Current challenges and future of agricultural genomes to phenomes in the USA

Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in genome to phenome (G2P) research is the focus of this paper. Previously (Genome Biol, 23(1):1-11, 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome to phenome (AG2P) work and envision the future of the AG2P field. The topic summaries composing this paper are distilled from two 1.5-h small group discussions. Challenges and solutions identified across multiple topics at the workshop were explored. We end our discussion with a vision for the future of agricultural progress, identifying two areas of innovation needed: (1) innovate in genetic improvement methods development and evaluation and (2) innovate in agricultural research processes to solve societal problems. To address these needs, we then provide six specific goals that we recommend be implemented immediately in support of advancing AG2P research.

Colorectal two-week wait service and quantitative FIT: it's not just about colon cancer

INTRODUCTION

The aim of this study was to assess faecal immunochemical test (FIT) negativity in terms of its effect on cancer risk in the local symptomatic two-week wait (2WW) population. FIT was introduced to the colorectal 2WW pathway at the start of the pandemic. This study analyses the FIT-negative (<10µg Hb/g) cohort and calculates the relative risk and odds ratio associated with a negative FIT test.

METHODS

FIT tests were sent to symptomatic 2WW patients without rectal bleeding, iron-deficient anaemia or palpable mass. Where FIT was <10µg Hb/g investigations were moved to a radiology protocol.

RESULTS

The test return rate was 91% with a FIT-negative (<10µg Hb/g) rate of 82%. The FIT-negative group in the symptomatic referral pathway in Cornwall have a low (1.4%) risk of colon cancer but a significant risk (6.6%) when all cancer types are considered. The impact of a negative quantitative FIT changes the odds ratio of a patient having a luminal cancer by 0.26. The odds ratio for 'all cancer' risk was affected by 0.83.

CONCLUSION

A negative FIT test within the local NG12 symptomatic patient group signifies a low risk of colon cancer and identifies patients who can be initially investigated with cross-sectional imaging. However, when all cancer types are considered, cancer prevalence in this group remains above 6%. In relative risk terms a negative FIT represents a small change in overall risk and this patient group still qualify for investigation through 2WW pathways.

Pre-clerkship physical examination assessment rubric

INTRODUCTION

The physical examination is a core competency in the training of pre-clerkship medical students. It is important to certify proficiency in the physical examination before students start their clinical rotations. Many institutions use home grown assessment tools for this purpose; however, there currently are no validated rubrics designed to assess the performance a head to toe physical examination by a pre-clerkship medical student. The goal of this study is to assess the reliability (inter-rater and intra-rater) of our institutionally developed rubric.

METHODS

Clinical faculty with various levels of teaching experience watched videos of students doing a head to toe physical examination and scored the students using our assessment rubric. These scores were evaluated for intra-rater and inter-rater reliability.

RESULTS

A total of 15 student videos were reviewed by five faculty members with varying levels of teaching experience. The degree of inter-rater agreement (between raters) for single and average measure was excellent and the degree of intra-rater agreement (same rater twice) for single and average measure was excellent.

DISCUSSION

We conclude that our institutionally developed physical examination assessment rubric is a reliable means to certify proficiency in the physical examination before students start their clinical clerkships.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

FRI0611-HPR EUROPEAN PRESCRIBERS’ PERSPECTIVES ON BIOSIMILARS

Background:

Biosimilars are highly similar, but not identical to originator biologics. In an increasingly resource-constrained environment, switching patients from originator biologics to biosimilars is a growing practice in many jurisdictions. Though automatic substitution of originator biologics with biosimilars is rare in Europe, this practice excludes physicians from decisions regarding the treatment of their patients.

Objectives:

As countries seek to control health costs and expand access to biologic therapies, building physician confidence in biosimilars is critical to promoting their use and reaping the cost benefits. This survey will empirically document their perspectives on biologic substitution. These findings may serve as a resource for countries in developing biosimilar policies which build physician confidence in biosimilars.

Methods:

The Alliance for Safe Biologic Medicines (ASBM) commissioned 15-minute web-based surveys among biologic prescribers in 6 Western European countries. Respondents must prescribe biologic medicines, must practice in France, Germany, Italy, Spain, Switzerland, or United Kingdom, must specialize in one of 10 practice areas: Dermatology, Endocrinology, Gastroenterology, Hematology Oncology, Immunology, Nephrology, Neurology, Oncology, Ophthalmology, Rheumatology. This survey is a refresh of one conducted in 2013 (n=470) available atwww.safebiologics.org/surveys.

Results:

579 responses were received, 14% from Rheumatologists (n=80). Biosimilar familiarity was high, increasing from 76% to 90% from the 2013 survey; with Rheumatologists the most familiar (99%). Similarly, the % of physicians who felt sole treatment decision authority was very important or critical had increased from 72% to 82%; among Rheumatologists again this figure was higher (85%). This pattern was found across many questions, for example the importance of retaining authority to prevent a substitution (a jump from 74% in 2013 to 84% in 2019 saying “very important or critical”, with Rheumatologists higher than average at 90%). Rheumatologists had a higher than average comfort level prescribing biosimilars to new patients, but were the least comfortable with a third party switching their patient for non-medical reasons (e.g. cost): 49% were “very uncomfortable” compared to an average of 29% across specialties.

Conclusion:

European physicians have increased their familiarity with biosimilars since 2013, with Rheumatologists the practice area with greatest familiarity. After 13 years of experience with biosimilars, Europe’s prescribers consider maintaining physician control of treatment decisions to be highly and increasingly important; Remain uncomfortable with switching a patient to a biosimilar for non-medical reasons; Are highly (and increasingly) uncomfortable with a non-medical substitution performed by a third party. When looking specifically at Rheumatologists, these trends are even more pronounced.

Disclosure of Interests:

Michael Reilly Grant/research support from: The organization of which I am executive director (ASBM) has received general grants from pharmaceutical companies., Madelaine Feldman: None declared

An Old Disease With an Unfamiliar Face: A Case Report of Ocular Syphilis

Syphilis is an infection caused by the bacterium Treponema pallidum. Patients with syphilis can present with a wide range of symptoms depending on the stage of disease. An underappreciated manifestation of syphilis is ocular involvement, which has been increasingly reported in the last several years. Delay in diagnosis and treatment of ocular syphilis can increase the risk of irreversible vision loss. Syphilis can affect almost every structure in the eye; however, most commonly presents with panuveitis. Ocular syphilis is treated similarly to neurosyphilis with prompt initiation of intravenous penicillin G.

Differences in medical student self-evaluations of clinical and professional skills

BACKGROUND

The skill of self-assessment is critical to medical students. We sought to determine whether there were differences between student self-assessments and their faculty assessments and if they were modified by gender. Additionally, we sought to determine the differences in these assessments between students in a traditional (core) versus an enhanced (SELECT) medical school curriculum.

METHODS

In this retrospective study, mid-term and final assessment and feedback forms from the first-year Doctoring 1 course were analyzed from three academic years: 2014-2015 through 2016-2017. Data were abstracted from the forms and de-identified for analysis. Class year, student gender, and class type were also abstracted from this "on the shelf" data from program assessment. The level of agreement between faculty and student assessments was investigated using Wilcoxon signed ranks test. The gender differences (male versus female students) between student assessments and their assessment by their faculty were investigated by using the Kruskal Wallis test.

RESULTS

Five hundred and thirty-five student self-assessments were analyzed. Fifty-six percent (301/535) were male while 44% (234/535) were female. Faculty assessments (P-value <0.001) were higher than students and this was not modified by student gender. Compared to the domain of "participation" in the core program, there was no difference between the student/faculty ratings based on student gender (P-value: 0.48); there was a difference in the SELECT program cohort (P-value: 0.02). Specifically, the female students appear to rate themselves lower (female student: mean/standard deviation: 2.07/0.52) compared to their faculty (faculty: mean/standard deviation: 2.42/0.55).

CONCLUSION

Faculty consistently assessed the students at a higher rating than the students rated themselves. The level of difference between student self-assessments and their assessment by their faculty was not modified by student gender. With the minor exception of "participation," there was no difference between students in the two different doctoring class curriculums.

Use of cell phone type cameras to enhance focusing and magnification in optical microscopes

Cameras with auto-focusing and zoom capability, such as those in cell phones, can simplify focusing a microscope and at the same time provide a wide range of magnification.

