Farm level bio-economic modelling of aquatic animal disease and health interventions

A farm level bio-economic model, for aquatic animal production, of the relationships between inputs (e.g. purchased animals), outputs (e.g. harvested animals) and gross margin (GM) was developed to assess ex-ante the economics of disease and animal health interventions. Feed costs were calculated from estimates of food conversion ratio (FCR), animals harvested and mortality. The model was applied to a typical grow-out rainbow trout (Oncorhynchus mykiss) farm on Lake Titicaca, Peru and a typical shrimp (Paenus vannamei) farm in the Mekong Delta, Vietnam. The model was used in two analyses. Firstly, an approach to assess the burden of disease developed by the Global Burden of Animal Diseases (GBADs) project was adopted. Output under conditions of 'ideal health' was estimated by reducing mortality to zero and removing health costs. GM in both systems increased by approximately 25% when production was kept constant (and stocking rates reduced) and more than doubled if production was allowed to rise (and initial stocking increased). The increase in GM under conditions of ideal compared with current production provided an estimate of the maximum possible benefit from improved health management. Secondly, break-even analysis was used to assess the economics of vaccination against infectious pancreatic necrosis (IPN) vaccine (rainbow trout - RBT) and probiotics (shrimp). If initial stocking was kept constant, and production allowed to rise, break-even points for the intervention (when GM was the same with and without the intervention) were achieved when mortality was reduced by 16% in RBT fry and juvenile and 28% in shrimp. If production was kept constant and benefit realised by reduced initial stocking, the break-even point was achieved for i) vaccination of RBT when mortality in fry and juveniles was reduced by 39%, and ii) probiotics in shrimp production when there was a 15% reduction in mortality (nursery and grow-out), 10% increase in shrimp weight at harvest and 10% improvement in FCR. The results demonstrate how relatively simple models, parameterised with basic farm production data, can assess the burden of disease and quantify ex-ante the potential benefit of interventions. In the absence of trial data, these analyses support decision-making by farmers. The models can be adapted for many aquaculture systems. Farm level results can be extrapolated to estimate disease burden, and benefits of interventions, at regional or national level and thus support informed decision-making and allocation of resources to health management.

Abstract P5-06-01: Talazoparib antitumor effects in BRCA-deficient breast cancer models

Background: BRCA1 and BRCA2 functions are essential for the DNA double-strand break repair process in living cells with DNA damages. Therefore, germline pathogenic mutations in BRCA1/2 increases the risk of developing cancer.1, 2Poly(ADP-ribose) polymerase (PARP) enzymes are proteins responsible for DNA single-strand break repair. Persistent inhibition of PARP-dependent DNA repair in BRCA-deficient breast cancer cells leads to increased DNA damages resulting in cancer cell death. Talazoparib is a novel and potent, orally bioavailable, small molecule PARP inhibitor. Talazoparib's dual mechanism of action inhibits PARP enzyme activity and effectively traps PARP on DNA, preventing DNA repair, resulting in cell death in BRCA1/2-mutated cells.3 In tissue culture studies, talazoparib is more potent at trapping PARP on DNA to induce cancer cell death compared to other PARP inhibitors.4 Previous studies have demonstrated talazoparib inhibited growth in tumors harboring BRCA1/2 gene mutations. In the MX-1 breast cancer model with BRCA1-deficiency, talazoparib inhibited cell growth in vitro and induced regression in solid mouse xenografts.5 Here, we demonstrate antitumor effects of talazoparib monotherapy in a panel of breast cancer cells and patient-derived breast cancer models with pathologic BRCA1/2 mutations.

Method: A panel of human breast cancer cell lines was treated with talazoparib to determine its cytotoxic effects. BRCA1/2 mutations status was correlated to talazoparib cytotoxic effects. At the molecular level, BRCA1/2-mutant and wild type breast cancer cell lines were treated with dose-escalating talazoparib to also assess the relationship between PARP-DNA trapping complex formation and treatment response. Patient-derived breast cancer xenograft models were used to assess talazoparib monotherapy on tumorigenesis. Immunohistochemistry assays were performed to determine Ki-67, gH2AX and caspase 3 marker expression following talazoparib treatment.

