthermore, we discovered metastasis-promoting genes, such as secreted phosphoprotein 1 by comparing with primary. Computational DR scores associated with CMS revealed drug candidates (n = 18), and it was successfully evaluated in cisplatin response of both patients and organoids. Our CMS recapitulated in-depth functional and cellular heterogeneity encompassing primary and metastatic TNBC. We suggest DR scores to predict CMS-specific DRs and to be successfully validated. Finally, our approach systemically proposes a relevant therapeutic prediction model as well as prognostic markers for TNBC. IMPLICATIONS: We delineated the genomic characteristic and computational DR prediction for TNBC CMS from gene expression profile. Our systematic approach provides diagnostic markers for subtype and metastasis verified by machine-learning and novel therapeutic candidates for patients with TNBC.

P2444Comparison of 3D and 2D echocardiography-derived indices of left ventricular function and structure to predict long-term mortality in the general population: Southall And Brent Revisited (SABRE) study

Background

Three-dimensional echocardiography (3DE) may have advantages over two-dimensional echocardiography (2DE) for the assessment of left ventricular (LV) function and structure. However, studies comparing 3DE and 2DE-derived indices in relation to mortality are limited, particularly in the general population.

Purpose

We examined associations between 2DE and 3DE-derived LV ejection fractions (LVEF) and volumes for all-cause mortality in a population-based sample.

Methods

A total of 899 individuals (age, 69.6±6.1 years; 77.5%male) from the SABRE study, a UK-based tri-ethnic community cohort, underwent a comprehensive transthoracic echocardiography examination. 2D LVEF and volumes were calculated, and full-volume 3D LV datasets acquired over 4 sub-volumes were obtained using a matrix-array transducer and were analysed offline using Qlab advanced, v7.0. The associations between both 2D- and 3D-derived LVEF (≥55% vs. <55%), body surface area indexed end-diastolic volume (iEDV) and end-systolic volume (iESV), and all-cause mortality were determined using Cox proportional hazards models. Survival curves were constructed using the Kaplan-Meier method.

Results

Of the 899 individuals, 118 (13.1%) died over a median follow-up period of 8 years to 2018. Kaplan Meier survival estimates (Figure 1 illustrates LVEF) and Cox regression revealed that 2D and 3D LVEF, iEDV and iESV were associated with increased risk of all-cause mortality (LVEF (≥55% vs. <55%), 3DE: HR=0.53 (0.35, 0.80); 2DE: HR=0.51 (0.34, 0.75), iEDV (per 1SD increment), 3DE: HR=1.20 (1.0, 1.41); 2DE: HR=1.19 (1.0–1.41), iESV (per 1SD increment), 3DE: HR=1.27 (1.1, 1.52), 2DE: HR=1.32 (1.15, 0.1.51)). However, 3DE associations tended to be stronger in models adjusted for classical risk factors including age, sex, ethnicity, systolic blood pressure, cholesterol:HDL ratio, body mass index, antihypertensive medications, diabetes, and smoking (LVEF (≥55% vs. <55%), 3DE: HR=0.59 (0.39, 0.90); 2DE: HR=0.69 (0.46, 1.0), iEDV (per 1SD increment), 3DE: HR=1.20 (1.0, 1.41); 2DE: HR=1.10 (0.93, 1.31), iESV (per 1SD increment), 3DE: HR=1.27 (1.1, 1.52), 2DE: HR=1.20 (1.04, 0.1.39)).

Figure 1. Kaplan-Meier curves.

Conclusions

In this population-based study, both 2DE and 3DE-derived indices of LV structure and function were associated with all-cause mortality independently of classical risk factors, with some indication that strengths of association were greater for 3DE-derived indices.

Acknowledgement/Funding

SABRE is funded by BHF, Diabetes UK, the MRC and the Wellcome Trust. LA holds a scholarship grant from Imam Abdulrahman Bin Faisal University, SA

6070Association of blood pressure measures with brain structure and function: the Southall and Brent REvisited (SABRE) study

Background

In our rapidly ageing society, dementia and neurocognitive decline are significant global public health problems. Blood pressure (BP), an established cardiovascular risk factor, has been extensively studied with respect to brain structure and function; however, findings across the literature differ depending on the BP component in consideration, and the use of brachial rather than central BP.

