A Network-Based Model of Oncogenic Collaboration for Prediction of Drug Sensitivity.

Tumorigenesis is a multi-step process, involving the acquisition of multiple oncogenic mutations that transform cells, resulting in systemic dysregulation that enables proliferation, invasion, and other cancer hallmarks. The goal of precision medicine is to identify therapeutically-actionable mutations from large-scale omic datasets. However, the multiplicity of oncogenes required for transformation, known as oncogenic collaboration, makes assigning effective treatments difficult. Motivated by this observation, we propose a new type of oncogenic collaboration where mutations in genes that interact with an oncogene may contribute to the oncogene's deleterious potential, a new genomic feature that we term "surrogate oncogenes." Surrogate oncogenes are representatives of these mutated subnetworks that interact with oncogenes. By mapping mutations to a protein-protein interaction network, we determine the significance of the observed distribution using permutation-based methods. For a panel of 38 breast cancer cell lines, we identified a significant number of surrogate oncogenes in known oncogenes such as BRCA1 and ESR1, lending credence to this approach. In addition, using Random Forest Classifiers, we show that these significant surrogate oncogenes predict drug sensitivity for 74 drugs in the breast cancer cell lines with a mean error rate of 30.9%. Additionally, we show that surrogate oncogenes are predictive of survival in patients. The surrogate oncogene framework incorporates unique or rare mutations from a single sample, and therefore has the potential to integrate patient-unique mutations into drug sensitivity predictions, suggesting a new direction in precision medicine and drug development. Additionally, we show the prevalence of significant surrogate oncogenes in multiple cancers from The Cancer Genome Atlas, suggesting that surrogate oncogenes may be a useful genomic feature for guiding pancancer analyses and assigning therapies across many tissue types.

Computational detection of alternative exon usage.

BACKGROUND: With the advent of the GeneChip Exon Arrays, it is now possible to extract "exon-level" expression estimates, allowing for detection of alternative splicing events, one of the primary mechanisms of transcript diversity. In the context of (1) a complex trait use case and (2) a human cerebellum vs. heart comparison on previously validated data, we present a transcript-based statistical model and validation framework to allow detection of alternative exon usage (AEU) between different groups. To illustrate the approach, we detect and confirm differences in exon usage in the two of the most widely studied mouse genetic models (the C57BL/6J and DBA/2J inbred strains) and in a human dataset. RESULTS: We developed a computational framework that consists of probe level annotation mapping and statistical modeling to detect putative AEU events, as well as visualization and alignment with known splice events. We show a dramatic improvement (∼25 fold) in the ability to detect these events using the appropriate annotation and statistical model which is actually specified at the transcript level, as compared with the transcript cluster/gene-level annotation used on the array. An additional component of this workflow is a probe index that allows ranking AEU candidates for validation and can aid in identification of false positives due to single nucleotide polymorphisms. DISCUSSION: Our work highlights the importance of concordance between the functional unit interrogated (e.g., gene, transcripts) and the entity (e.g., exon, probeset) within the statistical model. The framework we present is broadly applicable to other platforms (including RNAseq).

The melting of pulmonary surfactant monolayers.

Monomolecular films of phospholipids in the liquid-expanded (LE) phase after supercompression to high surface pressures (pi), well above the equilibrium surface pressure (pi(e)) at which fluid films collapse from the interface to form a three-dimensional bulk phase, and in the tilted-condensed (TC) phase both replicate the resistance to collapse that is characteristic of alveolar films in the lungs. To provide the basis for determining which film is present in the alveolus, we measured the melting characteristics of monolayers containing TC dipalmitoyl phosphatidylcholine (DPPC), as well as supercompressed 1-palmitoyl-2-oleoyl phosphatidylcholine and calf lung surfactant extract (CLSE). Films generated by appropriate manipulations on a captive bubble were heated from < or =27 degrees C to > or =60 degrees C at different constant pi above pi(e). DPPC showed the abrupt expansion expected for the TC-LE phase transition, followed by the contraction produced by collapse. Supercompressed CLSE showed no evidence of the TC-LE expansion, arguing that supercompression did not simply convert the mixed lipid film to TC DPPC. For both DPPC and CLSE, the melting point, taken as the temperature at which collapse began, increased at higher pi, in contrast to 1-palmitoyl-2-oleoyl phosphatidylcholine, for which higher pi produced collapse at lower temperatures. For pi between 50 and 65 mN/m, DPPC melted at 48-55 degrees C, well above the main transition for bilayers at 41 degrees C. At each pi, CLSE melted at temperatures >10 degrees C lower. The distinct melting points for TC DPPC and supercompressed CLSE provide the basis by which the nature of the alveolar film might be determined from the temperature-dependence of pulmonary mechanics.

Persistence of metastability after expansion of a supercompressed fluid monolayer.

Fluid monolayers of 1-palmitoyl-2-oleoyl-phosphatidylcholine collapse from an air/water interface to form a three-dimensional bulk phase at the equilibrium spreading pressure (pie) of approximately 47 mN/m. This phase transition limits access to higher surface pressures under equilibrium conditions or during slow continuous compressions. We have shown previously that these films avoid collapse and become metastable when compressed on a captive bubble to surface pressures above 60 mN/m and that the metastability persists during expansion at least to pie. Here, we first documented the extent of this persistent metastability. Rates of isobaric collapse during expansion of the metastable films were up to 3 orders of magnitude slower than those during the initial compression to high surface pressures. Recovery of the ability to collapse depended on the surface pressure to which the films were expanded and how long they were held there. Films reverted after brief exposure to 20 mN/m and after 1 h at 35 mN/m. At pie, films remained capable of reaching high surface pressures during slow compressions after 65 h, although an increase in compressibility above 55 mN/m suggested somewhat increased rates of collapse. We also determined if the films remained metastable when they acquired sufficient free area to allow reinsertion of collapsed material. Faster isobaric expansion in the presence of more collapsed material and with further deviation below pie supported the existence of reinsertion. The persistence of metastability to pie shows that films with sufficient free area to allow reinsertion remain resistant to collapse. Observations that suggest heterogeneous reinsertion, however, argue that free area may be distributed heterogeneously and leave open the possibility that metastability persists because significant regions retain a restricted free area.

Metastability of a supercompressed fluid monolayer.

Previous studies showed that monomolecular films of extracted calf surfactant collapse at the equilibrium spreading pressure during quasi-static compressions but become metastable at much higher surface pressures when compressed faster than a threshold rate. To determine the mechanism by which the films become metastable, we studied single-component films of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC). Initial experiments confirmed similar metastability of POPC if compressed above a threshold rate. Measurements at different surface pressures then showed that rates of collapse, although initially increasing above the equilibrium spreading pressure, reached a sharply defined maximum and then slowed considerably. When heated, rapidly compressed films recovered their ability to collapse with no discontinuous change in area, arguing that the metastability does not reflect transition of the POPC film to a new phase. These observations indicate that in several respects, the supercompression of POPC monolayers resembles the supercooling of three-dimensional liquids toward a glass transition.