Abstract P4-07-04: PARP1/2 inhibition in a subset of triple negative breast cancer (TNBC) patient-derived tumor xenografts (PDX) identifies predictive biomarkers of response

Background: BRCA1/2 mutation carriers (gBRCA) have a higher risk of breast or ovarian cancer, since BRCA1/2 mutation results in impaired high-fidelity DNA repair by homologous recombination (HR) and subsequently genetic instability. In non-gBRCA TNBC, HR deficiency occurs at the somatic level, by means of BRCA1 mutation, BRCA1 epigenetic loss or mutation in other HR-associated genes. Because PARP1/2 inhibitors (PARPi) are well-tolerated and active anti-cancer agents in the advanced setting of gBRCA tumors, we sought to expand their applicability by identifying response biomarkers in TNBC.

Methods: We have assessed the antitumor response of the PARP1/2 inhibitor olaparib as single agent in a panel of 12 primary and advanced TNBC PDX models. On PDXs exhibiting primary sensitivity to olaparib, we have developed models of acquired resistance by continuous exposure to the drug and identifying progression on treatment. We have characterized the models through targeted sequencing and the analysis of the hypermethylation and expression levels of BRCA1 transcript to find potential correlates of drug-sensitivity.

Results: Three out of 12 PDXs (25%) treated with single agent olaparib, exhibit tumor regression or disease stabilization. BRCA1 is hypermethylated in two of these PARPi-sensitive TNBC PDX models and is associated with loss of BRCA1 mRNA expression. The third PARPi-sensitive TNBC PDX harbors a frameshift, heterozygous PALB2 mutation, which is no longer detected in the acquired resistance PDX model. Acquired resistance in the hypermethylated PDXs is under study as well as the duration of response compared to gBRCA PDX models.

Conclusions: Our study highlights that somatic HR-deficiency is frequent in TNBC and provides the basis of sensitivity to PARPi.

Citation Format: Serra V, Cruz C, Bruna A, Ibrahim YH, Vivancos A, Vivancos A, Nuciforo P, Bellet M, Gómez P, Pérez JM, Saura C, Vidal M, Serres X, Rueda OM, Peg V, Caldas C, O'Connor MJ, Baselga J, Cortés J. PARP1/2 inhibition in a subset of triple negative breast cancer (TNBC) patient-derived tumor xenografts (PDX) identifies predictive biomarkers of response. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-07-04.

Abstract P2-08-13: Integrating multiplex and next generation sequencing (NGS) platforms in routine molecular profiling of metastatic breast cancer (MBC) patients (pts): Trends for enrollment in genotype-directed clinical trials (GDTs)

Background/aims: Multiplex or NGS platforms increase the number of mutations (mut) detected in tumor samples respect to single-gene sequencing techniques. We aimed to assess the actionable molecular alteration (ActMA) detection rate and the enrollment in GDTs derived from the integration of these platforms in routine molecular profiling of MBC pts, in addition to FISH and IHC techniques already in use. Methods: Consecutive MBC pts screened for gene mut by Sequenom (Seq) or AmpliconSeq (ASeq) were identified. Data on FGFR1 amplification (amp), PTEN IHC, and enrollment in GDTs were collected. ActMA: any mut, PTENnull (IHC score=0), or FGFR1/HER2amp for which a matched targeted drug might be available. Targeted therapy: treatment with PI3K/mTOR, novel anti-HER2, FGFR, or AKT inhibitors (inh) irrespective of having ActMA. GDT: treatment matched to ActMA. Results: From Oct2010-Apr2015, 260 pts screened (Seq 207, ASeq 53). IHC subtype: HR+/HER2- (LUM) 65%, HER2+ 13.5%, TN 19.6%, unk 1.9%. 84 samples from a metastatic site (32.3%).