Purpose

We set out to assess associations between detailed measures of brain structure and function with comprehensive measures of central and peripheral BP. Furthermore, we performed comprehensive mediation analyses on the associations to investigate potential micro and macro vascular mediatory pathways.

Methods

A community-based sample of 1438 individuals (69.7±6.2 years) from a tri-ethnic cohort. underwent vascular, cognitive and MRI based structural brain measures. BP measures included central (cSBP (Pulsecor)) and peripheral systolic BP (pSBP), diastolic BP (DBP), brachial (bPP) and central pulse pressure (cPP), and mean arterial pressure (MAP). Cognitive assessments comprised tests which explored global/overall function (CSID), executive function and memory. For brain structure, hippocampal brain volume was our key measure. Potential macro- and microvascular mediators included: arterial stiffness (cfPWV), carotid intima-media thickness, retinopathy, white matter hyperintensities and infarcts. Multivariable regression analyses were used to assess associations of BP components with cognitive function scores and brain volumes, adjusted for age, sex and ethnicity as well as macro- and microvascular risk factors. Multiple imputation was performed to account for missing data.

Results

After adjusting for age, sex and ethnicity, both cSBP and pSBP were negatively associated with memory (data are β±SE (z-score) −0.014±0.006, p=0.04), while DBP was positively associated with hippocampal volume (0.006±0.003, p=0.03). cPP was negatively associated with memory (−0.020±0.009, p=0.03), executive function (−0.018±0.006, p=0.002) and hippocampal volume (−0.007±0.003, p=0.005), while bPP was negatively associated with CSID (−0.008±0.004, p=0.04), memory (−0.020±0.008, p=0.02), executive function (−0.016±0.005, p=0.002) and hippocampal volume (−0.006±0.002, p=0.007). There was a stronger association between both PP measures and brain structure and function than with the other BP components, especially MAP. There was little difference in association between cPP and bPP measures with brain structure and function. Furthermore, these associations do not appear to be mediated by either macro- or microvascular disease.

Conclusion

These results suggest that there is a direct association between increased PP and a decline in brain structure and function. This implies that older patients with suboptimal PP control may be at increased risk of developing cognitive impairment and that measuring PP offers mechanistic information above and beyond conventional BP measures.

Acknowledgement/Funding

Wellcome Trust, British Heart Foundation

Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data

Insertions and deletions (INDELs) comprise a significant proportion of human genetic variation, and recent papers have revealed that many human diseases may be attributable to INDELs. With the development of next-generation sequencing (NGS) technology, many statistical/computational tools have been developed for calling INDELs. However, there are differences among those tools, and comparisons among them have been limited. In order to better understand these inter-tool differences, five popular and publicly available INDEL calling tools-GATK HaplotypeCaller, Platypus, VarScan2, Scalpel, and GotCloud-were evaluated using simulation data, 1000 Genomes Project data, and family-based sequencing data. The accuracy of INDEL calling by each tool was mainly evaluated by concordance rates. Family-based sequencing data, which consisted of 49 individuals from eight Korean families, were used to calculate Mendelian error rates. Our comparison results show that GATK HaplotypeCaller usually performs the best and that joint calling with Platypus can lead to additional improvements in accuracy. The result of this study provides important information regarding future directions for the variant detection and the algorithms development.

ASpedia: a comprehensive encyclopedia of human alternative splicing

Alternative splicing confers the human genome complexity by increasing the diversity of expressed mRNAs. Hundreds or thousands of splicing regions have been identified through differential alternative splicing analysis of high-throughput datasets. However, it is hard to explain the functional impact of each splicing event. Protein domain formation and nonsense-mediated decay are considered the main functional features of splicing. However, other functional features such as miRNA target sites, phosphorylation sites and single-nucleotide variations are directly affected by alternative splicing and affect downstream function. Hence, we established ASpedia: a comprehensive database for human alternative splicing annotation, which encompasses a range of functions, from genomic annotation to isoform-specific function (ASpedia, http://combio.snu.ac.kr/aspedia). The database provides three features: (i) genomic annotation extracted from DNA, RNA and proteins; (ii) transcription and regulation elements analyzed from next-generation sequencing datasets; and (iii) isoform-specific functions collected from known and published datasets. The ASpedia web application includes three components: an annotation database, a retrieval system and a browser specialized in the identification of human alternative splicing events. The retrieval system supports multiple AS event searches resulting from high-throughput analysis and the AS browser comprises genome tracks. Thus, ASpedia facilitates the systemic annotation of the functional impacts of multiple AS events.

