bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2019‒11‒10
38 papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. The PI3K-AKT network at the interface of oncogenic signalling and cancer metabolism.
  2. Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.
  3. Mitochondrial Perturbations Couple mTORC2 to Autophagy in C. elegans.
  4. A Genetic Screen in Drosophila To Identify Novel Regulation of Cell Growth by Phosphoinositide Signaling.
  5. Growth Factor-Dependent and -Independent Activation of mTORC2.
  6. DEPTOR is an in vivo tumor suppressor that inhibits prostate tumorigenesis via the inactivation of mTORC1/2 signals.
  7. Lipid signalling drives proteolytic rewiring of mitochondria by YME1L.
  8. Anabolic SIRT4 exerts retrograde control over TORC1 signalling by glutamine sparing in the mitochondria.
  9. Lactate production is a prioritised feature of adipocyte metabolism.
  10. A dyadic genotype-phenotype approach to diagnostic criteria for Proteus syndrome.
  11. PTENα and PTENβ promote carcinogenesis through WDR5 and H3K4 trimethylation.
  12. SIRT1 facilitates primordial follicle recruitment independent of deacetylase activity through directly modulating Akt1 and mTOR transcription.
  13. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome.
  14. A Crucial Role for the Small GTPase Rac1 Downstream of the Protein Kinase Akt2 in Insulin Signaling that Regulates Glucose Uptake in Mouse Adipocytes.
  15. The Mechanisms Underlying PTEN Loss in Human Tumors Suggest Potential Therapeutic Opportunities.
  16. Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models.
  17. Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
  18. LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.
  19. Lysine-specific demethylase 1 mediates AKT activity and promotes epithelial-mesenchymal transition in PIK3CA mutant colorectal cancer.
  20. Chromatin regulation at the intersection of estrogen receptor and PI3K pathways in breast cancer.
  21. Phosphoinositides in Autophagy: Current Roles and Future Insights.
  22. An Immunocompetent Mouse Model of HPV16(+) Head and Neck Squamous Cell Carcinoma.
  23. Unravelling cellular relationships during development and regeneration using genetic lineage tracing.
  24. A CD133-AKT-Wnt signaling axis drives glioblastoma brain tumor-initiating cells.
  25. Special issue: PI3K/Akt Signaling in Human Cancer.
  26. Tumor angiogenesis: causes, consequences, challenges and opportunities.
  27. The reactome pathway knowledgebase.
  28. Insulin-induced membrane permeability to glucose in human muscles at rest and following exercise.
  29. BioModels-15 years of sharing computational models in life science.
  30. MetaboLights: a resource evolving in response to the needs of its scientific community.
  31. A Phase Ib Study of Cetuximab and BYL719 (Alpelisib) Concurrent with Intensity-Modulated Radiation Therapy in Stage III-IVB Head and Neck Squamous Cell Carcinoma.
  32. Dynamic lineage priming is driven via direct enhancer regulation by ERK.
  33. Targeting glucose metabolism to suppress cancer progression: prospective of anti-glycolytic cancer therapy.
  34. Metformin Improves Mitochondrial Respiratory Activity through Activation of AMPK.
  35. PTEN isoforms with dual and opposing function.
  36. Novel and Alternative Targets Against Breast Cancer Stemness to Combat Chemoresistance.
  37. Crumbs organizes the transport machinery by regulating apical levels of PI(4,5)P2 in Drosophila.
  38. Context Dependency of Epithelial-to-Mesenchymal Transition for Metastasis.
  1. Nat Rev Cancer. 2019 Nov 04.
    The PI3K-AKT network at the interface of oncogenic signalling and cancer metabolism.
    Gerta Hoxhaj, Brendan D Manning.
      The altered metabolic programme of cancer cells facilitates their cell-autonomous proliferation and survival. In normal cells, signal transduction pathways control core cellular functions, including metabolism, to couple the signals from exogenous growth factors, cytokines or hormones to adaptive changes in cell physiology. The ubiquitous, growth factor-regulated phosphoinositide 3-kinase (PI3K)-AKT signalling network has diverse downstream effects on cellular metabolism, through either direct regulation of nutrient transporters and metabolic enzymes or the control of transcription factors that regulate the expression of key components of metabolic pathways. Aberrant activation of this signalling network is one of the most frequent events in human cancer and serves to disconnect the control of cell growth, survival and metabolism from exogenous growth stimuli. Here we discuss our current understanding of the molecular events controlling cellular metabolism downstream of PI3K and AKT and of how these events couple two major hallmarks of cancer: growth factor independence through oncogenic signalling and metabolic reprogramming to support cell survival and proliferation.
    DOI:  https://doi.org/10.1038/s41568-019-0216-7
  2. Science. 2019 11 08. 366(6466): 714-723
    Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.
    Neil Vasan, Pedram Razavi, Jared L Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S Taylor, Maura N Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Frauke Schimmoller, Timothy R Wilson, Lori S Friedman, Lewis C Cantley, Maurizio Scaltriti, José Baselga.
      Activating mutations in PIK3CA are frequent in human breast cancer, and phosphoinositide 3-kinase alpha (PI3Kα) inhibitors have been approved for therapy. To characterize determinants of sensitivity to these agents, we analyzed PIK3CA-mutant cancer genomes and observed the presence of multiple PIK3CA mutations in 12 to 15% of breast cancers and other tumor types, most of which (95%) are double mutations. Double PIK3CA mutations are in cis on the same allele and result in increased PI3K activity, enhanced downstream signaling, increased cell proliferation, and tumor growth. The biochemical mechanisms of dual mutations include increased disruption of p110α binding to the inhibitory subunit p85α, which relieves its catalytic inhibition, and increased p110α membrane lipid binding. Double PIK3CA mutations predict increased sensitivity to PI3Kα inhibitors compared with single-hotspot mutations.
    DOI:  https://doi.org/10.1126/science.aaw9032
  3. Cell Rep. 2019 Nov 05. pii: S2211-1247(19)31269-0. [Epub ahead of print]29(6): 1399-1409.e5
    Mitochondrial Perturbations Couple mTORC2 to Autophagy in C. elegans.
    Helena Aspernig, Thomas Heimbucher, Wenjing Qi, Dipak Gangurde, Sedric Curic, Yijian Yan, Erika Donner von Gromoff, Ralf Baumeister, Antje Thien.
      Autophagy is stimulated by stress conditions and needs to be precisely tuned to ensure cellular homeostasis and organismal development and health. The kinase mechanistic target of rapamycin (mTOR) forms the enzymatic core of the highly conserved mTOR complexes mTORC1 and mTORC2. mTORC1 is a key inhibitor of autophagy, yet the function of mTORC2 in autophagy is controversial. We here show that inactivation of mTORC2 and its direct target serum- and glucocorticoid-inducible kinase 1 (SGK-1) potently induces autophagy and the autophagic degradation of mitochondria in C. elegans. Enhanced autophagy in mTORC2- or SGK-1-deficient animals contributes to their developmental and reproductive defects and is independent of the canonical SGK-1 effector DAF-16/FOXO. Importantly, we find that inactivation of mTORC2-SGK-1 signaling impairs mitochondrial homeostasis and triggers an increased release of mitochondria-derived reactive oxygen species (mtROS) to induce autophagy. Thus, mitochondrial stress couples reduced mTORC2 activity to enhanced autophagic turnover.
