bims-pideca 2019-10-06 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2019–10–06
ten papers selected by
Ralitsa Radostinova Madsen, University College London

PTEN in Hereditary and Sporadic Cancer.
A triple drug combination targeting components of the nutrient-sensing network maximizes longevity.
PTEN Mouse Models of Cancer Initiation and Progression.
Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.
Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.
Pleiotropic Effects of mTOR and Autophagy During Development and Aging.
Distinct Alterations in Tricarboxylic Acid Cycle Metabolites Associate with Cancer and Autism Phenotypes in Cowden Syndrome and Bannayan-Riley-Ruvalcaba Syndrome.
Mouse embryo geometry drives formation of robust signaling gradients through receptor localization.
Thioredoxin-1 maintains mitochondrial function via mTOR signaling in the heart.
High levels of AAV vector integration into CRISPR-induced DNA breaks.

Cold Spring Harb Perspect Med. 2019 Sep 30. pii: a036087. [Epub ahead of print]

PTEN in Hereditary and Sporadic Cancer.

Joanne Ngeow, Charis Eng.

Germline pathogenic phosphatase and tensin homolog (PTEN) mutations cause PTEN hamartoma tumor syndrome (PHTS), characterized by various benign and malignant tumors of the thyroid, breast, endometrium, and other organs. Patients with PHTS may present with other clinical features such as macrocephaly, intestinal polyposis, cognitive changes, and pathognomonic skin changes. Clinically, deregulation of PTEN function is implicated in other human diseases in addition to many types of human cancer. PTEN is an important phosphatase that counteracts one of the most critical cancer pathways: the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathways. Although PTEN can dephosphorylate lipids and proteins, it also has functions independent of phosphatase activity in normal and pathological states. It is positively and negatively regulated at the transcriptional level as well as posttranslationally by phosphorylation, ubiquitylation, oxidation, and acetylation. Although most of its tumor-suppressor activity is likely to be caused by lipid dephosphorylation at the plasma membrane, PTEN also resides in the cytoplasm and nucleus, and its subcellular distribution is under strict control. In this review, we highlight our current knowledge of PTEN function and recent discoveries in understanding PTEN function regulation and how this can be exploited therapeutically for cancer treatment.

DOI: https://doi.org/10.1101/cshperspect.a036087
Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 201913212. [Epub ahead of print]

A triple drug combination targeting components of the nutrient-sensing network maximizes longevity.

Jorge Iván Castillo-Quan, Luke S Tain, Kerri J Kinghorn, Li Li, Sebastian Grönke, Yvonne Hinze, T Keith Blackwell, Ivana Bjedov, Linda Partridge.

  Increasing life expectancy is causing the prevalence of age-related diseases to rise, and there is an urgent need for new strategies to improve health at older ages. Reduced activity of insulin/insulin-like growth factor signaling (IIS) and mechanistic target of rapamycin (mTOR) nutrient-sensing signaling network can extend lifespan and improve health during aging in diverse organisms. However, the extensive feedback in this network and adverse side effects of inhibition imply that simultaneous targeting of specific effectors in the network may most effectively combat the effects of aging. We show that the mitogen-activated protein kinase kinase (MEK) inhibitor trametinib, the mTOR complex 1 (mTORC1) inhibitor rapamycin, and the glycogen synthase kinase-3 (GSK-3) inhibitor lithium act additively to increase longevity in Drosophila Remarkably, the triple drug combination increased lifespan by 48%. Furthermore, the combination of lithium with rapamycin cancelled the latter's effects on lipid metabolism. In conclusion, a polypharmacology approach of combining established, prolongevity drug inhibitors of specific nodes may be the most effective way to target the nutrient-sensing network to improve late-life health.

Keywords:  aging; lithium; polypharmacology; rapamycin; trametinib

DOI:  https://doi.org/10.1073/pnas.1913212116
Cold Spring Harb Perspect Med. 2019 Sep 30. pii: a037283. [Epub ahead of print]

PTEN Mouse Models of Cancer Initiation and Progression.

Yu-Ru Lee, Pier Paolo Pandolfi.