ActMA / n (%)LUMHER2+TNP value (Fisher's exact test)TotalTP53*11 (31.4)1 (50)9 (52.9)0.3421 (38.9)PIK3CA44 (26)10 (28.6)4 (7.8)0.158 (22.7)FGFR1amp21 (17.4)1 (5.3)6 (16.7)0.4728 (15.9)PTENnull12 (9.3)2 (7.7)9 (25)0.0323 (12)AKT110 (5.9)1 (2.9)-0.1511 (4.3)ERBB23 (1.8)---3 (1.2)EGFR1 (0.6)-2 (4.1)-3 (1.2)ESR1*1 (3)---1 (2)KRAS2 (1.2)---2 (0.8)Denominators vary according to platform. *Amplicon only

Proportion of PIK3CAmut was similar irrespective of the site of analysis (primary 25.5%, metastasis 21.4%; P=0.63) and platform (Seq 22.2%, ASeq 24.5%, P=0.72). ASeq detected more mutations in actionable genes than Seq (36% vs. 29%, P=0.01). At least 1 ActMA (range 0-3) was found in 53.5% of pts, with non-significant differences in HER2- subtypes (LUM 48.5% vs. TN 39.2%, P=0.32).

Subtype* / ActMA n (%)≥10123All139 (53.5)121 (46.5)111 (42.7)25 (9.6)3 (1.2)LUM82 (48.5)87 (51.5)71 (42)9 (5.3)2 (1.2)HER2+35 (100)-22 (62.9)12 (34.3)1 (28)TN20 (39.2)31 (60.8)16 (31.4)4 (7.8)-*5 pts with unk subtype not shown

Pts with ≥2 ActMA (excluding HER2amp): 11 LUM (interestingly, 3 pts with PIK3CAmut+FGFR1amp), 1 HER2+, and 4 TN. Overall, 56% of pts received ≥1 targeted therapy (range 0-4). From the 139 pts with ≥1 potential ActMA (including HER2amp if treated with a novel anti-HER2), 61.8% received a targeted therapy and 42.4% were enrolled in a GDT: PI3K/mTOR inhibitor (inh) 54 (64.3%), novel anti-HER2 16 (19.1%), FGFR inh 8 (9.5%), AKT inh 6 (7.1%). Of the 121 pts that did not have potentially ActMA, 50% received a targeted therapy. The OR for receiving targeted therapy if ActMA was present was 1.59 (95%CI 0.94-2.70, P=0.08). Conclusion: Integration of multiplex and NGS platforms in routine molecular profiling of MBC pts yields a detection rate of ActMA >50%, which translates into higher probability of receiving a targeted agent and enrollment in a GDT. This suggests that physicians are pushing towards matched targeted therapies for pts that participate in molecular screening programs and have ActMA. Results on the outcome of these pts will be presented.

Citation Format: Oliveira M, Dienstmann R, Bellet M, Pérez-Garcia JM, Gómez P, Muñoz-Couselo E, Vidal M, Ortega V, Zamora E, Soberino J, Meire A, Nuciforo P, Vivancos A, Cortés J, Saura C. Integrating multiplex and next generation sequencing (NGS) platforms in routine molecular profiling of metastatic breast cancer (MBC) patients (pts): Trends for enrollment in genotype-directed clinical trials (GDTs). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-08-13.

Siderophore cooperation of the bacterium Pseudomonas fluorescens in soil

While social interactions play an important role for the evolution of bacterial siderophore production in vitro, the extent to which siderophore production is a social trait in natural populations is less clear. Here, we demonstrate that siderophores act as public goods in a natural physical environment of Pseudomonas fluorescens: soil-based compost. We show that monocultures of siderophore producers grow better than non-producers in soil, but non-producers can exploit others' siderophores, as shown by non-producers' ability to invade populations of producers when rare. Despite this rare advantage, non-producers were unable to outcompete producers, suggesting that producers and non-producers may stably coexist in soil. Such coexistence is predicted to arise from the spatial structure associated with soil, and this is supported by increased fitness of non-producers when grown in a shaken soil–water mix. Our results suggest that both producers and non-producers should be observed in soil, as has been observed in marine environments and in clinical populations.

[Optimization and improvement of surgical indicators in the urology department of a regional hospital of the ministry of health of the Junta de Andalucía]

OBJECTIVES

To improve the rates of surgical activity and average waiting times for surgery, and to optimize the number of surgical indications in the Urology Department of a Regional Hospital.

METHODS

A study and analysis of the surgical activity and different indexes in 2014 was performed comparing the first half of the year and the second half after implementation of improvement measures.

STUDY VARIABLES

operating room occupancy rate, average hospital stay, cancellations, surgical complexity, average number of surgeries per operative room, average global waiting time and waiting time by 120 and 180 days guarantee decrees following the Junta de Andalucía standards.

RESULTS

In comparison with the first half of 2014, in the second half the operating room occupancy rate increased from 79% to 85%, the average stay decreased from 6 to 3 days, and a decrease in cancellations from 9% to 6% was observed. Moreover, a decrease in the mean waiting times was observed for surgeries subject to both the 120 days and 180 days guarantee decree and a decrease in the number of surgical indications in urology through the implementation of protocols based on clinical practice guidelines.

CONCLUSIONS

Despite the limitations of the study, and being a small Department in a district hospital, we observed that optimization of resources, implementation of protocols, and clinical pathways can improve and optimize different indicators of surgical activity.

Population mixing promotes arms race host-parasite coevolution

The consequences of host–parasite coevolution are highly contingent on the qualitative coevolutionary dynamics: whether selection fluctuates (fluctuating selection dynamic; FSD), or is directional towards increasing infectivity/resistance (arms race dynamic; ARD). Both genetics and ecology can play an important role in determining whether coevolution follows FSD or ARD, but the ecological conditions under which FSD shifts to ARD, and vice versa, are not well understood. The degree of population mixing is thought to increase host exposure to parasites, hence selecting for greater resistance and infectivity ranges, and we hypothesize this promotes ARD. We tested this by coevolving bacteria and viruses in soil microcosms and found that population mixing shifted bacteria–virus coevolution from FSD to ARD. A simple theoretical model produced qualitatively similar results, showing that mechanisms that increase host exposure to parasites tend to push dynamics towards ARD. The shift from FSD to ARD with increased population mixing may help to explain variation in coevolutionary dynamics between different host–parasite systems, and more specifically the observed discrepancies between laboratory and field bacteria–virus coevolutionary studies.

Expression Profile of Carotenoid Cleavage Dioxygenase Genes in Summer Squash (Cucurbita pepo L.)

Carotenoids are important dietary components that can be found in vegetable crops. The accumulation of these compounds in fruit and vegetables is altered by the activity of carotenoid cleavage dioxygenases (CCDs) enzymes that produce their degradation. The aim of this work was to study the possible implication of CCD genes in preventing carotenoid storage in the horticultural crop summer squash (Cucurbita pepo L.). The relationship between the presence of these compounds and gene expression for CCDs was studied in three varieties showing different peel and flesh colour. Expression analysis for the CCD genes CpNCED1, CpNCED2, CpNCED3, CpNCED9, CpCCD1, CpCCD4a, CpCCD4b and CpCCD8 was carried out on different organs and at several fruit developmental stages. The results showed that the CpCCD4a and CpCCD4b genes were highly expressed in the variety with lowest carotenoid content suggesting a putative role in carotenoid accumulation pattern in summer squash fruit.

The impact of resource availability on bacterial resistance to phages in soil

Resource availability can affect the coevolutionary dynamics between host and parasites, shaping communities and hence ecosystem function. A key finding from theoretical and in vitro studies is that host resistance evolves to greater levels with increased resources, but the relevance to natural communities is less clear. We took two complementary approaches to investigate the effect of resource availability on the evolution of bacterial resistance to phages in soil. First, we measured the resistance and infectivity of natural communities of soil bacteria and phage in the presence and absence of nutrient-providing plants. Second, we followed the real-time coevolution between defined bacteria and phage populations with resource availability manipulated by the addition or not of an artificial plant root exudate. Increased resource availability resulted in increases in bacterial resistance to phages, but without a concomitant increase in phage infectivity. These results suggest that phages may have a reduced impact on the control of bacterial densities and community composition in stable, high resource environments.

