Abstract P6-04-05: Genotype-phenotype classification of triple negative breast cancers (TNBC) in women of African descent using the PAM50 NanoString platform and genomic data

Introduction: TNBC has the highest mortality rate amongst all other breast cancer types due to its complex tumor heterogeneity and lack of well-defined molecular targets. It is known that women of African descent are two to three times more likely to develop TNBC compared to women of European ancestry, yet wide-scale genomic studies of African and African American breast tumors are limited. To elucidate genotypes and molecular subtypes associated with the most aggressive forms of breast cancer, we used the PAM50 NanoString platform to reclassify Nigerian (NG), African American (AA) and Caucasian (CA) tumors previously annotated by Immunohistochemistry (IHC), and correlated our findings to their germline genotype data obtained using high-throughput technologies.

Methods: RNAs were isolated from formalin-fixed, paraffin embedded (FFPE) tumor tissues using the High Pure Paraffin Kit (Roche) following manufacturer's protocol, and assayed on NanoString nCounter Analysis System using a custom Nano110 (PAM50 + claudin-low & VEGF signatures) probe set. Intrinsic subtyping and gene-expression data were evaluated using R statistical software. All study samples were previously annotated and subtyped by the ER/PR/HER2 IHC classifier. Genotypes were obtained from next generation sequencing or Illumina Human2.5M BeadChip platform using germline DNA from more than 2000 breast cancer cases and 2000 controls were studied.

Results: To date, Intrinsic molecular subtyping by Nano110 has been completed on 69 NG, 81 AA and 74 CA tumors. Concordance between IHC and PAM50 was 59%, which is adequate and comparable to previous studies. Basal-like subtype was overrepresented and accounted for nearly 30% of NG and AA cases, compared to 17% in CA cases. HER2-enriched subtype was overrepresented only in NG cases (9%). The proportion with Luminal A tumors were 44% NG, 56% AA and 68% CA, respectively.

Conclusions: PAM50 NanoString assay is reliable and high-throughput for molecular subtyping breast cancer using RNA extracted from FFPE tumors. Ongoing work will correlate PAM50 intrinsic subtypes to genotype data.

Citation Format: Olayiwola OA, Ogundiran TO, Hardeman A, Yoshimatsu TF, Clayton W, Adeoye A, Ademola A, Ajani MA, Khramtsova G, Grushko TA, Huo D, Zheng Y, Parker J, Perou C, Olopade OI. Genotype-phenotype classification of triple negative breast cancers (TNBC) in women of African descent using the PAM50 NanoString platform and genomic data. [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 P6-04-05.

Abstract PD6-07: Genomic sequencing in metastatic breast cancer patients to inform clinical practice at the University of North Carolina at Chapel Hill

Background: An increasing number of molecularly-targeted therapies for metastatic breast cancer (MBC) are clinically-available (approved and investigational). These anti-cancer agents target specific molecular abnormalities such as mutated, amplified, deleted, or rearranged genes. Reporting of unique tumor genetic alterations is not included in routine clinical/diagnostic panels. In MBC, knowledge of mutational status may foster efficient transitions in clinical care and trial enrollment at disease progression. We describe the development and implementation of a clinically-integrated genomic sequencing program and report how information regarding targetable genomic aberrations in MBC patients (pts) is used to improve clinical practice in an academic setting.

Methods: Genomic sequencing of investigative biomarkers was prospectively offered to pts with MBC. DNA libraries were prepared separately from a retrieved archival FFPE tumor sample and a matched normal sample from each pt. Relevant targets were enriched by custom Agilent SureSelect hybrid capture baits using standard protocols. Samples were sequenced on Illumina HiSeq 2000/2500 platforms. Mutational findings were reviewed by a molecular tumor board (MTB); variants identified to be potentially actionable underwent confirmatory testing in a CLIA-approved laboratory. Confirmed findings were inserted into the pt's EMR accessible by both the pt and the treating oncologist.

Results: Of the 725 MBC pts seen at UNC since 1/1/2012, 194 (27%) contributed samples for genomic sequencing. Of those whose tumors were sequenced, average age at MBC diagnosis was 54 (25 - 91); 73% were Caucasian, 16% African American. De novo MBC accounted for 39 (20%) sequenced pts. Of sequenced patients, sites of metastatic disease included bone only (7%), visceral only (46%), and both bone and visceral (47%). Approximately 1/3 of pts were consented for sequencing at time of initial MBC diagnosis, 1/4 after 1st line therapy for MBC, and the remaining at or beyond their 2nd line. In total, 131 (68%) pts have sequencing results available of which 43% of pts had reportable mutations deemed actionable by the MTB. Specific mutations and observed frequency by subtype are shown below. Pts (19%) whose tumors were sequenced were more commonly enrolled in a therapeutic clinical trial for MBC, a higher rate than seen in the non-sequenced group (7%) (p<0.001). To date, 27% of pts' tumors harbored an alteration that is an eligibility requirement for a molecularly-targeted therapeutic trial accruing pts at UNC.