Abstract P2-07-03: Refining neoadjuvant predictors of three year distant metastasis free survival: Integrating volume change as measured by MRI with residual cancer burden

Background: Patients achieving a pathologic complete response (pCR) following neoadjuvant therapy have significantly improved event-free survival relative to those who do not; and pCR is an FDA-accepted endpoint to support accelerated approval of novel agents/combinations in the neoadjuvant treatment of high risk early stage breast cancer. Previous studies have shown that recurrence risk increased with increasing burden of residual disease (as assessed by the RCB index). As well, these studies suggest that patients with minimum residual disease (RCB-I class) also have favorable outcomes (comparable to those achieving a pCR) within high risk tumor subtypes. In this study, we assess whether integrating RCB with MRI functional tumor volume (FTV), which in itself is prognostic, can improve prediction of distant recurrence free survival (DRFS); and identify a subset of patients with minimal residual disease with comparable DRFS as those who achieved a pCR. Imaging tools can then be used to identify the subset that will do well early and guide the timing of surgical therapy.

Method: We performed a pooled analysis of 596 patients from the I-SPY2 TRIAL with RCB, pre-surgical MRI FTV data and known follow-up (median 2.5 years). We first assessed whether FTV predicts residual disease (pCR or pCR/RCB-I) using ROC analysis. We applied a power transformation to normalize the pre-surgical FTV distribution; and assessed its association with DRFS using a bi-variate Cox proportional hazard model adjusting for HR/HER2 subtype. We also fitted a bivariate Cox model of RCB index adjusting for subtype; and assessed whether adding pre-surgical FTV to this model further improves association with DRFS using a likelihood ratio (LR) test. For the Cox modeling, penalized splines approximation of the transformed FTV and RCB index with 2 degrees of freedom was used to allow for non-linear effects of FTV and RCB on DRFS.

Result: Pre-surgical MRI FTV is significantly associated with DRFS (Wald p&lt;0.00001), and more effective at predicting pCR/RCB-I than predicting pCR alone (AUC: 0.72 vs. 0.65). Larger pre-surgical FTV remains associated with worse DRFS adjusting for subtype (Wald p &lt;0.00001). The RCB index is also significantly associated with DRFS adjusting for subtype (Wald p&lt;0.00001). Adding FTV to a model containing RCB and subtype further improves association with DRFS (LR p=0.0007). RCB-I patients have excellent DRFS (94% at 3 years compared to 95% in the pCR group). Efforts are underway to identify an optimal threshold for dichotomizing pre-surgical FTV and FTV change measures for use in combination with pCR/RCB-I class to generate integrated RCB (iRCB) groups as a composite predictor of DRFS.

Conclusion: Pre-surgical MRI FTV is effective at predicting minimal residual disease (RCB0/I) in the I-SPY 2 TRIAL. Despite the association between FTV and RCB, FTV appears to provide independent added prognostic value (to RCB and subtype), suggesting that integrating MRI volume measures and RCB into a composite predictor may improve DRFS prediction.

Citation Format: Hylton NM, Symmans WF, Yau C, Li W, Hatzis C, Isaacs C, Albain KS, Chen Y-Y, Krings G, Wei S, Harada S, Datnow B, Fadare O, Klein M, Pambuccian S, Chen B, Adamson K, Sams S, Mhawech-Fauceglia P, Magliocco A, Feldman M, Rendi M, Sattar H, Zeck J, Ocal I, Tawfik O, Grasso LeBeau L, Sahoo S, Vinh T, Yang S, Adams A, Chien AJ, Ferero-Torres A, Stringer-Reasor E, Wallace A, Boughey JC, Ellis ED, Elias AD, Lang JE, Lu J, Han HS, Clark AS, Korde L, Nanda R, Northfelt DW, Khan QJ, Viscusi RK, Euhus DM, Edmiston KK, Chui SY, Kemmer K, Wood WC, Park JW, Liu MC, Olopade O, Tripathy D, Moulder SL, Rugo HS, Schwab R, Lo S, Helsten T, Beckwith H, Haugen PK, van't Veer LJ, Perlmutter J, Melisko ME, Wilson A, Peterson G, Asare AL, Buxton MB, Paoloni M, Clennell JL, Hirst GL, Singhrao R, Steeg K, Matthews JB, Sanil A, Berry SM, Abe H, Wolverton D, Crane EP, Ward KA, Nelson M, Niell BL, Oh K, Brandt KR, Bang DH, Ojeda-Fournier H, Eghtedari M, Sheth PA, Bernreuter WK, Umphrey H, Rosen MA, Dogan B, Yang W, Joe B, I-SPY 2 TRIAL Consortium, Yee D, Pusztai L, DeMichele A, Asare SM, Berry DA, Esserman LJ. Refining neoadjuvant predictors of three year distant metastasis free survival: Integrating volume change as measured by MRI with residual cancer burden [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-03.

Abstract P4-09-11: Computer extracted features of tumor grade from H&E images predict oncotype DX risk categories for early stage ER+ breast cancer

Introduction: The ODx test is a 21 gene assay that is currently employed for separating Estrogen Receptor positive (ER+) breast cancer patients into low (L) and high (H) risk of recurrence categories, helping clinicians decide if adjuvant chemotherapy is appropriate. In this study, we sought to explore whether computer extracted features pertaining to tumor grade (nuclear pleomorphism, tubule count, mitotic index) in conjunction with a machine learning classifier were predictive of the corresponding ODx risk category for ER+ breast cancer patients.

Design: First, 2000x2000 pixel sub-regions of digitized H&E slides at 40x are processed to both identify and segment epithelial and stromal nuclei using a combination of watershed and deep learning (DL). 247 nuclear features consisting of architecture, shape, and texture features were extracted from these segmentations. Subsequently, the mitotic and tubule related features were extracted at each nuclei candidate using DL detectors. The input to this process was a binary mask computed by thresholding a blue ratio transformed image using Otsu's method. The identified regions were analyzed using DL to determine if a nucleus is a part of a tubule, and/or if it is mitotic. Finally, all of these features were combined, evaluated using Ranksum feature ranking, and then used to generate predictive models using four different supervised machine learning classifiers - random forest, support vector machine, linear discriminant analysis, and a neural network – via a 3-fold cross validation scheme. The classifiers were evaluated by their ability to distinguish between the four different classification tasks presented above using the area (AUC) under the Receiver Operating Characteristic (ROC) curve: 1) L ODx and L mBR grade vs. H ODx and H mBR grade (L-L vs. H-H), 2) L ODx vs. H ODx, 3) L ODx vs. Intermediate (T) and H ODx, 4) L and T ODx vs. H ODx.

Results: The highest performing features were consistently mitosis, epithelial architectural, and tubule features. Classification accuracy ranged from 0.61 (L vs. T and H) to 0.97 (L-L vs. H-H) (Table 1). These features were able to provide the highest level of classification utility for the most distinct cases (L-L vs. H-H) and had less classification accuracy with classification problems involving more difficult T cases.

  Number top 10 Features in each categoryNumber top 10 Features in each categoryNumber top 10 Features in each categoryExperimentMax AUCMitosisTubuleEpithelial ArchitectureL-L vs. H-H (N=36)0.97315L vs. H (N=72)0.77505L vs. T and H (N=125)0.61208L and T vs. H (N=125)0.75505Table 1: Maximum AUC, and best features used to obtain those results.

Conclusion: Computer derived features pertaining to nuclear architecture and mitotic index were predictive of ODx risk categories. Additional independent validation of these findings is needed in a separate test set.

Citation Format: Whitney JR, Romeo-Bucheli D, Janowczyk A, Ganesan S, Feldman M, Gilmore H, Madabhushi A. Computer extracted features of tumor grade from H&E images predict oncotype DX risk categories for early stage ER+ breast cancer [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 P4-09-11.

Abstract OT2-06-03: METAMORPH: METAstatic markers of recurrent tumor PHenotype for breast cancer

Up to 30% of patients diagnosed with breast cancer will develop recurrent disease within their lifetime, and currently this form of the disease is incurable. There are unmet needs to better understand underlying metastatic biology, identify new therapeutic targets and develop better methods for monitoring changes in disease, both to monitor response and elucidate resistance mechanisms. To address these needs, the METAMORPH Study encompasses a comprehensive approach that combines serial molecular tissue profiling at the RNA and DNA level with circulating markers (DTCs, CTCs, plasma tumor DNA), and ongoing assessment of therapeutic response.

