Abstract PD4-15: A tale of two pathways: Mutations in PI3K pathway in TNBC patients matter for the oncogenic cooperation with DNA damage repair pathway

Background: Mutations guide targeted therapy in the personalized medicine. In the opening chapter of our recently edited book (Dey et al., 2016), Prof. L. Cantley elegantly elucidated the basic signaling of the PI3K pathway in cancers. Mutations in the PI3K pathway are not only common and subtype-specific in BC but are also contextual. Alterations in DNA damage repair (DDR) pathway involving HRD (Homologous Recombination Defect) genes are one of the important contextual events of the upregulation of the PI3K pathway (De et al., 2016). Aim: Here we interrogated the contextuality of alterations of the PI3K and DDR pathway genes in our Avera patients. The mechanism of contextual cooperation between the pathwayswas experimentally validated. Methods: We examined mutation profile (FoundationOne) of our patients (Avera Cancer Institute) and patients fromthe TCGA data (cBioPortal). We validated the cooperation of the two pathwaysexperimentally by the synergy model of mutation-specific drugs; PI3K-PTEN-mTOR pathway inhibitor(s) and PARP inhibitor(s) using TNBC model.Results: We analyzed alterations of 17 and 12 genes of the PI3K and DDR pathways respectively in subtypes of BC. In luminal A and HER2-enriched (TCGA, Nature 2012), the alteration of PIK3CA reached 49 % and 47% as compared to 37 % in luminal B and 25% in basal-like.In the basal-like/TNBC subtype (cBioPortal) 12 DDR pathway genes (CHEK1/2, RAD51, BRCA1/2, MLH1, MSH2, ATM, ATR, MDC1, PARP1, FANCF) were altered in 90.1 % of cases, and 17 PI3K pathway genes were altered in 88.9 % of cases.Our ER+ve patients presented a diverse variety of PIK3CA mutations (E545K,  E545A, E545G, E542K, E453K, E762K, E365K, N345K, C420R, E81K, Q546R, C420R, E726K, E81K, E970K, H1047R, H1047L P104L, P539R, G106R,G1049R, R93Q,N345T, V105_E109>E, L113del, K111del) as compared to a less diverse type of PIK3CA mutations (Amplification, E542K, H1047R) in our TNBC patients. In our TNBC patients, the predominant type of mutation in PI3K pathway genes was found in PTEN consisting of Y68C, Y180*, loss, loss exons 1-5, and deletion exon1. The other most common mutation found in TNBC patients was in TP53 (>80%) and somatic BRCA1/2 (˜15%) genes. The interaction between the two pathways was evaluated using the mostly altered oncogenes and tumor suppressor genes (PTEN, AKT1/2, TSC1/2, mTOR, RICTOR, RHEB, BRCA1/2, ATM, ATR, FANCF) applying STRING10 to test the association at the highest 0.900 confidence views. Finally, we experimentally validated the contextual synergy of 2 pathways by demonstrating that a node-specific inhibition of the PI3K-mTOR pathway by GDC-0980 in the presence of carboplatin resulted in (1) an enhanced impairment of DSB repair and (2) a subsequent sensitization to PARPi (i). This effect occurred simultaneously with the inhibition of classic PI3K-mTOR survival signal(s) which induced a robust antiproliferative/proapoptotic effect even in BRCA-competent TNBC cells. The absence of PTEN, on the other hand, sensitized TNBC cells to PARPi in the presence of carboplatin, an effect more pronounced in BRCA-loss. Conclusion: Our data showed that the PI3K pathway cooperates with the DDR pathway in the breast oncogenesis especially basal-like and TNBC.

Citation Format: Dey N, Williams C, Krie A, Klein J, Williams K, Carlson JH, De PK, Leyland-Jones B. A tale of two pathways: Mutations in PI3K pathway in TNBC patients matter for the oncogenic cooperation with DNA damage repair pathway [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-15.

Mineral analysis of complete dog and cat foods in the UK and compliance with European guidelines

Mineral content of complete pet food is regulated to ensure health of the companion animal population. Analysis of adherence to these regulatory guidelines has not been conducted. Here, mineral composition of complete wet (n = 97) and dry (n = 80) canine and feline pet food sold in the UK was measured to assess compliance with EU guidelines. A majority of foods complied with ≥8 of 11 guidelines (99% and 83% for dry and wet food, respectively), but many failed to provide nutritional minimum (e.g. Cu, 20% of wet food) or exceeded nutritional maximum (e.g. Se, 76% of wet food). Only 6% (6/97) of wet and 38% (30/80) of dry food were fully compliant. Some foods (20–30% of all analysed) had mineral imbalance, such as not having the recommended ratio of Ca:P (between 1:1 to 2:1). Foods with high fish content had high levels of undesirable metal elements such as arsenic. This study highlights broad non-compliance of a range of popular pet foods sold in the UK with EU guidelines (94% and 61% of wet and dry foods, respectively). If fed exclusively and over an extended period, a number of these pet foods could impact the general health of companion animals.

Precise predictions for V + jets dark matter backgrounds

High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the Z ( ν ν ¯ ) +  jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by Z ( ℓ + ℓ - ) +  jet, W ( ℓ ν ) +  jet and γ +  jet production, and extrapolating to the Z ( ν ν ¯ ) +  jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the-art calculations for all relevant V +  jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different V +  jet processes play a key role. The anticipated theoretical uncertainty in the Z ( ν ν ¯ ) +  jet background is at the few percent level up to the TeV range.

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.

Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis

KEY MESSAGE

We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F6 recombinant inbred line and an F2 population, two genes were identified that mapped to the short arm of chromosome 1Ssh, designated as Sr-1644-1Sh, and the long arm of chromosome 5Ssh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.

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.