Genomewide Analysis of Inherited Variation Associated with Phosphorylation of PI3K/AKT/mTOR Signaling Proteins

While there exists a wealth of information about genetic influences on gene expression, less is known about how inherited variation influences the expression and post-translational modifications of proteins, especially those involved in intracellular signaling. The PI3K/AKT/mTOR signaling pathway contains several such proteins that have been implicated in a number of diseases, including a variety of cancers and some psychiatric disorders. To assess whether the activation of this pathway is influenced by genetic factors, we measured phosphorylated and total levels of three key proteins in the pathway (AKT1, p70S6K, 4E-BP1) by ELISA in 122 lymphoblastoid cell lines from 14 families. Interestingly, the phenotypes with the highest proportion of genetic influence were the ratios of phosphorylated to total protein for two of the pathway members: AKT1 and p70S6K. Genomewide linkage analysis suggested several loci of interest for these phenotypes, including a linkage peak for the AKT1 phenotype that contained the AKT1 gene on chromosome 14. Linkage peaks for the phosphorylated:total protein ratios of AKT1 and p70S6K also overlapped on chromosome 3. We selected and genotyped candidate genes from under the linkage peaks, and several statistically significant associations were found. One polymorphism in HSP90AA1 was associated with the ratio of phosphorylated to total AKT1, and polymorphisms in RAF1 and GRM7 were associated with the ratio of phosphorylated to total p70S6K. These findings, representing the first genomewide search for variants influencing human protein phosphorylation, provide useful information about the PI3K/AKT/mTOR pathway and serve as a valuable proof of concept for studies integrating human genomics and proteomics

PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis

TOR (Target of Rapamycin) is a highly conserved protein kinase and a central controller of cell growth. TOR is found in two functionally and structurally distinct multiprotein complexes termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). In the present study, we developed a two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) based proteomic strategy to identify new mammalian TOR (mTOR) binding proteins. We report the identification of Proline-rich Akt substrate (PRAS40) and the hypothetical protein Q6MZQ0/FLJ14213/CAE45978 as new mTOR binding proteins. PRAS40 binds mTORC1 via Raptor, and is an mTOR phosphorylation substrate. PRAS40 inhibits mTORC1 autophosphorylation and mTORC1 kinase activity toward eIF-4E binding protein (4E-BP) and PRAS40 itself. HeLa cells in which PRAS40 was knocked down were protected against induction of apoptosis by TNFα and cycloheximide. Rapamycin failed to mimic the pro-apoptotic effect of PRAS40, suggesting that PRAS40 mediates apoptosis independently of its inhibitory effect on mTORC1. Q6MZQ0 is structurally similar to proline rich protein 5 (PRR5) and was therefore named PRR5-Like (PRR5L). PRR5L binds specifically to mTORC2, via Rictor and/or SIN1. Unlike other mTORC2 members, PRR5L is not required for mTORC2 integrity or kinase activity, but dissociates from mTORC2 upon knock down of tuberous sclerosis complex 1 (TSC1) and TSC2. Hyperactivation of mTOR by TSC1/2 knock down enhanced apoptosis whereas PRR5L knock down reduced apoptosis. PRR5L knock down reduced apoptosis also in mTORC2 deficient cells. The above suggests that mTORC2-dissociated PRR5L may promote apoptosis when mTOR is hyperactive. Thus, PRAS40 and PRR5L are novel mTOR-associated proteins that control the balance between cell growth and cell death

Regulation of the TSC/mTOR pathway in human disease and cellular stress.

A fundamental question in cell biology is how various extracellular cues can cause changes in translational output and hence the growth of the cell. The mammalian target of rapamycin (mTOR) is a key regulator of translation that acts to stimulate protein synthesis by phosphorylating the ribosomal translation regulators p70 ribosomal S6 kinase (56K) and eukaryote initiation factor 4E binding protein 1 (4EBP1). mTOR is known to receive inputs from multiple signaling pathways and responds by increasing or decreasing protein synthesis appropriately. A prominent example of this phenomenon is how mTOR is stimulated by growth factors and the availability of nutrients, while it is inhibited by conditions such as low ATP levels, the absence of nutrients, or cellular stressors such as DNA damage or hypoxia. Regulation of protein synthesis by mTOR is responsible for controlling cell size and proliferation, and dysregulation of the mTOR pathway in vivo has been implicated in the pathogenesis of several hypertrophic and hamartoma (benign tumor) syndromes, including tuberous sclerosis complex and the pten-hamartoma tumor syndromes. Here we show that LKB1, the gene mutated in another hamartoma syndrome -- the Peutz-Jeghers hamartoma syndrome -- directly affects signaling through mTOR. We show that loss of LKB1 causes increased signaling through mTOR targets S6K and 4EBP1, and LKB1 over-expression causes physiological markers of mTOR signaling to decrease. Our results indicate that LKB1 plays a role in cell growth regulation in response to cellular energy levels; and they also suggest that rapamycin or rapamycin analogs might be of therapeutic benefit in Peutz-Jeghers syndrome. We also propose a provisional system to classify hamartoma and hypertrophic syndromes according to their potential or proven role in the mTOR pathway. Another area of investigation relates to how mTOR is regulated by stress conditions such as energy starvation, DNA damage, hypoxia, or glucocorticoid treatment. We observed that two stress-induced proteins, RTP801/Redd1 and RTP801L/Redd2, potently inhibit signaling through mTOR. Our data support the hypothesis that RTP801 functions downstream of AKT and upstream of TSC2 -- two known constituents of the mTOR pathway -- to inhibit mTOR functions. RTP801 and RTP801L are homologous, yet show little sequence similarity to known protein domains other than a coiled-coil domain. We also present evidence for a mechanism as to how these proteins may function to regulate the mTOR pathway. Taken together, these results add a new dimension to mTOR pathway regulation and provide a possible molecular mechanism of how cellular stress conditions may regulate mTOR function.Ph.D.BiochemistryBiological SciencesCellular biologyMolecular biologyPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/127009/2/3304953.pd

Regulation of the TSC pathway by LKB1: evidence of a molecular link between tuberous sclerosis complex and Peutz-Jeghers syndrome

Tuberous sclerosis complex (TSC) and Peutz-Jeghers syndrome (PJS) are dominantly inherited benign tumor syndromes that share striking histopathological similarities. Here we show that LKB1, the gene mutated in PJS, acts as a tumor suppressor by activating TSC2, the gene mutated in TSC. Like TSC2, LKB1 inhibits the phosphorylation of the key translational regulators S6K and 4EBP1. Furthermore, we show that LKB1 activates TSC2 through the AMP-dependent protein kinase (AMPK), indicating that LKB1 plays a role in cell growth regulation in response to cellular energy levels. Our results suggest that PJS and other benign tumor syndromes could be caused by dysregulation of the TSC2/mTOR pathway

A cluster randomized controlled trial for the Evaluation of routinely Measured PATient reported outcomes in HemodialYsis care (EMPATHY): a study protocol

Abstract Background Kidney failure requiring dialysis is associated with poor health outcomes and health-related quality of life (HRQL). Patient-reported outcome measures (PROMs) capture symptom burden, level of functioning and other outcomes from a patient perspective, and can support clinicians to monitor disease progression, address symptoms, and facilitate patient-centered care. While evidence suggests the use of PROMs in clinical practice can lead to improved patient experience in some settings, the impact on patients’ health outcomes and experiences is not fully understood, and their cost-effectiveness in clinical settings is unknown. This study aims to fill these gaps by evaluating the effectiveness and cost-effectiveness of routinely measuring PROMs on patient-reported experience, clinical outcomes, HRQL, and healthcare utilization. Methods The EMPATHY trial is a pragmatic multi-centre cluster randomized controlled trial that will implement and evaluate the use of disease-specific and generic PROMs in three kidney care programs in Canada. In-centre hemodialysis units will be randomized into four groups, whereby patients: 1) complete a disease-specific PROM; 2) complete a generic PROM; 3) complete both types of PROMs; 4) receive usual care and do not complete any PROMs. While clinical care pathways are available to all hemodialysis units in the study, for the three active intervention groups, the results of the PROMs will be linked to treatment aids for clinicians and patients. The primary outcome of this study is patient-provider communication, assessed by the Communication Assessment Tool (CAT). Secondary outcomes include patient management and symptoms, use of healthcare services, and the costs of implementing this intervention will also be estimated. The present protocol fulfilled the Standard Protocol Items: Recommendations for Intervention Trials (SPIRIT) checklist. Discussion While using PROMs in clinical practice is supported by theory and rationale, and may engage patients and enhance their role in decisions regarding their care and outcomes, the best approach of their use is still uncertain. It is important to rigorously evaluate such interventions and investments to ensure they provide value for patients and health systems. Trial registration Protocol version (1.0) and trial registration data are available on www.clinicaltrials.gov , identifier: NCT03535922 , registered May 24, 2018

Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging.

One of the core challenges in applying machine learning and artificial intelligence to medicine is the limited availability of annotated medical data. Unlike in other applications of machine learning, where an abundance of labeled data is available, the labeling and annotation of medical data and images require a major effort of manual work by expert clinicians who do not have the time to annotate manually. In this work, we propose a new deep learning technique (SLIVER-net), to predict clinical features from 3-dimensional volumes using a limited number of manually annotated examples. SLIVER-net is based on transfer learning, where we borrow information about the structure and parameters of the network from publicly available large datasets. Since public volume data are scarce, we use 2D images and account for the 3-dimensional structure using a novel deep learning method which tiles the volume scans, and then adds layers that leverage the 3D structure. In order to illustrate its utility, we apply SLIVER-net to predict risk factors for progression of age-related macular degeneration (AMD), a leading cause of blindness, from optical coherence tomography (OCT) volumes acquired from multiple sites. SLIVER-net successfully predicts these factors despite being trained with a relatively small number of annotated volumes (hundreds) and only dozens of positive training examples. Our empirical evaluation demonstrates that SLIVER-net significantly outperforms standard state-of-the-art deep learning techniques used for medical volumes, and its performance is generalizable as it was validated on an external testing set. In a direct comparison with a clinician panel, we find that SLIVER-net also outperforms junior specialists, and identifies AMD progression risk factors similarly to expert retina specialists

Adipose-Specific Knockout of raptor Results in Lean Mice with Enhanced Mitochondrial Respiration

raptor is a specific and essential component of mammalian TOR complex 1 (mTORC1), a key regulator of cell growth and metabolism. To investigate a role of adipose mTORC1 in regulation of adipose and whole-body metabolism, we generated mice with an adipose-specific knockout of raptor (raptor(ad-/-)). Compared to control littermates, raptor(ad-/-) mice had substantially less adipose tissue, were protected against diet-induced obesity and hypercholesterolemia, and exhibited improved insulin sensitivity. Leanness was in spite of reduced physical activity and unaffected caloric intake, lipolysis, and absorption of lipids from the food. White adipose tissue of raptor(ad-/-) mice displayed enhanced expression of genes encoding mitochondrial uncoupling proteins characteristic of brown fat. Leanness of the raptor(ad-/-) mice was attributed to elevated energy expenditure due to mitochondrial uncoupling. These results suggest that adipose mTORC1 is a regulator of adipose metabolism and, thereby, controls whole-body energy homeostasis