    Keywords:  ROS; SGK-1; autophagy; mTOR; mTORC2; mammalian target of rapamycin; mitochondria; mitophagy; reactive oxygen species; serum glucocorticoid-regulated kinase 1
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.072
  4. G3 (Bethesda). 2019 Nov 08. pii: g3.400851.2019. [Epub ahead of print]
    A Genetic Screen in Drosophila To Identify Novel Regulation of Cell Growth by Phosphoinositide Signaling.
    Vishnu Janardan, Sanjeev Sharma, Urbashi Basu, Padinjat Raghu.
      Phosphoinositides are lipid signaling molecules that regulate several conserved sub-cellular processes in eukaryotes, including cell growth. Phosphoinositides are generated by the enzymatic activity of highly specific lipid kinases and phosphatases. For example, the lipid PIP3, the Class I PI3 kinase that generates it and the phosphatase PTEN that metabolizes it are all established regulators of growth control in metazoans. To identify additional functions for phosphoinositides in growth control, we performed a genetic screen to identify proteins which when depleted result in altered tissue growth. By using RNA-interference mediated depletion coupled with mosaic analysis in developing eyes, we identified and classified additional candidates in the developing Drosophila melanogaster eye that regulate growth either cell autonomously or via cell-cell interactions. We report three genes: Pi3K68D, Vps34 and fwd that are important for growth regulation and suggest that these are likely to act via cell-cell interactions in the developing eye. Our findings define new avenues for the understanding of growth regulation in metazoan tissue development by phosphoinositide metabolizing proteins.
    Keywords:  Drosophila melanogaster; Phosphoinositides; cell growth; metazoan
    DOI:  https://doi.org/10.1534/g3.119.400851
  5. Trends Endocrinol Metab. 2019 Nov 04. pii: S1043-2760(19)30202-4. [Epub ahead of print]
    Growth Factor-Dependent and -Independent Activation of mTORC2.
    Jonas R Knudsen, Andreas M Fritzen, David E James, Thomas E Jensen, Maximilian Kleinert, Erik A Richter.
      The target of rapamycin complex 2 (TORC2) was discovered in 2002 in budding yeast. Its mammalian counterpart, mTORC2, was first described in 2004. Soon thereafter it was demonstrated that mTORC2 directly phosphorylates Akt on Ser473, ending a long search for the elusive 'second' insulin-responsive Akt kinase. In this review we discuss key evidence pertaining to the subcellular localization of mTORC2, highlighting a spatial heterogeneity that relates to mTORC2 activation. We summarize current models for how growth factors (GFs), such as insulin, trigger mTORC2 activation, and we provide a comprehensive discussion focusing on a new exciting frontier, the molecular mechanisms underpinning GF-independent activation of mTORC2.
    Keywords:  activation mechanisms; exercise.; mTORC2; subcellular localization
    DOI:  https://doi.org/10.1016/j.tem.2019.09.005
  6. Oncogene. 2019 Nov 04.
    DEPTOR is an in vivo tumor suppressor that inhibits prostate tumorigenesis via the inactivation of mTORC1/2 signals.
    Xiaoyu Chen, Xiufang Xiong, Danrui Cui, Fei Yang, Dongping Wei, Haomin Li, Jianfeng Shu, Yanli Bi, Xiaoqing Dai, Longyuan Gong, Yi Sun, Yongchao Zhao.
      The DEPTOR-mTORC1/2 axis has been shown to play an important, but a context dependent role in the regulation of proliferation and the survival of various cancer cells in cell culture settings. The in vivo role of DEPTOR in tumorigenesis remains elusive. Here we showed that the levels of both DEPTOR protein and mRNA were substantially decreased in human prostate cancer tissues, which positively correlated with disease progression. DEPTOR depletion accelerated proliferation and survival, migration, and invasion in human prostate cancer cells. Mechanistically, DEPTOR depletion not only activated both mTORC1 and mTORC2 signals to promote cell proliferation and survival, but also induced an AKT-dependent epithelial-mesenchymal transition (EMT) and β-catenin nuclear translocation to promote cell migration and invasion. Abrogation of mTOR or AKT activation rescued the biological consequences of DEPTOR depletion. Importantly, in a Deptor-KO mouse model, Deptor knockout accelerated prostate tumorigenesis triggered by Pten loss via the activation of mTOR signaling. Collectively, our study demonstrates that DEPTOR is a tumor suppressor in the prostate, and its depletion promotes tumorigenesis via the activation of mTORC1 and mTORC2 signals. Thus, DEPTOR reactivation via a variety of means would have therapeutic potential for the treatment of prostate cancer.
    DOI:  https://doi.org/10.1038/s41388-019-1085-y
  7. Nature. 2019 Nov 06.
    Lipid signalling drives proteolytic rewiring of mitochondria by YME1L.
    Thomas MacVicar, Yohsuke Ohba, Hendrik Nolte, Fiona Carola Mayer, Takashi Tatsuta, Hans-Georg Sprenger, Barbara Lindner, Yue Zhao, Jiahui Li, Christiane Bruns, Marcus Krüger, Markus Habich, Jan Riemer, Robin Schwarzer, Manolis Pasparakis, Sinika Henschke, Jens C Brüning, Nicola Zamboni, Thomas Langer.
      Reprogramming of mitochondria provides cells with the metabolic flexibility required to adapt to various developmental transitions such as stem cell activation or immune cell reprogramming, and to respond to environmental challenges such as those encountered under hypoxic conditions or during tumorigenesis1-3. Here we show that the i-AAA protease YME1L rewires the proteome of pre-existing mitochondria in response to hypoxia or nutrient starvation. Inhibition of mTORC1 induces a lipid signalling cascade via the phosphatidic acid phosphatase LIPIN1, which decreases phosphatidylethanolamine levels in mitochondrial membranes and promotes proteolysis. YME1L degrades mitochondrial protein translocases, lipid transfer proteins and metabolic enzymes to acutely limit mitochondrial biogenesis and support cell growth. YME1L-mediated mitochondrial reshaping supports the growth of pancreatic ductal adenocarcinoma (PDAC) cells as spheroids or xenografts. Similar changes to the mitochondrial proteome occur in the tumour tissues of patients with PDAC, suggesting that YME1L is relevant to the pathophysiology of these tumours. Our results identify the mTORC1-LIPIN1-YME1L axis as a post-translational regulator of mitochondrial proteostasis at the interface between metabolism and mitochondrial dynamics.
    DOI:  https://doi.org/10.1038/s41586-019-1738-6
  8. Mol Cell Biol. 2019 Nov 04. pii: MCB.00212-19. [Epub ahead of print]
    Anabolic SIRT4 exerts retrograde control over TORC1 signalling by glutamine sparing in the mitochondria.
    Eisha Shaw, Manasi Talwadekar, Zeenat Rashida, Nitya Mohan, Aishwarya Acharya, Subhash Khatri, Sunil Laxman, Ullas Kolthur-Seetharam.