Abstract 3424: Consensus molecular subtype of triple negative breast cancer to implicate in chemotherapy response

Objective: The heterogeneity of triple negative breast cancer (TNBC) confers the difficulties in chemotherapy and induces poor outcome. Subtype classification of TNBC using gene expression profile could achieve to identify molecular markers to suggest therapeutic guidance.

Methods: In this study, we collected gene expression profiles of 957 TNBC patients from GEO and integrated into one meta-data using meta analysis. We identified subtypes using nonnegative matrix factorization (NMF) and explored for comprehensive characteristics of consensus molecular subtype (CMS) by investigating key pathway activity, tumor microenvironment, stemness and so on. In addition, we computed the drug response score (DRscore) from MSigDB chemical perturbation signature gene set and examined drug associations with key pathways of CMS. Drug candidates were validated from independent two data sets; our patients’ expression profile (n = 38) and biobank TNBC organoids (n=64).

Results: We classified four different TNBC subtypes displaying gene expression patterns including mesenchymal-like (MSL), luminal-AR (LAR), immunomodulatory (IM), and stem-like (SL). MSL were activated pathways with epithelial-to-mesenchymal (EMT) and TGF-beta signaling whereas SL was up-regulation of cell cycle and WNT signaling pathway. The LAR subtype was activated of androgen and estrogen receptor pathway. Although metastatic TNBC generally shared equal activity of key pathways with primary, coagulation, toll-like receptors, TNF, and Jak-STAT signaling pathways were dysregulated in metastasis. Especially, SPP1 gene expression to induce metastasis was associated with poor prognosis. DRscores were discriminative in CMS of meta-data and biobank expression profile. We found subtype-specific 18 drugs as therapeutic candidates and these drugs were also correlated with key pathways. In a case of cisplatin, DRscores appear resistant in MSL while response in SL. Our patients’ expression profiles were shown to consistent result as well as biobank.

Conclusion: These finding might facilitate understanding heterogeneity of TNBC. Our novel approach to explore drug response suggested functional intervention landscape of drug

response without in-vivo experiment. Taken together, we propose biomarkers for diagnosis and also suggest therapeutic strategy depending on CMS.

Citation Format: Jihyun Kim, Doyeong Yu, Jiyoon Noh, Wooyeong Jang, Hanna Yang, Youngmee Kwon, Keun Seok Lee, Sung Hoon Sim, Sun-Young Kong, In Hae Park, Charny Park. Consensus molecular subtype of triple negative breast cancer to implicate in chemotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3424.

Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women

Very young breast cancer patients are more common in Asian countries than Western countries and are thought to have worse prognosis than older patients. The aim of the current study was to identify molecular characteristics of young patients with estrogen receptor (ER)-positive breast cancer by analyzing mutations and copy number variants (CNV), and by applying expression profiling. The whole exome and transcriptome of 47 Korean young breast cancer (KYBR) patients (age <35) were analyzed. Genomic profiles were constructed using mutations, CNV and differential gene expression from sequencing data. Pathway analyses were also performed using gene sets to identify biological processes. Our data were compared with young ER+ breast cancer patients in The Cancer Genome Atlas (TCGA) dataset. TP53, PIK3CA and GATA3 were highly recurrent somatic mutation genes. APOBEC-associated mutation signature was more frequent in KYBR compared with young TCGA patients. Integrative profiling was used to classify our patients into 3 subgroups based on molecular characteristics. Group A showed luminal A-like subtype and IGF1R signal dysregulation. Luminal B patients were classified into groups B and C, which showed chromosomal instability and enrichment for APOBEC3A/B deletions, respectively. Group B was characterized by 11q13 (CCND1) amplification and activation of the ubiquitin-mediated proteolysis pathway. Group C showed 17q12 (ERBB2) amplification and lower ER and progesterone receptor expression. Group C was also distinguished by immune activation and lower epithelial-mesenchyme transition (EMT) degree compared with group B. This study showed that integrative genomic profiling could classify very young patients with breast cancer into molecular subgroups that are potentially linked to different clinical characteristics.