METAMORPH is a prospective cohort study of women with suspected or confirmed recurrent breast cancer and accessible tumor by standard clinical biopsy, who are enrolled at the University of Pennsylvania prior to starting a new therapy for recurrent metastatic disease. The aims of this trial are to (1) evaluate the mechanisms through which recurrent breast cancer are genetically distinct from the primary tumor, (2) evaluate the circulating tumor biomarker trajectory of recurrent disease, (3) elucidate “escape pathways” of progressing tumors that emerge during the selective pressure of therapy, and (4) explore clinical utility of tumor and blood testing. The study protocol integrates research aims into clinical care, including a standardized approach to disease assessment and biopsy, pathologic confirmation of histology and receptor subtype, panel-based CLIA-approved genomic profiling, collection of research specimens, and standardized reporting of results, which are returned to patients and physicians. Patients are followed for treatment and outcome, and serial samples are collected at progression. A companion protocol, COMET, provides education about genomic testing and assesses patient understanding and impact of results. To date, 155 patients have enrolled, 142 (92%) have been biopsied, 120 (77%) have had sufficient DNA for molecular profiling and 109 (70%) have had genomic panel testing. Accrual is ongoing, with an initial target of 300 patients. Multiple sites within the UPHS Health System are enrolling. Contact information: angela.demichele@uphs.upenn.edu.

Key words: Metastatic disease, tumor profiling.

Citation Format: DeMichele A, Soucier-Ernst DJ, Clark C, Shih N, Stavropoulos W, Maxwell KN, Feldman M, Lierbamen D, Morrissette JJD, Paul MR, Pan T-C, Wang J, Belka GK, Chen Y, Yee S, Carpenter E, Fox K, Matro J, Clark A, Shah P, Domchek S, Bradbury A, Chodosh L. METAMORPH: METAstatic markers of recurrent tumor PHenotype for breast cancer [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 OT2-06-03.

Abstract PD8-04: Evolutionary history and genomic landscape of metastatic breast cancer

Background: The majority of deaths from breast cancer are due to distant metastatic disease. Despite this, few systematic genomic analyses have been performed on metastatic tumors. This results from the relative difficulty of performing biopsies on metastatic tumors, as well as the uncertainty regarding genomic determinism, according to which the majority of actionable mutations present in metastases can be discovered in the primary tumor.

Methods: “METAMORPH” is an ongoing prospective cohort study of women with suspected or confirmed recurrent breast cancer enrolled prior to starting a new therapy for recurrent metastatic disease. Biopsies of metastatic lesions were performed under radiologic guidance, and archival primary tumors were subsequently obtained. WES and sWGS were performed to determine coding mutations and aberrant copy-number in metastatic tumors from 67 patients, 33 of which were assayed with corresponding matched primary tumors.

Results: Using Bayesian approaches, we find that cancers fit one of two patterns: canonical linear evolution (whereby the metastatic tumor arises from one or more advanced primary tumor subclones) vs. branched evolution (whereby both primary and metastatic tumors develop mutations that go on to become clonal within their respective tumors after the time of dissemination). In cases where tumors show evidence of branched evolution or small subclone dissemination, we expect that a large proportion of mutations may not be represented in both the primary and corresponding metastatic tumors. Indeed, primary-metastatic tumor pairs show substantial discordance at the genomic level, sharing only ˜30% of mutations and ˜28% of copy-number alterations on average. Furthermore, we find that metastatic tumors have decreased clonal heterogeneity, suggesting a history of selection. Indeed, we find clinically relevant mutations that are present exclusively in the primary or the corresponding recurrent metastatic tumor, as well as genes that are recurrently altered in metastatic tumors, such as amplification of SRC-1, loss of genes encoding CDK inhibitors, and alterations in JAK1/2/3.Finally, compared to the primary tumors from which they arose, metastatic tumors exhibit increased frequencies of alterations in several discrete pathways, including those involving the extracellular matrix as well as PI3K/AKT/mTOR, estrogen, and HER2 signaling.

Conclusions: The low degree of genomic concordance between primary and metastatic tumors due to evolutionary distance, as well as the presence of activating and targetable mutations specifically in metastatic tumors, suggests that there is value in comprehensively characterizing metastatic tumors to inform patient treatment and identify novel targets underlying breast cancer progression.

Citation Format: Paul MR, Pan T-C, Pant D, Belka GK, Chen Y, Shih N, Lieberman D, Morrissette JJD, Soucier-Ernst D, Clark C, Stavropoulos W, Maxwell K, Feldman M, DeMichele A, Chodosh LA. Evolutionary history and genomic landscape of metastatic breast cancer [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 PD8-04.

Characterization of non-dialyzable constituents from cranberry juice that inhibit adhesion, co-aggregation and biofilm formation by oral bacteria

An extract prepared from cranberry juice by dialysis known as nondialyzable material (NDM) has been shown previously to possess anti-adhesion activity toward microbial species including oral bacteria, uropathogenic Escherichia coli and Helicobacter pylori. Bioassay-guided fractionation of cranberry NDM was therefore undertaken to identify the anti-adhesive constituents. An aqueous acetone-soluble fraction (NDMac) obtained from Sephadex LH-20 inhibited adhesion-linked activities by oral bacteria, including co-aggregation of oral bacteria Fusobacterium nucleatum with Streptococcus sanguinis or Porphyromonas gingivalis, and biofilm formation by Streptococcus mutans. Analysis of NDMac and subsequent subfractions by MALDI-TOF MS and ¹H NMR revealed the presence of A-type proanthocyanidin oligomers (PACs) of 3-6 degrees of polymerization composed of (epi)catechin units, with some (epi)gallocatechin and anthocyanin units also present, as well as quercetin derivatives. Subfractions containing putative xyloglucans in addition to the mixed polyphenols also inhibit biofilm formation by S. mutans (MIC = 125-250 μg mL^-1). These studies suggest that the anti-adhesion activities of cranberry NDM on oral bacteria may arise from a combination of mixed polyphenol and non-polyphenol constituents.

Abstract P2-08-03: Targeting inflammatory pathways: A phase 2 trial of the JAK-inhibitor ruxolitinib in combination with exemestane for aromatase inhibitor-resistant, estrogen receptor-positive breast cancer

Background: In vitro mechanisms link IL-6 to poor outcome in breast cancer via inflammatory pathways, activated JAK/STAT tumor signaling and upregulation of aromatase, leading to an aggressive tumor phenotype. Epidemiological data from our group and others support these mechanisms in women with ER-positive (+) disease. We therefore hypothesized that the JAK inhibitor, ruxolitinib (RUX, INCB018424; Incyte), would enhance activity of exemestane (EXE) in women with ER+ breast cancer who relapsed after non-steroidal aromatase inhibitor therapy, particularly among carriers of a germ-line polymorphism in IL-6, conferring elevated levels of IL-6 in the tumor microenvironment.

Methods: The “JAKEE trial” is a phase II trial to determine the safety and efficacy of RUX + EXE in postmenopausal women with relapsed, ER+ advanced breast cancer. Eligible patients were required to have progressed on a non-steroidal AI and either measureable or bone-only disease. CRP, a putative biomarker of tumor microenvironment inflammation, was measured at baseline and serially during treatment. Using a Simon 2-stage design, we treated 15 patients with RUX at 25 mg BID and EXE at 25mg daily on a continuous 28-day schedule. First stage results were previously presented (AACR, 2014). Accrual proceeded to second stage after no patient met the pre-defined stopping rule of grade (G) 3/4 toxicity requiring discontinuation from the study within the first treatment cycle. Due to the substantial rate of anemia requiring dose reductions, however, RUX dose was reduced to 15 mg BID in second stage.

Results: A total of 25 patients were enrolled; 24/25 had progressed on AI in metastatic setting; 1 relapsed on adjuvant AI. RUX+EXE was well-tolerated overall, with only 2 G4 events (creatinine elevation, hepatic failure); both were due to disease progression. 16% had G3 fatigue, anemia or hypertension; 12% had G3 neutropenia or depression. Other lower grade toxicities in &gt;20% included musculoskeletal pain, increased ALT, and headache. Overall, patients stayed on therapy for a median of 3 cycles (range 2 – 21). There were no CR or PR, but 6/25 (24%) had prolonged disease control (SD&gt; 6 months). Median CRP at study entry was 6.4 (range 0.3-38.9), with 8/25 (32%) having CRP&gt;10. Achieving SD&gt;6 months was not associated with baseline CRP (CRP&gt;10 in 32% with vs. 33% without SD&gt;6 months, p(exact)=1.0). A novel pharmacodynamic assay to assess STAT3 phosphorylation in peripheral blood mononuclear cells after RUX exposure demonstrated differential effects in patients with response.