      Anabolic and catabolic signalling mediated via mTOR and AMPK have to be intrinsically coupled to mitochondrial functions for maintaining homeostasis and mitigate cellular/organismal stress. Although, glutamine is known to activate mTOR, if/how differential mitochondrial utilization of glutamine impinges on mTOR signalling is less explored. Mitochondrial SIRT4, which unlike other sirtuins is induced in a fed state, is known to inhibit catabolic signalling/pathways through AMPK-PGC1α/SIRT1-PPARα axis and negatively regulate glutamine metabolism via TCA cycle. However, physiological significance of SIRT4 functions during a fed state is still unknown. Here, we establish SIRT4 as key anabolic factor that activates TORC1 signalling and regulates lipogenesis, autophagy and cell proliferation. Mechanistically, we demonstrate that the ability of SIRT4 to inhibit anaplerotic conversion of glutamine to α-ketoglutarate potentiates TORC1. Interestingly, we also show that mitochondrial glutamine sparing or utilization is critical for differentially regulating TORC1 under fed and fasted conditions. Moreover, we conclusively show that differential expression of SIRT4 during fed and fasted states is vital for coupling mitochondrial energetics and glutamine utilization with anabolic pathways. These significant findings also illustrate that SIRT4 integrates nutrient inputs with mitochondrial retrograde signals to maintain a balance between anabolic and catabolic pathways.
    DOI:  https://doi.org/10.1128/MCB.00212-19
  9. J Biol Chem. 2019 Nov 05. pii: jbc.RA119.011178. [Epub ahead of print]
    Lactate production is a prioritised feature of adipocyte metabolism.
    James R Krycer, Lake-Ee Quek, Deanne Francis, Daniel J Fazakerley, Sarah D Elkington, Alexis Diaz-Vegas, Kristen C Cooke, Fiona C Weiss, Xiaowen Duan, Sergey Kurdyukov, Ping-Xin Zhou, Uttam K Tambar, Akiyoshi Hirayama, Satsuki Ikeda, Yushi Kamei, Tomoyoshi Soga, Gregory J Cooney, David E James.
      Adipose tissue is essential for whole-body glucose homeostasis, with a primary role in lipid storage. It has been previously observed that lactate production is also an important metabolic feature of adipocytes, but its relationship to adipose and whole-body glucose disposal remains unclear. Therefore, using a combination of metabolic labeling techniques, here we closely examined lactate production of cultured and primary mammalian adipocytes. Insulin treatment increased glucose uptake and conversion to lactate, with the latter responding more to insulin than did other metabolic fates of glucose. However, lactate production did not just serve as a mechanism to dispose of excess glucose, since we also observed that lactate production in adipocytes did not solely depend on glucose availability and even occurred independently of glucose metabolism. This suggests that lactate production is prioritized in adipocytes. Furthermore, knocking down lactate dehydrogenase specifically in the fat body of Drosophila flies lowered circulating lactate and improved whole-body glucose disposal. These results emphasize lactate production is an additional metabolic role of adipose tissue beyond lipid storage and release.
    Keywords:  Drosophila; adipocyte; cell metabolism; fat tissue; glucose disposal; insulin; insulin resistance; lactate; metabolic regulation; whole-body glucose homeostasis
    DOI:  https://doi.org/10.1074/jbc.RA119.011178
  10. Am J Med Genet C Semin Med Genet. 2019 Nov 06.
    A dyadic genotype-phenotype approach to diagnostic criteria for Proteus syndrome.
    Julie C Sapp, Anna Buser, Jasmine Burton-Akright, Kim M Keppler-Noreuil, Leslie G Biesecker.
      Phenotype-based diagnostic criteria were developed for Proteus syndrome in 1999 and updated in 2006. Subsequently, the causative mosaic gene alteration was discovered, the c.49G>A p.E17K variant in AKT1. As well, a number of overlapping overgrowth disorders attributable to mosaic PIK3CA variants have now been characterized, leading to the designation of PIK3CA-related overgrowth spectrum (PROS). Finally, ongoing work to better characterize Proteus syndrome has led to identification of additional features of that disorder that could be useful in diagnostic criteria. We have taken the opportunity of these discoveries to re-evaluate the Proteus syndrome diagnostic criteria. Here we propose a new set of diagnostic criteria that establishes a weighted, point-based system for the phenotypic attributes and then integrates that with the potential molecular test results to result in one of two designations: AKT1-related Proteus syndrome or AKT1-related overgrowth spectrum. A patient whose only manifestation is an AKT1 c.49G>A-positive tumor would receive neither of these designations. Here we review the rational basis of diagnostic criteria and argue that a unitary diagnostic entity is a distinct gene-phenotype dyad and that this should be the model for all mendelian disorders. The gene-alone or phenotype-alone approach is inadequate to rigorously delineate a unitary diagnostic entity.
    DOI:  https://doi.org/10.1002/ajmg.c.31744
  11. Nat Cell Biol. 2019 Nov 04.
    PTENα and PTENβ promote carcinogenesis through WDR5 and H3K4 trimethylation.
    Shao-Ming Shen, Cheng Zhang, Meng-Kai Ge, Shuang-Shu Dong, Li Xia, Ping He, Na Zhang, Yan Ji, Shuo Yang, Yun Yu, Jun-Ke Zheng, Jian-Xiu Yu, Qiang Xia, Guo-Qiang Chen.
      PTENα and PTENβ are two longer translational variants of phosphatase and tensin homolog (PTEN) messenger RNA. Their expressional regulations and functions in carcinogenesis remain largely unknown. Here, we demonstrate that, in contrast with the well-established tumour-suppressive role of canonical PTEN, PTENα and PTENβ promote tumourigenesis by directly interacting with the histone H3 lysine 4 (H3K4) presenter WDR5 to promote H3K4 trimethylation and maintain a tumour-promoting signature. We also show that USP9X and FBXW11 bind to the amino-terminal extensions of PTENα/β, and respectively deubiquitinate and ubiquitinate lysines 235 and 239 in PTENα to regulate PTENα/β stability. In accordance, USP9X promotes tumourigenesis and FBXW11 suppresses tumourigenesis through PTENα/β. Taken together, our results indicate that the Pten gene is a double-edged sword for carcinogenesis, and reinterpretation of the importance of the Pten gene in carcinogenesis is warranted.
    DOI:  https://doi.org/10.1038/s41556-019-0409-z
  12. FASEB J. 2019 Nov 06. fj201900782R
    SIRT1 facilitates primordial follicle recruitment independent of deacetylase activity through directly modulating Akt1 and mTOR transcription.
    Tuo Zhang, Xinhua Du, Lihua Zhao, Meina He, Lin Lin, Chuanhui Guo, Xinran Zhang, Jun Han, Hao Yan, Kun Huang, Guanghong Sun, Lei Yan, Bo Zhou, Guoliang Xia, YingYing Qin, Chao Wang.