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is one of the most frequently mutated, deleted, and functionally inactivated tumor suppressor genes in human cancer. PTEN is found mutated both somatically and in the germline of patients with PTEN hamartoma tumor syndrome (PHTS). PTEN encodes a dual lipid and protein phosphatase that dephosphorylates the lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3), in turn negatively regulating the oncogenic PI3K-AKT pathway, a key proto-oncogenic player in cancer development and progression. Because of importance of PTEN in tumorigenesis, a large number of sophisticated genetically engineered mouse models (GEMMs) has been designed to elucidate the underlying mechanisms by which the "PTEN pathway" promotes tumorigenesis, while simultaneously providing a well-tailored system for the identification of novel therapies and offering platforms for new drug discoveries. This review summarizes the major cancer mouse models through which the PTEN pathway has been genetically deconstructed, and outlines the rapid development of GEMMs toward more detailed functional and tissue-specific analysis.

DOI: https://doi.org/10.1101/cshperspect.a037283
Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30504-2. [Epub ahead of print]30(4): 735-753.e4

Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.

Samir Softic, Jesse G Meyer, Guo-Xiao Wang, Manoj K Gupta, Thiago M Batista, Hans P M M Lauritzen, Shiho Fujisaka, Dolors Serra, Laura Herrero, Jennifer Willoughby, Kevin Fitzgerald, Olga Ilkayeva, Christopher B Newgard, Bradford W Gibson, Birgit Schilling, David E Cohen, C Ronald Kahn.

  Dietary sugars, fructose and glucose, promote hepatic de novo lipogenesis and modify the effects of a high-fat diet (HFD) on the development of insulin resistance. Here, we show that fructose and glucose supplementation of an HFD exert divergent effects on hepatic mitochondrial function and fatty acid oxidation. This is mediated via three different nodes of regulation, including differential effects on malonyl-CoA levels, effects on mitochondrial size/protein abundance, and acetylation of mitochondrial proteins. HFD- and HFD plus fructose-fed mice have decreased CTP1a activity, the rate-limiting enzyme of fatty acid oxidation, whereas knockdown of fructose metabolism increases CPT1a and its acylcarnitine products. Furthermore, fructose-supplemented HFD leads to increased acetylation of ACADL and CPT1a, which is associated with decreased fat metabolism. In summary, dietary fructose, but not glucose, supplementation of HFD impairs mitochondrial size, function, and protein acetylation, resulting in decreased fatty acid oxidation and development of metabolic dysregulation.

Keywords:  acetylation; fatty acid oxidation; fatty liver disease; fructose; glucose; ketohexokinase; mass spectrometry; mitochondria; obesity; sugar

DOI:  https://doi.org/10.1016/j.cmet.2019.09.003
Mol Cell. 2019 Sep 24. pii: S1097-2765(19)30683-5. [Epub ahead of print]

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.

Pei-Hsuan Chen, Ling Cai, Kenneth Huffman, Chendong Yang, Jiyeon Kim, Brandon Faubert, Lindsey Boroughs, Bookyung Ko, Jessica Sudderth, Elizabeth A McMillan, Luc Girard, Dong Chen, Michael Peyton, Misty D Shields, Bo Yao, David S Shames, Hyun Seok Kim, Brenda Timmons, Ikuo Sekine, Rebecca Britt, Stephanie Weber, Lauren A Byers, John V Heymach, Jing Chen, Michael A White, John D Minna, Guanghua Xiao, Ralph J DeBerardinis.

  Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes, including signal transduction and gene expression patterns, arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here, we quantified metabolic features, mostly from the 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression, and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.

Keywords:  (13)C stable isotope labeling; cancer metabolism; cell lines; gene expression; glucose; glutamine; non-small cell lung cancer; oncogenotypes; protein expression; therapeutic sensitivity

DOI:  https://doi.org/10.1016/j.molcel.2019.08.028
Front Cell Dev Biol. 2019 ;7 192

Pleiotropic Effects of mTOR and Autophagy During Development and Aging.

Kathrin Schmeisser, J Alex Parker.

  Autophagy as a ubiquitous catabolic process causes degradation of cytoplasmic components and is generally considered to have beneficial effects on health and lifespan. In contrast, inefficient autophagy has been linked with detrimental effects on the organism and various diseases, such as Parkinson's disease. Previous research, however, showed that this paradigm is far from being black and white. For instance, it has been reported that increased levels of autophagy during development can be harmful, but become advantageous in the aging cell or organism, causing enhanced healthspan and even longevity. The antagonistic pleiotropy hypothesis postulates that genes, which control various traits in an organism, can be fitness-promoting in early life, but subsequently trigger aging processes later. Autophagy is controlled by the mechanistic target of rapamycin (mTOR), a key player of nutrient sensing and signaling and classic example of a pleiotropic gene. mTOR acts upstream of transcription factors such as FOXO, NRF, and TFEB, controlling protein synthesis, degradation, and cellular growth, thereby regulating fertility as well as aging. Here, we review recent findings about the pleiotropic role of autophagy during development and aging, examine the upstream factors, and contemplate specific mechanisms leading to disease, especially neurodegeneration.