Integrated molecular characterization of adult soft tissue sarcoma for therapeutic targets

Background

Several studies have investigated the molecular drivers and therapeutic targets in adult soft tissue sarcomas. However, such studies are limited by the genomic heterogeneity and rarity of sarcomas, particularly in those with complex and unbalanced karyotypes. Additional biomarkers are needed across sarcoma types to improve therapeutic strategies. To investigate the molecular characteristics of complex karyotype sarcomas (CKSs) for therapeutic targets, we performed genomic profiling.

Results

The mutational landscape showed that TP53, ATRX, and PTEN genes were highly mutated. CKS samples were categorized into three groups based on copy number variations that were associated with CDK4 and RB1 signatures. Integrated analysis of genomic and transcriptomic data revealed several pathways related to PDGFR, which could be a strategic target for anti-sarcoma therapy.

Conclusions

This study provides a detailed molecular classification of CKSs and proposes several therapeutic targets. Targeted or combinational therapies for treating CKS should be considered before chemotherapy.

Electronic supplementary material

The online version of this article (10.1186/s12881-018-0722-6) contains supplementary material, which is available to authorized users.

A new software scheme for scatter correction based on a simple radiographic scattering model

In common radiography, image contrast is often limited due mainly to scattered x-rays and noise, decreasing the quantitative usefulness of x-ray images. Several scatter reduction methods based on software correction schemes have been extensively investigated in an attempt to overcome these difficulties, most of which are based on measurement, mathematical-physical modeling, or a combination of both. However, those methods require special equipment, system geometry, and extra manual work to measure scatter characteristics. In this study, we investigated a new software scheme for scatter correction based on a simple radiographic scattering model where the intensity of the scattered x-rays was directly estimated from a single x-ray image using a weighted l¹-norm contextual regularization framework. We implemented the proposed algorithm and performed a systematic simulation and experiment to demonstrate its viability. We also conducted some clinical image studies using patient's image data of breast and L-spine to verify the clinical effectiveness of the proposed scheme. Our results indicate that the degradation of image characteristics by scattered x-rays and noise was effectively recovered by using the proposed software scheme, thus improving radiographic visibility considerably. Graphical abstract The schematic illustrations of scatter suppression methods by using a an antiscatter grid and b a scatter estimation algorithm.

Integrative Profiling of Alternative Splicing Induced by U2AF1 S34F Mutation in Lung Adenocarcinoma Reveals a Mechanistic Link to Mitotic Stress

Mutations in spliceosome components have been implicated in carcinogenesis of various types of cancer. One of the most frequently found is U2AF1 S34F missense mutation. Functional analyses of this mutation have been largely limited to hematological malignancies although the mutation is also frequently seen in other cancer types including lung adenocarcinoma (LUAD). We examined the impact of knockdown (KD) of wild type (wt) U2AF1 and ectopic expression of two splice variant S34F mutant proteins in terms of alternative splicing (AS) pattern and cell cycle progression in A549 lung cancer cells. We demonstrate that induction of distinct AS events and disruption of mitosis at distinct sub-stages result from KD and ectopic expression of the mutant proteins. Importantly, when compared with the splicing pattern seen in LUAD patients with U2AF1 S34F mutation, ectopic expression of S34F mutants but not KD was shown to result in common AS events in several genes involved in cell cycle progression. Our study thus points to an active role of U2AF1 S34F mutant protein in inducing cell cycle dysregulation and mitotic stress. In addition, alternatively spliced genes which we describe here may represent novel potential markers of lung cancer development.

Correction to: Acceptability of HIV self-sampling kits (TINY vial) among people of black African ethnicity in the UK: a qualitative study

It has been highlighted that in the original article [1] there is a typesetting mistake in the name of I. Fakoya. This was incorrectly captured as F. Fakoya. This correction article clarifies the correct name of the author.

