bims-pideca 2020-01-19 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2020–01–19
nineteen papers selected by
Ralitsa Radostinova Madsen, University College London

Efficacy of PI3K inhibitors in advanced breast cancer.
Posttranslational Regulation and Conformational Plasticity of PTEN.
Crosstalk between PTEN/PI3K/Akt Signalling and DNA Damage in the Oocyte: Implications for Primordial Follicle Activation, Oocyte Quality and Ageing.
Management of toxicity to isoform α-specific PI3K inhibitors.
Overview of the relevance of PI3K pathway in HR-positive breast cancer.
Biomarkers of response and resistance to PI3K inhibitors in estrogen receptor-positive breast cancer patients and combination therapies involving PI3K inhibitors.
A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.
mTOR at the nexus of nutrition, growth, ageing and disease.
Autophagy drives fibroblast senescence through MTORC2 regulation.
In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.
TrkB hyperactivity contributes to brain dysconnectivity, epileptogenesis, and anxiety in zebrafish model of Tuberous Sclerosis Complex.
Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
Sestrin prevents atrophy of disused and aging muscles by integrating anabolic and catabolic signals.
First-in-human Phase I study to evaluate the brain-penetrant PI3K/mTOR inhibitor GDC-0084 in patients with progressive or recurrent high-grade glioma.
A Phase II Open Label Study of Everolimus in Combination With Endocrine Therapy in Resistant Hormone Receptor-Positive HER2-Negative Advanced Breast Cancer.
Fructose and hepatic insulin resistance.
The PI3K subunits, P110α and P110β are potential targets for overcoming P-gp and BCRP-mediated MDR in cancer.
Therapeutic Targeting of mTORC2 in mTORopathies.
Primary Cilia and Brain Wiring, Connecting the Dots.

Ann Oncol. 2019 Dec;pii: S0923-7534(20)34374-X. [Epub ahead of print]30 Suppl 10 x12-x20

Efficacy of PI3K inhibitors in advanced breast cancer.

B Verret, J Cortes, T Bachelot, F Andre, M Arnedos.

  The phosphoinositide 3 (PI3)-kinase/Akt signaling pathway has always been a focus of interest in breast cancer due to its role in cell growth, cell proliferation, cell migration and deregulated apoptosis. Its activation has been linked to endocrine resistance and worse prognosis in certain subgroups of breast cancer. In addition, deregulation of the PI3K/Akt pathway including PIK3CA activating mutation is frequently present in breast cancer. Multiple efforts have been carried out to target this pathway, initially with pan-PI3K inhibitors with some hint of activity but hampered by their limiting side-effects. A recent large randomized trial in patients with endocrine-resistant PIK3CA-mutant hormone receptor (HR)-positive tumors led to the approval of the first PI3K inhibitor, alpelisib, in combination with fulvestrant. The specificity of alpelisib against the p110α catalytic isoform provided additional efficacy and a better toxicity profile. In this review, we summarize the main research with PI3K inhibitors in breast cancer and we provide some insight of potential future combinations of this treatment in breast cancer patients.

Keywords:  PI3K inhibitors; breast cancer; targeted therapy

DOI:  https://doi.org/10.1093/annonc/mdz381
Cold Spring Harb Perspect Med. 2020 Jan 13. pii: a036095. [Epub ahead of print]

Posttranslational Regulation and Conformational Plasticity of PTEN.

Larissa Kotelevets, Barbara Trifault, Eric Chastre, Mark G H Scott.

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor that is frequently down-modulated in human cancer. PTEN inhibits the phosphatidylinositol 3-phosphate kinase (PI3K)/AKT pathway through its lipid phosphatase activity. Multiple PI3K/AKT-independent actions of PTEN, protein-phosphatase activities and functions within the nucleus have also been described. PTEN, therefore, regulates many cellular processes including cell proliferation, survival, genomic integrity, polarity, migration, and invasion. Even a modest decrease in the functional dose of PTEN may promote cancer development. Understanding the molecular and cellular mechanisms that regulate PTEN protein levels and function, and how these may go awry in cancer contexts, is, therefore, key to fully understanding the role of PTEN in tumorigenesis. Here, we discuss current knowledge on posttranslational control and conformational plasticity of PTEN, as well as therapeutic possibilities toward reestablishment of PTEN tumor-suppressor activity in cancer.

DOI: https://doi.org/10.1101/cshperspect.a036095
Cells. 2020 Jan 14. pii: E200. [Epub ahead of print]9(1):

Crosstalk between PTEN/PI3K/Akt Signalling and DNA Damage in the Oocyte: Implications for Primordial Follicle Activation, Oocyte Quality and Ageing.

Mila Maidarti, Richard A Anderson, Evelyn E Telfer.

  The preservation of genome integrity in the mammalian female germline from primordial follicle arrest to activation of growth to oocyte maturation is fundamental to ensure reproductive success. As oocytes are formed before birth and may remain dormant for many years, it is essential that defence mechanisms are monitored and well maintained. The phosphatase and tensin homolog of chromosome 10 (PTEN)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB, Akt) is a major signalling pathway governing primordial follicle recruitment and growth. This pathway also contributes to cell growth, survival and metabolism, and to the maintenance of genomic integrity. Accelerated primordial follicle activation through this pathway may result in a compromised DNA damage response (DDR). Additionally, the distinct DDR mechanisms in oocytes may become less efficient with ageing. This review considers DNA damage surveillance mechanisms and their links to the PTEN/PI3K/Akt signalling pathway, impacting on the DDR during growth activation of primordial follicles, and in ovarian ageing. Targeting DDR mechanisms within oocytes may be of value in developing techniques to protect ovaries against chemotherapy and in advancing clinical approaches to regulate primordial follicle activation.

Keywords:  DNA damage response (DDR); PTEN/PI3K/Akt; ageing; follicle activation

DOI:  https://doi.org/10.3390/cells9010200
Ann Oncol. 2019 Dec;pii: S0923-7534(20)34376-3. [Epub ahead of print]30 Suppl 10 x21-x26

Management of toxicity to isoform α-specific PI3K inhibitors.

S E Nunnery, I A Mayer.

  Alterations in the phosphoinositide 3-kinase (PI3K)/AKT pathway are frequently found in cancer and are especially common in breast cancer, where it is estimated that 70% of tumors have some type of genetic alteration that could lead to pathway hyperactivation. A variety of PI3K pathway inhibitors have been developed in an attempt to target this pathway and improve cancer control. One of the challenges in treating patients with PI3K/AKT pathway inhibitors is the associated toxicity from on-target and off-target effects. Such side-effects are common, but reversible, and include hyperglycemia, rash, stomatitis, diarrhea, nausea, and fatigue. As a result, dose reductions, treatment delays, and treatment discontinuation are frequently reported. This impairs not only patients' quality of life but also treatment efficacy. Most side-effects are reversible with drug interruption, since these drugs typically have a short half-life and are manageable with early intervention. An interdisciplinary approach with proactive management of patients receiving PI3K pathway inhibitors should include comprehensive education of patients about the range of toxicities, frequent monitoring, early toxicity recognition, active intervention, as well as prophylactic strategies.

Keywords:  PI3K inhibitors; supportive care; toxicities

DOI:  https://doi.org/10.1093/annonc/mdz440
Ann Oncol. 2019 Dec;pii: S0923-7534(20)34373-8. [Epub ahead of print]30 Suppl 10 x3-x11

Overview of the relevance of PI3K pathway in HR-positive breast cancer.

N Vasan, E Toska, M Scaltriti.

  One of the hallmarks of hormone receptor (HR)-positive breast cancer is its dependence on the phosphatidylinositol-3-kinase (PI3K) pathway. Here, we review the epidemiologic, functional, and pharmacologic interactions between oncogenic PI3K and the estrogen receptor (ER). We discuss the epidemiology of PI3K pathway alterations, mechanisms of resistance to PI3K inhibitors, and the current mechanistic landscape of crosstalk between PI3K and ER, which provide the rationale for dual ER and PI3K inhibition and is now a standard of care in the treatment of ER+ PIK3CA-mutant metastatic breast cancer. We outline newer studies in this field that delineate the clinically relevant overlaps between PI3K and parallel signaling pathways, insulin signaling, and ER epigenetic modifiers. We also identify several caveats with the current data and propose new strategies to overcome these bottlenecks.

Keywords:  AKT; PI3K inhibitors; PI3K pathway; PIK3CA; breast cancer; estrogen receptor

DOI:  https://doi.org/10.1093/annonc/mdz281
Ann Oncol. 2019 Dec;pii: S0923-7534(20)34372-6. [Epub ahead of print]30 Suppl 10 x27-x42

Biomarkers of response and resistance to PI3K inhibitors in estrogen receptor-positive breast cancer patients and combination therapies involving PI3K inhibitors.

M Brandão, R Caparica, D Eiger, E de Azambuja.

  In this review, we discuss biomarkers of response and resistance to PI3K inhibitors (PI3Ki) in estrogen receptor-positive breast cancer, both in the early and advanced settings. We analyse data regarding PIK3CA mutations, PI3K pathway activation, PTEN expression loss, Akt signalling, insulin levels, 18FFDG-PET/CT imaging, FGFR1/2 amplification, KRAS and TP53 mutations. Most of the discussed data comprise retrospective and exploratory studies, hence many results are not conclusive. Therefore, among all of these biomarkers, only PIK3CA mutations have proved to have a predictive value for treatment with the α-selective PI3Ki alpelisib (SOLAR-1 trial) and the β-sparing PI3Ki taselisib (SANDPIPER trial) in the advanced setting. Since the accuracy of current individual biomarkers is not optimal, a composite biomarker, including DNA, RNA and protein expression data, to more precisely assess the PI3K/AKT/mTOR pathway activation status, may arise as a promising approach. Finally, we describe the rational for new combination therapies involving PI3Ki and anti-HER2 agents, chemotherapy, CDK4/6 inhibitors, mTOR inhibitors or new endocrine treatments and discuss the ongoing trials in this field.

Keywords:  PI3K inhibitors; PIK3CA; breast neoplasms; gene sequencing; predictive biomarkers

DOI:  https://doi.org/10.1093/annonc/mdz280
Nat Commun. 2020 Jan 16. 11(1): 312

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.

Maria Escala-Garcia, Jean Abraham, Irene L Andrulis, Hoda Anton-Culver, Volker Arndt, Alan Ashworth, Paul L Auer, Päivi Auvinen, Matthias W Beckmann, Jonathan Beesley, Sabine Behrens, Javier Benitez, Marina Bermisheva, Carl Blomqvist, William Blot, Natalia V Bogdanova, Stig E Bojesen, Manjeet K Bolla, Anne-Lise Børresen-Dale, Hiltrud Brauch, Hermann Brenner, Sara Y Brucker, Barbara Burwinkel, Carlos Caldas, Federico Canzian, Jenny Chang-Claude, Stephen J Chanock, Suet-Feung Chin, Christine L Clarke, Fergus J Couch, Angela Cox, Simon S Cross, Kamila Czene, Mary B Daly, Joe Dennis, Peter Devilee, Janet A Dunn, Alison M Dunning, Miriam Dwek, Helena M Earl, Diana M Eccles, A Heather Eliassen, Carolina Ellberg, D Gareth Evans, Peter A Fasching, Jonine Figueroa, Henrik Flyger, Manuela Gago-Dominguez, Susan M Gapstur, Montserrat García-Closas, José A García-Sáenz, Mia M Gaudet, Angela George, Graham G Giles, David E Goldgar, Anna González-Neira, Mervi Grip, Pascal Guénel, Qi Guo, Christopher A Haiman, Niclas Håkansson, Ute Hamann, Patricia A Harrington, Louise Hiller, Maartje J Hooning, John L Hopper, Anthony Howell, Chiun-Sheng Huang, Guanmengqian Huang, David J Hunter, Anna Jakubowska, Esther M John, Rudolf Kaaks, Pooja Middha Kapoor, Renske Keeman, Cari M Kitahara, Linetta B Koppert, Peter Kraft, Vessela N Kristensen, Diether Lambrechts, Loic Le Marchand, Flavio Lejbkowicz, Annika Lindblom, Jan Lubiński, Arto Mannermaa, Mehdi Manoochehri, Siranoush Manoukian, Sara Margolin, Maria Elena Martinez, Tabea Maurer, Dimitrios Mavroudis, Alfons Meindl, Roger L Milne, Anna Marie Mulligan, Susan L Neuhausen, Heli Nevanlinna, William G Newman, Andrew F Olshan, Janet E Olson, Håkan Olsson, Nick Orr, Paolo Peterlongo, Christos Petridis, Ross L Prentice, Nadege Presneau, Kevin Punie, Dhanya Ramachandran, Gad Rennert, Atocha Romero, Mythily Sachchithananthan, Emmanouil Saloustros, Elinor J Sawyer, Rita K Schmutzler, Lukas Schwentner, Christopher Scott, Jacques Simard, Christof Sohn, Melissa C Southey, Anthony J Swerdlow, Rulla M Tamimi, William J Tapper, Manuel R Teixeira, Mary Beth Terry, Heather Thorne, Rob A E M Tollenaar, Ian Tomlinson, Melissa A Troester, Thérèse Truong, Clare Turnbull, Celine M Vachon, Lizet E van der Kolk, Qin Wang, Robert Winqvist, Alicja Wolk, Xiaohong R Yang, Argyrios Ziogas, Paul D P Pharoah, Per Hall, Lodewyk F A Wessels, Georgia Chenevix-Trench, Gary D Bader, Thilo Dörk, Douglas F Easton, Sander Canisius, Marjanka K Schmidt.

Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

DOI: https://doi.org/10.1038/s41467-019-14100-6
Nat Rev Mol Cell Biol. 2020 Jan 14.

mTOR at the nexus of nutrition, growth, ageing and disease.

Grace Y Liu, David M Sabatini.

The mTOR pathway integrates a diverse set of environmental cues, such as growth factor signals and nutritional status, to direct eukaryotic cell growth. Over the past two and a half decades, mapping of the mTOR signalling landscape has revealed that mTOR controls biomass accumulation and metabolism by modulating key cellular processes, including protein synthesis and autophagy. Given the pathway's central role in maintaining cellular and physiological homeostasis, dysregulation of mTOR signalling has been implicated in metabolic disorders, neurodegeneration, cancer and ageing. In this Review, we highlight recent advances in our understanding of the complex regulation of the mTOR pathway and discuss its function in the context of physiology, human disease and pharmacological intervention.

DOI: https://doi.org/10.1038/s41580-019-0199-y
Autophagy. 2020 Jan 13. 1-13

Autophagy drives fibroblast senescence through MTORC2 regulation.

Monique Bernard, Bing Yang, Francis Migneault, Julie Turgeon, Mélanie Dieudé, Marc-Alexandre Olivier, Guillaume B Cardin, Mostafa El-Diwany, Katy Underwood, Francis Rodier, Marie-Josée Hébert.

  Sustained macroautophagy/autophagy favors the differentiation of fibroblasts into myofibroblasts. Cellular senescence, another means of responding to long-term cellular stress, has also been linked to myofibroblast differentiation and fibrosis. Here, we evaluate the relationship between senescence and myofibroblast differentiation in the context of sustained autophagy. We analyzed markers of cell cycle arrest/senescence in fibroblasts in vitro, where autophagy was triggered by serum starvation (SS). Autophagic fibroblasts expressed the senescence biomarkers CDKN1A/p21 and CDKN2A/p16 and exhibited increased senescence-associated GLB1/beta-galactosidase activity. Inhibition of autophagy in serum-starved fibroblasts with 3-methyladenine, LY294002, or ATG7 (autophagy related 7) silencing prevented the expression of senescence-associated markers. Similarly, suppressing MTORC2 activation using rapamycin or by silencing RICTOR also prevented senescence hallmarks. Immunofluorescence microscopy showed that senescence and myofibroblast differentiation were induced in different cells, suggesting mutually exclusive activation of senescence and myofibroblast differentiation. Reactive oxygen species (ROS) are known inducers of senescence and exposing fibroblasts to ROS scavengers decreased ROS production during SS, inhibited autophagy, and significantly reduced the expression of senescence and myofibroblast differentiation markers. ROS scavengers also curbed the AKT1 phosphorylation at Ser473, an MTORC2 target, establishing the importance of ROS in fueling MTORC2 activation. Inhibition of senescence by shRNA to TP53/p53 and shRNA CDKN2A/p16 increased myofibroblast differentiation, suggesting a negative feedback loop of senescence on autophagy-induced myofibroblast differentiation. Collectively, our results identify ROS as central inducers of MTORC2 activation during chronic autophagy, which in turn fuels senescence activation and myofibroblast differentiation in distinct cellular subpopulations.Abbreviations: 3-MA: 3-methyladenine; ACTA2: actin, alpha 2, smooth muscle, aorta; AKT1: AKT serine/threonine kinase 1; p-AKT1: AKT1 Ser473 phosphorylation; t-AKT1: total AKT serine/threonine kinase 1; ATG4A: autophagy related 4A cysteine peptidase; ATG7: autophagy gene 7; C12FDG: 5-dodecanoylaminofluorescein Di-β-D-Galactopyranoside; CDKN1A: cyclin dependent kinase inhibitor 1A; CDKN2A: cyclin dependent kinase inhibitor 2A; Ctl: control; DAPI: 4',6-diamidino-2-phenylindole, dilactate; ECM: extracellular matrix; GSH: L-glutathione reduced; H2O2: hydrogen peroxide; HLF: adult human lung fibroblasts; Ho: Hoechst 33342 (2'-[4-ethoxyphenyl]-5-[4-methyl-1-piperazinyl]-2.5'-bi-1H-benzimidazole); HSC: hepatic stellate cells; LY: LY294002; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MTORC1/2: mechanistic target of rapamycin kinase complex 1/2; N: normal growth medium; NAC: N-acetyl-L-cysteine; PBS: phosphate-buffered saline; PDGFA: platelet derived growth factor subunit A; PRKCA/PKCα: protein kinase C alpha; PtdIns3K: class III phosphatidylinositol 3-kinase; PTEN: phosphatase and tensin homolog; R: rapamycin; RICTOR: RPTOR independent companion of MTOR complex 2; ROS: reactive oxygen species; RPTOR: regulatory associated protein of MTOR complex 1; SA-GLB1/β-gal: senescence-associated galactosidase beta 1; SGK1: serum/glucocorticoid regulated kinase 1; shRNA: short hairpin RNA; siCtl: control siRNA; siRNA: small interfering RNA; SQSTM1: sequestosome 1; SS: serum-free (serum starvation) medium; TP53: tumor protein p53; TUBA: tubulin alpha; V: vehicle.

Keywords:  Autophagy; MTORC2; myofibroblast; rapamycin; senescence

DOI:  https://doi.org/10.1080/15548627.2020.1713640
EMBO J. 2020 Jan 13. e102169

In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.

Stefano Annunziato, Catrin Lutz, Linda Henneman, Jinhyuk Bhin, Kim Wong, Bjørn Siteur, Bas van Gerwen, Renske de Korte-Grimmerink, Maria Paz Zafra, Emma M Schatoff, Anne Paulien Drenth, Eline van der Burg, Timo Eijkman, Siddhartha Mukherjee, Katharina Boroviak, Lodewyk Fa Wessels, Marieke van de Ven, Ivo J Huijbers, David J Adams, Lukas E Dow, Jos Jonkers.

  Genetically engineered mouse models (GEMMs) of cancer have proven to be of great value for basic and translational research. Although CRISPR-based gene disruption offers a fast-track approach for perturbing gene function and circumvents certain limitations of standard GEMM development, it does not provide a flexible platform for recapitulating clinically relevant missense mutations in vivo. To this end, we generated knock-in mice with Cre-conditional expression of a cytidine base editor and tested their utility for precise somatic engineering of missense mutations in key cancer drivers. Upon intraductal delivery of sgRNA-encoding vectors, we could install point mutations with high efficiency in one or multiple endogenous genes in situ and assess the effect of defined allelic variants on mammary tumorigenesis. While the system also produces bystander insertions and deletions that can stochastically be selected for when targeting a tumor suppressor gene, we could effectively recapitulate oncogenic nonsense mutations. We successfully applied this system in a model of triple-negative breast cancer, providing the proof of concept for extending this flexible somatic base editing platform to other tissues and tumor types.

Keywords:  CRISPR-Cas9; base editing; breast cancer; genetically engineered mouse models; intraductal injections

DOI:  https://doi.org/10.15252/embj.2019102169
Proc Natl Acad Sci U S A. 2020 Jan 13. pii: 201910834. [Epub ahead of print]

TrkB hyperactivity contributes to brain dysconnectivity, epileptogenesis, and anxiety in zebrafish model of Tuberous Sclerosis Complex.

Magdalena Kedra, Katarzyna Banasiak, Katarzyna Kisielewska, Lidia Wolinska-Niziol, Jacek Jaworski, Justyna Zmorzynska.

  Tuberous Sclerosis Complex (TSC) is a rare genetic disease that manifests with early symptoms, including cortical malformations, childhood epilepsy, and TSC-associated neuropsychiatric disorders (TANDs). Cortical malformations arise during embryonic development and have been linked to childhood epilepsy before, but the underlying mechanisms of this relationship remain insufficiently understood. Zebrafish have emerged as a convenient model to study elementary neurodevelopment; however, without in-depth functional analysis, the Tsc2-deficient zebrafish line cannot be used for studies of TANDs or new drug screening. In this study, we found that the lack of Tsc2 in zebrafish resulted in heterotopias and hyperactivation of the mTorC1 pathway in pallial regions, which are homologous to the mammalian cortex. We observed commissural thinning that was responsible for brain dysconnectivity, recapitulating TSC pathology in human patients. The lack of Tsc2 also delayed axonal development and caused aberrant tract fasciculation, corresponding to the abnormal expression of genes involved in axon navigation. The mutants underwent epileptogenesis that resulted in nonmotor seizures and exhibited increased anxiety-like behavior. We further mapped discrete parameters of locomotor activity to epilepsy-like and anxiety-like behaviors, which were rescued by reducing tyrosine receptor kinase B (TrkB) signaling. Moreover, in contrast to treatment with vigabatrin and rapamycin, TrkB inhibition rescued brain dysconnectivity and anxiety-like behavior. These data reveal that commissural thinning results in the aberrant regulation of anxiety, providing a mechanistic link between brain anatomy and human TANDs. Our findings also implicate TrkB signaling in the complex pathology of TSC and reveal a therapeutic target.

Keywords:  TANDs; TrkB; Tuberous Sclerosis Complex; anxiety; brain dysconnectivity

DOI:  https://doi.org/10.1073/pnas.1910834117
Nat Biotechnol. 2020 Jan 13.

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.

Marco Jost, Daniel A Santos, Reuben A Saunders, Max A Horlbeck, John S Hawkins, Sonia M Scaria, Thomas M Norman, Jeffrey A Hussmann, Christina R Liem, Carol A Gross, Jonathan S Weissman.

A lack of tools to precisely control gene expression has limited our ability to evaluate relationships between expression levels and phenotypes. Here, we describe an approach to titrate expression of human genes using CRISPR interference and series of single-guide RNAs (sgRNAs) with systematically modulated activities. We used large-scale measurements across multiple cell models to characterize activities of sgRNAs containing mismatches to their target sites and derived rules governing mismatched sgRNA activity using deep learning. These rules enabled us to synthesize a compact sgRNA library to titrate expression of ~2,400 genes essential for robust cell growth and to construct an in silico sgRNA library spanning the human genome. Staging cells along a continuum of gene expression levels combined with single-cell RNA-seq readout revealed sharp transitions in cellular behaviors at gene-specific expression thresholds. Our work provides a general tool to control gene expression, with applications ranging from tuning biochemical pathways to identifying suppressors for diseases of dysregulated gene expression.

DOI: https://doi.org/10.1038/s41587-019-0387-5
Nat Commun. 2020 Jan 13. 11(1): 189

Sestrin prevents atrophy of disused and aging muscles by integrating anabolic and catabolic signals.

Jessica Segalés, Eusebio Perdiguero, Antonio L Serrano, Pedro Sousa-Victor, Laura Ortet, Mercè Jardí, Andrei V Budanov, Laura Garcia-Prat, Marco Sandri, David M Thomson, Michael Karin, Jun Hee Lee, Pura Muñoz-Cánoves.

A unique property of skeletal muscle is its ability to adapt its mass to changes in activity. Inactivity, as in disuse or aging, causes atrophy, the loss of muscle mass and strength, leading to physical incapacity and poor quality of life. Here, through a combination of transcriptomics and transgenesis, we identify sestrins, a family of stress-inducible metabolic regulators, as protective factors against muscle wasting. Sestrin expression decreases during inactivity and its genetic deficiency exacerbates muscle wasting; conversely, sestrin overexpression suffices to prevent atrophy. This protection occurs through mTORC1 inhibition, which upregulates autophagy, and AKT activation, which in turn inhibits FoxO-regulated ubiquitin-proteasome-mediated proteolysis. This study reveals sestrin as a central integrator of anabolic and degradative pathways preventing muscle wasting. Since sestrin also protected muscles against aging-induced atrophy, our findings have implications for sarcopenia.

DOI: https://doi.org/10.1038/s41467-019-13832-9
Clin Cancer Res. 2020 Jan 14. pii: clincanres.2808.2019. [Epub ahead of print]

First-in-human Phase I study to evaluate the brain-penetrant PI3K/mTOR inhibitor GDC-0084 in patients with progressive or recurrent high-grade glioma.

Patrick Y Wen, Timothy F Cloughesy, Alan G Olivero, Kari M Morrissey, Timothy R Wilson, Xuyang Lu, Lars U Mueller, Alexandre F Coimbra, Benjamin M Ellingson, Elizabeth Gerstner, Eudocia Q Lee, Jordi Rodon.

PURPOSE: GDC-0084 is an oral, brain-penetrant small molecule inhibitor of phosphoinositide 3-kinase (PI3K) and mammalian target of rapamycin (mTOR). A first-in-human, Phase I study was conducted in patients with recurrent high-grade glioma.
EXPERIMENTAL DESIGN: GDC-0084 was administered orally, once-daily to evaluate safety, pharmacokinetics (PK) and activity. Fluorodeoxyglucose positron emission tomography (FDG-PET) was performed to measure metabolic responses.
RESULTS: Forty-seven heavily pretreated patients enrolled in eight cohorts (2-65 mg). Dose-limiting toxicities (DLTs) included one case of Grade 2 bradycardia and Grade 3 myocardial ischemia (15 mg), Grade 3 stomatitis (45 mg) and 2 cases of Grade 3 mucosal inflammation (65 mg); the maximum tolerated dose (MTD) was 45 mg/day. GDC-0084 demonstrated linear and dose-proportional PK, with a half-life (~19 hr) supportive of once-daily dosing. At 45 mg/day, steady-state concentrations exceeded pre-clinical target concentrations producing antitumor activity in xenograft models. FDG-PET in 7 of 27 patients (26%) showed metabolic partial response. At doses ≥ 45 mg/day, a trend towards decreased median SUV in normal brain was observed, suggesting central nervous system penetration of drug. In 2 resection specimens, GDC-0084 was detected at similar levels in tumor and brain tissue, with a brain tissue/tumor to plasma ratio of > 1 and > 0.5 for total and free drug, respectively. Best overall response was stable disease in 19 patients (40%), and progressive disease in 26 patients (55%); 2 patients (4%) were non-evaluable.
CONCLUSIONS: GDC-0084 demonstrated classic PI3K/mTOR-inhibitor related toxicities. FDG-PET and concentration data from brain tumor tissue suggest that GDC-0084 crossed the blood-brain barrier.

DOI: https://doi.org/10.1158/1078-0432.CCR-19-2808
Clin Breast Cancer. 2019 Jun 26. pii: S1526-8209(19)30164-8. [Epub ahead of print]

A Phase II Open Label Study of Everolimus in Combination With Endocrine Therapy in Resistant Hormone Receptor-Positive HER2-Negative Advanced Breast Cancer.

Denise A Yardley, William Liggett, Mark Mainwaring, Aurelio Castrellon, Laura Blakely, Brian Hemphill, Bertrand Anz, Robyn R Young, Mythili Shastry, Laura M DeBusk, John D Hainsworth, Howard A Burris.

   BACKGROUND: Therapies targeting estrogen receptor signaling are standard for patients with hormone receptor (HR)-positive (HR+) metastatic breast cancer (MBC). Dysregulation of the phosphoinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is associated with treatment resistance. Addition of the mTOR inhibitor, everolimus, to exemestane doubled progression-free survival (PFS) in HR+/HER2- MBC patients whose disease had previously progressed during endocrine therapy. In this phase II study, we used everolimus in addition to the most recent endocrine therapy during which a patient's disease progressed, in an attempt to restore and extend the benefit of the antiestrogen therapy in patients with HR+/HER2- MBC.
PATIENTS AND METHODS: Patients with HR+ MBC who progressed on antiestrogen therapy received everolimus (10 mg orally daily) in combination with the antiestrogen therapy most recently administered. Treatment was administered in 4-week cycles and continued until disease progression or unacceptable toxicity. Blood and archival tumor specimens were collected for VeriStrat (Biodesix, Inc) and Foundation One (Foundation Medicine) assays, respectively. Accrual of 42 evaluable patients allowed detection of improvement in median PFS from 2.8 months (expected with hormonal treatment alone) to 5 months (power 80%, α = 5%).
RESULTS: Forty-seven patients were enrolled and treated. After a median follow-up of 22.2 months, median PFS was 6.6 months. Secondary efficacy end points included: overall response rate, 6%; clinical benefit rate, 40%; and median overall survival, 21.1 months. No unexpected toxicity was observed. Efficacy could not be correlated with PI3K/AKT/mTOR alterations or VeriStrat (Biodesix, Inc) prognostic signatures.
CONCLUSION: After progression during antiestrogen therapy, the addition of everolimus, without changing the hormonal therapy, resulted in a median PFS of 6.6 months, suggesting efficacy in patients with HR+/HER2- MBC.

Keywords:  Antiestrogen therapy; Endocrine therapy-resistant breast cancer; HER2-negative breast cancer; Hormone receptor-positive breast cancer; Mammalian target of rapamycin (mTOR) inhibitor

DOI:  https://doi.org/10.1016/j.clbc.2019.06.005
Crit Rev Clin Lab Sci. 2020 Jan 14. 1-15

Fructose and hepatic insulin resistance.

Samir Softic, Kimber L Stanhope, Jeremie Boucher, Senad Divanovic, Miguel A Lanaspa, Richard J Johnson, C Ronald Kahn.

  Excessive caloric intake in a form of high-fat diet (HFD) was long thought to be the major risk factor for development of obesity and its complications, such as fatty liver disease and insulin resistance. Recently, there has been a paradigm shift and more attention is attributed to the effects of sugar-sweetened beverages (SSBs) as one of the culprits of the obesity epidemic. In this review, we present the data invoking fructose intake with development of hepatic insulin resistance in human studies and discuss the pathways by which fructose impairs hepatic insulin action in experimental animal models. First, we described well-characterized pathways by which fructose metabolism indirectly leads to hepatic insulin resistance. These include unequivocal effects of fructose to promote de novo lipogenesis (DNL), impair fatty acid oxidation (FAO), induce endoplasmic reticulum (ER) stress and trigger hepatic inflammation. Additionally, we entertained the hypothesis that fructose can directly impede insulin signaling in the liver. This appears to be mediated by reduced insulin receptor and insulin receptor substrate 2 (IRS2) expression, increased protein-tyrosine phosphatase 1B (PTP1b) activity, whereas knockdown of ketohexokinase (KHK), the rate-limiting enzyme of fructose metabolism, increased insulin sensitivity. In summary, dietary fructose intake strongly promotes hepatic insulin resistance via complex interplay of several metabolic pathways, at least some of which are independent of increased weight gain and caloric intake. The current evidence shows that the fructose, but not glucose, component of dietary sugar drives metabolic complications and contradicts the notion that fructose is merely a source of palatable calories that leads to increased weight gain and insulin resistance.

Keywords:  NAFLD; Sugar; fructose; insulin resistance; obesity; sugar-sweetened beverages

DOI:  https://doi.org/10.1080/10408363.2019.1711360
Mol Cancer. 2020 Jan 17. 19(1): 10

The PI3K subunits, P110α and P110β are potential targets for overcoming P-gp and BCRP-mediated MDR in cancer.

Lei Zhang, Yidong Li, Qianchao Wang, Zhuo Chen, Xiaoyun Li, Zhuoxun Wu, Chaohua Hu, Dan Liao, Wei Zhang, Zhe-Sheng Chen.

   BACKGROUND: PI3K/AKT is a vital signaling pathway in humans. Recently, several PI3K/AKT inhibitors were reported to have the ability to reverse cancer multidrug resistance (MDR); however, specific targets in the PI3K/AKT pathways and the mechanisms associated with MDR have not been found because many of the inhibitors have multiple targets within a large candidate protein pool. AKT activation is one presumed mechanism by which MDR develops during cancer treatment.
METHODS: The effects of inhibiting PI3K 110α and 110β by BAY-1082439 treatment and CRISPR/Cas9 knockout were examined to determine the possible functions of BAY-1082439 and the roles of PI3K 110α and 110β in the reversal of MDR that is mediated by the downregulation of P-gp and BCRP. Inhibition of AKT with GSK-2110183 showed that the downregulation of P-gp and BCRP is independent of generalized AKT inactivation. Immunofluorescence, immunoprecipitation, MTT, flow cytometry and JC-1 staining analyses were conducted to study the reversal of MDR that is mediated by P-gp and BCRP in cancer cells. An ATPase assay and a structural analysis were also used to analyze the potential mechanisms by which BAY-1082439 specifically targets PI3K 110α and 110β and nonspecifically influences P-gp and BCRP.
RESULTS: By inhibiting the activation of the PI3K 110α and 110β catalytic subunits through both the administration of BAY-1082439 and the CRISPR/Cas9 deletion of Pik3ca and Pik3cb, the ATP-binding cassette transporters P-gp/ABCB1 and BCRP/ABCG2 were downregulated, thereby reestablishing the drug sensitivity of human epidermoid carcinoma and non-small cell lung cancer (NSCLC) MDR cells. Inhibition of AKT did not reverse the MDR mediated by P-gp or BCRP. The ABC family proteins and AKT may play MDR-enhancing roles independently.
CONCLUSIONS: The reversal of the dual functions of ABC-transporter-mediated and AKT-activation-enhanced MDR through the inhibition or knockout of PI3K 110α or 110β promises to improve current strategies based on combined drug treatments to overcome MDR challenges.

Keywords:  Breast cancer resistance protein (BCRP/ABCG2/ABCP/MXR); Cancer; Multidrug resistance (MDR); P-glycoprotein (P-gp/ABCB1/MDR1); P110α/PIK3CA; P110β/PIK3CB; PI3K; Reversal of MDR

DOI:  https://doi.org/10.1186/s12943-019-1112-1
Neuron. 2019 Dec 18. pii: S0896-6273(19)31035-9. [Epub ahead of print]104(6): 1032-1033

Therapeutic Targeting of mTORC2 in mTORopathies.

Brianne Dentel, Christine Ochoa Escamilla, Peter T Tsai.

Dysregulated mTOR contributes to neurodevelopmental dysfunction. A new study (Chen et al., 2019) demonstrates that suppression of mTORC2, not mTORC1, ameliorates survival, seizures, and abnormal behaviors in a Pten mutant model, highlighting mTORC2 as a potential therapeutic target in mTORopathies.

DOI: https://doi.org/10.1016/j.neuron.2019.11.026
Dev Cell. 2019 Dec 16. pii: S1534-5807(19)30988-8. [Epub ahead of print]51(6): 661-663

Primary Cilia and Brain Wiring, Connecting the Dots.

Qiong Song, Joseph G Gleeson.

Primary cilia function as cellular signaling hubs, integrating multiple signaling pathways. Patients with the ciliopathy Joubert syndrome have been suggested to have axonal tract defects. In this issue of Developmental Cell, Guo et al. (2019) demonstrate a ciliary signaling requirement for axonal tract development and connectivity through dysregulated PI3K/AKT/ACIII signaling.

DOI: https://doi.org/10.1016/j.devcel.2019.11.017