Keywords:  C. elegans; aging; autophagy; genetics; pleiotropy

DOI:  https://doi.org/10.3389/fcell.2019.00192
Am J Hum Genet. 2019 Oct 03. pii: S0002-9297(19)30343-X. [Epub ahead of print]105(4): 813-821

Distinct Alterations in Tricarboxylic Acid Cycle Metabolites Associate with Cancer and Autism Phenotypes in Cowden Syndrome and Bannayan-Riley-Ruvalcaba Syndrome.

Lamis Yehia, Ying Ni, Fang Feng, Marilyn Seyfi, Tammy Sadler, Thomas W Frazier, Charis Eng.

  Germline heterozygous PTEN mutations cause subsets of Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome (BRRS); these subsets are characterized by high risks of breast, thyroid, and other cancers and, in one subset, autism spectrum disorder (ASD). Up to 10% of individuals with PTENMUT CS, CS-like syndrome, or BRRS have germline SDHx (succinate dehydrogenase, mitochondrial complex II) variants, which modify cancer risk. PTEN contributes to metabolic reprogramming; this is a well-established role in a cancer context. Relatedly, SDH sits at the crossroad of the electron transport chain and tricarboxylic acid (TCA) cycle, two central bioenergetic pathways. Intriguingly, PTENMUT and SDHMUT individuals have reduced SDH catalytic activity, resulting in succinate accumulation; this indicates a common genotype-independent biochemical alteration. Here, we conducted a TCA targeted metabolomics study on 511 individuals with CS, CS-like syndrome, or BRRS with various genotypes (PTEN or SDHx, mutant or wild type [WT]) and phenotypes (cancer or ASD) and a series of 187 population controls. We found consistent TCA cycle metabolite alterations in cases with various genotypes and phenotypes compared to controls, and we found unique correlations of individual metabolites with particular genotype-phenotype combinations. Notably, increased isocitrate (p = 1.2 × 10-3), but reduced citrate (p = 5.0 × 10-4), were found to be associated with breast cancer in individuals with PTENMUT/SDHxWT. Conversely, increased lactate was associated with neurodevelopmental disorders regardless of genotype (p = 9.7 × 10-3); this finding was replicated in an independent validation series (n = 171) enriched for idiopathic ASD (PTENWT, p = 5.6 × 10-4). Importantly, we identified fumarate (p = 1.9 × 10-2) as a pertinent metabolite, distinguishing individuals who develop ASD from those who develop cancer. Our observations suggest that TCA cycle metabolite alterations are germane to the pathobiology of PTEN-related CS and BRRS, as well as genotype-independent ASD, with implications for potential biomarker and/or therapeutic value.

Keywords:  Krebs cycle; PTEN hamartoma tumor syndrome; autism spectrum disorder; hereditary cancer; neurodevelopmental disorders; targeted metabolomics

DOI:  https://doi.org/10.1016/j.ajhg.2019.09.004
Nat Commun. 2019 Oct 04. 10(1): 4516

Mouse embryo geometry drives formation of robust signaling gradients through receptor localization.

Zhechun Zhang, Steven Zwick, Ethan Loew, Joshua S Grimley, Sharad Ramanathan.

Morphogen signals are essential for cell fate specification during embryogenesis. Some receptors that sense these morphogens are known to localize to only the apical or basolateral membrane of polarized cell lines in vitro. How such localization affects morphogen sensing and patterning in the developing embryo remains unknown. Here, we show that the formation of a robust BMP signaling gradient in the early mouse embryo depends on the restricted, basolateral localization of BMP receptors. The mis-localization of receptors to the apical membrane results in ectopic BMP signaling in the mouse epiblast in vivo. With evidence from mathematical modeling, human embryonic stem cells in vitro, and mouse embryos in vivo, we find that the geometric compartmentalization of BMP receptors and ligands creates a signaling gradient that is buffered against fluctuations. Our results demonstrate the importance of receptor localization and embryo geometry in shaping morphogen signaling during embryogenesis.

DOI: https://doi.org/10.1038/s41467-019-12533-7
Cardiovasc Res. 2019 Oct 04. pii: cvz251. [Epub ahead of print]

Thioredoxin-1 maintains mitochondrial function via mTOR signaling in the heart.