Abstract 3294: Functional annotation for alternative splicing to investigate disrupted splicing in cancer

Alternative splicing (AS) plays a key role to confer human genome complexity. The advent of mRNA high-throughput sequencing facilitates to identify precise differential alternative splicing analysis. Massive result estimated from RNA-Seq should be sorted out whether AS has functional impact or not. Previous studies investigated protein domain or nonsense-mediated decay of AS event region. However other functional sites on exon inclusion region also exist. For example, miRNA binding site, and post-translational modification of AS site already are reported to assign functional impact. Therefore we developed ASpedia (http://combio.snu.ac.kr/aspedia/) to annotation functional impact of AS event. AS events of our database were generated from human genome hg19 ENSEMBL and Refseq. ASpedia provides a database, explore system, and AS browser to annotate functional impact evidence encompassing DNA, RNA, and protein. The user could query multiple AS events from differential AS analysis result. Currently our system supports a jar execution file to convert input query file from MISO or rMATS result.

The variant of splicing factor (SF) disrupts normal splicing. It could be assumed that target genes of mutated SF could be transcribed to aberrant isoforms by changed splicing machinery. Therefore we investigated the comprehensive SF variant status from TCGA somatic mutation and copy number. SF3B1 (2% in BRCA) and U2AF1 (4% in AML, and 2% in LUAD) were shown to recurrent mutation including hotspot. ELAVL2 known dispensable splicing factor to brain tissue were highly recurrent in deletion (18% in GBM). In order to examine aberrant AS events caused SF variants, we estimated exon-inclusion proportion Percent-Spliced-In (PSI) values for identifiable AS events using TCGA RNA-Seq dataset. Using differentially AS event analysis, we identified AS events that were significantly differentially spliced in the presence of a U2AF S34F/Y mutation (119 in AML). And we purposed to finding In order to investigate functional site, the differentially spliced AS events were additionally annotated using ASpedia. Finally we identified the landscape of that AS events were altered by SF variants, and we proved that a part of the events was involved in cancer-associated functions.

Citation Format: Daejin Hyung, Jihyun Kim, Soo Young Cho, Charny Park. Functional annotation for alternative splicing to investigate disrupted splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3294.

The Efficacy of Platelet-Rich Plasma on Tendon and Ligament Healing: A Systematic Review and Meta-analysis With Bias Assessment

BACKGROUND

There has been a surge in high-level studies investigating platelet-rich plasma (PRP) for tendon and ligament injuries. A number of meta-analyses have been published, but few studies have focused exclusively on tendon and ligament injuries.

PURPOSE

To perform a meta-analysis assessing the ability of PRP to reduce pain in patients with tendon and ligament injuries.

STUDY DESIGN

Systematic review and meta-analysis.

METHODS

This study followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. A comprehensive search of the literature was carried out in April 2017 using electronic databases PubMed, MEDLINE, and the Cochrane Library. Only level 1 studies were included. Platelet and leukocyte count, injection volume, kit used, participant age/sex, comparator, and activating agent used were recorded. The short-term and long-term efficacy of PRP was assessed using the visual analog scale (VAS) to measure pain intensity. Injury subgroups (rotator cuff, tendinopathy, anterior cruciate ligament, and lateral epicondylitis) were evaluated. Funnel plots and the Egger test were used to screen for publication bias, and sensitivity analysis was performed to evaluate the effect of potential outliers by removing studies one at a time.

RESULTS

Thirty-seven articles were included in this review, 21 (1031 participants) of which could be included in the quantitative analysis. The majority of studies published investigated rotator cuff injuries (38.1%) or lateral epicondylitis (38.1%). Seventeen studies (844 participants) reported short-term VAS data, and 14 studies (771 participants) reported long-term VAS data. Overall, long-term follow-up results showed significantly less pain in the PRP group compared with the control group (weighted mean difference [WMD], -0.84; 95% CI, -1.23 to -0.44; P < .01). Patients treated with PRP for rotator cuff injuries (WMD, -0.53; 95% CI, -0.98 to -0.09; P = .02) and lateral epicondylitis (WMD, -1.39; 95% CI, -2.49 to -0.29; P = .01) reported significantly less pain in the long term. Substantial heterogeneity was reported at baseline ( I² = 72.0%; P < .01), short-term follow-up ( I² = 72.5%; P < .01), long-term follow-up ( I² = 76.1%; P < .01), and overall ( I² = 75.8%; P < .01). The funnel plot appeared to be asymmetric, with some missingness at the lower right portion of the plot suggesting possible publication bias.

CONCLUSION

This review shows that PRP may reduce pain associated with lateral epicondylitis and rotator cuff injuries.

