bims-pideca 2019-10-27 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2019–10–27
eleven papers selected by
Ralitsa Radostinova Madsen, University College London

Therapeutic inhibition of mTORC2 rescues the behavioral and neurophysiological abnormalities associated with Pten-deficiency.
Mutations in the sonic hedgehog pathway cause macrocephaly-associated conditions due to crosstalk to the PI3K/AKT/mTOR pathway.
Differential effects of various genetic mouse models of the mechanistic target of rapamycin complex I inhibition on heart failure.
PIK3CA Cooperates with KRAS to Promote MYC Activity and Tumorigenesis via the Bromodomain Protein BRD9.
Nutrient mTORC1 signaling underpins regulatory T cell control of immune tolerance.
Soft tissue angiomatosis: another PIK3CA-related disorder.
Role of mTOR Signaling in Female Reproduction.
Aberrant lipid metabolism as an emerging therapeutic strategy to target cancer stem cells: Concise review.
Pan-cancer whole-genome analyses of metastatic solid tumours.
Structural Mechanisms of PTEN Regulation.
High-performance chemical- and light-inducible recombinases in mammalian cells and mice.

Nat Med. 2019 Oct 21.

Therapeutic inhibition of mTORC2 rescues the behavioral and neurophysiological abnormalities associated with Pten-deficiency.

Chien-Ju Chen, Martina Sgritta, Jacqunae Mays, Hongyi Zhou, Rocco Lucero, Jin Park, I-Ching Wang, Jun Hyoung Park, Benny Abraham Kaipparettu, Loredana Stoica, Paymaan Jafar-Nejad, Frank Rigo, Jeannie Chin, Jeffrey L Noebels, Mauro Costa-Mattioli.

Dysregulation of the mammalian target of rapamycin (mTOR) signaling, which is mediated by two structurally and functionally distinct complexes, mTORC1 and mTORC2, has been implicated in several neurological disorders1-3. Individuals carrying loss-of-function mutations in the phosphatase and tensin homolog (PTEN) gene, a negative regulator of mTOR signaling, are prone to developing macrocephaly, autism spectrum disorder (ASD), seizures and intellectual disability2,4,5. It is generally believed that the neurological symptoms associated with loss of PTEN and other mTORopathies (for example, mutations in the tuberous sclerosis genes TSC1 or TSC2) are due to hyperactivation of mTORC1-mediated protein synthesis1,2,4,6,7. Using molecular genetics, we unexpectedly found that genetic deletion of mTORC2 (but not mTORC1) activity prolonged lifespan, suppressed seizures, rescued ASD-like behaviors and long-term memory, and normalized metabolic changes in the brain of mice lacking Pten. In a more therapeutically oriented approach, we found that administration of an antisense oligonucleotide (ASO) targeting mTORC2's defining component Rictor specifically inhibits mTORC2 activity and reverses the behavioral and neurophysiological abnormalities in adolescent Pten-deficient mice. Collectively, our findings indicate that mTORC2 is the major driver underlying the neuropathophysiology associated with Pten-deficiency, and its therapeutic reduction could represent a promising and broadly effective translational therapy for neurological disorders where mTOR signaling is dysregulated.

DOI: https://doi.org/10.1038/s41591-019-0608-y
Am J Med Genet A. 2019 Oct 22.

Mutations in the sonic hedgehog pathway cause macrocephaly-associated conditions due to crosstalk to the PI3K/AKT/mTOR pathway.

Steven D Klein, Dzung C Nguyen, Viraj Bhakta, Derek Wong, Vivian Y Chang, Tom B Davidson, Julian A Martinez-Agosto.

The hedgehog (Hh) pathway is highly conserved and required for embryonic patterning and determination. Mutations in the Hh pathway are observed in sporadic tumors as well as under syndromic conditions. Common to these syndromes are the findings of polydactyly/syndactyly and brain overgrowth. The latter is also a finding most commonly observed in the cases of mutations in the PI3K/AKT/mTOR pathway. We have identified novel Hh pathway mutations and structural copy number variations in individuals with somatic overgrowth, macrocephaly, dysmorphic facial features, and developmental delay, which phenotypically closely resemble patients with phosphatase and tensin homolog (PTEN) mutations. We hypothesized that brain overgrowth and phenotypic overlap with syndromic overgrowth syndromes in these cases may be due to crosstalk between the Hh and PI3K/AKT/mTOR pathways. To test this, we modeled disease-associated variants by generating PTCH1 and Suppressor of Fused (SUFU) heterozygote cell lines using the CRISPR/Cas9 system. These cells demonstrate activation of PI3K signaling and increased phosphorylation of its downstream target p4EBP1 as well as a distinct cellular phenotype. To further investigate the mechanism underlying this crosstalk, we treated human neural stem cells with sonic hedgehog (SHH) ligand and performed transcriptional analysis of components of the mTOR pathway. These studies identified decreased expression of a set of mTOR negative regulators, leading to its activation. We conclude that there is a significant crosstalk between the SHH and PI3K/AKT/mTOR. We propose that this crosstalk is responsible for why mutations in PTCH1 and SUFU lead to macrocephaly phenotypes similar to those observed in PTEN hamartoma and other overgrowth syndromes associated with mutations in PI3K/AKT/mTOR pathway genes.

