Sensitivity analysis for lexicographic ordering in radiation therapy treatment planning

PURPOSE

To introduce a method to efficiently identify and calculate meaningful tradeoffs between criteria in an interactive IMRT treatment planning procedure. The method provides a systematic approach to developing high-quality radiation therapy treatment plans.

METHODS

Treatment planners consider numerous dosimetric criteria of varying importance that, when optimized simultaneously through multicriteria optimization, yield a Pareto frontier which represents the set of Pareto-optimal treatment plans. However, generating and navigating this frontier is a time-consuming, nontrivial process. A lexicographic ordering (LO) approach to IMRT uses a physician's criteria preferences to partition the treatment planning decisions into a multistage treatment planning model. Because the relative importance of criteria optimized in the different stages may not necessarily constitute a strict prioritization, the authors introduce an interactive process, sensitivity analysis in lexicographic ordering (SALO), to allow the treatment planner control over the relative sequential-stage tradeoffs. By allowing this flexibility within a structured process, SALO implicitly restricts attention to and allows exploration of a subset of the Pareto efficient frontier that the physicians have deemed most important.

RESULTS

Improvements to treatment plans over a LO approach were found by implementing the SALO procedure on a brain case and a prostate case. In each stage, a physician assessed the tradeoff between previous stage and current stage criteria. The SALO method provided critical tradeoff information through curves approximating the relationship between criteria, which allowed the physician to determine the most desirable treatment plan.

CONCLUSIONS

The SALO procedure provides treatment planners with a directed, systematic process to treatment plan selection. By following a physician's prioritization, the treatment planner can avoid wasting effort considering clinically inferior treatment plans. The planner is guided by criteria importance, but given the information necessary to accurately adjust the relative importance at each stage. Through these attributes, the SALO procedure delivers an approach well balanced between efficiency and flexibility.

Abstract 5239: Use of bioscaffolds to study escape from tumor dormancy

Tumor dormancy and escape from dormancy remains an elusive mystery in cancer progression; clinically, escape from dormancy is thought to result in recurrent, aggressive disease. Over 70% of prostate cancer patients have disseminated tumor cells (DTCs) in their bone marrow at the time of primary treatment, yet less than 30% of those patients developed recurrent disease 5-15+ years post-initial treatment. Currently there are no good methods for studying tumor dormancy and escape from dormancy. Imaging studies using mouse models of dormancy and examination of DTCs from patients for gene signatures that may give clues to such dormancy are still in the early stages of development. Other tools for studying dormancy in vitro and in vivo need to be developed, especially for prostate cancer, in which no mouse models of dormancy currently exist. Here we present a study in which we implanted porous polyHEMA scaffolds pre-seeded with human prostate cells (benign, malignant or dormant) into athymic nude mice and compared growth to that in Matrigel. The malignant line had similar growth curves in the pHEMA bioscaffold and Matrigel. Likewise the failure to grow in vivo for a benign prostate epithelial line was similar in Matrigel and the bioscaffold. However, while a human prostate cancer cell line engineered to overexpress the senescence-associated gene insulin-like growth factor binding protein 7 (IGFBP7), and thus mimic dormancy, failed to grow in vivo with Matrigel, it grew when placed in a pHEMA bioscaffold. Because of this difference in growth, we further explored the BP7 expressing prostate cancer cell line. We measured the mRNA and protein levels of BP7 in the implants to determine if loss of BP7 would, in part, explain the growth of the BP7 cell line in the scaffolds. mRNA levels of BP7 were actually significantly higher in the pHEMA (growth group) compared to the Matrigel (non-growth group), p<0.0001. Protein levels of BP7 were not significantly different between the groups, however, there was a trend for higher BP7 expression in the pHEMA group. Angiogenesis is important in metastatic spread and growth, however, there were no significant differences in vessel density between the Matrigel and bioscaffold implants. Other factors that influence metastasis include activation of immune cells; in particular, macrophages are hypothesized to play an important role in metastasis. We stained the implants for macrophages and saw increased numbers of macrophages in the pHEMA implants compared with the Matrigel implants. We will present data from transcript profiles and cytokine antibody arrays that examine differences that occur between the dormant and growing BP7 prostate cancer implants. We hypothesize that infiltration of macrophages into bioscaffolds seeded with dormant cells creates a microenvironment that favors cancer cell escape from dormancy. Thus the use of pHEMA scaffolds provides an in vivo model for studying escape from dormancy in prostate cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5239. doi:1538-7445.AM2012-5239

Chloroform Cometabolism by Butane-Grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and Methane-Grown Methylosinus trichosporium OB3b