Conclusions: Targeting JAK/STAT signaling in AI-resistant breast cancer with RUX+EXE was safe and well-tolerated. 24% of patients had prolonged SD, but baseline CRP level did not predict response. Correlative studies to determine whether host and/or tumor biomarkers predict response to therapy, including germline IL-6 genotype, immune profiles, p-STAT3 and estradiol levels, are currently underway.

Citation Format: DeMichele AM, Clark AS, Holmes R, Volpe M, Medrano C, Troxel A, Fox K, Domchek S, Matro J, Bradbury A, Shih N, Feldman M, Hexner E, Bromberg J. Targeting inflammatory pathways: A phase 2 trial of the JAK-inhibitor ruxolitinib in combination with exemestane for aromatase inhibitor-resistant, estrogen receptor-positive breast cancer [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 P2-08-03.

Unilateral retinitis pigmentosa. A case report

CLINICAL CASE

A 27-year-old woman with a history of nyctalopia and constriction of visual field of the right eye. The ophthalmological examination showed a visual field and electroretinogram that were compatible with unilateral retinitis pigmentosa (RP). After a one year follow-up, the unilateral condition remained.

DISCUSSION

Unilateral retinitis pigmentosa is a rare condition, with a frequency between 0.2%-5% of the RP. It mainly affects women and older age groups than bilateral RP. For a definitive diagnosis, it is necessary to have a funduscopy and electroretinogram (ERG) altered unilaterally, and exclude infectious, inflammatory, and vascular causes.

Grasses suppress shoot-borne roots to conserve water during drought

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Abstract P6-13-08: Palbociclib and paclitaxel on an alternating schedule for advanced breast cancer: Results of a phase Ib trial

Background: Palbociclib (P) is an oral CDK 4/6 inhibitor (CDKi) that was recently FDA approved in combination with endocrine therapy for metastatic breast cancer. We have performed a Phase I trial of P in combination with paclitaxel (T) based on preclinical studies suggesting that P synergizes with T when given on an alternating schedule, enabling cell cycle synchronization in tumor cells. We now present the dose expansion cohort.

Methods: Patients (Pts) enrolled on the trial had Rb-expressing tumors of any estrogen/progesterone/HER2 receptor type, adequate organ function, and ≤3 prior chemotherapy regimens for metastatic breast cancer (mBC). Prior adjuvant or metastatic taxane was allowed. Dose escalation led to expansion at P100mg or 75mg, starting with 3 days of P (run-in) and reduction of P dosing from 5-day to 3-day intervals (days 2-4, 9-11, 16-18 of each 28 day cycle). T at 80mg/m2 was given weekly for 3 cycles; thereafter, T was administered days 1, 8 and 15 of 28 day cycle. Weekly toxicity assessments were performed; RECIST 1.0 response was assessed every 2 cycles as partial response (PR), stable disease (SD) or progressive disease (PD). Pts had the option to discontinue T and continue on P alone (3 on/1 off schedule) if they attained SD after cycle 6.

Results: 27 pts enrolled on study (15- dose escalation, 12- dose expansion). Results are shown in the Table. 21 pts had received prior taxane; pts had received a median of 2 chemotherapy regimens for mBC. DLTs were grade 3 AST/ALT (n=1, at 125 mg) and febrile neutropenia (FN) (n=1, at 100 mg). Uncomplicated grade 3/4 NTP was common and frequently led to dose reduction or dose interruption during the first cycle of therapy. Frequency of NTP did not change with reducing the days of P. Among 24 evaluable patients, 14 (58%), had PR or SD ≥ 6 months across all dose levels. Of 14 pts who responded, 10 (71%) had received prior taxane. 20 pts are off study; 19 for PD, and 2 for toxicity (NTP in cycle 17 and FN in cycle 1); 7 pts remain on study. Prolonged tumor responses were seen.

Conclusions: P and T can be safely combined on an alternating dosing schedule; the optimal combination dose is 75 mg of P and 80mg/m2 of weekly T. The high response rate warrants a randomized trial to determine the incremental benefit over T alone. Additional mechanistic studies are in progress to understand the in vivo effects of the alternating dosing schedule on cell cycle activity and tumor proliferation.

Starting Dose Level P (mg)Number (Total 27)DLTGrade 3/4 NTP (n)Final Dose P mg (n)Dose Interruption (n)Best Response (n)5030050 (1) 50 (1) 50 (1)No (2) Yes (1)PR (1) SD (1) PD (1)7530275 (1) 50 (1) 25 (1)No (1) Yes (2)PR (2) SD (1)100605100 (2) 75 (3) 25 (1)No (1) Yes (5)PR (2) SD (1) PD (3)12531- LFT375 (1) 50 (2)No (0) Yes (3)PR (1) SD (2)75 (Run-In)60175 (5) 50 (1)No (4) Yes (2)PR (1) SD (2) PD (1) N/A (2)*100 (Run-In)61- FN5100 (1) 75 (4) 25(1)No (1) Yes (5)PR (4) SD (1) N/A (1)^*2 pts not yet evaluable. ^1 pt went off study due to FN after cycle 1.

Citation Format: Clark AS, O'Dwyer P, Troxel A, Lal P, Feldman M, Gallagher M, Driscoll A, Colameco C, Lewis D, Rosen M, Matro J, Bradbury A, Domchek S, Fox K, DeMichele A. Palbociclib and paclitaxel on an alternating schedule for advanced breast cancer: Results of a phase Ib trial. [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 P6-13-08.

Abstract P3-07-49: Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial

Background: I-SPY2 is a multicenter phase 2 trial in high risk stage II/III breast cancer (BC) using adaptive randomization within biomarker subtypes to evaluate novel agents added to standard neoadjuvant chemotherapy. The first regimen to graduate based on the predicted probability of a higher pCR rate within predefined subsets was veliparib/carboplatin + paclitaxel (VC+T→AC vs T→AC) in triple negative BC (TNBC). In TNBC the residual cancer burden (RCB) is prognostic, whether as a continuous index or grouped into classes, with pCR (RCB-0) and RCB-I classes having identical survival. Therefore, we evaluated the use of RCB to further discriminate between investigational and control arms.

Methods: Site pathologists reported RCB for 99% of subjects in the primary efficacy analysis based on pCR (n=114/115). We compared the distribution of RCB reported as a continuous index in each treatment-subset combination to matched concurrently randomized controls using the Wilcoxon rank sum test for RCB index, and Fisher's Exact test for RCB classes (RCB-0/I vs RCB-II/III). The statistics are descriptive rather than inferential, and given the small sample size have no claim on generalizability. We modified the Bayesian model used to compute the estimated probability of success in a future, randomized, phase 3 trial of 300 subjects, if response were defined by either pCR or RCB-I (RCB0/I), or separately if it were defined by pCR alone.

Results: VC+T→AC led to a significantly lower RCB index than T→AC in TNBC (p=0.0021), with a near-significant trend when those with pCR were excluded (p=0.06). There was no significant difference in RCB distributions in the other breast cancer subtypes treated. In TNBC, the odds ratio (OR) for achieving RCB-0/I in the VC+T→AC arm vs control was 8.2 (95% confidence interval (CI): 2.1–35), whereas the OR for achieving pCR was 4.56 (95% CI: 1.25–19.53). The simulations using response information from I-SPY2 to predict the probability of success for VC+T→AC for TNBC in a future phase 3 trial estimated this probability to be 0.99 if modeled using RCB-0/I as the response endpoint, and 0.90 if modeled using pCR as the response endpoint.

Conclusions: Use of RCB index and classes provided additional insight into the effect of adding VC to T, appearing to magnify the improved treatment response that had been observed with pCR rates in TNBC. It will be important to test in randomized trials whether a decrease in the RCB index relative to controls, and/or increased rates of RCB-0/I class, are predictive of survival benefit in TNBC.