      In female mammals, the majority of primordial follicles (PFs) are physiologically quiescent, and only a few of them are activated and enter the growing follicle pool. Specific molecules, such as mammalian target of rapamycin (mTOR) and the serine/threonine kinase Akt (AKT), have been proven to be important for PF activation. However, how the transcription of these genes is regulated is not clear. Although activators of mTOR or AKT have been successfully used to rescue the fertility of patients with premature ovarian insufficiency, the low efficacy and unclear safety profile of these drugs hinder their clinical use in the in vitro activation (IVA) of PFs. Here, sirtuin 1 (SIRT1), an NAD-dependent deacetylase, was demonstrated to activate mouse PFs independent of its deacetylase activity. SIRT1 was prominently expressed in pregranulosa cells (pGCs) and oocytes, and its expression was increased during PF activation. PF activation was achieved by either up-regulating SIRT1 with a specific activator or overexpressing SIRT1. Moreover, SIRT1 knockdown in oocytes or pGCs could significantly suppress PF activation. Further studies demonstrated that SIRT1 enhanced both Akt1 and mTOR expression by acting more as a transcription cofactor, directly binding to the respective gene promoters, than as a deacetylase. Importantly, we explored the potential clinical applications of targeting SIRT1 in IVA via short-term treatment of cultured ovaries from mice and human ovarian tissues to activate PFs by applying the SIRT1 activator resveratrol. RSV-induced IVA could be a candidate strategy to develop more efficient procedures for future clinical treatment of infertility.-Zhang, T., Du, X., Zhao, L., He, M., Lin, L., Guo, C., Zhang, X., Han, J., Yan, H., Huang, K., Sun, G., Yan, L., Zhou, B., Xia, G., Qin, Y., Wang, C. SIRT1 facilitates primordial follicle recruitment independent of deacetylase activity through directly modulating Akt1 and mTOR transcription.
    Keywords:  in vitro activation; ovary; primordial follicle activation; resveratrol
    DOI:  https://doi.org/10.1096/fj.201900782R
  13. Nat Struct Mol Biol. 2019 Nov 06.
    An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome.
    Chenxu Zhu, Miao Yu, Hui Huang, Ivan Juric, Armen Abnousi, Rong Hu, Jacinta Lucero, M Margarita Behrens, Ming Hu, Bing Ren.
      Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.
    DOI:  https://doi.org/10.1038/s41594-019-0323-x
  14. Int J Mol Sci. 2019 Oct 31. pii: E5443. [Epub ahead of print]20(21):
    A Crucial Role for the Small GTPase Rac1 Downstream of the Protein Kinase Akt2 in Insulin Signaling that Regulates Glucose Uptake in Mouse Adipocytes.
    Nobuyuki Takenaka, Mika Nakao, Sayaka Matsui, Takaya Satoh.
      Insulin-stimulated glucose uptake is mediated by translocation of the glucose transporter GLUT4 to the plasma membrane in adipocytes and skeletal muscle cells. In both types of cells, phosphoinositide 3-kinase and the protein kinase Akt2 have been implicated as critical regulators. In skeletal muscle, the small GTPase Rac1 plays an important role downstream of Akt2 in the regulation of insulin-stimulated glucose uptake. However, the role for Rac1 in adipocytes remains controversial. Here, we show that Rac1 is required for insulin-dependent GLUT4 translocation also in adipocytes. A Rac1-specific inhibitor almost completely suppressed GLUT4 translocation induced by insulin or a constitutively activated mutant of phosphoinositide 3-kinase or Akt2. Constitutively activated Rac1 also enhanced GLUT4 translocation. Insulin-induced, but not constitutively activated Rac1-induced, GLUT4 translocation was abrogated by inhibition of phosphoinositide 3-kinase or Akt2. On the other hand, constitutively activated Akt2 caused Rac1 activation, and insulin-induced Rac1 activation was suppressed by an Akt2-specific inhibitor. Moreover, GLUT4 translocation induced by a constitutively activated mutant of Akt2 or Rac1 was diminished by knockdown of another small GTPase RalA. RalA was activated by a constitutively activated mutant of Akt2 or Rac1, and insulin-induced RalA activation was suppressed by an Akt2- or Rac1-specific inhibitor. Collectively, these results suggest that Rac1 plays an important role in the regulation of insulin-dependent GLUT4 translocation downstream of Akt2, leading to RalA activation in adipocytes.
    Keywords:  Akt2; GLUT4; GTPase; Rac1; adipocyte; glucose uptake; insulin
    DOI:  https://doi.org/10.3390/ijms20215443
  15. Biomolecules. 2019 Nov 07. pii: E713. [Epub ahead of print]9(11):
    The Mechanisms Underlying PTEN Loss in Human Tumors Suggest Potential Therapeutic Opportunities.
    Hyeyoun Chang, Zhenying Cai, Thomas M Roberts.
      In this review, we will first briefly describe the diverse molecular mechanisms associated with PTEN loss of function in cancer. We will then proceed to discuss the molecular mechanisms linking PTEN loss to PI3K activation and demonstrate how these mechanisms suggest possible therapeutic approaches for patients with PTEN-null tumors.
    Keywords:  PI3K; PTEN; cancer
    DOI:  https://doi.org/10.3390/biom9110713
  16. J Clin Invest. 2019 Nov 05. pii: 127425. [Epub ahead of print]
    Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models.
    Santiago Ruiz, Haitian Zhao, Pallavi Chandakkar, Julien Papoin, Hyunwoo Choi, Aya Nomura-Kitabayashi, Radhika Patel, Matthew Gillen, Li Diao, Prodyot K Chatterjee, Mingzhu He, Yousef Al-Abed, Ping Wang, Christine N Metz, S Paul Oh, Lionel Blanc, Fabien Campagne, Philippe Marambaud.
      Hereditary hemorrhagic telangiectasia (HHT), a genetic bleeding disorder leading to systemic arteriovenous malformations (AVMs), is caused by loss-of-function mutations in the ALK1-ENG-Smad1/5/8 pathway. Evidence suggests that HHT pathogenesis strongly relies on overactivated PI3K-Akt-mTOR and VEGFR2 pathways in endothelial cells (ECs). In the BMP9/10-immunoblocked (BMP9/10ib) neonatal mouse model of HHT, we report here that the mTOR inhibitor, sirolimus, and the receptor tyrosine-kinase inhibitor, nintedanib, could synergistically fully block, but also reversed, retinal AVMs to avert retinal bleeding and anemia. Sirolimus plus nintedanib prevented vascular pathology in the oral mucosa, lungs, and liver of the BMP9/10ib mice, as well as significantly reduced gastrointestinal bleeding and anemia in inducible ALK1-deficient adult mice. Mechanistically, in vivo in BMP9/10ib mouse ECs, sirolimus and nintedanib blocked the overactivation of mTOR and VEGFR2, respectively. Furthermore, we found that sirolimus activated ALK2-mediated Smad1/5/8 signaling in primary ECs-including in HHT patient blood outgrowth ECs-and partially rescued Smad1/5/8 activity in vivo in BMP9/10ib mouse ECs. These data demonstrate that the combined correction of endothelial Smad1/5/8, mTOR, and VEGFR2 pathways opposes HHT pathogenesis. Repurposing of sirolimus plus nintedanib might provide therapeutic benefit in HHT patients.
    Keywords:  Cell Biology; Drug therapy; Genetic diseases; Mouse models; Vascular Biology
    DOI:  https://doi.org/10.1172/JCI127425
  17. Cell. 2019 Nov 05. pii: S0092-8674(19)31213-9. [Epub ahead of print]
    Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
    Kuang Shen, Kacper B Rogala, Hui-Ting Chou, Rick K Huang, Zhiheng Yu, David M Sabatini.
      mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
    DOI:  https://doi.org/10.1016/j.cell.2019.10.036
  18. Nucleic Acids Res. 2019 Nov 08. pii: gkz1023. [Epub ahead of print]
    LINCS Data Portal 2.0: next generation access point for perturbation-response signatures.