Determining the mineral composition in Cucurbita pepo fruit using near infrared reflectance spectroscopy

BACKGROUND

Efforts through conventional breeding to improve the mineral content in horticultural crops have not always been successful mainly due to the fact that standard analytical methods are both costly and time-consuming. We investigated the feasibility of applying near infrared reflectance spectroscopy (NIRS) to the estimation of essential mineral composition in the skin and flesh of summer squash fruits (Cucurbita pepo subsp. pepo) using a 200-sample set from diverse morphotypes.

RESULTS

The coefficients of determination in the external validation (R(2) VAL) obtained for the skin and flesh of the fruit were: total mineral content, 0.84 and 0.70; P, 0.74 and 0.62; K, 0.83 and 0.67; Ca, 0.57 and 0.60; Mg, 0.78 and 0.45; Fe, 0.78 and 0.65; Cu, 0.67 and 0.66; Mn, 0.67 and 0.64; Zn, 0.80 and 0.79 and Na, 0.33 and 0.33; respectively.

CONCLUSIONS

NIRS combined with different spectral transformations by modified partial least-squares (MPLS) regression has shown to be useful in determining the mineral composition of summer squash fruit, being a fast and low-cost analytical technique. Components such as chlorophyll, starch and lipids were used by MPLS for modelling the predicting equations. The promotion of micronutrient-rich summer squash varieties could have a significant long-term beneficial impact on the health of mineral deficient human populations.

Characterisation of nasal Staphylococcus delphini and Staphylococcus pseudintermedius isolates from healthy donkeys in Tunisia

REASONS FOR PERFORMING STUDY

Staphylococcus intermedius group (SIG) bacteria can colonise the nares of some animals but are also emerging pathogens in humans and animals.

OBJECTIVES

To analyse SIG nasal carriage in healthy donkeys destined for food consumption in Tunisia and to characterise recovered isolates.

METHODS

Nasal swabs from 100 healthy donkeys were tested for SIG recovery, and isolates were identified by biochemical and molecular methods. Antimicrobial susceptibility of isolates was tested and detection of antimicrobial resistance and virulence genes was performed. Isolates were typed at the clonal level by multilocus sequence typing and SmaI pulsed-field gel electrophoresis.

RESULTS

Staphylococcus delphini and Staphylococcus pseudintermedius (included in SIG) were obtained in 19% and 2% of the tested samples, respectively, and one isolate per sample was characterised. All isolates were meticillin susceptible and mecA negative. Most S. delphini and S. pseudintermedius isolates showed susceptibility to all antimicrobials tested, with the exception of 2 isolates resistant to tetracycline (tet(M) gene) or fusidic acid. The following toxin genes were identified (percentage of isolates): lukS-I (100%), lukF-I (9.5%), siet (100%), se-int (90%), seccanine (19%) and expA (9.5%). Thirteen different pulsed-field gel electrophoresis profiles were identified among the 21 SIG isolates. Additionally, the following 9 different sequence types (STs) were detected by multilocus sequence typing, 6 of them new: ST219 (6 isolates), ST12 (5 isolates), ST220 (3 isolates), ST13, ST50, ST193, ST196, ST218 and ST221 (one isolate each).

CONCLUSIONS

Staphylococcus delphini and S. pseudintermedius are common nasal colonisers of donkeys, generally susceptible to the antimicrobials tested; nevertheless, these SIG isolates contain virulence genes, including the recently described exfoliative gene (expA) and several enterotoxin genes, with potential implications for public health. This is the first description of S. delphini in Tunisia. The Summary is available in Chinese - see Supporting information.