Shin-Ichi Oka, Adave Chin, Ji Yeon Park, Shohei Ikeda, Wataru Mizushima, Guersom Ralda, Peiyong Zhai, Mingming Tong, Jaemin Byun, Fan Tang, Yudai Einaga, Chun-Yang Huang, Toshihide Kashihara, Mengyuan Zhao, Jihoon Nah, Bin Tian, Yoko Hirabayashi, Junji Yodoi, Junichi Sadoshima.

   AIMS: Thioredoxin 1 (Trx1) is an evolutionarily conserved oxidoreductase that cleaves disulfide bonds in oxidized substrate proteins such as mechanistic target of rapamycin (mTOR) and maintains nuclear-encoded mitochondrial gene expression. The cardioprotective effect of Trx1 has been demonstrated via cardiac-specific overexpression of Trx1 and dominant negative Trx1. However, the pathophysiological role of endogenous Trx1 has not been defined with a loss-of-function model. To address this, we have generated cardiac-specific Trx1 knockout (Trx1cKO) mice.
METHODS AND RESULTS: Trx1cKO mice were viable but died with a median survival age of 25.5 days. They developed heart failure, evidenced by contractile dysfunction, hypertrophy, and increased fibrosis and apoptotic cell death. Multiple markers consistently indicated increased oxidative stress and RNA-sequencing revealed downregulation of genes involved in energy production in Trx1cKO mice. Mitochondrial morphological abnormality was evident in these mice. Although heterozygous Trx1cKO mice did not show any significant baseline phenotype, pressure-overload-induced cardiac dysfunction and downregulation of metabolic genes were exacerbated in these mice. mTOR was more oxidized and phosphorylation of mTOR substrates such as S6K and 4EBP1 was impaired in Trx1cKO mice. In cultured cardiomyocytes, Trx1 knockdown inhibited mitochondrial respiration and metabolic gene promoter activity, suggesting that Trx1 maintains mitochondrial function in a cell autonomous manner. Importantly, mTOR-C1483F, an oxidation resistant mutation, prevented Trx1 knockdown-induced mTOR oxidation and inhibition and attenuated suppression of metabolic gene promoter activity.
CONCLUSION(S): Endogenous Trx1 is essential for maintaining cardiac function and metabolism, partly through mTOR regulation via Cys1483.
TRANSLATIONAL PERSPECTIVE: Although cell protective effects of Trx1 have been demonstrated previously, the in vivo function and the direct target of endogenous Trx1 remain to be elucidated. Using cardiac-specific Trx1 KO mice, this study demonstrates that endogenous Trx1 plays an essential role in maintaining cardiac function and redox homeostasis and confers stress resistance to the heart. The salutary effect of Trx1 in the heart is primarily mediated through reduction of mTOR in vivo.

Keywords:  Heart; Redox; Thioredoxin-1(Trx1); mechanistic target of rapamycin (mTOR); metabolism

DOI:  https://doi.org/10.1093/cvr/cvz251
Nat Commun. 2019 Sep 30. 10(1): 4439

High levels of AAV vector integration into CRISPR-induced DNA breaks.

Killian S Hanlon, Benjamin P Kleinstiver, Sara P Garcia, Mikołaj P Zaborowski, Adrienn Volak, Stefan E Spirig, Alissa Muller, Alexander A Sousa, Shengdar Q Tsai, Niclas E Bengtsson, Camilla Lööv, Martin Ingelsson, Jeffrey S Chamberlain, David P Corey, Martin J Aryee, J Keith Joung, Xandra O Breakefield, Casey A Maguire, Bence György.

Adeno-associated virus (AAV) vectors have shown promising results in preclinical models, but the genomic consequences of transduction with AAV vectors encoding CRISPR-Cas nucleases is still being examined. In this study, we observe high levels of AAV integration (up to 47%) into Cas9-induced double-strand breaks (DSBs) in therapeutically relevant genes in cultured murine neurons, mouse brain, muscle and cochlea. Genome-wide AAV mapping in mouse brain shows no overall increase of AAV integration except at the CRISPR/Cas9 target site. To allow detailed characterization of integration events we engineer a miniature AAV encoding a 465 bp lambda bacteriophage DNA (AAV-λ465), enabling sequencing of the entire integrated vector genome. The integration profile of AAV-465λ in cultured cells display both full-length and fragmented AAV genomes at Cas9 on-target sites. Our data indicate that AAV integration should be recognized as a common outcome for applications that utilize AAV for genome editing.

DOI: https://doi.org/10.1038/s41467-019-12449-2