Chloroform (CF) degradation by a butane-grown enrichment culture, CF8, was compared to that by butane-grown Pseudomonas butanovora and Mycobacterium vaccae JOB5 and to that by a known CF degrader, Methylosinus trichosporium OB3b. All three butane-grown bacteria were able to degrade CF at rates comparable to that of M. trichosporium. CF degradation by all four bacteria required O(inf2). Butane inhibited CF degradation by the butane-grown bacteria, suggesting that butane monooxygenase is responsible for CF degradation. P. butanovora required exogenous reductant to degrade CF, while CF8 and M. vaccae utilized endogenous reductants. Prolonged incubation with CF resulted in decreased CF degradation. CF8 and P. butanovora were more sensitive to CF than either M. trichosporium or M. vaccae. CF degradation by all three butane-grown bacteria was inactivated by acetylene, which is a mechanism-based inhibitor for several monooxygenases. Butane protected all three butane-grown bacteria from inactivation by acetylene, which indicates that the same monooxygenase is responsible for both CF and butane oxidation. CF8 and P. butanovora were able to degrade other chlorinated hydrocarbons, including trichloroethylene, 1,2-cis-dichloroethylene, and vinyl chloride. In addition, CF8 degraded 1,1,2-trichloroethane. The results indicate the potential of butane-grown bacteria for chlorinated hydrocarbon transformation.

Abstract C15: A novel panel of serum biomarkers distinguishes asthma from non-small cell lung cancer

Purpose: Asthma affects an increasing proportion of the population and may predispose sufferers to lung cancer. Frequent misdiagnosis of asthma and lack of early detection tests for lung cancer might be mitigated by better diagnostic tests. We used multiplexed immunoassays and mass spectrometry to identify serum biomarkers capable of distinguishing asthma from non-small cell lung cancer, the most common type of lung cancer.

Methods: Sera from normal subjects (NO; n = 300), patients with asthma (AST; n=180), and non-small cell lung cancer (LC; n = 334) were acquired from commercial vendors. Levels of 58 cytokines, chemokines and growth factors were quantified using multiplexed immunoassays. For biomarker discovery, specimens were digested with trypsin and analyzed by liquid chromatography electrospray ionization MS (LC ESI MS/MS). Proteins were identified using Mascot search software. Validation of select biomarkers identified by MS was achieved by immunodetection of target proteins in serum specimens. Data were reduced using inter-pathology comparisons with statistical significance determined using Student's t-test.

Results: Multiplexed immunoassays identified 29 analytes with significant (t<0.05) inter-pathology differences; 14 of these were highly significant (t < 0.0001). We fund a subset of biomarkers with unexpectedly large inter-gender differences and distinct gender-specific expression patterns. Serum levels of interleukin-13 and small inducible cytokine b11 (I-TAC) showed the greatest difference between AST, LC, and NO sera. MS analysis to date identified 11 differentially expressed proteins that included 3 putative yet unnamed proteins identified by gene sequencing and 1 protein product corresponding to chromosome X open reading frame 38. The presence of select proteins discovered by MS (syntaxin 11, cAMP-specific 3′,5′-cyclic phosphodiesterase type 7, and arginase) was confirmed and quantified by immunobloting.

Conclusion: We have identified a group of serum biomarkers having high inter-pathology discrimination power that are capable of differentiating AST and LC from normal controls and that may potentially be used in diagnostic tests for early detection of lung pathologies. Our experimental strategy is widely applicable to discovery and validation of biomarkers for diverse human diseases, response to a therapy, or pre-selection of patients for clinical trials.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C15.

Traffic and meteorological impacts on near-road air quality: summary of methods and trends from the Raleigh Near-Road Study

A growing number of epidemiological studies conducted worldwide suggest an increase in the occurrence of adverse health effects in populations living, working, or going to school near major roadways. A study was designed to assess traffic emissions impacts on air quality and particle toxicity near a heavily traveled highway. In an attempt to describe the complex mixture of pollutants and atmospheric transport mechanisms affecting pollutant dispersion in this near-highway environment, several real-time and time-integrated sampling devices measured air quality concentrations at multiple distances and heights from the road. Pollutants analyzed included U.S. Environmental Protection Agency (EPA)-regulated gases, particulate matter (coarse, fine, and ultrafine), and air toxics. Pollutant measurements were synchronized with real-time traffic and meteorological monitoring devices to provide continuous and integrated assessments of the variation of near-road air pollutant concentrations and particle toxicity with changing traffic and environmental conditions, as well as distance from the road. Measurement results demonstrated the temporal and spatial impact of traffic emissions on near-road air quality. The distribution of mobile source emitted gas and particulate pollutants under all wind and traffic conditions indicated a higher proportion of elevated concentrations near the road, suggesting elevated exposures for populations spending significant amounts of time in this microenvironment. Diurnal variations in pollutant concentrations also demonstrated the impact of traffic activity and meteorology on near-road air quality. Time-resolved measurements of multiple pollutants demonstrated that traffic emissions produced a complex mixture of criteria and air toxic pollutants in this microenvironment. These results provide a foundation for future assessments of these data to identify the relationship of traffic activity and meteorology on air quality concentrations and population exposures.

Sweet's syndrome--like neutrophilic lobular panniculitis associated with all-trans-retinoic acid chemotherapy in a patient with acute promyelocytic leukemia

Sweet's syndrome-like (Sweet's-like) neutrophilic panniculitis is usually idiopathic, but is frequently associated with hematologic, inflammatory, and immunologic disease. Drug-related cases of Sweet's syndrome have been reported. Of relevance, chemotherapy with the retinoid all-trans-retinoic acid (ATRA) infrequently induces Sweet's-like neutrophilic panniculitis that occurs concomitantly with neutrophilic differentiation. The pathologic features are limited to the adipose tissue or include both the dermis and the subcutaneous fat; the neutrophilic infiltrate can be observed in the lobules, the septae, or both. We present this case because of the unusual subcutaneous neutrophilic infiltrate consistent with Sweet's-like neutrophilic lobular panniculitis in a patient with acute promyelocytic leukemia receiving ATRA chemotherapy. This case highlights the important connection between ATRA and Sweet's syndrome.

Genetic correlations between two strains of Durocs and crossbreds from differing production environments for slaughter traits

The aim of this study was to estimate the genetic correlations between 2 purebred Duroc pig populations (P1 and P2) and their terminal crossbreds [C1 = P1 x (Landrace x Large White) and C2 = P2 x (Landrace x Large White)] raised in different production environments. The traits analyzed were backfat (BF), muscle depth (MD), BW at slaughter (WGT), and weight per day of age (WDA). Data sets from P1, P2, C1, and C2 included 26,674, 8,266, 16,806, and 12,350 animals, respectively. Two-trait models (nucleus and commercial crossbreds) for each group included fixed (contemporary group, sex, weight, and age), random additive (animal for P1 and P2 and sire for C1 and C2), random litter, and random dam (C1 and C2 only) effects. Heritability estimates (+/-SE) for BF were 0.46 +/- 0.04, 0.38 +/- 0.02, 0.32 +/- 0.02, and 0.33 +/- 0.02 for P1, P2, C1, and C2, respectively. Heritability estimates for MD were 0.31 +/- 0.01, 0.23 +/- 0.02, 0.19 +/- 0.01, and 0.12 +/- 0.01 for P1, P2, C1, and C2, respectively. The estimates for WGT and WDA were 0.31 +/- 0.01, 0.21 +/- 0.02, 0.16 +/- 0.01, and 0.18 +/- 0.01 and 0.32 +/- 0.01, 0.22 +/- 0.02, 0.16 +/- 0.01, and 0.19 +/- 0.01, respectively. Genetic correlations between purebreds and crossbreds for BF were 0.83 +/- 0.09 (P1 x C1) and 0.89 +/- 0.05 (P2 x C2), for MD 0.78 +/- 0.05 (P1 x C1) and 0.80 +/- 0.08 (P2 x C2). For WGT and WDA, the correlations were 0.53 +/- 0.08 (P1 x C1), 0.80 +/- 0.10 (P2 x C2), and 0.60 +/- 0.07 (P1 x C1) and 0.79 +/- 0.09 (P2 x C2), respectively. (Co)variances in crossbreds were adjusted to a live BW scale. Compared with purebreds, the genetic variances in crossbreds were lower, and the residual variances were greater. Sire variances in crossbreds were approximately 20 to 30% of the animal variances in purebreds for BF and MD but were 13 to 25% for WGT and WDA. The efficiency of purebred selection on crossbreds, assessed by EBV prediction weights, ranged from 0.43 to 0.91 for line 1 and 0.70 to 0.92 for line 2. When nucleus and commercial environments differ substantially, the efficiency of selection varies by line and traits, and selection strategies that include crossbred data from typical production environments may therefore be desirable.

Long-term storage and safe retrieval of DNA from microorganisms for molecular analysis using FTA matrix cards

We assessed the potential use of Whatman FTA paper as a device for archiving and long-term storage of bacterial cell suspensions of over 400 bacterial strains representing 61 genera, the molecular applications of immobilised DNA on FTA paper, and tested its microbial inactivation properties. The FTA paper extracted bacterial DNA is of sufficiently high quality to successfully carryout the molecular detection of several key genes including 16S rRNA, esp (Enterococcus surface protein), Bft (Bacteroides fragilis enterotoxin) and por (porin protein) by PCR and for DNA fingerprinting by random amplified polymorphic DNA-PCR (RAPD-PCR). To test the long-term stability of the FTA immobilised DNA, 100 of the 400 archived bacterial samples were randomly selected following 3 years of storage at ambient temperature and PCR amplification was used to monitor its success. All of the 100 samples were successfully amplified using the 16S rDNA gene as a target and confirmed by DNA sequencing. Furthermore, the DNA was eluted into solution from the FTA cards using a new alkaline elution procedure for evaluation by real-time PCR-based assays. The viability of cells retained on the FTA cards varied among broad groups of bacteria. For the more fragile gram-negative species, no viable cells were retained even at high cell densities of between 10(7) and 10(8) colony forming units (cfu) ml(-1), and for the most robust species such as spore-formers and acid-fast bacteria, complete inactivation was achieved at cell densities ranging between 10(1) and 10(4) cfu ml(-1). The inactivation of bacterial cells on FTA cards suggest that this is a safe medium for the storage and transport of bacterial nucleic acids.