Transcriptional and hormonal regulation of petal and stamen development by STAMENLESS, the tomato (Solanum lycopersicum L.) orthologue to the B-class APETALA3 gene

Four B-class MADS box genes specify petal and stamen organ identities in tomato. Several homeotic mutants affected in petal and stamen development were described in this model species, although the causal mutations have not been identified for most of them. In this study we characterized a strong stamenless mutant in the tomato Primabel cultivar (sl-Pr), which exhibited homeotic conversion of petals into sepals and stamens into carpels and we compared it with the stamenless mutant in the LA0269 accession (sl-LA0269). Genetic complementation analysis proved that both sl mutants were allelic. Sequencing revealed point mutations in the coding sequence of the Tomato APETALA3 (TAP3) gene of the sl-Pr genome, which lead to a truncated protein, whereas a chromosomal rearrangement in the TAP3 promoter was detected in the sl-LA0269 allele. Moreover, the floral phenotype of TAP3 antisense plants exhibited identical homeotic changes to sl mutants. These results demonstrate that SL is the tomato AP3 orthologue and that the mutant phenotype correlated to the SL silencing level. Expression analyses showed that the sl-Pr mutation does not affect the expression of other tomato B-class genes, although SL may repress the A-class gene MACROCALYX. A partial reversion of the sl phenotype by gibberellins, gene expression analysis, and hormone quantification in sl flowers revealed a role of phytohormones in flower development downstream of the SL gene. Together, our results indicated that petal and stamen identity in tomato depends on gene-hormone interactions, as mediated by the SL gene.

Genetic diversity and potential vectors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain

The genetic variability of a Cucurbit aphid-borne yellows virus (CABYV) (genus Polerovirus, family Luteoviridae) population was evaluated by determining the nucleotide sequences of two genomic regions of CABYV isolates collected in open-field melon and squash crops during three consecutive years in Murcia (southeastern Spain). A phylogenetic analysis showed the existence of two major clades. The sequences did not cluster according to host, year, or locality of collection, and nucleotide similarities among isolates were 97 to 100 and 94 to 97% within and between clades, respectively. The ratio of nonsynonymous to synonymous nucleotide substitutions reflected that all open reading frames have been under purifying selection. Estimates of the population's genetic diversity were of the same magnitude as those previously reported for other plant virus populations sampled at larger spatial and temporal scales, suggesting either the presence of CABYV in the surveyed area long before it was first described, multiple introductions, or a particularly rapid diversification. We also determined the full-length sequences of three isolates, identifying the occurrence and location of recombination events along the CABYV genome. Furthermore, our field surveys indicated that Aphis gossypii was the major vector species of CABYV and the most abundant aphid species colonizing melon fields in the Murcia (Spain) region. Our surveys also suggested the importance of the weed species Ecballium elaterium as an alternative host and potential virus reservoir.

Coevolution with phages does not influence the evolution of bacterial mutation rates in soil

Coevolution with phages drive the evolution of high bacterial mutation rates in vitro, but the relevance of this finding to natural populations is unclear. Here, we investigated how coevolution affects mutation rate evolution in soil, in the presence and absence of the rest of the natural microbial community. Although mutation rate on average increased threefold, neither coevolving phages nor the rest of natural community significantly affected mutation rates. Our results suggest that features of the soil over and above directly interacting organisms constrain the evolution of strong mutators, helping to explain their relatively low frequency compared with some laboratory and clinical settings.

