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A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening.

Demethylation of histones by lysine demethylases (KDMs) plays a critical role in controlling gene transcription. Aberrant demethylation may play a causal role in diseases such as cancer. Despite the biological significance of these enzymes, there are limited assay technologies for study of KDMs and few quality chemical probes available to interrogate their biology. In this report, we demonstrate the utility of self-assembled monolayer desorption/ionization (SAMDI) mass spectrometry for the investigation of quantitative KDM enzyme kinetics and for high-throughput screening for KDM inhibitors. SAMDI can be performed in 384-well format and rapidly allows reaction components to be purified prior to injection into a mass spectrometer, without a throughput-limiting liquid chromatography step. We developed sensitive and robust assays for KDM1A (LSD1, AOF2) and KDM4C (JMJD2C, GASC1) and screened 13,824 compounds against each enzyme. Hits were rapidly triaged using a redox assay to identify compounds that interfered with the catalytic oxidation chemistry used by the KDMs for the demethylation reaction. We find that overall this high-throughput mass spectrometry platform coupled with the elimination of redox active compounds leads to a hit rate that is manageable for follow-up work.
© 2015 Society for Laboratory Automation and Screening.

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Genomic analysis and selective small molecule inhibition identifies BCL-X(L) as a critical survival factor in a subset of colorectal cancer.

Defects in programmed cell death, or apoptosis, are a hallmark of cancer. The anti-apoptotic B-cell lymphoma 2 (BCL-2) family proteins, including BCL-2, BCL-X(L), and MCL-1 have been characterized as key survival factors in multiple cancer types. Because cancer types with BCL2 and MCL1 amplification are more prone to inhibition of their respectively encoded proteins, we hypothesized that cancers with a significant frequency of BCL2L1 amplification would have greater dependency on BCL-X(L) for survival.
To identify tumor subtypes that have significant frequency of BCL2L1 amplification, we performed data mining using The Cancer Genome Atlas (TCGA) database. We then assessed the dependency on BCL-X(L) in a panel of cell lines using a selective and potent BCL-X(L) inhibitor, A-1155463, and BCL2L1 siRNA. Mechanistic studies on the role of BCL-X(L) were further undertaken via a variety of genetic manipulations.
We identified colorectal cancer as having the highest frequency of BCL2L1 amplification across all tumor types examined. Colorectal cancer cell lines with BCL2L1 copy number &gt;3 were more sensitive to A-1155463. Consistently, cell lines with high expression of BCL-XL and NOXA, a pro-apoptotic protein that antagonizes MCL-1 activity were sensitive to A-1155463. Silencing the expression of BCL-X(L) via siRNA killed the cell lines that were sensitive to A-1155463 while having little effect on lines that were resistant. Furthermore, silencing the expression of MCL-1 in resistant cell lines conferred sensitivity to A-1155463, whereas silencing NOXA abrogated sensitivity.
This work demonstrates the utility of characterizing frequent genomic alterations to identify cancer survival genes. In addition, these studies demonstrate the utility of the highly potent and selective compound A-1155463 for investigating the role of BCL-X(L) in mediating the survival of specific tumor types, and indicate that BCL-X(L) inhibition could be an effective treatment for colorectal tumors with high BCL-X(L) and NOXA expression.

Development of Teratocarcinomas and Teratomas in Severely Immunodeficient NOD.Cg-Prkdc(scid) Il2rg(tm1Wjl)/Szj (NSG) Mice.

The embryonic portion of 7-day-old mouse embryos transplanted to extrauterine sites of syngeneic adult animals gives rise to teratoid tumors, which may be either benign [teratomas (T)] or malignant [teratocarcinomas (TC)]. The incidence of embryo-derived TC varies from one mouse strain to another, indicating that some strains are TC-permissive whereas others are relatively TC-nonpermissive. Embryos of a TC-permissive mouse strain (DBA/2J) and a TC-nonpermissive one (C57BL/6J) were transplanted into NOD.Cg-Prkdc(scid) Il2rg(tm1Wjl)/SzJ (NSG) mice to determine their tumorigenic potential in the absence of functional adaptive and innate immune responses in the hosts. C57BL/6J embryos transplanted to NSG mice gave rise to TC in 31% of cases, whereas the incidence of TC produced from DBA/2J transplanted embryos was 71%. The NSG embryos transplanted to syngeneic hosts gave rise to TC in 67% of cases, allowing the classification of NSG as a TC-permissive strain. A previously reported correlation between teratocarcinoma and splenomegaly was also observed in the NSG mice. The capacity of these tumors to differentiate into the cells and tissues of the normal embryo is mapped through a detailed histological analysis. These data suggest that teratocarcinogenesis, in the absence of host innate and adaptive immunity, is largely determined by the genetic background of the embryo.

Sequential and compartmentalized action of Rabs, SNAREs and MAL in the apical delivery of fusiform vesicles in urothelial umbrella cells.

Uroplakins (UPs) are major differentiation products of urothelial umbrella cells, playing important roles in forming the permeability barrier, and in the expansion/stabilization of the apical membrane. Further, UPIa serves as a uropathogenic E. coli receptor. While it is understood that UPs are delivered to the apical membrane via fusiform vesicles (FVs), the mechanisms that regulate this exocytic pathway remain poorly understood. Immuno-microscopy of normal and mutant mouse urothelia showed that the UP-delivering FVs contained Rab8/11 and Rab27b/Slac2-a, which mediate apical transport along actin filaments. Subsequently, a Rab27b/Slp2-a complex mediated FV-membrane anchorage before SNARE-mediated and MAL-facilitated apical fusion. We also showed that keratin 20 (K20), which formed a chicken-wire network 150-300 nm below the apical membrane and had hole sizes allowing FV passage, defined a subapical compartment containing FVs primed and strategically located for fusion. Finally, we showed that Rab8/11 and Rab27b function in the same pathway, that Rab27b-knockout leads to uroplakin and Slp2-a destabilization, and that Rab27b works upstream from MAL. These data support a unifying model in which UP cargoes are targeted for apical insertion via sequential interactions with Rabs and their effectors, SNAREs and MAL, and in which K20 plays a key role in regulating vesicular trafficking.
© 2016 by The American Society for Cell Biology.

Extending the Classification Approach for Comparing Two Active Treatment Arms to Binary and Time-to-Event Outcomes.

For regulatory purposes, in a trial comparing two active treatments, a hypothesis such as noninferiority or superiority must be prespecified even when there is little known about how they compare against each other or when the objective is simply to identify the best. In this paper, we extend an alternative classification methodology, the classification approach of Qu et al (Statistics in Medicine, 30:3488-3495), to compare two active treatments when outcomes are binary and time-to-event variables. This method based on estimation approach instead of hypothesis testing can be useful when little prior information is available on which treatment has better efficacy. The entire decision space is divided into eight distinct possible outcomes based on predefined lower and upper non-inferiority margins, and the conclusion will be drawn according to the location of the confidence interval for relative risk or hazard ratio (or its logarithm transformation). We demonstrate theoretically that this method controls the misclassification rate at the specified level. We also illustrate the method by simulations and using data from a Phase 3 first-line nonsmall cell lung cancer study.