MRI analysis of extra-capsular ganglia at the gastrocnemius origin and their association with osteoarthritis

AIM

To evaluate the prevalence, clinical relevance, and magnetic resonance imaging (MRI) features of extra-capsular ganglia at the gastrocnemius origin and to assess their association with internal derangement and osteoarthritis of the knee.

MATERIALS AND METHODS

One hundred consecutive knee MRI examinations, obtained within a 6-month period from patients with no history of recent knee trauma, recent injections, inflammatory arthritis, infection, or tumours, were evaluated retrospectively for the presence of ganglia at the gastrocnemius origin. The lesions were divided into two groups: an intra-capsular and an extra-capsular group. Cyst morphology (size, shape, and internal septa), internal derangement of the knee (cartilage lesion, cruciate ligament injury, meniscal tear, and corner injury on MRI, and osteoarthritis of the knee on radiographs) were evaluated. The chi-square, Fisher's exact, and t-tests were used to compare the two groups, in addition to multivariate stepwise logistic regression analysis.

RESULTS

Thirty-nine ganglia with an extra-capsular location were identified on 100 knee MRI (39 %). Rounded shape and internal septa were more common in the extra-capsular than in the intra-capsular group (p<0.001). Frequencies of high-grade cartilage, meniscal tear, and high-grade osteoarthritis significantly differed between the groups (p≤0.038). In multivariate analysis, the only significant association was between high-grade osteoarthritis and the extra-capsular group.

CONCLUSION

Extra-capsular ganglia at the gastrocnemius origin were not uncommon on knee MRI and had features typical of ganglia found at other sites. High-grade osteoarthritis was significantly associated with extra-capsular ganglia.

Development of a new analgesic index using nasal photoplethysmography

Although surrogate measures to quantify pain intensity have been commercialised, there is a need to develop a new index with improved accuracy. The aim of this study was to develop a new analgesic index using nasal photoplethysmography data. The specially designed sensor was placed between the columella and the nasal septum to acquire nasal photoplethysmography in surgical patients. Nasal photoplethysmography and Surgical Pleth Index^® (GE Healthcare) data were obtained for 14 min both in the absence (pre-operatively) or presence (postoperatively) of pain in a group of surgical patients, each patient acting as their own control. Various dynamic photoplethysmography variables were extracted to quantify pain intensity; the most accurate index was selected using logistic regression as a classifier. The area under the curve of the receiver-operating characteristic curve was measured to evaluate the accuracy of final model predictions. In total, 12,012 heart beats from 89 patients were used to develop a new Nasal Photoplethysmography Index for analgesic depth quantification. The two-variable model (a combination of diastolic peak point variation and heart beat interval variation) was most accurate in discriminating between the presence and absence of pain (numerical rating scale (NRS) ≥ 3). The accuracy and area under the curve of the receiver-operating characteristic curve for the Nasal Photoplethysmography Index were 75.3% and 0.8018, respectively, and 64.8% and 0.7034, respectively, for the Surgical Pleth Index. The Nasal Photoplethysmography Index clearly distinguished pain (NRS ≥ 3) in awake surgical patients with postoperative pain. The Nasal Photoplethysmography Index performed better than the Surgical Pleth Index. Further validation studies are needed to evaluate its feasibility to quantify pain intensity during general anaesthesia.

Acceptability of HIV self-sampling kits (TINY vial) among people of black African ethnicity in the UK: a qualitative study

Background

Increasing routine HIV testing among key populations is a public health imperative, so improving access to acceptable testing options for those in need is a priority. Despite increasing targeted distribution and uptake of HIV self-sampling kits (SSKs) among men who have sex with men in the UK, little is known about why targeted SSK interventions for black African users are not as wide-spread or well-used. This paper addresses this key gap, offering insight into why some groups may be less likely than others to adopt certain types of SSK interventions in particular contexts. These data were collected during the development phase of a larger study to explore the feasibility and acceptability of targeted distribution of SSKs to black African people.

Methods

We undertook 6 focus groups with members of the public who self-identified as black African (n = 48), 6 groups with specialists providing HIV and social services to black African people (n = 53), and interviews with HIV specialist consultants and policy-makers (n = 9). Framework analysis was undertaken, using inductive and deductive analysis to develop and check themes.

