114 research outputs found
Synthetic lethal screening in the mammalian central nervous system identifies Gpx6 as a modulator of Huntingtonâs disease
Huntingtonâs disease, the most common inherited neurodegenerative disease, is characterized by a dramatic loss of deep-layer cortical and striatal neurons, as well as morbidity in midlife. Human genetic studies led to the identification of the causative gene, huntingtin. Recent genomic advances have also led to the identification of hundreds of potential interacting partners for huntingtin protein and many hypotheses as to the molecular mechanisms whereby mutant huntingtin leads to cellular dysfunction and death. However, the multitude of possible interacting partners and cellular pathways affected by mutant huntingtin has complicated efforts to understand the etiology of this disease, and to date no curative therapeutic exists. To address the general problem of identifying the disease-phenotype contributing genes from a large number of correlative studies, here we develop a synthetic lethal screening methodology for the mammalian central nervous system, called SLIC, for synthetic lethal in the central nervous system. Applying SLIC to the study of Huntingtonâs disease, we identify the age-regulated glutathione peroxidase 6 (Gpx6) gene as a modulator of mutant huntingtin toxicity and show that overexpression of Gpx6 can dramatically alleviate both behavioral and molecular phenotypes associated with a mouse model of Huntingtonâs disease. SLIC can, in principle, be used in the study of any neurodegenerative disease for which a mouse model exists, promising to reveal modulators of neurodegenerative disease in an unbiased fashion, akin to screens in simpler model organisms.National Institute of Neurological Disorders and Stroke (U.S.) (Award R01NS085880)William N. and Bernice E. Bumpus Foundation (Early Career Investigator Innovation Award)JPB FoundationEuropean Molecular Biology Organization (Long-term Fellowship
ZFIRE: The Evolution of the Stellar Mass Tully-Fisher Relation to Redshift 2.0 < Z < 2.5 with MOSFIRE
Using observations made with MOSFIRE on Keck I as part of the ZFIRE survey,
we present the stellar mass Tully-Fisher relation at 2.0 < z < 2.5. The sample
was drawn from a stellar mass limited, Ks-band selected catalog from ZFOURGE
over the CANDELS area in the COSMOS field. We model the shear of the Halpha
emission line to derive rotational velocities at 2.2X the scale radius of an
exponential disk (V2.2). We correct for the blurring effect of a
two-dimensional PSF and the fact that the MOSFIRE PSF is better approximated by
a Moffat than a Gaussian, which is more typically assumed for natural seeing.
We find for the Tully-Fisher relation at 2.0 < z < 2.5 that logV2.2 =(2.18 +/-
0.051)+(0.193 +/- 0.108)(logM/Msun - 10) and infer an evolution of the
zeropoint of Delta M/Msun = -0.25 +/- 0.16 dex or Delta M/Msun = -0.39 +/- 0.21
dex compared to z = 0 when adopting a fixed slope of 0.29 or 1/4.5,
respectively. We also derive the alternative kinematic estimator S0.5, with a
best-fit relation logS0.5 =(2.06 +/- 0.032)+(0.211 +/- 0.086)(logM/Msun - 10),
and infer an evolution of Delta M/Msun= -0.45 +/- 0.13 dex compared to z < 1.2
if we adopt a fixed slope. We investigate and review various systematics,
ranging from PSF effects, projection effects, systematics related to stellar
mass derivation, selection biases and slope. We find that discrepancies between
the various literature values are reduced when taking these into account. Our
observations correspond well with the gradual evolution predicted by
semi-analytic models.Comment: 21 pages, 14 figures, 1 appendix. Accepted for publication by Apj,
February 28, 201
ZFOURGE: Using Composite Spectral Energy Distributions to Characterize Galaxy Populations at 1<z<4
We investigate the properties of galaxies as they shut off star formation
over the 4 billion years surrounding peak cosmic star formation. To do this we
categorize galaxies from into groups based on the shape
of their spectral energy distributions (SEDs) and build composite SEDs with
resolution. These composite SEDs show a variety of spectral shapes
and also show trends in parameters such as color, mass, star formation rate,
and emission line equivalent width. Using emission line equivalent widths and
strength of the 4000\AA\ break, , we categorize the composite SEDs
into five classes: extreme emission line, star-forming, transitioning,
post-starburst, and quiescent galaxies. The transitioning population of
galaxies show modest H emission (\AA) compared to
more typical star-forming composite SEDs at
(\AA). Together with their smaller sizes (3 kpc vs. 4 kpc)
and higher S\'ersic indices (2.7 vs. 1.5), this indicates that morphological
changes initiate before the cessation of star formation. The transitional group
shows a strong increase of over one dex in number density from to
, similar to the growth in the quiescent population, while
post-starburst galaxies become rarer at . We calculate average
quenching timescales of 1.6 Gyr at and 0.9 Gyr at and
conclude that a fast quenching mechanism producing post-starbursts dominated
the quenching of galaxies at early times, while a slower process has become
more common since .Comment: Accepted for publication in The Astrophysical Journa
The distribution of satellites around massive galaxies at 1<z<3 in ZFOURGE/CANDELS: dependence on star formation activity
We study the statistical distribution of satellites around star-forming and
quiescent central galaxies at 1<z<3 using imaging from the FourStar Galaxy
Evolution Survey (ZFOURGE) and the Cosmic Assembly Near-IR Deep Extragalactic
Legacy Survey (CANDELS). The deep near-IR data select satellites down to
at z<3. The radial satellite distribution around centrals
is consistent with a projected NFW profile. Massive quiescent centrals,
, have 2 times the number of satellites compared
to star-forming centrals with a significance of 2.7 even after
accounting for differences in the centrals' stellar-mass distributions. We find
no statistical difference in the satellite distributions of intermediate-mass
quiescent and star-forming centrals, . Comparing
to the Guo2011 semi-analytic model, the excess number of satellites indicates
that quiescent centrals have halo masses 0.3 dex larger than star-forming
centrals, even when the stellar-mass distributions are fixed. We use a simple
toy model that relates halo mass and quenching, which roughly reproduces the
observed quenched fractions and the differences in halo mass between
star-forming and quenched galaxies only if galaxies have a quenching
probability that increases with halo mass from 0 for
11 to 1 for 13.5. A single
halo-mass quenching threshold is unable to reproduce the quiescent fraction and
satellite distribution of centrals. Therefore, while halo quenching may be an
important mechanism, it is unlikely to be the only factor driving quenching. It
remains unclear why a high fraction of centrals remain star-forming even in
relatively massive halos.Comment: 19 pages, 17 figures, accepted by ApJ. Information on ZFOURGE can be
found at http://zfourge.tamu.ed
Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML
Leukemia stem cells (LSCs) have the capacity to self-renew and propagate disease upon serial transplantation in animal models, and elimination of this cell population is required for curative therapies. Here, we describe a series of pooled, in vivo RNAi screens to identify essential transcription factors (TFs) in a murine model of acute myeloid leukemia (AML) with genetically and phenotypically defined LSCs. These screens reveal the heterodimeric, circadian rhythm TFs Clock and Bmal1 as genes required for the growth of AML cells in vitro and in vivo. Disruption of canonical circadian pathway components produces anti-leukemic effects, including impaired proliferation, enhanced myeloid differentiation, and depletion of LSCs. We find that both normal and malignant hematopoietic cells harbor an intact clock with robust circadian oscillations, and genetic knockout models reveal a leukemia-specific dependence on the pathway. Our findings establish a role for the core circadian clock genes in AML.National Institutes of Health (U.S.) (Grant P01 CA066996)National Institutes of Health (U.S.) (Grant R01 HL082945)National Cancer Institute (U.S.) (Grant P30-CA14051
PIK3CA mutant tumors depend on oxoglutarate dehydrogenase
Oncogenic PIK3CA mutations are found in a significant fraction of human cancers, but therapeutic inhibition of PI3K has only shown limited success in clinical trials. To understand how mutant PIK3CA contributes to cancer cell proliferation, we used genome scale loss-of-function screening in a large number of genomically annotated cancer cell lines. As expected, we found that PIK3CA mutant cancer cells require PIK3CA but also require the expression of the TCA cycle enzyme 2-oxoglutarate dehydrogenase (OGDH). To understand the relationship between oncogenic PIK3CA and OGDH function, we interrogated metabolic requirements and found an increased reliance on glucose metabolism to sustain PIK3CA mutant cell proliferation. Functional metabolic studies revealed that OGDH suppression increased levels of the metabolite 2-oxoglutarate (2OG). We found that this increase in 2OG levels, either by OGDH suppression or exogenous 2OG treatment, resulted in aspartate depletion that was specifically manifested as auxotrophy within PIK3CA mutant cells. Reduced levels of aspartate deregulated the malate-aspartate shuttle, which is important for cytoplasmic NAD + regeneration that sustains rapid glucose breakdown through glycolysis. Consequently, because PIK3CA mutant cells exhibit a profound reliance on glucose metabolism, malate-aspartate shuttle deregulation leads to a specific proliferative block due to the inability to maintain NAD + /NADH homeostasis. Together these observations define a precise metabolic vulnerability imposed by a recurrently mutated oncogene. Keyword: PIK3CA; 2OG; OGDH; TCA cycle; glycolysisDamon Runyon Cancer Research Foundation (HHMI Fellowship
A comprehensive platform for highly multiplexed mammalian functional genetic screens
<p>Abstract</p> <p>Background</p> <p>Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens.</p> <p>Results</p> <p>Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens.</p> <p>Conclusion</p> <p>Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.</p
The receptor TREML4 amplifies TLR7-mediated signaling during antiviral responses and autoimmunity
The genes and pathways that fine-tune TLR7-mediated innate inflammatory responses remain to be fully elucidated. Using an unbiased genome-scale shRNA screen, we identified the receptor TREML4 as an essential positive regulator of TLR7 signaling. Macrophages from Treml4â/â mice were hyporesponsive to TLR7 agonists and failed to produce type I interferon due to impaired phosphorylation of the transcription factor STAT1 by the MAP kinase p38 and decreased recruitment of MyD88 to TLR7. TREML4 deficiency reduced production of inflammatory cytokines and autoantibodies in SLE-prone MRL/lpr mice and inhibited the antiviral immune response to influenza. Our data identify TREML4 as a positive regulator of TLR7 signaling and provide insight into the molecular mechanisms that control antiviral immunity and the development of autoimmunity
Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia
Despite extensive insights into the underlying genetics and biology of acute myeloid leukemia (AML), overall survival remains poor and new therapies are needed. We found that casein kinase 1 α (Csnk1a1), a serine-threonine kinase, is essential for AML cell survival in vivo. Normal hematopoietic stem and progenitor cells (HSPCs) were relatively less affected by shRNA-mediated knockdown of Csnk1a1. To identify downstream mediators of Csnk1a1 critical for leukemia cells, we performed an in vivo pooled shRNA screen and gene expression profiling. We found that Csnk1a1 knockdown results in decreased Rps6 phosphorylation, increased p53 activity, and myeloid differentiation. Consistent with these observations, p53-null leukemias were insensitive to Csnk1a1 knockdown. We further evaluated whether D4476, a casein kinase 1 inhibitor, would exhibit selective antileukemic effects. Treatment of leukemia stem cells (LSCs) with D4476 showed highly selective killing of LSCs over normal HSPCs. In summary, these findings demonstrate that Csnk1a1 inhibition causes reduced Rps6 phosphorylation and activation of p53, resulting in selective elimination of leukemia cells, revealing Csnk1a1 as a potential therapeutic target for the treatment of AML
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