DOI: https://doi.org/10.1002/ajmg.a.61368
Geroscience. 2019 Oct 24.

Differential effects of various genetic mouse models of the mechanistic target of rapamycin complex I inhibition on heart failure.

Dao-Fu Dai, Yonggang Liu, Nathan Basisty, Pabalu Karunadharma, Somasish G Dastidar, Ying Ann Chiao, Tony Chen, Richard P Beyer, Michael T Chin, Michael Maccoss, Albert R La Spada, Peter S Rabinovitch.

  Inhibition of mammalian target of rapamycin complex I (mTORC1) by rapamycin improves cardiac function in both aging and heart failure. While the protective mechanisms are not fully understood in mammals, they are presumably mediated through metabolic regulation and suppression of protein translation by reduced phosphorylation of 4EBP1, a target of mTORC1. Using transverse aortic constriction (TAC) and Gαq overexpression-induced heart failure models, we examined the effect of cardiac-specific heterozygous deletion (het) of Raptor, a component of mTORC1, and cardiac-specific transgenic overexpression of wild type or phosphorylation site mutant 4EBP1. In wild-type mice with TAC-induced heart failure, quantitative shotgun proteomics revealed decreased abundance of proteins of mitochondrial metabolism and increased abundance of proteins in oxidative stress response, ubiquitin, and other pathways. The Raptor het ameliorated both TAC- and Gαq overexpression-induced heart failure and the associated proteomic remodeling, especially those pathways involved in mitochondrial function, citric acid cycle, and ubiquitination. In contrast, transgenic overexpression of either wild type or mutant 4EBP1 aggravated TAC and Gαq, consistent with reduced adaptive hypertrophy by suppression of protein translation, in parallel with adverse remodeling of left ventricular proteomes. Partial mTORC1 inhibition by Raptor heterozygous deletion ameliorates heart failure and is associated with better preservation of the mitochondrial proteome; however, this effect does not appear to be mediated through suppression of protein translation by increased 4EBP1. Increased activity of 4EBP1 reduced adaptive hypertrophy and aggravated heart failure, suggesting that protein translation is essential for adaptive hypertrophy in pressure overload.

Keywords:  Aging; Heart failure; Nutrient signaling; Proteomics; mTOR

DOI:  https://doi.org/10.1007/s11357-019-00119-6
Cancers (Basel). 2019 Oct 24. pii: E1634. [Epub ahead of print]11(11):

PIK3CA Cooperates with KRAS to Promote MYC Activity and Tumorigenesis via the Bromodomain Protein BRD9.

Catherine M Bell, Philipp Raffeiner, Jonathan R Hart, Peter K Vogt.

  Tumor formation is generally linked to the acquisition of two or more driver genes that cause normal cells to progress from proliferation to abnormal expansion and malignancy. In order to understand genetic alterations involved in this process, we compared the transcriptomes of an isogenic set of breast epithelial cell lines that are non-transformed or contain a single or double knock-in (DKI) of PIK3CA (H1047R) or KRAS (G12V). Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. This gene signature was mediated in part by the bromodomain-containing protein 9 (BRD9) that was found in the SWI-SNF chromatin-remodeling complex, bound to the MYC super-enhancer locus. Small molecule inhibition of BRD9 reduced MYC transcript levels. Critically, only DKI cells had the capacity for anchorage-independent growth in semi-solid medium, and CRISPR-Cas9 manipulations showed that PIK3CA and BRD9 expression were essential for this phenotype. In contrast, KRAS was necessary for DKI cell migration, and BRD9 overexpression induced the growth of KRAS single mutant cells in semi-solid medium. These results provide new insight into the earliest transforming events driven by oncoprotein cooperation and suggest BRD9 is an important mediator of mutant PIK3CA/KRAS-driven oncogenic transformation.

Keywords:  CRISPR-Cas9; GTPase Kras (KRAS); MYC (c-Myc); bromodomain-containing protein 9 (BRD9); chromatin remodeling; oncogene; phosphatidylinositol 3-kinase (PI 3-kinase); transcriptomics; transformation; tumor cell biology

DOI:  https://doi.org/10.3390/cancers11111634
J Exp Med. 2019 Oct 24. pii: jem.20190848. [Epub ahead of print]

Nutrient mTORC1 signaling underpins regulatory T cell control of immune tolerance.

Mytrang H Do, Xinxin Wang, Xian Zhang, Chun Chou, Briana G Nixon, Kristelle J Capistrano, Min Peng, Alejo Efeyan, David M Sabatini, Ming O Li.

Foxp3+ regulatory T (T reg) cells are pivotal regulators of immune tolerance, with T cell receptor (TCR)-driven activated T reg (aT reg) cells playing a central role; yet how TCR signaling propagates to control aT reg cell responses remains poorly understood. Here we show that TCR signaling induces expression of amino acid transporters, and renders amino acid-induced activation of mTORC1 in aT reg cells. T reg cell-specific ablation of the Rag family small GTPases RagA and RagB impairs amino acid-induced mTORC1 signaling, causing defective amino acid anabolism, reduced T reg cell proliferation, and a rampant autoimmune disorder similar in severity to that triggered by T reg cell-specific TCR deficiency. Notably, T reg cells in peripheral tissues, including tumors, are more sensitive to Rag GTPase-dependent nutrient sensing. Ablation of RagA alone impairs T reg cell accumulation in the tumor, resulting in enhanced antitumor immunity. Thus, nutrient mTORC1 signaling is an essential component of TCR-initiated T reg cell reprogramming, and Rag GTPase activities may be titrated to break tumor immune tolerance.

DOI: https://doi.org/10.1084/jem.20190848
Histopathology. 2019 Oct 20.

Soft tissue angiomatosis: another PIK3CA-related disorder.

Olivia Boccara, Louise Galmiche-Rolland, Bérengère Dadone-Montaudié, Sonia Ariche-Maman, Florence Coulet, Mélanie Eyries, Stéphanie Pannier, Véronique Soupre, Thierry Molina, Florence Pedeutour, Sylvie Fraitag.

   AIM: Angiomatosis of soft tissue (AST) is a, rare, high-flow, intramuscular vascular anomaly. In the context of PTEN hamartoma tumor syndrome (PHTS), this AST is referred to as PTEN hamartoma of soft tissue. Given that AST is observed in patients with no history of PHTS, we hypothesized that non-syndromic AST arises as a consequence of a somatic mutation.
METHODS AND RESULTS: Thirteen patients with histologically confirmed AST were retrospectively studied. Details of the patients' personal and family medical histories and symptoms were retrieved from their medical records. The histological analyses were reviewed, and a tissue sample was used for genetic testing. Somatic mutations in the PIK3CA gene (p.Glu542Lys; p.Glu545Lys; p.His1047Arg) were identified in the tissue samples from seven patients, all of whom had unremarkable medical histories and had presented with a single lesion located in the lower limb. Five pathogenic variations in the PTEN gene (mutations: p.Lys263Arg; c.1026+2T>A; p.Ala126Thr; p.Leu108Arg; deletion, log ratio -0.55) were identified in the lesions of four patients; two of the latter had multifocal lesions. All four patients displayed macrocephaly, three boys presented with penile freckles, but none had a family history of PHTS. There were no histological differences between the PIK3CA and PTEN groups.
CONCLUSIONS: AST can be related to either PTEN or PIK3CA mutations and may be multifocal in PHTS. AST appears to be a manifestation of PHTS that occurs in early childhood. The patient's medical history and clinical presentation should prompt the physician to perform specific genetic testing.

Keywords:  PIK3CA-related overgrowth syndrome; PTEN hamartoma of soft tissue; PTEN hamartoma tumor syndrome; soft tissue angiomatosis

DOI:  https://doi.org/10.1111/his.14021
Front Endocrinol (Lausanne). 2019 ;10 692

Role of mTOR Signaling in Female Reproduction.

Zaixin Guo, Qi Yu.

  Mammalian target of rapamycin (mTOR) is a conserved serine/threonine kinase of the phosphatidylinositol kinase-related kinase family that regulates cell growth, metabolism, and autophagy. Extensive research has linked mTOR to several human diseases including cancer, neurodegenerative disorders, and aging. In this review, recent publications regarding the mechanisms underlying the role of mTOR in female reproduction under physiological and pathological conditions are summarized. Moreover, we assess whether strategies to improve or suppress mTOR expression could have therapeutic potential for reproductive diseases like premature ovarian failure, polycystic ovarian syndrome, and endometriosis.

Keywords:  endometriosis; follicular development; gonadotoxicity; mTOR signaling; oocyte maturation; ovulation; polycystic ovarian syndrome (PCOS); steroidogenesis

DOI:  https://doi.org/10.3389/fendo.2019.00692
Stem Cells. 2019 Oct 24.

Aberrant lipid metabolism as an emerging therapeutic strategy to target cancer stem cells: Concise review.

Malini Visweswaran, Frank Arfuso, Sudha Warrier, Arun Dharmarajan.

