The amino-acid stress sensing eIF2α kinase GCN2 is a survival biomarker for malignant mesothelioma

BackgroundMalignant mesothelioma is a tumour that is strongly associated with a history of asbestos exposure, and which derives from mesothelial cells that line the serous cavities of the body. The tumour most commonly arises in the pleural cavity, but can also arise in the pericardium, peritoneum, and tunica vaginalis. At present the lesion has a very poor prognosis and is an incurable form of cancer with median survival times of up to 19 months being quoted for some histological subtypes. A large proportion of mesotheliomas have been shown to be arginine auxotrophic, leading to new research for therapeutics which might exploit this potential vulnerability.MethodsWe measured the levels of General Control Non-derepressible 2 (GCN2) protein in malignant mesothelioma tumour samples and determined whether these levels correlate with clinical outcomes.ResultsWe observed that the expression levels of GCN2 correlated with patient survival and was an independent prognostic variable in pairwise comparisons with all available clinical data.ConclusionThese findings suggest that GCN2 levels provides prognostic information and may allow for stratification of care pathways. It may suggest that targeting GCN2 is a viable strategy for mesothelioma therapy development

Architecture of human Rag GTPase heterodimers and their complex with mTORC1

© 2019 American Association for the Advancement of Science. All rights reserved. The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo–electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDPnucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes

Studies of Millimeter-Wave Atmospheric Noise Above Mauna Kea

We report measurements of the fluctuations in atmospheric emission (atmospheric noise) above Mauna Kea recorded with Bolocam at 143 and 268 GHz from the Caltech Submillimeter Observatory (CSO). The 143 GHz data were collected during a 40 night observing run in late 2003, and the 268 GHz observations were made in early 2004 and early 2005 over a total of 60 nights. Below 0.5 Hz, the data time-streams are dominated by atmospheric noise in all observing conditions. The atmospheric noise data are consistent with a Kolmogorov-Taylor (K-T) turbulence model for a thin wind-driven screen, and the median amplitude of the fluctuations is 280 mK^2 rad^(-5/3) at 143 GHz and 4000 mK^2 rad^(-5/3) at 268 GHz. Comparing our results with previous ACBAR data, we find that the normalization of the power spectrum of the atmospheric noise fluctuations is a factor of 80 larger above Mauna Kea than above the South Pole at millimeter wavelengths. Most of this difference is due to the fact that the atmosphere above the South Pole is much drier than the atmosphere above Mauna Kea. However, the atmosphere above the South Pole is slightly more stable as well: the fractional fluctuations in the column depth of precipitable water vapor are a factor of sqrt(2) smaller at the South Pole compared to Mauna Kea. Based on our atmospheric modeling, we developed several algorithms to remove the atmospheric noise, and the best results were achieved when we described the fluctuations using a low-order polynomial in detector position over the 8 arcmin field of view (FOV). However, even with these algorithms, we were not able to reach photon-background-limited instrument photometer (BLIP) performance at frequencies below 0.5 Hz in any observing conditions.Comment: 48 pages, 16 figures, accepted for publication in Ap

Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System

Receptor tyrosine kinase FGFR3 is involved in many signaling networks and is frequently mutated in developmental disorders and cancer. The Hsp90/ Cdc37 chaperone system is essential for function of normal and neoplastic cells. Here we uncover the mechanistic inter-relationships between these pro- teins by combining approaches including NMR, HDX-MS, and SAXS. We show that several disease- linked mutations convert FGFR3 to a stronger client, where the determinant underpinning client strength involves an allosteric network through the N-lobe and at the lobe interface. We determine the architec- ture of the client kinase/Cdc37 complex and dem on- strate, together with site-speci?c information, that binding of Cdc37 to unrelated kinases induces a common, extensive conformational remodeling of the kinase N-lobe, beyond localized changes and in- teractions within the binary complex. As further shown for FGFR3, this processing by Cdc37 deacti- vates the kinase and presents it, in a speci ?c orienta- tion established in the complex, for direct recognition by Hsp90

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.

The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition