A nonvoxel-based dose convolution/superposition algorithm optimized for scalable GPU architectures

PURPOSE

Real-time adaptive planning and treatment has been infeasible due in part to its high computational complexity. There have been many recent efforts to utilize graphics processing units (GPUs) to accelerate the computational performance and dose accuracy in radiation therapy. Data structure and memory access patterns are the key GPU factors that determine the computational performance and accuracy. In this paper, the authors present a nonvoxel-based (NVB) approach to maximize computational and memory access efficiency and throughput on the GPU.

METHODS

The proposed algorithm employs a ray-tracing mechanism to restructure the 3D data sets computed from the CT anatomy into a nonvoxel-based framework. In a process that takes only a few milliseconds of computing time, the algorithm restructured the data sets by ray-tracing through precalculated CT volumes to realign the coordinate system along the convolution direction, as defined by zenithal and azimuthal angles. During the ray-tracing step, the data were resampled according to radial sampling and parallel ray-spacing parameters making the algorithm independent of the original CT resolution. The nonvoxel-based algorithm presented in this paper also demonstrated a trade-off in computational performance and dose accuracy for different coordinate system configurations. In order to find the best balance between the computed speedup and the accuracy, the authors employed an exhaustive parameter search on all sampling parameters that defined the coordinate system configuration: zenithal, azimuthal, and radial sampling of the convolution algorithm, as well as the parallel ray spacing during ray tracing. The angular sampling parameters were varied between 4 and 48 discrete angles, while both radial sampling and parallel ray spacing were varied from 0.5 to 10 mm. The gamma distribution analysis method (γ) was used to compare the dose distributions using 2% and 2 mm dose difference and distance-to-agreement criteria, respectively. Accuracy was investigated using three distinct phantoms with varied geometries and heterogeneities and on a series of 14 segmented lung CT data sets. Performance gains were calculated using three 256 mm cube homogenous water phantoms, with isotropic voxel dimensions of 1, 2, and 4 mm.

RESULTS

The nonvoxel-based GPU algorithm was independent of the data size and provided significant computational gains over the CPU algorithm for large CT data sizes. The parameter search analysis also showed that the ray combination of 8 zenithal and 8 azimuthal angles along with 1 mm radial sampling and 2 mm parallel ray spacing maintained dose accuracy with greater than 99% of voxels passing the γ test. Combining the acceleration obtained from GPU parallelization with the sampling optimization, the authors achieved a total performance improvement factor of >175 000 when compared to our voxel-based ground truth CPU benchmark and a factor of 20 compared with a voxel-based GPU dose convolution method.

CONCLUSIONS

The nonvoxel-based convolution method yielded substantial performance improvements over a generic GPU implementation, while maintaining accuracy as compared to a CPU computed ground truth dose distribution. Such an algorithm can be a key contribution toward developing tools for adaptive radiation therapy systems.

Development and implementation of a high-throughput AlphaLISA assay for identifying inhibitors of EZH2 methyltransferase

The methylation state of lysine residues within histone H3 is a major determinant of active and inactive regions of the genome. Enhancer of Zeste homolog 2 (EZH2) is a histone lysine methyltransferase that is part of the polycomb repressive complex 2 (PRC2). Elevated EZH2 expression levels have been linked to hypertrimethylation of histone H3 lysine 27 (H3K27), repression of tumor repressor genes, and the onset of several types of cancers. We used the AlphaLISA technology to develop a high-throughput assay for identifying small molecule inhibitors of EZH2. AlphaLISA Acceptor Beads coated with antibodies directed against methylated H3K27 provided a sensitive method of detecting EZH2 activity through measurement of K27 methylation of a biotinylated H3-based peptide substrate. Optimized assay conditions resulted in a robust assay (Z'>0.7) which was successfully implemented in a high-throughput screening campaign. Small molecule inhibitors identified by this method may serve as powerful tools to further elucidate the potential importance of EZH2 in the development and treatment of cancer.

Structure-Based Design of Potent and Selective CK1γ Inhibitors

Aberrant activation of the Wnt pathway is believed to drive the development and growth of some cancers. The central role of CK1γ in Wnt signal transduction makes it an attractive target for the treatment of Wnt-pathway dependent cancers. We describe a structure-based approach that led to the discovery of a series of pyridyl pyrrolopyridinones as potent and selective CK1γ inhibitors. These compounds exhibited good enzyme and cell potency, as well as selectivity against other CK1 isoforms. A single oral dose of compound 13 resulted in significant inhibition of LRP6 phosphorylation in a mouse tumor PD model.

Discovery of potent and highly selective thienopyridine Janus kinase 2 inhibitors

Developing Janus kinase 2 (Jak2) inhibitors has become a significant focus for small molecule drug discovery programs in recent years due to the identification of a Jak2 gain-of-function mutation in the majority of patients with myeloproliferative disorders (MPD). Here, we describe the discovery of a thienopyridine series of Jak2 inhibitors that culminates with compounds showing 100- to >500-fold selectivity over the related Jak family kinases in enzyme assays. Selectivity for Jak2 was also observed in TEL-Jak cellular assays, as well as in cytokine-stimulated peripheral blood mononuclear cell (PBMC) and whole blood assays. X-ray cocrystal structures of 8 and 19 bound to the Jak2 kinase domain aided structure-activity relationship efforts and, along with a previously reported small molecule X-ray cocrystal structure of the Jak1 kinase domain, provided structural rationale for the observed high levels of Jak2 selectivity.

Lymph node yield following injection of patent blue V dye into colorectal cancer specimens

AIM

The study aimed to assess whether the ex vivo injection of patent blue V dye would increase lymph node yield in operative specimens of colorectal cancer.

METHOD

A randomized controlled trial was carried out in which patients undergoing resection for colonic cancer were allocated to patent V blue or no patent blue V dye submucosal injection of the operative specimen. The number of lymph nodes found in each group was compared.

RESULTS

Between 1 January and 31 December 2008, 68 patients were randomized. Thirty-three patients received patent blue V dye and 34 did not. In the former group the median number of blue nodes identified was 11, compared with a median of 9 in the no dye group. After the application of Carnoy's solution lymph node count was 16 in each group. There was no significant difference between all these results.

CONCLUSION

Ex vivo injection of patent blue V dye submucosally in a peritumour location did not increase the lymph node count or the percentage of specimens having more than 12 lymph nodes identified.

High-throughput TR-FRET assays for identifying inhibitors of LSD1 and JMJD2C histone lysine demethylases

Lysine demethylase 1 (LSD1) and Jumonji C domain-containing oxygenase D2C (JMJD2C) participate in regulating the methylation status of histone H3 lysine residues. In some contexts, LSD1 and JMJD2C activity causes enhanced cellular proliferation, which may lead to tumorigenesis. The authors explored the utility of time-resolved fluorescence resonance energy transfer (TR-FRET) immunoassays, which employed peptides consisting of the first 21 amino acids of histone H3 in which lysine 4 (H3K4) or lysine 9 (H3K9) was methylated (me) to quantify LSD1 and JMJD2C activity. The LSD1 assay monitored demethylation of the H3K4me1 peptide using an antibody that recognizes H3K4me1 but not the unmethylated peptide product. The JMJD2C assay measured demethylation of H3K9me3 with an antibody that selectively recognizes H3K9me2. The optimized conditions resulted in robust assays (Z' > 0.7) that required only 3 to 6 nM of enzyme in a reaction volume of 6 to 10 µL. These assays were used to compare the activity of different LSD1 constructs and to determine the apparent K(m) of each JMJD2C substrate. Finally, both assays were used in a high-throughput setting for identifying demethylase inhibitors. Compounds discovered by these TR-FRET methods may lead to powerful tools for ascertaining the roles of demethylases in a cellular context and ultimately for potential cancer treatments.

Comparison of 2 cell-based phosphoprotein assays to support screening and development of an ALK inhibitor

Anaplastic lymphoma kinase (ALK) when expressed as a fusion protein with nucleophosmin (NPM) has been implicated as a driving oncogene in a subset of lymphomas. Recent reports of ALK expression in a number of other cancers have raised the possibility that an ALK inhibitor may benefit patients with these diseases as well. In a campaign to identify and develop a selective ALK inhibitor, 2 assays were devised to measure the phosphorylation of tyrosine residue 1604 of ALK (pY(1604) ALK). Amplified Luminescent Proximity Homogeneous Assay (AlphaScreen(®)) and phosflow platforms were used to detect modulation of pY(1604) ALK to determine the relative potency of a set of small-molecule inhibitors. Prior to making use of these assays in diverse settings, the authors attempted to ensure their equivalence with a direct comparison of their performance. The pY(1604) ALK assays correlated well both with each other and with assays of ALK enzyme activity or ALK-dependent cell proliferation. The AlphaScreen(®) assay was amenable to automation and enabled rapid, high-throughput compound assessment in an NPM-ALK-driven cell line, whereas the phosflow assay enabled the authors to characterize the activity of compounds with respect to their impact on targeted enzymes and pathways. Results show that both AlphaScreen(®) and phosflow ALK assays exhibited diverse characteristics that made them desirable for different applications but were determined to be equally sensitive and robust in the detection of inhibition of pY(1604) ALK.

Abstract 1975: Discovery of a potent and selective Jak2 inhibitor that suppresses GM-CSF-induced STAT5 phosphorylation and Erythropoietin-induced reticulocytosis in vivo

Essential thrombocythemia (ET), polythemia vera (PV) and myelofibrosis (MF) are myeloproliferative disorders (MPDs) characterized by a chronic excessive production of cells from one or more myeloid lineages and/or bone marrow fibrosis, and have the potential to progress to AML. Recently, gain-of-function mutations in intracellular tyrosine kinase Janus kinase 2 (Jak2) were identified to be associated with MPDs. Jak2 is a member of the Jak family of kinases including Jak1, Jak3, and Tyk2 and is the most proximal signaling component for a number of cytokine receptors. The most common Jak2 mutation identified in MPDs is a substitution of valine to phenylalanine at codon 617 (V617F) located in the pseudokinase domain, which results in the loss of its repressive function, and subsequently leads to the constitutive activation of Jak2 and downstream signaling pathways (STAT, MAP kinase, and PI3 kinase) which affect the survival, differentiation and proliferation of hematopoietic progenitors.

Highly selective Jak2 inhibitors may provide a better therapeutic window in chronic dosing settings (ET and PV patients) than non-selective Jak inhibitors. Here we report the discovery of a potent and highly selective Jak2 inhibitor, AMG-Jak2-01. In enzyme assays, AMG-Jak2-01 was potent (3 nM) and selective over other Jak family kinases (> 2000-fold over Jak1, 10-fold over Jak3 and > 400-fold over Tyk2). In isogenic BaF3 cell lines expressing constitutively active Jak kinases (Tel-Jak fusion), AMG-Jak2-01 showed over 40-fold Jak2 selectivity against Jak1 or Tyk2 and 10-fold selectivity against Jak3 based on the inhibition of STAT5 phosphorylation (pSTAT5 – detected with AlphaScreen®). In cytokine-stimulated primary PBMC or whole blood assays, AMG-Jak2-01 demonstrated more than 25-fold Jak2 selectivity over Jak1and Jak3 based on inhibition of pSTAT5 (detected by flow cytometry). In vivo, oral administration of AMG-Jak2-01 at 100 mg/kg for 1 hr inhibited GM-CSF-induced pSTAT5 by approximately 70% (p<0.01) in a mouse peripheral blood pharmacodynamic assay. Finally, two doses of AMG-Jak2-01(100 mg/kg) given 4 hrs apart were able to suppress Epo-induced reticulocytosis in the mouse by 70% (p<0.02).

In summary, we have discovered a potent Jak2 inhibitor, AMG-Jak2-01, which is selective over other Jak family members in both enzyme and cell-based assays and demonstrates inhibitory activity in GM-CSF-induced STAT5 phosphorylation and erythropoietin-induced reticulocytosis in vivo.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1975. doi:10.1158/1538-7445.AM2011-1975