Results

We found three valuable components of targeted SSK interventions for this population: the use of settings and technologies that increase choice and autonomy; targeted offers of HIV testing that preserve privacy and do not exacerbate HIV stigma; and ensuring that the specific kit being used (in this case, the TINY vial) is perceived as simple and reliable.

Conclusions

This unique and rigorous research offers insights into participants’ views on SSK interventions, offering key considerations when targeting this population.. Given the plethora of HIV testing options, our work demonstrates that those commissioning and delivering SSK interventions will need to clarify (for users and providers) how each kit type and intervention design adds value. Most significantly, these findings demonstrate that without a strong locus of control over their own circumstances and personal information, black African people are less likely to feel that they can pursue an HIV test that is safe and secure. Thus, where profound social inequalities persist, so will inequalities in HIV testing uptake – by any means.

Electronic supplementary material

The online version of this article (10.1186/s12889-018-5256-5) contains supplementary material, which is available to authorized users.

KidsBrainIT: A New Multi-centre, Multi-disciplinary, Multi-national Paediatric Brain Monitoring Collaboration

OBJECTIVES

Validated optimal cerebral perfusion pressure (CPP) treatment thresholds in children do not exist. To improve the intensive care unit (ICU) management of the paediatric traumatic brain injury (TBI) population, we are forming a new paediatric multi-centre collaboration to recruit standardised ICU data for running and reporting upon models for assessing autoregulation and optimal CCP (CPPopt).

MATERIALS AND METHODS

We are adapting the adult BrainIT group's approach to develop a new Paediatric Brain Monitoring and Information Technology Group (KidsBrainIT), which will include a repository to store prospectively collected high-resolution physiological, clinical, and outcome data. In the first phase of this project there are 7 UK Paediatric Intensive Care Units, 1 Spanish, 1 Belgium, and 1 Romanian Centre interested in participating. In subsequent phases, we plan to open recruitment to other centres both within Europe, US and abroad. We are collaborating with the Leuven Group and plan to use their LAx (low-frequency autoregulation index), DATACAR (dynamic adaptive target of active cerebral autoregulation), CPPopt and visualisation methodologies. We also plan to use the continuous diffuse optical monitoring and tomography technology developed in Barcelona as an acute surrogate end-point for optimising brain perfusion. This technology allows non-invasive continuous monitoring of deep tissue perfusion and oxygenation in adults but its clinical application in infants and children with TBI has not been studied previously.

RESULTS

We report on the current status of setting up this new collaboration and also on pilot analyses in two centres which are the basis of our rationale for the need for a prospective validation study of CPPopt in children. Specifically, we demonstrated that CPPopt varied with time for each patient during their paediatric intensive care unit (PICU) stay, and the median overall CPPopt levels for children aged 2-6 years, 7-11 years and 12-16 years were 68.83, 68.09, and 72.17 mmHg respectively. Among survivors and patients with favourable outcome (GOS 4 and 5), there were significantly higher proportions with CPP monitoring time within CPPopt (p = 0.04 and p = 0.01 respectively).

CONCLUSIONS

There is a need and an interest in forming a multi-centre PICU collaboration for acquiring data and performing analyses for determining validated CPPopt thresholds in the paediatric TBI population. KidsBrainIT is being formed to meet that need.

Isolation and Functional Examination of the Long Non-Coding RNA Redrum

Here, we report isolation of multiple long non-coding RNAs (lncRNAs) expressed tissue-specifically during murine embryogenesis. One of these, subsequently came to be known as Redrum, is expressed in erythropoietic cells in fetal liver and adult bone marrow. Redrum transcription is also detected during pregnancy in the spleen where extramedullary hematopoiesis takes place. In order to examine the function of Redrum in vivo, we generated a gene-targeted murine model and analyzed its embryonic and adult erythropoiesis. The homozygous mutant embryo showed no apparent deficiency or defect in erythropoiesis. Adult erythropoiesis in bone marrow and in the spleen during pregnancy likewise showed no detectable phenotype as red blood cells matured in normal fashion. The phenotype is in contrast to the reported function of Redrum in vitro, and our observation implies that Redrum plays in vivo an accessory or supplementary role whose loss is compatible with normal erythropoiesis.