Development of BromoTag:A “Bump-&-Hole”-PROTAC system to induce potent, rapid, and selective degradation of tagged target proteins

[Image: see text] Small-molecule-induced protein depletion technologies, also called inducible degrons, allow degradation of genetically engineered target proteins within cells and animals. Here, we design and develop the BromoTag, a new inducible degron system comprising a Brd4 bromodomain L387A variant as a degron tag that allows direct recruitment by heterobifunctional bumped proteolysis targeting chimeras (PROTACs) to hijack the VHL E3 ligase. We describe extensive optimization and structure–activity relationships of our bump-and-hole–PROTACs using a CRISPR knock-in cell line expressing model target BromoTag-Brd2 at endogenous levels. Collectively, our cellular and mechanistic data qualifies bumped PROTAC AGB1 as a potent, fast, and selective degrader of BromoTagged proteins, with a favorable pharmacokinetic profile in mice. The BromoTag adds to the arsenal of chemical genetic degradation tools allowing us to manipulate protein levels to interrogate the biological function and therapeutic potential in cells and in vivo

New Hubble Space Telescope Discoveries of Type Ia Supernovae at z > 1: Narrowing Constraints on the Early Behavior of Dark Energy

We have discovered 21 new Type Ia supernovae (SNe Ia) with the Hubble Space Telescope (HST) and have used them to trace the history of cosmic expansion over the last 10 billion years. These objects, which include 13 spectroscopically confirmed SNe Ia at z > 1, were discovered during 14 epochs of reimaging of the GOODS fields North and South over two years with the Advanced Camera for Surveys on HST. Together with a recalibration of our previous HST-discovered SNe Ia, the full sample of 23 SNe Ia at z > 1 provides the highest-redshift sample known. Combined with previous SN Ia datasets, we measured H(z) at discrete, uncorrelated epochs, reducing the uncertainty of H(z>1) from 50% to under 20%, strengthening the evidence for a cosmic jerk--the transition from deceleration in the past to acceleration in the present. The unique leverage of the HST high-redshift SNe Ia provides the first meaningful constraint on the dark energy equation-of-state parameter at z >1. The result remains consistent with a cosmological constant (w(z)=-1), and rules out rapidly evolving dark energy (dw/dz >>1). The defining property of dark energy, its negative pressure, appears to be present at z>1, in the epoch preceding acceleration, with ~98% confidence in our primary fit. Moreover, the z>1 sample-averaged spectral energy distribution is consistent with that of the typical SN Ia over the last 10 Gyr, indicating that any spectral evolution of the properties of SNe Ia with redshift is still below our detection threshold.Comment: typos, references corrected, minor additions to exposition 82 pages, 17 figures, 6 tables. Data also available at: http://braeburn.pha.jhu.edu/~ariess/R06. Accepted, Astrophysical Journal vol. 656 for March 10, 200

Evidence for dark energy from the cosmic microwave background alone using the Atacama Cosmology Telescope lensing measurements

For the first time, measurements of the cosmic microwave background radiation (CMB) alone favor cosmologies with $w=-1$ dark energy over models without dark energy at a 3.2-sigma level. We demonstrate this by combining the CMB lensing deflection power spectrum from the Atacama Cosmology Telescope with temperature and polarization power spectra from the Wilkinson Microwave Anisotropy Probe. The lensing data break the geometric degeneracy of different cosmological models with similar CMB temperature power spectra. Our CMB-only measurement of the dark energy density $\Omega_\Lambda$ confirms other measurements from supernovae, galaxy clusters and baryon acoustic oscillations, and demonstrates the power of CMB lensing as a new cosmological tool.Comment: 4 pages, 3 figures; replaced with version accepted by Physical Review Letters, added sentence on models with non-standard primordial power spectr

Mean first-passage time of surface-mediated diffusion in spherical domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: to appear in J. Stat. Phy

Kinetics of active surface-mediated diffusion in spherically symmetric domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: Published online in J. Stat. Phy