Citation Format: Liu MC, Symmans WF, Yau C, Chen Y-Y, Rugo HS, Olopade OF, Datnow B, Chen B, Feldman M, Kallakury B, Hasteh F, Tickman R, Ritter J, Troxel M, Mhawech-Fauceglia P, Duan X, Berry D, Esserman L, DeMichele A. Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial. [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 P3-07-49.

Abstract P6-07-05: Mutational spectrum and tumor response in metastatic breast cancer

Background: While several comprehensive genomic sequencing tests are clinically available for breast cancer(BC), little is known about the spectrum of findings reported in the general population and clinical utility of findings for patients(pts). Here we report tumor sequencing from the METAMORPH study, a comprehensive genomic testing approach in pts with metastatic(met) BC.

Methods: Pts with either known or suspected BC mets consented to and clinically underwent concurrent diagnostic and research tumor biopsies(bx). FFPE specimens were profiled via Illumina TruSeq Cancer Panel next generation sequencing platform covering 212 amplicons in 47 cancer genes. Pathology, treatment and outcome data were prospectively collected and tracked. Aside from Her2-directed treatment, therapy was not mutation (mut)-matched.

Results: 64 pts enrolled between 11/2013 – 05/2015. Of these, 48 had bx successfully sequenced (75%). Of those without sequencing, 5 had negative/insufficient tissue, 2 had insufficient DNA, remainder no bx/pending. Median age of those sequenced was 56 (range 31-78); 81% Caucasian, 17% African American. 25% (12 pts) presented with de novo stage IV disease. Of those with recurrence (n=36), 83% had prior adjuvant chemotherapy; 81% hormone receptor positive(HR+) had prior endocrine therapy. Median # prior lines of therapy for met disease was 2 (IQR 0 – 8). Tumor characteristics, including mut analyses, are shown in Table 1. # muts did not differ significantly by subtype(p=0.22). Frequency of TP53 and PIK3CA hotspot muts was nearly identical to TCGA. Median # muts was 1 for pts with both de novo mets and recurrence(p=0.79). # of muts was not associated with time to recurrence(p=0.80). Excluding pts found to have TP53 mut only or ERBB2 alterations in known Her2+ disease, 42% of pts were identified as having at least one potentially actionable alteration (PIK3CA mut, AKT1 mut or EGFR amplification). Median time to treatment failure(TTF) on subsequent therapy was 4.1 months for overall group, and 4.1, 6.2, and 1.6 months for HR+/Her2-, any Her2+ and TN, respectively, adjusted for line of therapy(p=0.03). After adjustment for # lines of prior met therapy, TTF was 4.7 vs. 4.1 months for pts with any mut vs. none(p=0.89); 5.7 vs 4.1 months for PIK3CA+ vs. not (p=0.94); 3.3 vs. 6.5 months for TP53+ vs. not (p=0.03).

Conclusion: Pts with met BC have frequent and potentially actionable muts.While overall # of muts did not affect response, tumors with TP53 muts had shorter response to subsequent therapy in this cohort. Additional data are needed to determine the clinical utility of mut testing in met BC, for both standard and mut-matched therapy.

 Total (n=48)HR+/Her2- (n=28)Any HER2+ (n=7)TN (n=13)Receptor concordant with primary 100%78%77%# Mutations Median (Range)1 (0-4)1 (0-3)1 (1-2)1 (0-4)014 (29%)10 (36 %)04 (31%)118 (38%)11 (39%)4 (57%)3 (23%)213 (27%)5 (18%)3 (43%)5 (38%)3+3 (6%)2 (7%)01 (8%)Prevalent Mutations (&gt;20%)TP53 (38%), PIK3CA (35%)PIK3CA (50%), TP53 (25%)TP53 (60%), ERBB2amp (86%)TP53 (62%),PIK3CA (23%)Other Alterations (#)ATM (1), KIT (1), PDGFRA (1), PTEN(1), RB1 (1), SMAD4 (1), SMO (1), STK11 (1)AKT1 (1), ATM VUS (1), ERBB2 (1), PTEN (1), SMAD4 VUS (1), SMO VUS (1)ERBB2 (1), STK11(1)EGFR amp (2), KIT amp (1),PDGFRA amp (1), RB1 VUS (1)

Citation Format: Soucier-Ernst D, Colameco C, Troxel AB, Clark C, Shih N, Maxwell KN, Morrissette J, Lieberman D, Feldman M, Goodman N, Bradbury A, Clark A, Domchek S, Fox K, Glick J, Matro J, Nathanson K, Chodosh L, DeMichele A. Mutational spectrum and tumor response in metastatic breast cancer. [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 P6-07-05.

Risk of malignant progression in Barrett's esophagus indefinite for dysplasia

Barrett's esophagus is a well-recognized risk factor for esophageal adenocarcinoma. The natural history of Barrett's esophagus classified as ‘indefinite for dysplasia’ (IND) is poorly characterized. The aim of this study is to characterize the natural history of IND by determining the rate of neoplastic progression and identifying risk factors for progression. Patients from the University of Pennsylvania Health System pathology database and Barrett's esophagus registry with a diagnosis of IND between 2000 and 2014 were identified. Exclusion criteria included: (1) prior diagnosis of low-grade dysplasia (LGD), high-grade dysplasia (HGD), or esophageal adenocarcinoma (EAC); (2) presence of LGD, HGD, or EAC at the time of diagnosis of IND; and (3) lack of follow-up endoscopy after diagnosis. Patients with neoplastic progression were classified as having either prevalent disease (LGD, HGD, or EAC on surveillance biopsy within 12 months of IND diagnosis) or incident disease (LGD, HGD, or EAC on surveillance biopsy >12 months after IND diagnosis). One hundred six patients were eligible for analysis. Of 87 patients with follow-up endoscopy and biopsies within 1 year of IND diagnosis, 7 (8%) had prevalent disease (2 LGD, 4 HGD, 1 EAC). The prevalence of LGD was 2.3%, HGD was 4.6%, and EAC was 1.1%. Importantly, four of the seven prevalent (2 LGD, 2 HGD) cases were found to have dysplasia within 6 months of IND diagnosis. No demographic or endoscopic characteristics studied were associated with prevalent disease. Of the 106 IND patients, there were 66 patients without prevalent dysplasia with >1-year follow-up. Three (4.5%) progressed (1 to LGD after 12 months, 2 to HGD after 16.5 and 28 months), yielding an incidence rate for any dysplasia of 1.4 cases/100 person-years and HGD/EAC of 0.9/100 person-years. Risk factors for incident disease were smoking (p = 0.02) and Barrett's esophagus segment length (p = 0.03). IND is associated with considerable risk of prevalent dysplasia, especially within the first 6 months after diagnosis. However, the incidence of HGD/EAC is low and similar to previous studies of IND. These data suggest that IND patients should have repeat endoscopy within 6 months with careful surveillance protocols. Longer BE length and smoking history may help predict which patients are more likely to develop dysplasia, and therefore identify patients who may warrant even closer monitoring.

Entomological surveillance following a long-lasting insecticidal net universal coverage campaign in Midwestern Uganda

BACKGROUND

A universal coverage campaign (UCC) with long-lasting insecticidal nets (LLINs) was implemented in four districts in Midwestern Uganda in 2009-2010. Entomological surveys were carried out to monitor changes in vector density, behaviour and malaria transmission following this intervention.

METHODS

Anopheles mosquitoes were collected using CDC light traps quarterly and human landing catch twice a year in four sites. Collections were done at baseline before the campaign and over a three-year period following the campaign. Plasmodium falciparum circumsporozoite enzyme-linked immunosorbent assays were performed. A subset of anophelines were molecularly identified to species, and kdr L1014S frequencies were determined.

RESULTS

The prevailing malaria vector in three sites was Anopheles gambiae s.l. (>97 %), with An. funestus s.l. being present in low numbers only. An. gambiae s.s. dominated (> 95 %) over An. arabiensis within A. gambiae s.l. In the remaining site, all three vector species were observed, although their relative densities varied among seasons and years. Vector densities were low in the year following the UCC but increased over time. Vector infectivity was 3.2 % at baseline and 1.8 % three years post-distribution (p = 0.001). The daily entomological inoculation rate (EIR) in 2012 varied between 0.0-0.98 for the different sites compared to a baseline EIR that was between 0.0-5.8 in 2009. There was no indication of a change in indoor feeding times, and both An. gambiae s.l. and An. funestus s.l. continued to feed primarily after midnight with vectors being active until the early morning. Kdr L1014S frequencies were already high at baseline (53-85 %) but increased significantly in all sites over time.