Observed Mutation by Clinical Subype Genes Total # (56 pts)HR+/HER2- (25 pts)HER2+ (13 pts)TNBC (18pts)PIK3CA15933TP5315456CCND19531NF-14103FGFR13300PTEN3012KRAS2011MDM22110PIK3R12002ROS12011TSC12011Other*14518TOTAL73281728*Mutations observed only once

Conclusion: Preemptive genomic sequencing can be integrated into the clinical and operational practice of a comprehensive cancer center. Currently this research tool and program provides valuable information that has the potential to foster both clinical trial eligibility and/or enrollment. With longer follow-up, we hope such an approach ultimately will improve patient outcomes.

Citation Format: Grilley-Olsen J, Keith KC, Hayward M, Dees EC, Deal A, Ivanova A, Benbow JM, Parker J, Patel NM, Eberhard D, Mieczkowski P, Weck KE, Hayes DN, Muss H, Jolly T, Reeder-Hayes K, Earp HS, Sharpless N, Carey L, Anders CK. Genomic sequencing in metastatic breast cancer patients to inform clinical practice at the University of North Carolina at Chapel Hill. [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 PD6-07.

Bacterial filtration efficiency of green soy protein based nanofiber air filter

High bacterial filtration efficiency (BFE) filters, based on nanofibers derived from blends of grain proteins and poly-ethylene-oxide (PEO), were produced by an electrospinning process. Specifically, polymer blends consisting of purified soy flour/PEO with a ratio of 7/3 were spun into nanofibers and characterized. A new laboratory based experimental apparatus for testing BFE was designed and used to test BFE of bacterial aerosols consisting of Escherichia coli (E. coli). Performances of soy protein based nanofiber filters with nanofiber mass varying from 1 to 5 g/m2 as well as a nanofiber filters prepared from pure PEO were compared. The results showed that BFE values for filters containing 5 g/m2 protein based nanofibers and PEO nanofiber filter were 100 and 81.5%, respectively. The results also indicated that the BFE increased as the protein content in the nanofiber filter increased. These novel protein based nanofiber filters have demonstrated a clear potential for effective removal and retention of E. coli bacteria during air-filtration. These filters can be effectively deployed in environments such as hospitals and senior residential areas to reduce bacterial infections.

Systematic review and meta-analysis of enhanced recovery programmes in surgical patients

BACKGROUND

Enhanced recovery programmes (ERPs) have been developed over the past 10 years to improve patient outcomes and to accelerate recovery after surgery. The existing literature focuses on specific specialties, mainly colorectal surgery. The aim of this review was to investigate whether the effect of ERPs on patient outcomes varies across surgical specialties or with the design of individual programmes.

METHODS

MEDLINE, Embase, CINAHL and the Cochrane Central Register of Controlled Trials were searched from inception to January 2013 for randomized or quasi-randomized trials comparing ERPs with standard care in adult elective surgical patients.

RESULTS

Thirty-eight trials were included in the review, with a total of 5099 participants. Study design and quality was poor. Meta-analyses showed that ERPs reduced the primary length of stay (standardized mean difference -1·14 (95 per cent confidence interval -1·45 to -0·85)) and reduced the risk of all complications within 30 days (risk ratio (RR) 0·71, 95 per cent c.i. 0·60 to 0·86). There was no evidence of a reduction in mortality (RR 0·69, 95 per cent c.i. 0·34 to 1·39), major complications (RR 0·95, 0·69 to 1·31) or readmission rates (RR 0·96, 0·59 to 1·58). The impact of ERPs was similar across specialties and there was no consistent evidence that elements included within ERPs affected patient outcomes.

CONCLUSION

ERPs are effective in reducing length of hospital stay and overall complication rates across surgical specialties. It was not possible to identify individual components that improved outcome. Qualitative synthesis may be more appropriate to investigate the determinants of success.

Behavioural response of wheat bulb fly (Delia coarctata, Diptera: Anthomyiidae) larvae to the primary plant metabolite carbon dioxide

Wheat bulb fly (WBF) larvae use chemotaxis to orientate towards host-plant root exudates. This study aimed to investigate the role of the primary plant metabolite carbon dioxide (CO2) in host-plant location by WBF. Arena based behavioural experiments were used to identify whether CO2 induced chemotaxis (directional movement in response to a chemical stimulus) or kinesis (non-directional movement in response to a stimulus) from WBF larvae. No chemotactic response was observed when larvae were presented to a point source of CO2. However, elevated levels of CO2 induced kinesis, with both track length and tortuosity (number of twists and turns in the movement path) increasing at elevated CO2 levels of 1000-2000 ppm, demonstrating increased searching behaviour. Soil emission of CO2 was quantified to compare soil levels with those identified as eliciting behavioural effects on the larvae. Samples removed from soil gave a mean CO2 concentration of 557 (±46) ppm, which is lower than the lowest concentration of CO2 found to induce a behavioural response and higher than the lowest CO2 concentration tested, which was found not to alter behaviour. It is proposed that increased CO2 concentrations in the soil act as a behavioural trigger, inducing intensive searching of an area by WBF larvae. This increases the likelihood of finding more host-specific identifiers, such as secondary metabolites when near a potential host-plant.