Results: Cytotoxicity was observed in 50% (7/14) cell lines at IC50 values that are achieved in the clinic. BRCA1/2 alterations were detected in 21.4% (3/14) of cell lines sensitive to talazoparib treatment. In 14 patient-derived breast cancer xenograft models selected for this study, 57.1% (8/14) responded to talazoparib monotherapy. Of these, 35.7% had mutations in the BRCA1 (28.6%) and BRCA2 (7.1%) genes. Stable disease was observed in 14.2% (2/14). One stable model had BRCA1 mutations. Tumor regression was observed in 42.8% (6/14) of the models treated with talazoparib monotherapy. Importantly, 66.7% (4/6) of patient-derived breast cancer models that regressed on talazoparib monotherapy had mutations in BRCA1/2 genes.

Conclusions: Cytotoxicity was observed with talazoparib monotherapy in breast cancer cell lines and in patient-derived xenograft tumor models harboring BRCA1 or BRCA2 mutations. Our data demonstrate therapeutic potential of talazoparib monotherapy in breast cancer associated with pathologic BRCA1/2 mutations.

1.Couch FJ et al. J Clin Oncol. 2015;33:304-11.

2. Petrucelli N et al. Genet Med. 2010;12:245-59.

3. Wang B et al. J Med Chem. 2016;59:335-57.

4. Murai J et al. Mol Cancer Ther. 2014;13:433-43.

5. Shen Y et al. Clin Cancer Res. 2013;19:5003-15.

Citation Format: Phan VT, Protter AA, Peterson A, Uppal H. Talazoparib antitumor effects in BRCA-deficient breast cancer models [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 P5-06-01.

Abstract P2-07-04: A novel diagnostic androgen receptor gene signature links clinical outcomes and preclinical response to enzalutamide, paclitaxel or the combination in triple-negative breast cancer

Background: The androgen receptor (AR) is expressed in ≈70% of all breast cancers (BCs) and may be necessary for proliferation and survival advantage in AR+ tumors. A novel gene signature associated with AR-signaling biology (PREDICT AR) was developed by sequencing triple-negative BC (TNBC) tumors collected in a phase 2 study evaluating enzalutamide (ENZA) monotherapy1; clinical outcomes were superior in patients (pts) with PREDICT AR+ vs PREDICT AR- tumors.1,2 ENZA blocks nuclear localization and suppresses its activity.3 Paclitaxel (PTX) stabilizes microtubules and may also block AR nuclear localization. Thus we hypothesize that response to PTX-based therapy may be additive in PREDICT AR+ vs PREDICT AR- disease. This study sought to identify independent clinical datasets with PREDICT AR+ gene signature to assess outcomes following PTX-based therapy. Preclinically, we investigated the antitumor activity of ENZA, PTX, or ENZA+PTX in AR-driven TNBC models.

Methods: We probed publicly available TNBC clinical databases from Gene Expression Omnibus datasets to assess PREDICT AR status and clinical outcomes. Similarly, we assessed 21 TNBC lines for PREDICT AR status. BT549, MDA-MB-436, and MDA-MB-453 were treated with ENZA, PTX, or ENZA+PTX to determine activity. Cell signaling and pathway activation were assessed by western blot. ENZA and PTX activity was assessed in PREDICT AR+ xenograft models. Tumor RNA sequencing and immunohistochemistry were used to identify gene signatures, potentially predictive biomarkers, and potential synergistic effects of ENZA+PTX.

Results: The prevalence of PREDICT AR+ tumors in one cohort of 182 pts with primary TNBC4 was 51%. Distant relapse-free survival following PTX-based adjuvant/neoadjuvant therapy was not statistically different between pts with PREDICT AR+ vs PREDICT AR- TNBC (p=0.605). Pathologic complete response rates were 12.5% for PREDICT AR+ vs 21.0% for PREDICT AR- TNBC. Additional sets of pts with primary TNBC are being evaluated. Preclinically, we observed a dose-dependent inhibition of cell viability with either ENZA or PTX in AR+ TNBC cell lines and additive effects from ENZA+PTX. In PREDICT AR+ xenograft models, ENZA or PTX treatment resulted in a dose-dependent antitumor response. Combination studies are underway. Tumor RNA sequencing are being evaluated for gene signature of synergistic antitumor response to ENZA+PTX.

Conclusion: Analyzing publicly available clinical datasets, we found that PREDICT AR+ status was not associated with differential outcomes following PTX-based therapy in primary TNBC, suggesting there is potential to provide additive benefits in PTX-based therapy with ENZA. In preclinical studies, we observed additive effects when combining ENZA+PTX in PREDICT AR+ TNBC lines compared with single agent treatments. Taken together, these data suggest ENZA combined with PTX might provide additive benefits in a clinical setting for pts with PREDICT AR+ TNBC.

References

1. Traina TA et al. J Clin Oncol 2015:33(suppl):abstr 1003.

2. Parker J et al. J Clin Oncol 2015;33(suppl):abstr 1083.

3. Tran C et al. Science 2009;324:787-90.

4. Hatzis C et al. JAMA 2011;305:1873-81.

Citation Format: Phan VT, Protter AA, Peterson AC, Parker JS, Yoon K, Tudor IC, Paton V, Noonberg S, Uppal H. A novel diagnostic androgen receptor gene signature links clinical outcomes and preclinical response to enzalutamide, paclitaxel or the combination in triple-negative 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 P2-07-04.

Activities of ABT-773 against microaerophilic and fastidious organisms

ABT-773 was tested against 317 fastidious isolates; it inhibited 99% of organisms at a concentration of 4.0 microg/ml. With ampicillin-sulbactam and levofloxacin, only 2 and 6% of these strains, respectively, were resistant at the breakpoint. With clindamycin, penicillin G, and metronidazole, 22, 26, and 58% of the strains, respectively, were resistant.

Dealing with errors in interactive sequencing by hybridization

MOTIVATION

A realistic approach to sequencing by hybridization must deal with realistic sequencing errors. The results of such a method can surely be applied to similar sequencing tasks.

RESULTS

We provide the first algorithms for interactive sequencing by hybridization which are robust in the presence of hybridization errors. Under a strong error model allowing both positive and negative hybridization errors without repeated queries, we demonstrate accurate and efficient reconstruction with error rates up to 7%. Under the weaker traditional error model of Shamir and Tsur (Proceedings of the Fifth International Conference on Computational Molecular Biology (RECOMB-01), pp 269-277, 2000), we obtain accurate reconstructions with up to 20% false negative hybridization errors. Finally, we establish theoretical bounds on the performance of the sequential probing algorithm of Skiena and Sundaram (J. Comput. Biol., 2, 333-353, 1995) under the strong error model.

AVAILABILTY

Freely available upon request.

CONTACT

skiena@cs.sunysb.edu.

The epidemiology and disease burden of rotavirus in Vietnam: sentinel surveillance at 6 hospitals

The disease burden of rotavirus diarrhea in Vietnam was assessed by surveillance of children <5 years old who were hospitalized for diarrhea at 3 centers in the north and 3 centers in the south. Rotavirus was identified in 56% (range, 47%-60%) of the 5768 patients surveyed between July 1998 and June 2000. G-typing of the first 224 strains indicated that only 2% were non-typeable, 9% were in mixed infections, and the remainder were of the common serotypes G1, G2, G3, G4, and G9. In Vietnam, diarrhea accounts for 9880 deaths per year, which is approximately 15% of all deaths among children <5 years old, or 6.5 deaths per 1000 children. If even 50% of these diarrhea-related deaths in Vietnam were due to rotavirus, the number would represent 4%-8% of all deaths among children <5 years old, 2700-5400 rotavirus-related deaths per year, and 1 death per 280-560 children during the first 5 years of life. Thus, the disease burden of rotavirus in Vietnam is substantial, and programs to encourage the use of oral rehydration should be encouraged while efforts to develop vaccines continue.

Two major strains of type 1 wild poliovirus circulating in Indochina

Two hundred ninety-four isolates from 329 patients with acute flaccid paralysis in Cambodia and Vietnam during 1992-1995 were identified as type 1 wild polioviruses. Among these isolates, 85 were selected as geographic representatives and were examined by determining the nucleotide sequences of their genome in the VP1 region. The phylogenic analysis revealed that all of the isolates examined were classified into groups A and B. Isolates belonging to group A had been found only in northern Vietnam until 1993 but not in 1994 and 1995. Group B isolates were located in both northern and southern Vietnam and Cambodia. In 1994 and 1995, however, only group B isolates were found in the Mekong Delta area in southern Vietnam and Cambodia. Isolates of groups A and B were genetically different from strains previously isolated in other Asian countries. One of the two indigenous wild polioviruses still remains to be eliminated in this area.