    Vasileios Stathias, John Turner, Amar Koleti, Dusica Vidovic, Daniel Cooper, Mehdi Fazel-Najafabadi, Marcin Pilarczyk, Raymond Terryn, Caty Chung, Afoma Umeano, Daniel J B Clarke, Alexander Lachmann, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C Schürer.
      The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures by utilizing a diverse collection of perturbations across many model systems and assay types. The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized. Here, we report the first major update of LDP (http://lincsportal.ccs.miami.edu/signatures) with substantial changes in the data architecture and APIs, a completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries. A newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
    DOI:  https://doi.org/10.1093/nar/gkz1023
  19. Mol Cancer Res. 2019 Nov 08. pii: molcanres.0748.2019. [Epub ahead of print]
    Lysine-specific demethylase 1 mediates AKT activity and promotes epithelial-mesenchymal transition in PIK3CA mutant colorectal cancer.
    Samuel A Miller, Robert A Policastro, Sudha S Savant, Shruthi Sriramkumar, Ning Ding, Xiaoyu Lu, Helai P Mohammad, Sha Cao, Jay H Kalin, Philip A Cole, Gabriel E Zentner, Heather M O'Hagan.
      Activation of the epithelial-mesenchymal transition (EMT) program is a critical mechanism for initiating cancer progression and migration. Colorectal cancers (CRCs) contain many genetic and epigenetic alterations that can contribute to EMT. Mutations activating the PI3K/AKT signaling pathway are observed in >40% of patients with CRC contributing to increased invasion and metastasis. Little is known about how oncogenic signaling pathways such as PI3K/AKT synergize with chromatin modifiers to activate the EMT program. Lysine Specific Demethylase 1 (LSD1) is a chromatin-modifying enzyme that is overexpressed in colorectal cancer (CRC) and enhances cell migration. In this study we determine that LSD1 expression is significantly elevated in CRC patients with mutation of the catalytic subunit of PI3K, PIK3CA, compared to CRC patients with WT PIK3CA. LSD1 enhances activation of the AKT kinase in CRC cells through a non-catalytic mechanism, acting as a scaffolding protein for the transcription-repressing CoREST complex. Additionally, growth of PIK3CA mutant CRC cells is uniquely dependent on LSD1. Knockdown or CRISPR knockout of LSD1 blocks AKT-mediated stabilization of the EMT-promoting transcription factor Snail and effectively blocks AKT-mediated EMT and migration. Overall we uniquely demonstrate that LSD1 mediates AKT activation in response to growth factors and oxidative stress, and LSD1-regulated AKT activity promotes EMT-like characteristics in a subset of PIK3CA mutant cells. Implications: Our data supports the hypothesis that inhibitors targeting the CoREST complex may be clinically effective in CRC patients harboring PIK3CA mutations.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-19-0748
  20. Mol Cell Oncol. 2019 ;6(6): e1625620
    Chromatin regulation at the intersection of estrogen receptor and PI3K pathways in breast cancer.
    Pau Castel, Eneda Toska.
      Estrogen Receptor (ER) and the phosphoinositide 3-kinase (PI3K) pathways participate in regulatory crosstalk in breast cancer. We identified that chromatin regulation is at the intersection of oncogenic PI3K and ER. The PI3K effectors AKT, also known as protein kinase B (PKB), and SGK (serum/glucocorticoid-regulated kinase) play a redundant role by phosphorylating the chromatin regulator KMT2D and modulating ER activity and therapy resistance.
    Keywords:  AKT1; KMT2D; PI3K inhibitors; PI3K pathway; SGK1; breast cancer; chromatin regulation; estrogen receptor; therapy resistance
    DOI:  https://doi.org/10.1080/23723556.2019.1625620
  21. FEBS J. 2019 Nov 06.
    Phosphoinositides in Autophagy: Current Roles and Future Insights.
    Lavinia Palamiuc, Archna Ravi, Brooke M Emerling.
      Today the importance of autophagy in physiological processes and pathological conditions is undeniable. Initially autophagy merely was described as an evolutionarily conserved mechanism to maintain metabolic homeostasis in times of starvation, however in recent years it is now apparent that autophagy is a powerful regulator of many facets of cellular metabolism, that its deregulation contributes to various human pathologies, including cancer and neurodegeneration, and its modulation has considerable potential as a therapeutic approach. Different lipid species, including sphingolipids, sterols, and phospholipids play important roles in the various steps of autophagy. In particular, there is accumulating evidence indicating the minor group of phospholipids called the phosphoinositides as key modulators of autophagy, including the signaling processes underlying autophagy initiation, autophagosome biogenesis and maturation. In this review we discuss the known functions to date of the phosphoinositides in autophagy and attempt to summarize the kinases and phosphatases that regulate them as well as the proteins that bind to them throughout the autophagy program. We will also provide examples of how the control of phosphoinositides and their metabolizing enzymes is relevant to understanding many human diseases.
    Keywords:  autophagy; lysosome; mTORC1; phosphoinositide; phosphoinositide kinase; phosphoinositide phosphatase
    DOI:  https://doi.org/10.1111/febs.15127
  22. Cell Rep. 2019 Nov 05. pii: S2211-1247(19)31298-7. [Epub ahead of print]29(6): 1660-1674.e7
    An Immunocompetent Mouse Model of HPV16(+) Head and Neck Squamous Cell Carcinoma.
    Miranda B Carper, Scott Troutman, Bethany L Wagner, Kevin M Byrd, Sara R Selitsky, Kshitij Parag-Sharma, Erin C Henry, Weimin Li, Joel S Parker, Stephanie A Montgomery, John L Cleveland, Scott E Williams, Joseph L Kissil, David N Hayes, Antonio L Amelio.
      The incidence of human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) is increasing and implicated in more than 60% of all oropharyngeal carcinomas (OPSCCs). Although whole-genome, transcriptome, and proteome analyses have identified altered signaling pathways in HPV-induced HNSCCs, additional tools are needed to investigate the unique pathobiology of OPSCC. Herein, bioinformatics analyses of human HPV(+) HNSCCs revealed that all tumors express full-length E6 and identified molecular subtypes based on relative E6 and E7 expression levels. To recapitulate the levels, stoichiometric ratios, and anatomic location of E6/E7 expression, we generated a genetically engineered mouse model whereby balanced expression of E6/E7 is directed to the oropharyngeal epithelium. The addition of a mutant PIK3CAE545K allele leads to the rapid development of pre-malignant lesions marked by immune cell accumulation, and a subset of these lesions progress to OPSCC. This mouse provides a faithful immunocompetent model for testing treatments and investigating mechanisms of immunosuppression.
    Keywords:  GEMM, human papilloma virus; HNSCC; HPV; HPV16; LumiFluor; OPSCC; genetically engineered mouse model; head and neck squamous cell carcinoma; immunocompetent; oncogene; oropharyngeal squamous cell carcinoma; tumor suppressor; tumorigenesis
    DOI:  https://doi.org/10.1016/j.celrep.2019.10.005
  23. Nat Rev Mol Cell Biol. 2019 Nov 05.
    Unravelling cellular relationships during development and regeneration using genetic lineage tracing.
    Chloé S Baron, Alexander van Oudenaarden.