Carotenogenic gene expression and carotenoid accumulation in three varieties of Cucurbita pepo during fruit development

The control of gene expression is a crucial regulatory mechanism in carotenoid accumulation of fruits and flowers. We investigated the role of transcriptional regulation of nine genes involved in the carotenoid biosynthesis pathway in three varieties of Cucurbita pepo with evident differences in fruit color. The transcriptional levels of the key genes involved in the carotenoid biosynthesis were higher in flower-, leaf-, and fruit skin tissues than flesh tissues. This correlated with higher concentration of carotenoid content in these tissues. The differential expression among the colored and white cultivars detected for some genes, such as LCYe, in combination with other regulatory mechanisms, could explain the large differences found in terms of carotenoid content among the three varieties. These results are a first step to elucidate carotenogenesis in C. pepo and demonstrate that, in general, regulation of the pathway genes is a critical factor that determines the accumulation of these compounds.

First detection of methicillin-resistant Staphylococcus aureus ST398 and Staphylococcus pseudintermedius ST68 from hospitalized equines in Spain

Eight coagulase-positive staphylococci from equines with different pathologies obtained between 2005 and 2011 were investigated. Isolates were characterized by different molecular techniques (spa-, agr-, MLST), and clonal relatedness of strains was investigated by ApaI and SmaI PFGE. Anti-microbial resistance and virulence profiles were determined. Six isolates were identified as Staphylococcus aureus, and two as Staphylococcus pseudintermedius. Of these, four isolates were methicillin-resistant S. aureus (MRSA) ST398 and one S. pseudintermedius was mecA positive and typed as ST68. One MRSA ST398 strain was isolated in 2005 and might be one of the earliest MRSA ST398 descriptions in Spain. All 5 mecA-positive strains were multidrug resistant and were isolated from hospitalized equines. Three MRSA ST398 strains carried the recently described transposon Tn559 within the chromosomal radC gene. The mecA-positive S. pseudintermedius ST68 strain was also multidrug resistant and harboured the erm(B)-Tn5405-like element. This ST68 strain presented a clear susceptible phenotype to oxacillin and cefoxitin regardless of the presence of an integral and conserved mecA gene and mecA promoter, which enhances the need for testing the presence of this gene in routine analysis to avoid treatment failures. These data reflect the extended anti-microbial resistance gene acquisition capacities of both bacterial species and evidence their pathogenic properties. The first detection of MRSA ST398 and S. pseudintermedius ST68 in horses in Spain is reported.

Homogeneous sonophotolysis of food processing industry wastewater: Study of synergistic effects, mineralization and toxicity removal

The mineralization of industrial wastewater coming from food industry using an emerging homogeneous sonophotolytic oxidation process was evaluated as an alternative to or a rapid pretreatment step for conventional anaerobic digestion with the aim of considerably reducing the total treatment time. At the selected operation conditions ([H(2)O(2)]=11,750ppm, pH=8, amplitude=50%, pulse length (cycles)=1), 60% of TOC is removed after 60min and 98% after 180min when treating an industrial effluent with 2114ppm of total organic carbon (TOC). This process removed completely the toxicity generated during storing or due to intermediate compounds. An important synergistic effect between sonolysis and photolysis (H(2)O(2)/UV) was observed. Thus the sonophotolysis (ultrasound/H(2)O(2)/UV) technique significantly increases TOC removal when compared with each individual process. Finally, a preliminary economical analysis confirms that the sono-photolysis with H(2)O(2) and pretreated water is a profitable system when compared with the same process without using ultrasound waves and with no pretreatment.

Real-time microbial adaptive diversification in soil

Bacteria undergo adaptive diversification over a matter of days in test tubes, but the relevance to natural populations remains unclear. Here, we report real-time adaptive diversification of the bacterium Pseudomonas fluorescens in its natural environment, soil. Crucially, adaptive diversification was much greater in the absence of the established natural microbial community, suggesting that resident diversity is likely to inhibit, rather than promote, adaptive radiations in natural environments. Rapid diversification is therefore likely to play an important role in the population and community dynamics of microbes in environments where resident communities are perturbed, such as by agriculture, pollution and antibiotics.

Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding

INTRODUCTION

Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent.

OBJECTIVE

To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA.

METHODOLOGY

Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification.

RESULTS

In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols.

CONCLUSION

Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue.