Foetal haemoglobin, blood transfusion, and retinopathy of prematurity in very preterm infants: a pilot prospective cohort study

PurposeTo identify if there is an association between foetal haemoglobin (HbF) concentration and retinopathy of prematurity (ROP) in very preterm infants.Patients and methodsProspective cohort study. Infants born <32 weeks' gestational age or <1501 g in two tertiary neonatal units between January 2012 and May 2013 (n=42) were enrolled. HbF and adult haemoglobin (HbA) concentrations were measured using high-pressure liquid chromatography from blood samples sent as part of routine neonatal care once routinely requested laboratory tests had been performed. Clinical data were obtained from case notes. We calculated odds ratios (ORs) (95% confidence intervals (CIs)) to quantify the relationship between initial and mean %HbF with ROP severity (none, stages 1-3).ResultsA total of 42 infants were recruited: mean gestation 28.0 weeks (SD 1.91); mean birth weight 1042 g (SD 264). Six infants died before ROP screening; 14/36 developed ROP (39%); and 22/36 (61%) did not. Infants who developed ROP had similar initial %HbF (83.3 vs 92.3%, P=0.06), but significantly lower mean %HbF (61.75 vs 91.9%, P=0.0001) during their inpatient stay than those who did not develop ROP. In ordinal logistic regression models adjusted for birth weight, gestation and transfusion volume, mean post-natal %HbF was negatively associated with ROP severity: adjusted OR 0.94 (0.90-0.99), while initial %HbF at birth was not: adjusted OR 1.05 (0.97-1.16).ConclusionReplacing HbF by HbA during transfusion may promote ROP development by rapidly increasing oxygen availability to the retina. Conversely, maintaining a higher %HbF may be a protective factor against ROP.

An international comparison of retinopathy of prematurity grading performance within the Benefits of Oxygen Saturation Targeting II trials

Purpose

To investigate whether the observed international differences in retinopathy of prematurity (ROP) treatment rates within the Benefits of Oxygen Saturation Targeting (BOOST) II trials might have been caused by international variation in ROP disease grading.

Methods

Groups of BOOST II trial ophthalmologists in UK, Australia, and New Zealand (ANZ), and an international reference group (INT) used a web based system to grade a selection of RetCam images of ROP acquired during the BOOST II UK trial. Rates of decisions to treat, plus disease grading, ROP stage grading, ROP zone grading, inter-observer variation within groups and intra-observer variation within groups were measured.

Results

Forty-two eye examinations were graded. UK ophthalmologists diagnosed treat-requiring ROP more frequently than ANZ ophthalmologists, 13.9 (3.49) compared to 9.4 (4.46) eye examinations, P=0.038. UK ophthalmologists diagnosed plus disease more frequently than ANZ ophthalmologists, 14.1 (6.23) compared to 8.5 (3.24) eye examinations, P=0.021. ANZ ophthalmologists diagnosed stage 2 ROP more frequently than UK ophthalmologists, 20.2 (5.8) compared to 12.7 (7.1) eye examinations, P=0.026. There were no other significant differences in the grading of ROP stage or zone. Inter-observer variation was higher within the UK group than within the ANZ group. Intra-observer variation was low in both groups.

Conclusions

We have found evidence of international variation in the diagnosis of treatment-requiring ROP. Improved standardisation of the diagnosis of treatment-requiring ROP is required. Measures might include improved training in the grading of ROP, using an international approach, and further development of ROP image analysis software.

Tolerance of Pseudomonas aeruginosa in in-vitro biofilms to high-level peracetic acid disinfection

BACKGROUND

Biofilm has been suggested as a cause of disinfection failures in flexible endoscopes where no lapses in the decontamination procedure can be identified. To test this theory, the activity of peracetic acid, one of the widely used disinfectants in the reprocessing of flexible endoscopes, was evaluated against both planktonic and sessile communities of Pseudomonas aeruginosa.

AIM

To investigate the ability of P. aeruginosa biofilm to survive high-level peracetic acid disinfection.

METHOD

The susceptibility of planktonic cells of P. aeruginosa and biofilms aged 24, 48, 96, and 192 h to peracetic acid was evaluated by estimating their viability using resazurin viability and plate count methods. The biomass of the P. aeruginosa biofilms was also quantified using Crystal Violet assay. Planktonic cells of P. aeruginosa were treated with 5-30 ppm concentration of peracetic acid in the presence of 3.0 g/L of bovine serum albumin (BSA) for 5 min. Biofilms of P. aeruginosa were also treated with various peracetic acid concentrations (100-3000 ppm) for 5 min.

FINDINGS

Planktonic cells of P. aeruginosa were eradicated by 20 ppm of peracetic acid, whereas biofilms showed an age-dependent tolerance to peracetic acid, and 96 h biofilm was only eradicated at peracetic acid concentration of 2500 ppm.

CONCLUSION

Ninety-six-hour P. aeruginosa biofilm survives 5 min treatment with 2000 ppm of peracetic acid, which is the working concentration used in some endoscope washer-disinfectors. This implies that disinfection failure of flexible endoscopes might occur when biofilms build up in the lumens of endoscopes.

Abstract P6-08-04: Preclinical efficacy of dasatinib in combination with PARP inhibitor plus standard cytotoxic agent in triple-negative breast cancer xenograft model

Background: Dasatinib is an orally-active ATP-competitive small molecule kinase inhibitor that potently inhibits Abl kinase, Src family kinases and other kinases (Lombardo et al., 2004). Src, one of the key targets of dasatinib is involved in the regulation of cell proliferation, survival and apoptotic ability of cancer cells (Tryfonopoulos et al., 2011; Pusztai et al., 2014). Dasatinib has shown its anti-proliferative and anti-metastatic effectiveness against triple-negative breast cancer (TNBC) in both preclinical and clinical studies (Finn et al., 2011). Several molecular targets including poly ADP ribose polymerase (PARP) are under clinical investigation for the treatment of TNBC. Recently, PARP inhibitors in combination with chemotherapy have shown promising results in this disease in clinical and preclinical studies (Tutt et al., 2010; Kim et al., 2013; De et al., 2014). Here, we hypothesize that dasatinib in combination with PARP inhibitor (ABT888) plus standard cytotoxic agent (carboplatin) will attenuate the growth of both TNBC cell lines and xenograft tumors. Methodology:We have used BT-20 (PIK3CA mutated, H1047R), HCC70 (PTEN null), HCC1937 (BRCA1 mutated, PTEN null), MDA-MB-231 (KRAS/BRAF mutated), MDA-MB-468 (PTEN null) and SUM149PT (BRCA1 mutated, PTEN null) cells for in vitro study. Survival/proliferation, colony formation and apoptosis were examined by using 2D proliferative/growth assay, 3D-ON-TOP assays, and annexinV staining respectively. We next studied the activation status of Src and its downstream signaling. We also have evaluated the effects on tumor growth inhibition of dasatinib/ABT888/carboplatin as a single agent or in combination by using mouse xenograft model. Results: We observed that 1) Dasatinib inhibited Src activation in all tested lines, induced dephosphorylation of ERK1/2 and S6 RP; 2) level of Cyclin D1 was decreased by dasatinib treatment; 3) high anti-proliferative activities were observed following the treatment of dasatinib along with ABT888 plus carboplatin in both 2D proliferation assay and 3D-ON TOP colony formation assay; 4) dasatinib in combination with ABT888 plus carboplatin inducing early stage apoptosis was seen by Annexin V staining in all tested cell lines; 5) dasatinib alone or combined with ABT888 or carboplatin or in triple combination inhibited tumor growth in TNBC xenograft models, the best tumor inhibition result was induced by triple combination (comparing to no treatment control, the mean tumor volume was decreased ~ 87% ). Conclusion: Our in vitro and in vivo studies suggest that dasatinib may enhance the antitumor activity of PARP inhibitor plus standard cytotoxic agent in TNBC. Mechanistic studies of xenograft tumor samples are ongoing, the results of which will be presented in the meeting.

Citation Format: Sun Y, Lin X, Carlson JH, De P, Dey N, Jepperson T, R & D NCI, Williams C, Leyland-Jones B. Preclinical efficacy of dasatinib in combination with PARP inhibitor plus standard cytotoxic agent in triple-negative breast cancer xenograft model [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-08-04.

Abstract P1-05-23: Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting

Introduction

Variant calling based on DNA samples has been the gold standard of clinical testing since the advent of Sanger sequencing. The use of DNA variants has proved a great value to guide treatment in cancer patients. However, DNA based analysis will not inform about expression status of the gene harboring a particular variant. RNA has long been used to monitor expression. To this point RNA assays and analysis are confined to the research laboratory and rarely used clinically except in specifically defined gene signatures such as PAM50 and OncoType Dx. Beyond expression, RNA has the ability to confirm expression of DNA variants and identify fusion events. We hypothesize that the combination of DNA and RNA based data will allow the determination of variant specific expression status and improve clinical diagnostics. It has been previously shown that RNA sequencing (RNA-Seq) based variant calls are highly accurate and confirm DNA based variant calls. In this study we investigated the utility of RNA-Seq as a diagnostic assay integrated with DNA based sequencing data.

Materials and Methods

Targeted DNA sequencing of 321 genes was performed on 37 patient samples (FFPE), including 22 breast cancer samples by a commercial vendor. RNA-Seq on the same patient samples was performed using 100ng of total RNA. Libraries were run on the Illumina NextSeq 500 with a minimum of 75M paired 75bp reads. To evaluate RNA-seq expression reproducibility, replicates of 6 normal ovarian tissue samples (min. 50M reads) were run in sets of triplicates. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). RNA-Seq based variant calling was performed using the SNPiR pipeline. Based on the results of the commercial assay, DNA based variants were examined for expression of the corresponding genes and ability to confirm variants in the RNA-Seq data.

Results

RNA expression data showed no corresponding gene expression for at least one single nucleotide variant (SNV) in 9/37 patients analyzed (24.3%). In 18/37 patients (48.6%) SNV corresponding expression was in the lowest quartile of expression values. Variant calls could be confirmed by RNA-Seq for 95/455 SNVs, with adequate coverage in 263 of the remaining 360 variant locations (median coverage: 34). Of these, a homozygous reference call was made in 166/263 SNVs. Concordance for RNA-Seq gene level expression data between replicates was &gt; 0.995.

Conclusions

These findings suggest that RNA-Seq based data can provide clinical value when using gene expression values in combination with DNA based variant calls. We found gene level expression to be highly reproducible and will further investigate the use of spike in controls to determine clinically usable expression ranges and lower limit of expression values. To our knowledge, it has not been shown that RNA-Seq based variant calls are reproducible which is the focus of our current research as this will be one requirement for usage in a regulated environment. While our use of RNA Seq is currently limited to gene expression level data, we have demonstrated a clinically relevant benefit to using RNA Seq data as an additive feature to the current standard of DNA variant calling.

Citation Format: Young B, Mark A, Meissner T, Amallraja A, Andrews A, Connolly C, Williams C, Leyland-Jones B. Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-23.

Abstract P6-08-09: Cancer stem cells define 3D clonogenic growth response to rational combinations of PI3K-isoform specific inhibitors in TNBC

This abstract was not presented at the symposium.

Abstract P1-05-22: The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis

Introduction

Next generation sequencing has facilitated the understanding of pathogenesis and molecular heterogeneity of breast cancer (BC) as well as accelerated the path towards precision medicine. DNA sequencing (DNA-Seq) based assays for the detection of mutations and alterations in solid and hematologic cancers are finding their way into clinical practice and are readily available as clinical products. RNA sequencing (RNA-Seq), so far being vastly applied in the research context, promises to expand the diagnostic, prognostic and therapeutic use of this technology in cancer. Beyond mutational status, RNA-Seq enables the detection of fusions, quantification of gene expression level, detection of differentially expressed genes, molecular based subtyping, and risk-stratification. In this study we analyzed RNA-Seq and copy number data from BC patients that had undergone DNA-Seq based diagnostics through commercial providers with the goal to detect additional actionable targets.

Materials and Methods

We included 18 BC patients (5/18 triple negative) that had previously undergone DNA-based targeted (321 genes) sequencing. RNA-Seq to a minimum of 75M reads (75pb) was performed using 100 ng of total RNA on the Illumina NextSeq 500 platform. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). Fusions were detected using STAR-Fusion. DESeq2 was utilized to identify patient specific differentially expressed genes by analyzing samples individually against a set of 13 controls from healthy breast tissue generated in-house. Copy number variations (CNVs) were detected using the Nanostring CNV Cancer panel (89 genes) on the Nanostring nCounter platform. Differentially upregulated or amplified genes were queried against DGIdb and Gene Drug Knowledge database for suitable drug matches, limiting the queries to clinically actionable antineoplastic drugs.

Results

Analyzing the cohort of 18 BC patients, we detected on average 26 BC relevant genes (526 total, log2 FC &gt; 2) to be upregulated per patient. Querying the upregulated genes against DGIdb, we found a total of 18 genes that had drug matches and fulfilled the criteria of being actionable antineoplastic drugs, with 17/18 samples having a minimum of two gene targets (avg: 4). Most frequent upregulated genes were TOP2A (83%), AURKA (61%), AURKB (56%), RET (39%)and FGFR3 (28%). In the case of CNVs, 12/18 patients showed at least one gene target with clinically actionable drugs associated. This was observed across 12 gene targets that were amplified (avg: 3) and 4 gene targets that underwent deletions (avg: 1). Most frequent CNVs included MYC (14%) and CCND1 (12%). 4/7 patients having an AURKA overexpression also showed an AURKA amplification on the CNV assay. 10/18 patients had fusions events, with an average of three fusions per patient, including GAB2-WNT11, PAK1-TENM4 and FGFR2-CEP55 fusions.

Conclusions

We show that RNA-Seq and copy number assays provide additional clinical value by detecting suitable drug targets beyond traditional DNA-based approaches. We are conducting further analysis on how these additionally derived drug targets could improve the current treatment schedule of those patients.

Citation Format: Meissner T, Amallraja A, Mark A, Andrews A, Connolly C, Young B, De P, Williams C, Leyland-Jones B. The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-22.

Abstract P2-03-02: Differential mutation pattern between neoadjuvant and metastatic settings in breast cancer patients

Background: Dysregulated signaling pathways occur in human cancers including breast cancer, making it a rational target for novel genome guided combinatorial personalized therapies. The aim of the present study was to investigate the different genetic mutation pattern between neoadjuvant and metastatic settings in breast cancer patients to guide research and clinical treatment.

Material and Methods: 150 breast cancer patients were involved in this study. 38 patients were receiving neoadjuvant treatment and 112 patients were in the metastatic setting. Tumor specimens obtained from the 150 patients were subjected to genetic mutation testing by FoundationOne. Genetic alterations detected by FoundationOne test were collected and analyzed.

Results: 96 and 149 different genes where reported by FoundationOne in neoadjuvant and metastatic setting respectively. The average number of non-synonymous mutation was five per case in the neoadjuvant setting and six per case in the metastatic setting. TP53 (58%), MYC (32%), PIK3CA (29%), PTEN (16%), CDH1 (13%), CCND1 (11%), EMSY (11%), LYN (11%) and ZNF703 (11%) were the most seen mutations in neoadjuvant setting. TP53 (40%), PIK3CA (39%), MYC (22%), CCND1 (21%), FGF19 (21%), FGF4 (21%), CDH1 (20%), FGF3 (19%), ERBB2 (17%), ESR1 (14%), FGFR1 (14%), ZNF703 (14%), GATA3 (13%), MYST3 (11%), PTEN (11%), EMSY (10%), NF1 (10%) and ZNF217 (10%) were the most seen mutations in metastatic setting. ESR1 and GATA3, which are seen in 14% and 13% of metastatic breast cancer patients, were not reported in neoadjuvant breast patients. Moreover, among the 16 metastatic breast cancer patients who has ESR1 mutation, 9 (56%) of them presented with PIK3CA or other genetic mutations which are directly involved in the phosphoinositide 3-kinase (PI3K)/AKT pathway.

Conclusion: A significantly more mutation in Receptor Tyrosine Kinases (RTKs)/ Growth Factor Signaling ( especially ERBB and FGFR pathways) was reported in the metastatic setting compare to the neoadjuvant setting, suggesting a critical role of the RTKs in metastatic breast cancer patients. The coexisting of ESR1 and PI3K/AKT pathway alteration and the absence of ESR1 in neoadjuvant setting also suggested that in early stage breast cancer patients who have a PI3K pathway alterations; there is a higher chance to develop ESR1 mutation with disease progression.

Citation Format: Xu B, Williams C, De P, Dey N, Klein J, Williams K, McMillan A, Leyland-Jones B. Differential mutation pattern between neoadjuvant and metastatic settings in breast cancer patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-02.

Predicting recovery in patients with acute low back pain: A Clinical Prediction Model

BACKGROUND

There is substantial variability in the prognosis of acute low back pain (LBP). The ability to identify the probability of individual patients recovering by key time points would be valuable in making informed decisions about the amount and type of treatment to provide. Predicting recovery based on presentation 1-week after initially seeking care is clinically important and may be more accurate than predictions made at initial presentation. The aim of this study was to predict the probability of recovery at 1-week, 1-month and 3-months after 1-week review in patients who still have LBP 1-week after initially seeking care.

METHODS

The study sample comprised 1070 patients with acute LBP, with a pain score of ≥2 1-week after initially seeking care. The primary outcome measure was days to recovery from pain. Ten potential prognostic factors were considered for inclusion in a multivariable Cox regression model.

RESULTS

The final model included duration of current episode, number of previous episodes, depressive symptoms, intensity of pain at 1-week, and change in pain over the first week after seeking care. Depending on values of the predictor variables, the probability of recovery at 1-week, 1-month and 3-months after 1-week review ranged from 4% to 59%, 19% to 91% and 30% to 97%, respectively. The model had good discrimination (C = 0.758) and calibration.

CONCLUSIONS

This study found that a model based on five easily collected variables could predict the probability of recovery at key time points in people who still have LBP 1-week after seeking care.

SIGNIFICANCE

A clinical prediction model based on five easily collected variables was able to predict the likelihood of recovery from an episode of acute LBP at three key time points. The model had good discrimination (C = 0.758) and calibration.

Development and Testing of a Cognitive Behavioral Therapy Resource for Children's Dental Anxiety

Cognitive Behavioral Therapy (CBT) is an evidence-based treatment for dental anxiety; however, access to therapy is limited. The current study aimed to develop a self-help CBT resource for reducing dental anxiety in children, and to assess the feasibility of conducting a trial to evaluate the treatment efficacy and cost-effectiveness of such an intervention. A mixed methods design was employed. Within phase 1, a qualitative "person-based" approach informed the development of the self-help CBT resource. This also employed guidelines for the development and evaluation of complex interventions. Within phase 2, children, aged between 9 and 16 y, who had elevated self-reported dental anxiety and were attending a community dental service or dental hospital, were invited to use the CBT resource. Children completed questionnaires, which assessed their dental anxiety and health-related quality of life (HRQoL) prior to and following their use of the resource. Recruitment and completion rates were recorded. Acceptability of the CBT resource was explored using interviews and focus groups with children, parents/carers and dental professionals. For this analysis, the authors adhered to the Mixed Methods Appraisal Tool criteria. There were 24 families and 25 dental professionals participating in the development and qualitative evaluation of the CBT resource for children with dental anxiety. A total of 56 children agreed to trial the CBT resource (66% response rate) and 48 of these children completed the study (86% completion rate). There was a significant reduction in dental anxiety (mean score difference = 7.7, t = 7.9, df = 45, P < 0.001, Cohen's d ES = 1.2) and an increase in HRQoL following the use of the CBT resource (mean score difference = -0.03, t = 2.14, df = 46, P < 0.05, Cohen's d ES = 0.3). The self-help approach had high levels of acceptability to stakeholders. These findings provide preliminary evidence for the effectiveness and acceptability of the resource in reducing dental anxiety in children and support the further evaluation of this approach in a randomized control trial. Knowledge Transfer Statement: This study details the development of a guided self-help Cognitive Behavioral Therapy resource for the management of dental anxiety in children and provides preliminary evidence for the feasibility and acceptability of this approach with children aged between 9 and 16 y. The results of this study will inform the design of a definitive trial to examine the treatment- and cost-effectiveness of the resource for reducing dental anxiety in children.

Experts' Perceptions on China's Capacity to Manage Emerging and Re-emerging Zoonotic Diseases in an Era of Climate Change

Zoonotic diseases transmitted by arthropods and rodents are a major public health concern in China. However, interventions in recent decades have helped lower the incidence of several diseases despite the country's large, frequently mobile population and socio-economic challenges. Increasing globalization, rapid urbanization and a warming climate now add to the complexity of disease control and prevention and could challenge China's capacity to respond to threats of emerging and re-emerging zoonoses. To investigate this notion, face-to-face interviews were conducted with 30 infectious disease experts in four cities in China. The case study diseases under discussion were malaria, dengue fever and haemorrhagic fever with renal syndrome, all of which may be influenced by changing meteorological conditions. Data were analysed using standard qualitative techniques. The study participants viewed the current disease prevention and control system favourably and were optimistic about China's capacity to manage climate-sensitive diseases in the future. Several recommendations emerged from the data including the need to improve health literacy in the population regarding the transmission of infectious diseases and raising awareness of the health impacts of climate change amongst policymakers and health professionals. Participants thought that research capacity could be strengthened and human resources issues for front-line staff should be addressed. It was considered important that authorities are well prepared in advance for outbreaks such as dengue fever in populous subtropical areas, and a prompt and coordinated response is required when outbreaks occur. Furthermore, health professionals need to remain skilled in the identification of diseases for which incidence is declining, so that re-emerging or emerging trends can be rapidly identified. Recommendations such as these may be useful in formulating adaptation plans and capacity building for the future control and prevention of climate-sensitive zoonotic diseases in China and neighbouring countries.