The Atacama Cosmology Telescope: A Measurement of the Thermal Sunyaev-Zel'dovich Effect Using the Skewness of the CMB Temperature Distribution

We present a detection of the unnormalized skewness induced by the thermal Sunyaev-Zel'dovich (tSZ) effect in filtered Atacama Cosmology Telescope (ACT) 148 GHz cosmic microwave background temperature maps. Contamination due to infrared and radio sources is minimized by template subtraction of resolved sources and by constructing a mask using outlying values in the 218 GHz (tSZ-null) ACT maps. We measure = -31 +- 6 \mu K^3 (measurement error only) or +- 14 \mu K^3 (including cosmic variance error) in the filtered ACT data, a 5-sigma detection. We show that the skewness is a sensitive probe of sigma_8, and use analytic calculations and tSZ simulations to obtain cosmological constraints from this measurement. From this signal alone we infer a value of sigma_8= 0.79 +0.03 -0.03 (68 % C.L.) +0.06 -0.06 (95 % C.L.). Our results demonstrate that measurements of non-Gaussianity can be a useful method for characterizing the tSZ effect and extracting the underlying cosmological information.Comment: 9 pages, 5 figures. Replaced with version accepted by Phys. Rev. D, with improvements to the likelihood function and the IR source treatment; only minor changes in the result

Stereoselective synthesis of allele-specific BET inhibitors

Developing stereoselective synthetic routes that are efficient and cost-effective is important to allow easy access to biologically active molecules. Our previous syntheses of allele-selective bumped inhibitors of the Bromo and Extra-Terminal (BET) bromodomain proteins, Brd2, Brd3, Brd4 and BrdT, required a wasteful, late-stage alkylation step and expensive chiral separation. To circumvent these limitations, we developed a route based on stereocontrolled alkylation of an aspartic acid derivative that was used in a divergent, racemisation-free protocol to yield structurally diverse and enantiopure triazolodiazepines. With this approach, we synthesized bumped thienodiazepine-based BET inhibitor, ET-JQ1-OMe, in five steps and 99% ee without the need for chiral chromatography. Exquisite selectivity of ET-JQ1-OMe for Leu-Ala and Leu-Val mutants over wild-type bromodomain was confirmed by isothermal titration calorimetry and X-ray crystallography. Our new approach provides unambiguous chemical evidence for the absolute stereochemistry of the active, allele-specific BET inhibitor and a viable route that will facilitate wider access to this compound class

A Rasch and factor analysis of the Functional Assessment of Cancer Therapy-General (FACT-G)

BACKGROUND: Although the Functional Assessment of Cancer Therapy – General questionnaire (FACT-G) has been validated few studies have explored the factor structure of the instrument, in particular using non-sample dependent measurement techniques, such as Rasch Models. Furthermore, few studies have explored the relationship between item fit to the Rasch Model and clinical utility. The aim of this study was to investigate the dimensionality and measurement properties of the FACT-G with Rasch Models and Factor analysis. METHODS: A factor analysis and Rasch analysis (Partial Credit Model) was carried out on the FACT-G completed by a heterogeneous sample of cancer patients (n = 465). For the Rasch analysis item fit (infit mean squares ≥ 1.30), dimensionality and item invariance were assessed. The impact of removing misfitting items on the clinical utility of the subscales and FACT-G total scale was also assessed. RESULTS: The factor analysis demonstrated a four factor structure of the FACT-G which broadly corresponded to the four subscales of the instrument. Internal consistency for these four scales was very good (Cronbach's alpha 0.72 – 0.85). The Rasch analysis demonstrated that each of the subscales and the FACT-G total scale had misfitting items (infit means square ≥ 1.30). All these scales with the exception of the Social & Family Well-being Scale (SFWB) were unidimensional. When misfitting items were removed, the effect sizes and the clinical utility of the instrument were maintained for the subscales and the total FACT-G scores. CONCLUSION: The results of the traditional factor analysis and Rasch analysis of the FACT-G broadly agreed. Caution should be exercised when utilising the Social & Family Well-being scale and further work is required to determine whether this scale is best represented by two factors. Additionally, removing misfitting items from scales should be performed alongside an assessment of the impact on clinical utility