      Tracking the progeny of single cells is necessary for building lineage trees that recapitulate processes such as embryonic development and stem cell differentiation. In classical lineage tracing experiments, cells are fluorescently labelled to allow identification by microscopy of a limited number of cell clones. To track a larger number of clones in complex tissues, fluorescent proteins are now replaced by heritable DNA barcodes that are read using next-generation sequencing. In prospective lineage tracing, unique DNA barcodes are introduced into single cells through genetic manipulation (using, for example, Cre-mediated recombination or CRISPR-Cas9-mediated editing) and tracked over time. Alternatively, in retrospective lineage tracing, naturally occurring somatic mutations can be used as endogenous DNA barcodes. Finally, single-cell mRNA-sequencing datasets that capture different cell states within a developmental or differentiation trajectory can be used to recapitulate lineages. In this Review, we discuss methods for prospective or retrospective lineage tracing and demonstrate how trajectory reconstruction algorithms can be applied to single-cell mRNA-sequencing datasets to infer developmental or differentiation tracks. We discuss how these approaches are used to understand cell fate during embryogenesis, cell differentiation and tissue regeneration.
    DOI:  https://doi.org/10.1038/s41580-019-0186-3
  24. Oncogene. 2019 Nov 06.
    A CD133-AKT-Wnt signaling axis drives glioblastoma brain tumor-initiating cells.
    Branavan Manoranjan, Chirayu Chokshi, Chitra Venugopal, Minomi Subapanditha, Neil Savage, Nazanin Tatari, John P Provias, Naresh K Murty, Jason Moffat, Bradley W Doble, Sheila K Singh.
      Mechanistic insight into signaling pathways downstream of surface receptors has been revolutionized with integrated cancer genomics. This has fostered current treatment modalities, namely immunotherapy, to capitalize on targeting key oncogenic signaling nodes downstream of a limited number of surface markers. Unfortunately, rudimentary mechanistic understanding of most other cell surface proteins has reduced the clinical utility of these markers. CD133 has reproducibly been shown to correlate with disease progression, recurrence, and poor overall survivorship in the malignant adult brain tumor, glioblastoma (GBM). Using several patient-derived CD133high and CD133low GBMs we describe intrinsic differences in determinants of stemness, which we owe to a CD133-AKT-Wnt signaling axis in which CD133 functions as a putative cell surface receptor for AKT-dependent Wnt activation. These findings may have implications for personalized oncology trials targeting PI3K/AKT or Wnt as both pathways may be activated independent of their canonical drivers, leading to treatment resistance and disease relapse.
    DOI:  https://doi.org/10.1038/s41388-019-1086-x
  25. Semin Cancer Biol. 2019 Nov 02. pii: S1044-579X(19)30373-6. [Epub ahead of print]
    Special issue: PI3K/Akt Signaling in Human Cancer.
    Avaniyapuram Kannan Murugan.
      
    DOI:  https://doi.org/10.1016/j.semcancer.2019.10.022
  26. Cell Mol Life Sci. 2019 Nov 06.
    Tumor angiogenesis: causes, consequences, challenges and opportunities.
    Roberta Lugano, Mohanraj Ramachandran, Anna Dimberg.
      Tumor vascularization occurs through several distinct biological processes, which not only vary between tumor type and anatomic location, but also occur simultaneously within the same cancer tissue. These processes are orchestrated by a range of secreted factors and signaling pathways and can involve participation of non-endothelial cells, such as progenitors or cancer stem cells. Anti-angiogenic therapies using either antibodies or tyrosine kinase inhibitors have been approved to treat several types of cancer. However, the benefit of treatment has so far been modest, some patients not responding at all and others acquiring resistance. It is becoming increasingly clear that blocking tumors from accessing the circulation is not an easy task to accomplish. Tumor vessel functionality and gene expression often differ vastly when comparing different cancer subtypes, and vessel phenotype can be markedly heterogeneous within a single tumor. Here, we summarize the current understanding of cellular and molecular mechanisms involved in tumor angiogenesis and discuss challenges and opportunities associated with vascular targeting.
    Keywords:  Angiogenesis; Anti-angiogenic therapy; Cancer; Endothelial; VEGF; Vascular targeting
    DOI:  https://doi.org/10.1007/s00018-019-03351-7
  27. Nucleic Acids Res. 2019 Nov 06. pii: gkz1031. [Epub ahead of print]
    The reactome pathway knowledgebase.
    Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw, Fred Loney, Bruce May, Marija Milacic, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio.
      The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.
    DOI:  https://doi.org/10.1093/nar/gkz1031
  28. J Physiol. 2019 Nov 07.
    Insulin-induced membrane permeability to glucose in human muscles at rest and following exercise.
    Glenn K McConell, Kim A Sjøberg, Frederik Ceutz, Lasse Gliemann, Michael P Nyberg, Ylva Hellsten, Christian Frøsig, Bente Kiens, Jørgen F P Wojtaszewski, Erik A Richter.
      KEY POINTS: Increased insulin action is an important component of the health benefits of exercise, but its regulation is complex and not fully elucidated. Previous studies of insulin-stimulated GLUT4 translocation to the skeletal muscle membrane found insufficient increases to explain the increases in glucose uptake. By determination of leg glucose uptake and interstitial muscle glucose concentration we calculated insulin-induced muscle membrane permeability to glucose 4 h after one-legged knee-extensor exercise during a submaximal euglycaemic hyperinsulinaemic clamp. We found during submaximal insulin stimulation that muscle membrane permeability to glucose in humans increases twice as much in previously exercised vs. rested muscle and it outstrips the supply of glucose which then becomes limiting for glucose uptake. This methodology can now be employed to determine muscle membrane permeability to glucose in people with diabetes, who have reduced insulin action, and in principle can also be used to determine membrane permeability to other substrates or metabolites.ABSTRACT: Increased insulin action is an important component of the health benefits of exercise, but the regulation of insulin action in vivo is complex and not fully elucidated. Increases in skeletal muscle insulin-stimulated GLUT4 translocation are inconsistent and mostly cannot explain the increases in insulin action in humans. Here we used leg glucose uptake (LGU) and interstitial muscle glucose concentration to calculate insulin-induced muscle membrane permeability to glucose, a variable not previously possible to quantify in humans. Muscle membrane permeability to glucose, measured 4 h after one-legged knee-extensor exercise, increased ∼17-fold during a submaximal euglycaemic hyperinsulinaemic clamp in rested muscle (R) and ∼36-fold in exercised muscle (EX). Femoral arterial infusion of L-NMMA or ATP decreased and increased, respectively, leg blood flow (LBF) in both legs but did not affect membrane glucose permeability. Decreasing LBF reduced interstitial glucose concentrations to ∼2 mM in the exercised but only to ∼3.5 mM in non-exercised muscle and abrogated the augmented effect of insulin on LGU in the EX leg. Increasing LBF by ATP infusion increased LGU in both legs with uptake higher in the EX leg. We conclude that it is possible to measure functional muscle membrane permeability to glucose in humans and it increases twice as much in exercised vs. rested muscle during submaximal insulin stimulation. We also show that muscle perfusion is an important regulator of muscle glucose uptake when membrane permeability to glucose is high and we show that the capillary wall can be a significant barrier for glucose transport. This article is protected by copyright. All rights reserved.
    Keywords:  Insulin sensitivity; glucose uptake; microdialysis
    DOI:  https://doi.org/10.1113/JP278600
  29. Nucleic Acids Res. 2019 Nov 08. pii: gkz1055. [Epub ahead of print]
    BioModels-15 years of sharing computational models in life science.
    Rahuman S Malik-Sheriff, Mihai Glont, Tung V N Nguyen, Krishna Tiwari, Matthew G Roberts, Ashley Xavier, Manh T Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L Fairbanks, Johannes P Meyer, Chinmay Arankalle, Thawfeek M Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M Keating, Young M Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob.
      Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world's largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.
    DOI:  https://doi.org/10.1093/nar/gkz1055
  30. Nucleic Acids Res. 2019 Nov 06. pii: gkz1019. [Epub ahead of print]
    MetaboLights: a resource evolving in response to the needs of its scientific community.
    Kenneth Haug, Keeva Cochrane, Venkata Chandrasekhar Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan, Claire O'Donovan.
      MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological roles and locations. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information. In this article, we describe the significant updates that we have made over the last two years to the resource to respond to the increasing amount and diversity of data being submitted by the metabolomics community. We refreshed the website and most importantly, our submission process was completely overhauled to enable us to deliver a far more user-friendly submission process and to facilitate the growing demand for reproducibility and integration with other 'omics. Metabolomics resources and data are available under the EMBL-EBI's Terms of Use via the web at https://www.ebi.ac.uk/metabolights and under Apache 2.0 at Github (https://github.com/EBI-Metabolights/).
    DOI:  https://doi.org/10.1093/nar/gkz1019
  31. Int J Radiat Oncol Biol Phys. 2019 Oct 31. pii: S0360-3016(19)33963-X. [Epub ahead of print]
    A Phase Ib Study of Cetuximab and BYL719 (Alpelisib) Concurrent with Intensity-Modulated Radiation Therapy in Stage III-IVB Head and Neck Squamous Cell Carcinoma.
    Lara A Dunn, Nadeem Riaz, Matthew G Fury, Sean M McBride, Loren Michel, Nancy Y Lee, Eric J Sherman, Shrujal S Baxi, Sofia S Haque, Nora Katabi, Richard J Wong, Han Xiao, Alan L Ho, David G Pfister.
      PURPOSE: Activation of the PI3K/mTOR signaling pathway is common in head and neck squamous cell carcinoma (HNSCC). BYL719 is an α-specific PI3K inhibitor that is synergistic and efficacious when combined with cetuximab, an FDA-approved radiosensitizing agent in the treatment of HNSCC. The agent independently has been shown to enhance radiosensitivity. This study evaluates the addition of BYL719 to cetuximab and radiation in the treatment of locally advanced HNSCC.METHODS AND MATERIALS: This is a single-institution, phase I study. Patients with the AJCC 7th Edition stage III-IVB HNSCC received standard cetuximab (400 mg/m2 intravenous loading dose) prior to intensity-modulated radiation therapy (IMRT) followed by 250 mg/m2 weekly infusions during IMRT. BYL719 was given orally during IMRT in 3 dose levels: 1) 200 mg/day, 2) 250 mg/day, or 3) 300 mg/day in a standard 3 + 3 dose-escalation design.
    RESULTS: Eleven patients were evaluable. Dose level 2 was the maximum tolerated dose for BYL719. Two patients on dose level 3 had dose-limiting toxicities (DLTs) of oral mucositis that required a dose reduction of BYL719. One patient on dose level 2 had a DLT of nausea that led to withdrawal of on-study treatment. Related grade 3 or higher adverse events consisted of decreased lymphocyte count, oral mucositis, dysphagia, hyperglycemia, maculopapular rash, and palmar-plantar erythrodysesthesia syndrome. All 11 patients had a complete response on post-treatment imaging and 10 remain disease free. Of the 8 patients with mutational analysis, 1 had an activating PIK3CA mutation associated with a rapid response on serial intra-treatment magnetic resonance imaging scans.
    CONCLUSION: The recommended phase II dose of BYL719 is 250 mg/day in combination with cetuximab and IMRT in patients with locally advanced HNSCC. Further evaluation of the addition of BYL719 to the platinum-sparing regimen of cetuximab and IMRT in the treatment of locally advanced HNSCC is warranted.
    DOI:  https://doi.org/10.1016/j.ijrobp.2019.09.050
  32. Nature. 2019 Nov 06.
    Dynamic lineage priming is driven via direct enhancer regulation by ERK.
    William B Hamilton, Yaron Mosesson, Rita S Monteiro, Kristina B Emdal, Teresa E Knudsen, Chiara Francavilla, Naama Barkai, Jesper V Olsen, Joshua M Brickman.
      Central to understanding cellular behaviour in multi-cellular organisms is the question of how a cell exits one transcriptional state to adopt and eventually become committed to another. Fibroblast growth factor-extracellular signal-regulated kinase (FGF -ERK) signalling drives differentiation of mouse embryonic stem cells (ES cells) and pre-implantation embryos towards primitive endoderm, and inhibiting ERK supports ES cell self-renewal1. Paracrine FGF-ERK signalling induces heterogeneity, whereby cells reversibly progress from pluripotency towards primitive endoderm while retaining their capacity to re-enter self-renewal2. Here we find that ERK reversibly regulates transcription in ES cells by directly affecting enhancer activity without requiring a change in transcription factor binding. ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. Though the binding of mediator components responds directly to signalling, the persistent binding of pluripotency factors to both induced and repressed genes marks them for activation and/or reactivation in response to fluctuations in ERK activity. Among the repressed genes are several core components of the pluripotency network that act to drive their own expression and maintain the ES cell state; if their binding is lost, the ability to reactivate transcription is compromised. Thus, as long as transcription factor occupancy is maintained, so is plasticity, enabling cells to distinguish between transient and sustained signals. If ERK signalling persists, pluripotency transcription factor levels are reduced by protein turnover and irreversible gene silencing and commitment can occur.
    DOI:  https://doi.org/10.1038/s41586-019-1732-z
  33. Pharmacol Res. 2019 Oct 30. pii: S1043-6618(19)31673-1. [Epub ahead of print] 104511
    Targeting glucose metabolism to suppress cancer progression: prospective of anti-glycolytic cancer therapy.
    Ali F Abdel-Wahab, Waheed Mahmoud, Randa M Al-Harizy.
      Most solid tumor cells adapt to their heterogeneous microenvironment by depending largely on aerobic glycolysis for energy production, a phenomenon called the Warburg effect, which is a hallmark of cancer. The altered energy metabolism not only provides cancer cell with ATP for cellular energy, but also generate essential metabolic intermediates that play a pivotal role in the biosynthesis of macromolecules, to support cell proliferation, invasiveness, and chemoresistance. The cellular metabolic reprogramming in cancer is regulated by several oncogenic proteins and tumor suppressors such as hypoxia-inducible factor (HIF-1), Myc, p53, and PI3K/Akt/mTOR pathway. A better understanding of the mechanisms involved in the regulation of aerobic glycolysis can help in developing glycolytic inhibitors as anticancer agents. These metabolic antiglycolytic agents could be more effective if used in drug combinations to combat cancer. Several preclinical and early clinical studies have shown the effectiveness of targeting the glycolytic pathway as a therapeutic approach to suppress cancer progression. This review aimed to present the most recent data on the emerging drug candidate targeting enzymes and intermediates involved in glucose metabolism to provide therapeutic opportunities and challenges for antiglycolytic cancer therapy.
    Keywords:  3-Bromopyruvate (PubChem CID: 70684); Aerobic glycolysis; Dichloroacetate (PubChem CID: 517326); Fasentin (PubChem CID: 879520); Koningic acid (PubChem CID: 124361); Lonidamine (PubChem CID: 39562); Metformin (PubChem CID: 4091); Omeprazole (PubChem CID:4549); Oxamate (PubChem CID: 974); Phloretin (PubChem CID: 4788); Rapamycin (PubChem CID: 5284616); Warburg effect; antiglycolytic agents; cancer therapy
    DOI:  https://doi.org/10.1016/j.phrs.2019.104511
  34. Cell Rep. 2019 Nov 05. pii: S2211-1247(19)31267-7. [Epub ahead of print]29(6): 1511-1523.e5
    Metformin Improves Mitochondrial Respiratory Activity through Activation of AMPK.
    Yu Wang, Hongying An, Ting Liu, Caolitao Qin, Hiromi Sesaki, Shaodong Guo, Sally Radovick, Mehboob Hussain, Akhil Maheshwari, Fredric E Wondisford, Brian O'Rourke, Ling He.
      Impaired mitochondrial respiratory activity contributes to the development of insulin resistance in type 2 diabetes. Metformin, a first-line antidiabetic drug, functions mainly by improving patients' hyperglycemia and insulin resistance. However, its mechanism of action is still not well understood. We show here that pharmacological metformin concentration increases mitochondrial respiration, membrane potential, and ATP levels in hepatocytes and a clinically relevant metformin dose increases liver mitochondrial density and complex 1 activity along with improved hyperglycemia in high-fat- diet (HFD)-fed mice. Metformin, functioning through 5' AMP-activated protein kinase (AMPK), promotes mitochondrial fission to improve mitochondrial respiration and restore the mitochondrial life cycle. Furthermore, HFD-fed-mice with liver-specific knockout of AMPKα1/2 subunits exhibit higher blood glucose levels when treated with metformin. Our results demonstrate that activation of AMPK by metformin improves mitochondrial respiration and hyperglycemia in obesity. We also found that supra-pharmacological metformin concentrations reduce adenine nucleotides, resulting in the halt of mitochondrial respiration. These findings suggest a mechanism for metformin's anti-tumor effects.
    Keywords:  AMPK; Drp1; adenine nucleotides; diabetes; insulin resistance; membrane potential; metformin; mitochondrial respiration/fission
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.070
  35. Nat Cell Biol. 2019 Nov 04.
    PTEN isoforms with dual and opposing function.
    Justin Taylor, Omar Abdel-Wahab.
      
    DOI:  https://doi.org/10.1038/s41556-019-0405-3
  36. Front Oncol. 2019 ;9 1003
    Novel and Alternative Targets Against Breast Cancer Stemness to Combat Chemoresistance.
    Sangita Sridharan, Cory M Howard, Augustus M C Tilley, Boopathi Subramaniyan, Amit K Tiwari, Randall J Ruch, Dayanidhi Raman.
      Breast cancer stem cells (BCSCs) play a vital role in tumor progression and metastasis. They are heterogeneous and inherently radio- and chemoresistant. They have the ability to self-renew and differentiate into non-BCSCs. These determinants of BCSCs including the plasticity between the mesenchymal and epithelial phenotypes often leads to minimal residual disease (MRD), tumor relapse, and therapy failure. By studying the resistance mechanisms in BCSCs, a combinatorial therapy can be formulated to co-target BCSCs and bulk tumor cells. This review addresses breast cancer stemness and molecular underpinnings of how the cancer stemness can lead to pharmacological resistance. This might occur through rewiring of signaling pathways and modulated expression of various targets that support survival and self-renewal, clonogenicity, and multi-lineage differentiation into heterogeneous bulk tumor cells following chemotherapy. We explore emerging novel and alternative molecular targets against BC stemness and chemoresistance involving survival, drug efflux, metabolism, proliferation, cell migration, invasion, and metastasis. Strategic targeting of such vulnerabilities in BCSCs may overcome the chemoresistance and increase the longevity of the metastatic breast cancer patients.
    Keywords:  CSC-directed therapy; breast cancer stemness; chemoresistance; minimal residual disease; novel targets; plasticity; therapy failure
    DOI:  https://doi.org/10.3389/fonc.2019.01003
  37. Elife. 2019 Nov 07. pii: e50900. [Epub ahead of print]8
    Crumbs organizes the transport machinery by regulating apical levels of PI(4,5)P2 in Drosophila.
    Johanna Lattner, Weihua Leng, Elisabeth Knust, Marko Brankatschk, David Flores-Benitez.
      An efficient vectorial intracellular transport machinery depends on a well-established apico-basal polarity and is a prerequisite for the function of secretory epithelia. Despite extensive knowledge on individual trafficking pathways, little is known about the mechanisms coordinating their temporal and spatial regulation. Here, we report that the polarity protein Crumbs is essential for apical plasma membrane phospholipid-homeostasis and efficient apical secretion. Through recruiting βHeavy-Spectrin and MyosinV to the apical membrane, Crumbs maintains the Rab6-, Rab11- and Rab30-dependent trafficking and regulates the lipid phosphatases Pten and Ocrl. Crumbs knock-down results in increased apical levels of PI(4,5)P2 and formation of a novel, Moesin- and PI(4,5)P2-enriched apical membrane sac containing microvilli-like structures. Our results identify Crumbs as an essential hub required to maintain the organization of the apical membrane and the physiological activity of the larval salivary gland.
    Keywords:  D. melanogaster; cell biology
    DOI:  https://doi.org/10.7554/eLife.50900
  38. Cell Rep. 2019 Nov 05. pii: S2211-1247(19)31285-9. [Epub ahead of print]29(6): 1458-1468.e3
    Context Dependency of Epithelial-to-Mesenchymal Transition for Metastasis.
    Tatiana Revenco, Adeline Nicodème, Ievgenia Pastushenko, Magdalena K Sznurkowska, Mathilde Latil, Panagiota A Sotiropoulou, Christine Dubois, Virginie Moers, Sophie Lemaire, Viviane de Maertelaer, Cédric Blanpain.
      Epithelial-to-mesenchymal transition (EMT) has been proposed to be important for metastatic dissemination. However, recent studies have challenged the requirement of EMT for metastasis. Here, we assessed in different models of primary skin squamous cell carcinomas (SCCs) whether EMT is associated with metastasis. The incidence of metastasis was much higher in SCCs presenting EMT compared to SCCs without EMT, supporting the notion that a certain degree of EMT is required to initiate the metastatic cascade in primary skin SCCs. Most circulating tumor cells presented EMT, whereas most lung metastasis did not present EMT, showing that mesenchymal-to-epithelial transition is important for metastatic colonization. In contrast, immunodeficient mice transplanted with SCCs, whether displaying EMT or not, presented metastasis. Altogether, our data demonstrate that the association of EMT and metastasis is model dependent, and metastasis of primary skin SCCs is associated with EMT.
    Keywords:  EMT; MET; cancer; cancer stem cells; circulating tumor cells; metastasis; niche; primary tumor; tumor transplantation
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.081
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