CONCLUSIONS

The entomological surveys indicate that there was a reduction in transmission intensity coinciding with an increase in use of LLINs and other antimalarial interventions in areas of high malaria transmission. There was no change in feeding behaviour, and human-vector contact occurred indoors and primarily after midnight constantly throughout the study. Although the study was not designed to evaluate the effectiveness of the intervention compared to areas with no such intervention, the reduction in transmission occurred in an area with previously stable malaria, which seems to indicate a substantial contribution of the increased LLIN coverage.

Paracetamol treatment of patent ductus arteriosus in preterm infants

OBJECTIVE

To determine the effectiveness of paracetamol in closing patent ductus arteriosus (PDA) in preterm infants of our population.

STUDY DESIGN

Infants with symptomatic PDA who failed or could not get ibuprofen treatment, and who were candidates for surgical ligation, were administered oral paracetamol 15 mg kg⁻¹ every 6h, for up to 7 days and were monitored for clinical, echocardiographic and laboratorial courses.

RESULT

Seven infants, between 24-27 weeks' gestation, were included. In four the DA was closed while treated by paracetamol-in one of them the DA reopened, treated with paracetamol again, and closed. In one infant, the DA almost closed, symptoms disappeared, and the DA subsequently closed spontaneously later. Two needed surgical ligation. There were no hematologic or biochemical abnormalities.

CONCLUSION

Although there is the possibility that PDA may have closed spontaneously, it is proposed that paracetamol could contribute to the closure of PDA in preterm infants.

Note: folded optical system for narrow forward looking probe

An optical system is described in which a laser beam makes three passes through a single graded index lens, forming a focus along the optic axis. It has important applications in endoscopic probes, where the forward looking characteristic permits the avoidance of obstacles and the narrow structure makes it minimally invasive.

Abstract P4-03-04: Computer extracted image measurements of nuclear shape and texture from H&E images appear to stratify low and high risk ER+ breast cancers assessed via oncotype DX

Background: In this study we investigate the ability of computer extracted image features (nuclear morphology and texture) from digitized H&E tissue slides to stratify women with lymph node negative (LN-), estrogen receptor positive (ER+) breast cancer (BCa) as low or high risk as determined by Oncotype DX (ODX), a 21 gene-expression assay. Each year, over 120,000 women in the United States (1 million worldwide) are diagnosed with ER+ BCa. Treatment guidelines recommend hormone therapy (HT) plus chemotherapy (CT); however, up to 85% of ER+ BCa patients will not benefit from CT, yet will still suffer its side effects. ODX yields a numeric risk score (RS) ranging from 1-100; RS&lt;18 suggests patients will respond to HT alone while RS&gt;30 indicates need for adjuvant CT. Unfortunately, this test is expensive (&gt;$4000), time-consuming, and involves destructive tissue testing. The goal of this study is to show that quantitative features calculated from H&E images can accurately predict risk stratification as determined by ODX in women with LN-, ER+ BCa, suggesting a histologic image based classifier could serve as a low-cost alternative.

Methods: Digitized H&E-stained ER+ BCa tissue sampled from 111 patients (34 high and 77 low-risk as determined by ODX) were obtained from the University of Pennsylvania, the University of Medicine and Dentistry of NJ, and Case Western Reserve University. Regions of cancer were annotated manually by an expert pathologist, and representative fields of view (FOV) were chosen at 20x magnification (2000 by 2000 pixels) for each patient. A selection of nuclear boundaries was annotated manually in each FOV. For each nucleus, a set of 2343 features was extracted, including 21 morphological (size, shape, and boundary) and 2322 texture (Gabor, Local Binary Pattern, Greylevel, and Laws filter features). Using Minimum Redundancy Maximum Relevance (mRMR) feature selection, the 3 features best able to separate low and high ODX risk categories were identified and used to build a supervised Bayesian classifier. Classifier training employed a randomized 3-fold cross-validation scheme; in each trial, two-thirds of the dataset were randomly selected for training, and the remaining one-third employed for independent testing. Classifier performance was evaluated using area under the receiver operating characteristic curve (AUC), positive predictive value (PPV), and negative predictive value (NPV) with respect to low and high ODX risk categorization. Performance metrics were averaged over 100 trials of 3-fold cross-validation (see table).

Results: The mRMR method selected one morphological feature (nuclear area) and two Laws-based texture features as being highly discriminating between risk categories. The Bayesian classifier trained with these 3 features yielded high AUC, PPV, and NPV measures with low variance in distinguishing ODX risk categories. The supervised classification results indicate that quantitative image features from H&E-stained histopathology are able to accurately discriminate between low and high risk patients as determined by ODX.

Classification PerformancePerformance MetricAverage (100 Trials)Standard DeviationAUC0.870.018PPV0.810.039NPV0.880.017

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-03-04.

Abstract P2-16-20: Biomarkers to predict response to the CDK 4/6 inhibitor, palbociclib (PD 0332991) in a single-agent phase II trial in advanced breast cancer

Background: The Cyclin D1-CDK4/6 complex is critical in regulating the G1/S checkpoint and phosphorylation of retinoblastoma protein (Rb); palbociclib is a highly-selective CDK 4/6 inhibitor. CCND1, the gene encoding Cyclin D1, is amplified in 15% of breast tumors; p16, the endogenous inhibitor of the complex is lost in up to half of breast tumors. We hypothesized that breast tumors containing either alteration or a high proliferative rate would have enhanced sensitivity to palbociclib. We conducted a single-agent, phase II trial of palbociclib in patients with advanced breast cancer (UPCC03909). In this trial, the clinical benefit rate (partial response [PR] + stable disease ≥6 months [6mSD]) was 17% (DeMichele, ASCO, 2013). The current analysis was a secondary endpoint to determine whether Rb expression, p16 loss, Ki-67 index or CCND1 amplification predicted response in the phase II trial.

Methods: Enrollment on UPCC03909 required archival tumor collection from either primary tumor or metastatic lesions. Fresh frozen paraffin-embedded (FFPE) tumor sections were tested for expression of Rb, Ki-67 and p16 by immunohistochemistry (IHC), and CCND1 amplification by fluorescence in situ hybridization. Categorical variables based on% tumor staining and intensity scores (negative defined as 0 or 1+ intensity staining, equivocal defined as 2+ staining or 3+ in &lt;30%, or positive defined as 3+ staining intensity in 30%) were generated for Rb and p16 nuclear staining. Fisher's Exact test was used to test for associations between nominal factors, the Cochran-Mantel-Hænszel test for associations between ordinal factors, and the Cox proportional hazard model for association of progression-free survival (PFS) with biomarkers.

Results: Thirty-seven patients were enrolled; response evaluation is available in 36/37. All had FFPE tumor available for Rb, 33/37 (89%)for CCND1 amplification and 29/37 (78%) for Ki-67 and p16 analyses. For complete results see Table 1.

Conclusions: These results provide preliminary evidence that breast tumors more likely to respond to palbociclib may have higher Rb nuclear expression, lower Ki67 indices and/or loss of p16. Larger studies are needed to confirm these results.

Table 1: Biomarker Summary and ResponseBiomarkerBiomarker CategoizationFrequency (%)Response Rate PR+6mSD/total (%)PFS Hazard Ratio (95%CI)Overall Population (n = 37)  6/36 (17%) Ki-67 (n = 29)≤ 10 (n = 20)69%4/19 (21%)1.00 &gt; 10 (n = 9)31%1/9 (11%)1.20 (0.50, 2.88)Rb (n = 37)Nuclear Score: Negative (n = 11)30%0/11 (0%)1.00 Equivocal (n = 15)40%2/14 (14.3%)0.72 (0.28, 1.84) Positive (n = 11)30%4/11 (36.4%)0.71 (0.28, 1.80)p16 (n = 29)Loss or Low Expression (n = 16)55%4/16 (25%)1.00 Moderate or High Expression (n = 13)45%1/12 (8.3%)1.08 (0.47, 2.49)CCND1 Amplification (n = 34)Non-amplified (n = 25)88%4/25 (16%)1.00 Amplified (n = 9)12%1/8 (12.5%)1.06 (0.46, 2.4)

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-16-20.