The SDSS-III Baryon Oscillation Spectroscopic Survey: Quasar Target Selection for Data Release Nine

The SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), a five-year spectroscopic survey of 10,000 deg^2, achieved first light in late 2009. One of the key goals of BOSS is to measure the signature of baryon acoustic oscillations in the distribution of Ly-alpha absorption from the spectra of a sample of ~150,000 z>2.2 quasars. Along with measuring the angular diameter distance at z\approx2.5, BOSS will provide the first direct measurement of the expansion rate of the Universe at z > 2. One of the biggest challenges in achieving this goal is an efficient target selection algorithm for quasars over 2.2 < z < 3.5, where their colors overlap those of stars. During the first year of the BOSS survey, quasar target selection methods were developed and tested to meet the requirement of delivering at least 15 quasars deg^-2 in this redshift range, out of 40 targets deg^-2. To achieve these surface densities, the magnitude limit of the quasar targets was set at g <= 22.0 or r<=21.85. While detection of the BAO signature in the Ly-alpha absorption in quasar spectra does not require a uniform target selection, many other astrophysical studies do. We therefore defined a uniformly-selected subsample of 20 targets deg^-2, for which the selection efficiency is just over 50%. This "CORE" subsample will be fixed for Years Two through Five of the survey. In this paper we describe the evolution and implementation of the BOSS quasar target selection algorithms during the first two years of BOSS operations. We analyze the spectra obtained during the first year. 11,263 new z>2.2 quasars were spectroscopically confirmed by BOSS. Our current algorithms select an average of 15 z > 2.2 quasars deg^-2 from 40 targets deg^-2 using single-epoch SDSS imaging. Multi-epoch optical data and data at other wavelengths can further improve the efficiency and completeness of BOSS quasar target selection. [Abridged]Comment: 33 pages, 26 figures, 12 tables and a whole bunch of quasars. Submitted to Ap

High-Grade B-cell Lymphoma, Not Otherwise Specified: A Multi-Institutional Retrospective Study

In this multi-institutional retrospective study, we examined the characteristics and outcomes of 160 patients with high-grade B-cell lymphoma, not otherwise specified (HGBL-NOS)-a rare category defined by high-grade morphologic features and lack of MYC rearrangements with BCL2 and/or BCL6 rearrangements ( double hit ). Our results show that HGBL-NOS tumors are heterogeneous: 83% of patients had a germinal center B-cell immunophenotype, 37% a dual-expressor immunophenotype (MYC and BCL2 expression), 28% MYC rearrangement, 13% BCL2 rearrangement, and 11% BCL6 rearrangement. Most patients presented with stage IV disease, a high serum lactate dehydrogenase, and other high-risk clinical factors. Most frequent first-line regimens included dose-adjusted cyclophosphamide, doxorubicin, vincristine, and etoposide, with rituximab and prednisone (DA-EPOCH-R; 43%); rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP; 33%); or other intensive chemotherapy programs. We found no significant differences in the rates of complete response (CR), progression-free survival (PFS), or overall survival (OS) between these chemotherapy regimens. CR was attained by 69% of patients. PFS at 2 years was 55.2% and OS was 68.1%. In a multivariable model, the main prognostic factors for PFS and OS were poor performance status, lactate dehydrogenase \u3e3 × upper limit of normal, and a dual-expressor immunophenotype. Age \u3e60 years or presence of MYC rearrangement were not prognostic, but patients with TP53 alterations had a dismal PFS. Presence of MYC rearrangement was not predictive of better PFS in patients treated with DA-EPOCH-R vs R-CHOP. Improvements in the diagnostic criteria and therapeutic approaches beyond dose-intense chemotherapy are needed to overcome the unfavorable prognosis of patients with HGBL-NOS