Abstract P2-02-04: Kinetic heterogeneity features on breast DCE-MRI as prognostic markers of breast cancer recurrence

PURPOSE

Breast tumors have been shown to be heterogeneous lesions, and tumor heterogeneity is one of the major difficulties in the way of an effective cancer diagnosis and successful treatment. We evaluate the predictive capacity of DCE-MRI kinetic heterogeneity features for assessing the risk of breast cancer recurrence as determined by a validated tumor gene expression assay.

METHOD AND MATERIALS

Bilateral Breast DCE-MRI scans were retrospectively analyzed from 57 women with estrogen receptor positive/node negative invasive breast cancer. The ages of the women at the time of the imaging ranged from 37 to 74 years with a mean age of 55.5 years. The women were imaged prone in a 1.5T scanner (GE LX echo, GE Healthcare, or Siemens Sonata, Siemens); matrix size: 512 × 512; slice thickness: 2.4-4.4 mm; flip angle: 25° or 30°. The images were collected before and after the administration of gadodiamide (Omniscan) or gadobenate dimeglumine (MultiHance) contrast agents. Dynamic contrast enhanced images were acquired at 90 second intervals for 3 post contrast time points. The women had previously undergone Oncotype Dx (Genomic Health Inc.) profiling of their tumor. The Oncotype DX assay provides the likelihood of 10-year breast cancer recurrence, using a score stratified into 3 risk categories (risk: low ≤17, medium = 18-30, high ≥ 31). Pixel-wise relative enhancement curves were computed using three post-contrast time points. Fuzzy C-means clustering was applied to partition the tumor pixels according to the variance of their relative enhancement. To capture kinetic heterogeneity, wavelet features were extracted within each tumor partition as a measure of spatial variation. Mean and variance of these features were further estimated within each region. Using these features, multivariable logistic regression was performed with leave-one-out cross-validation and feature selection to classify the tumors as high or low/medium risk. We compared our kinetic heterogeneity features against standard kinetics and texture features. Area under the curve (AUC) of the receiver operating characteristic (ROC) was used to evaluate classification performance.

RESULTS

Feature selection indicated an optimal set of 7 kinetic heterogeneity features (out of 54). The classifier based on these features had an AUC = 0.82 in classifying high versus low/medium risk tumors. Classifiers based on standard kinetics and texture features performed with AUCs of 0.69 and 0.64 respectively.

CONCLUSION

Wavelet kinetic features from breast DCE-MRI could be used to capture the spatial pattern of kinetic heterogeneity of and potentially serve as prognostic markers for the risk of recurrence. In addition, breast DCE-MRI kinetic heterogeneity features could be used to assess likelihood of recurrence and ultimately help guide therapeutic decisions. Larger studies are needed to validate these findings.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-02-04.

Phylogenetic resolution power of microsatellites and various single-nucleotide polymorphism types assessed in 10 divergent chicken populations

There has been some debate over the question of which types of DNA variation are most appropriate to accurately reconstruct evolutionary events. We compared the capacity of microsatellites (STRs) and various types of single-nucleotide polymorphism (SNP) loci in the chicken genome. The SNP types differ in their location: in exons, introns and promoters. Genetic distances between all possible pairs of 10 populations were calculated for each marker type. STR loci, which are much more polymorphic than are SNPs, are considered to have occurred at recent time compared with old evolutionary events of SNPs. Using structure software, STR loci assigned individuals to their population much more correctly than did any other marker types, whereas SNPs at promoter regions gave the poorest ascription. Furthermore, 29 STR markers were even better than all 152 SNPs together. Ancient evolutionary events that produced genetic differences between the most distant populations such as Red Jungle Fowl and domestic chicken were detected better by exons and introns than by STR loci and promoters. The significant interactions found between marker types and populations suggest that marker types had different phylogenetic histories, possibly related to a different timescale.

Above-Label Doses of Octreotide-LAR in Patients With Metastatic Small Intestinal Carcinoid Tumors

BACKGROUND

Octreotide LAR is indicated for treatment of malignant carcinoid syndrome and has been studied at doses of 10 to 30 mg intramuscularly every 4 weeks. In clinical practice, higher doses are often prescribed for patients who experience refractory carcinoid syndrome (flushing and/or diarrhea) or tumor growth while on the maximum label-recommended dose.

METHODS

We performed a retrospective, longitudinal review of octreotide LAR administration at a tertiary institution to determine the frequency of above-label dosing and outcomes.

RESULTS

Three hundred thirty-eight patients were considered evaluable, among whom 100 (30%) underwent at least 1 increase in dose or frequency of octreotide-LAR above the standard label dose. The most common maximum doses were 40 mg every 4 weeks (n = 37 patients), 60 mg every 4 weeks (n = 34), and 30 mg every 3 weeks (n = 18). The indications for dose increase were worsening carcinoid syndrome (n = 60), radiographic progression (n = 33), and rising urine 5-HIAA (n = 6). Of the patients whose doses were increased for refractory carcinoid syndrome, 62% (n = 34) experienced improvement in diarrhea, and 56% (n = 28) experienced improvement in flushing.

CONCLUSIONS

In conclusion, octreotide LAR is commonly prescribed in doses or schedules above the recommended dose and frequency. Patients with refractory carcinoid syndrome appear to experience a clinical benefit from this change. Prospective data may be used to further evaluate this strategy.

Prognostic validity of the American Joint Committee on Cancer staging classification for midgut neuroendocrine tumors

PURPOSE

The American Joint Committee on Cancer (AJCC) staging manual has introduced a TNM staging classification for jejunal-ileal (midgut) neuroendocrine tumors (NETs). This classification has not been validated in a population consisting solely of midgut NETs. The purpose of this study was to test the prognostic validity of the classification in such a population.

METHODS

Patients with jejunal and ileocecal NETs who were treated at the Moffitt Cancer Center between 2000 and 2010 were assigned stages (I through IV). Kaplan-Meier analyses for overall survival (OS) were performed on the basis of TNM stage and pathologic grade. Multivariate modeling was performed using Cox proportional hazards regression.

RESULTS

We identified 691 patients with jejunal-ileocecal NETs. The AJCC classification in aggregate was highly prognostic for OS (P < .001). Five-year OS rates for stages I through IV were 100%, 100%, 91%, and 72%, respectively. The survival difference between stages III and IV was significant (P < .001); the difference between stages I/II versus III was not statistically significant (P = .1). Among patients with stage IIIB tumors, 5-year survival rates were 95% for resectable tumors versus 78% for unresectable mesenteric tumors (P = .02). A proliferative threshold of five mitoses per 10 high-power fields (HPF) was of greater prognostic value than a threshold of two mitoses per 10 HPF for discriminating between low- and intermediate-grade tumors.

CONCLUSION

Stage I and II midgut NETs are associated with identical survival rates. Stage IIIB tumors are heterogeneous, with significant differences in survival observed between resectable mesenteric lymph nodes versus unresectable masses in the root of the mesentery. A higher mitotic cutoff of five per 10 HPF may lead to improved prognostic differentiation between low- and intermediate-grade tumors. Revisions to the current AJCC staging and grading classification may be warranted.

Note: digital optical zoom by selection of polarization

The combination of a liquid crystal cell with a polarizing beam splitter is used to select one of the two paths through an optical imaging system. The paths both focus the same image on a CCD detector, but one has 4 times the magnification of the other.

Universal newborn hearing screening

The present statement reviews the evidence for universal newborn hearing screening (UNHS). A systematic review of the literature was conducted using Medline and using search dates from 1996 to the third week of August 2009. The following search terms were used: neonatal screening AND hearing loss AND hearing disorders. The key phrase "universal newborn hearing screening" was also searched. The Cochrane Central Register of Controlled Trials and systematic reviews was searched. Three systematic reviews, one controlled non-randomized trial and multiple cohort studies were found. It was determined that there was satisfactory evidence to support UNHS. The results of the available literature are consistent and indicate clear evidence that without UNHS, delayed diagnosis leads to significant harm for children and their families; with UNHS, diagnosis and intervention occur earlier; earlier intervention translates to improved language outcomes; and in well-run programs, there is negligible harm from screening.

Above-label doses of octreotide-LAR in patients with metastatic small-intestinal carcinoid tumors

e14579

Background: Octreotide LAR is indicated for treatment of the malignant carcinoid syndrome, and has been studied at doses of 10-30mg intramuscularly every 4 weeks. It has also been proven to delay time to progression of metastatic midgut carcinoid tumors at a dose of 30mg every 4 weeks. In clinical practice, higher doses are often prescribed for patients who experience refractory carcinoid syndrome (flushing and/or diarrhea) or tumor growth while on the maximal labeled dose. We performed a retrospective, longitudinal review of octreotide LAR administration at a tertiary institution to determine the frequency of ‘above-label’ dosing and outcomes. Methods: A retrospective chart-review was performed using a database of patients with metastatic small-bowel carcinoid tumors treated at the Moffitt Cancer Center between the years 2000 and 2010. Data included the maximal dose of octreotide LAR administered, reasons for change in dose or frequency (above the labeled dose of 30mg every 4 weeks), and clinical responses to dose change. Results: 337 patients were considered evaluable, among whom 99 patients (27%) underwent at least one increase in dose or frequency of octreotide-LAR above the standard labeled dose. The most common maximal doses were 40mg every 4 weeks (37 patients), 60mg every 4 weeks (34 patients), and 30mg every 3 weeks (17 patients). The indications for dose increase were worsening carcinoid syndrome (60 patients), radiographic progression (33 patients) and rising urine 5-HIAA (6 patients). Among patients whose doses were increased for refractory carcinoid syndrome, 62% experienced improvement in diarrhea and 56% experienced improvement in flushing. Conclusions: In clinical practice, octreotide LAR is commonly prescribed in doses or schedules above the labled dose and frequency. Patients with refractory carcinoid syndrome appear to experience a clinical benefit from the change. Prospective data is needed to evaluate this strategy.

Evaluation of plant and fungal extracts for their potential antigingivitis and anticaries activity

The link between diet and health has lead to the promotion of functional foods which can enhance health. In this study, the oral health benefits of a number of food homogenates and high molecular mass and low molecular mass fractions were investigated. A comprehensive range of assays were performed to assess the action of these foods on the development of gingivitis and caries using bacterial species associated with these diseases. Both antigingivitis and anticaries effects were investigated by assays examining the prevention of biofilm formation and coaggregation, disruption of preexisting biofilms, and the foods' antibacterial effects. Assays investigating interactions with gingival epithelial cells and cytokine production were carried out to assess the foods' anti- gingivitis properties. Anti-caries properties such as interactions with hydroxyapatite, disruption of signal transduction, and the inhibition of acid production were investigated. The mushroom and chicory homogenates and low molecular mass fractions show promise as anti-caries and anti-gingivitis agents, and further testing and clinical trials will need to be performed to evaluate their true effectiveness in humans.

P1-17-06: A Phase II Trial of the CDK 4/6 Inhibitor PD0332991 in Women with Advanced Breast Cancer

Background: Dysregulation of the G1/S checkpoint of the cell cycle is a feature of many breast cancers. PD0332991, a potent oral inhibitor of cyclin-dependent kinases (CDKs) 4 and 6 is well-tolerated and has demonstrated activity in a phase I trial in a variety of solid tumors at a phase II dose of 125 mg daily on a 3 week on/1 week off schedule. Preclinical data suggest that this agent is most active in ER+ (luminal) breast cancers. We are performing a phase II study of PD0332991 in women with advanced breast cancer, one of several parallel disease cohorts under study.

Methods: Patients with histologically-confirmed stage IV breast cancer were eligible if they had primary or metastatic tumor which stained positive for retinoblastoma (Rb) protein by immunohistochemistry, disease measureable by RECIST criteria and adequate organ function/performance status. Treatment was initiated with PD0332991 at 125 mg orally, days 1 - 21 of a 28-day treatment cycle. Tumor assessments occurred after every 2 cycles (8-week intervals). The primary objective was to determine the safety and response rates in cohorts of 15 patients per tumor type; 15 patients per arm provided 80% power to detect a 15% (1/15) response rate per disease that would lead to further cohort expansion. Secondary objectives include PK, PD and predictive biomarker assessment.

Results: 36 patients were screened, 32 (89%) stained positive for Rb, and 14 have enrolled on study. The only reported toxicites are neutropenia (7 patients, 4 grade 3/4), thrombocytopenia (1 patient, grade 1) and fatigue (1 patient, grade 2). 3 patients (23%) have had dose interruptions and 5 (38%) have had dose-reduction for neutropenia, though no episodes of febrile neutropenia have occurred. Among 11 patients assessable for response to date, there is 1(7%) partial response (PR), 6 (43%) with stable disease (SD) and 4 (29%) with progressive disease (PD). 3 of 6 patients with stable disease have received greater than 6 months of therapy, and these sustained responses have occurred with dosing as low as 50 mg/day. All PR/SD have occurred in patients with ER+ tumors; all PD have been in patients with triple negative (ER-/PR-/Her2-) disease. The cyclin D1 status of all patients are being assessed. Of the 10 ER+ patients, 3 are cyclin D1 amplified, 5 are non-amplified and 2 are pending assessment. 2 in 4 cyclin D1 non-amplified patients had SD, while 2 of 2 evaluable patients with amplification had SD. PK and PD analyses are in progress.

Conclusions: PD 0332991 is an extremely well-tolerated, oral CDK 4/6 inhibitor that demonstrates prolonged single-agent activity in ER+ breast cancer patients who have progressed on hormonal therapy. These data have prompted expansion of this breast cancer cohort to further delineate activity and translational studies examining predictors of response are underway.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-17-06.

P2-10-03: Non-Invasive In Vivo Characterization of Cancer-Cell Proliferation & Angiogenesis in Cancer-Cell-Surrounding Stromal Microenvironment In-Vivo Using Diffuse Optical Tomography

Background: Cancer cell proliferation and stromal microenvironment changes have been shown to indicate tumor growth (Orimo, Weinberg et al., Cell, 2005, Coussens and Werb, Nature, 2002). However, most studies were performed using excised tissue samples or cultured cells. In-vivo characterization of these properties in human breast cancer could magnify the importance of recent findings from in-vitro tissues. Diffuse Optical Tomography (DOT) provides quantitative three-dimensional (3D) images of the physiological and pathological properties of breast cancer tissues in vivo. In this study, we investigate the relationship between DOT measured physiological parameters, such as hemoglobin & tissue oxygenation that differentiate malignant, benign and normal breast tissues (Choe, Yodh et al. JBO, 2009), and histologically quantified Ki67 expression in cancer cell nuclei and vasculature in the stromal microenvironment surrounding breast cancer cells.

Methods: DOT was employed to measure 20 infiltrating ductal carcinoma patients. DOT utilizes non-ionizing low power near infrared light to examine a subject laying in the prone position on a bed with her breasts inside a breast box. DOT quantifies oxy- and deoxy-hemoglobin concentration and tissue oxygenation. Cancer proliferation was quantified by calculating Ki67 stained nuclei percent and vascular area (calculated by detecting CD34 stained vascular structure using automated RGB based software).

Results: The ratio of Ki67 expression in cancer cells to surrounding normal cells was correlated with DOT-measured tumor-to-normal ratio of volume-averaged oxy-hemoglobin and tissue oxygen saturation (R=0.72, p-value: 0.0197 and R=0.68, p-value: 0.0293, respectively, N=10). The vascular area (μm2) the surrounding stroma was correlated with total hemoglobin concentration and oxy-hemoglobin (R=0.49, p-value: 0.1238 and R=0.43, p-value: 0.1819, respectively, N=11). Additionally, cancer-to-normal ratio of nuclei compactness and cancer micro-vessel density was correlated with tumor-to-normal ratio of oxy-hemoglobin concentration (R=0.43, p-value: 0.056 and R=0.43, p-value:0.058, respectively, N=20).

Discussion: The positive correlations between Ki67 cancer-proliferation-marker and tissue oxy-hemoglobin concentration indicate that DOT detects increased oxygenated environment for proliferating cells. The observation that nuclei compactness increases with oxy-hemoglobin concentration also supports the statement above, and, the correlation between hemoglobin concentration and vascular area in surrounding stroma suggests that DOT measures tumor growth stimulated by stromal micro-environment changes. The difference between the field of view needed to calculate a parameter value (i.e., macroscopic (cm3) for DOT and microscopic (|im3) for histology) likely lowers the correlation between the two technologies. However, the results of this study clearly suggest that DOT measures tumor growth due to proliferation of cancer cells and angiogenesis in cancer-cell-surrounding stroma. This work was supported by NIH and the Susan G. Komen for the Cure foundation.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-10-03.