  Emerging evidences in cancer metabolomics have identified reprogrammed metabolic pathways to be a major hallmark of cancer, amongst which deregulated lipid metabolism is a prominent field receiving increasing attention. Cancer stem cells (CSCs) comprise <0.1% of the tumour bulk and possess high self-renewal, tumour initiating properties, and are responsible for therapeutic resistance, disease recurrence, and tumour metastasis. Hence, it is imperative to understand the metabolic rewiring occurring in CSCs, especially their lipid metabolism, on which there have been recent reports. CSCs rely highly upon lipid metabolism for maintaining their stemness properties and fulfilling their biomass and energy demands, ultimately leading to cancer growth and invasion. Hence, in this review we will shed light on the aberrant lipid metabolism that CSCs exploit to boost their survival, which comprises upregulation in de novo lipogenesis, lipid droplet synthesis, lipid desaturation, and β-oxidation. Further, the metabolic regulators involved in the process, such as key lipogenic enzymes, are also highlighted. Finally, we also summarise the therapeutic strategies targeting the key regulators involved in CSCs' lipid metabolism, which thereby demonstrate the potential to develop powerful and novel therapeutics against the CSC lipid metabolome. © AlphaMed Press 2019 SIGNIFICANCE STATEMENT: This review describes the significance of altered lipid metabolism present in cancer stem cells (CSCs) originating from various cancers. It discusses the critical metabolic modifications occurring in CSCs that enable advanced growth and tumorigenesis through enhanced dependence on fatty acid synthesis and β-oxidation to fulfil their heightened energy and biomass requirements. Further, this review also summarises the various anti-cancer therapeutic strategies targeting CSC lipid metabolism.

Keywords:  Cancer stem cells; fatty acid synthesis; lipid metabolism; metabolic rewiring; β-oxidation

DOI:  https://doi.org/10.1002/stem.3101
Nature. 2019 Oct 23.

Pan-cancer whole-genome analyses of metastatic solid tumours.

Peter Priestley, Jonathan Baber, Martijn P Lolkema, Neeltje Steeghs, Ewart de Bruijn, Charles Shale, Korneel Duyvesteyn, Susan Haidari, Arne van Hoeck, Wendy Onstenk, Paul Roepman, Mircea Voda, Haiko J Bloemendal, Vivianne C G Tjan-Heijnen, Carla M L van Herpen, Mariette Labots, Petronella O Witteveen, Egbert F Smit, Stefan Sleijfer, Emile E Voest, Edwin Cuppen.

Metastatic cancer is a major cause of death and is associated with poor treatment efficacy. A better understanding of the characteristics of late-stage cancer is required to help adapt personalized treatments, reduce overtreatment and improve outcomes. Here we describe the largest, to our knowledge, pan-cancer study of metastatic solid tumour genomes, including whole-genome sequencing data for 2,520 pairs of tumour and normal tissue, analysed at median depths of 106× and 38×, respectively, and surveying more than 70 million somatic variants. The characteristic mutations of metastatic lesions varied widely, with mutations that reflect those of the primary tumour types, and with high rates of whole-genome duplication events (56%). Individual metastatic lesions were relatively homogeneous, with the vast majority (96%) of driver mutations being clonal and up to 80% of tumour-suppressor genes being inactivated bi-allelically by different mutational mechanisms. Although metastatic tumour genomes showed similar mutational landscape and driver genes to primary tumours, we find characteristics that could contribute to responsiveness to therapy or resistance in individual patients. We implement an approach for the review of clinically relevant associations and their potential for actionability. For 62% of patients, we identify genetic variants that may be used to stratify patients towards therapies that either have been approved or are in clinical trials. This demonstrates the importance of comprehensive genomic tumour profiling for precision medicine in cancer.

DOI: https://doi.org/10.1038/s41586-019-1689-y
Cold Spring Harb Perspect Med. 2019 Oct 21. pii: a036152. [Epub ahead of print]

Structural Mechanisms of PTEN Regulation.

Glenn R Masson, Roger L Williams.

The tumor suppressor phosphatase and tensin homolog on chromosome 10 (PTEN) is a tightly regulated enzyme responsible for dephosphorylating the progrowth lipid messenger molecule phosphatidylinositol 3,4,5-trisphosphate (PIP3) on the plasma membrane. The carboxy-terminal tail (CTT) of PTEN is key for regulation of the enzyme. When phosphorylated, the unstructured CTT interacts with the phosphatase-C2 superdomain to inactivate the enzyme by preventing membrane association. PTEN mutations associated with cancer also inactivate the enzyme. Alternate translation-initiation sites generate extended isoforms of PTEN, such as PTEN-L that has multiple roles in cells. The extended amino-terminal region bears a signal sequence and a polyarginine sequence to facilitate exit from and entry into cells, respectively, and a membrane-binding helix that activates the enzyme. This amino-terminal region also facilitates mitochondrial and nucleolar localization. This review explores PTEN structure and its impact on localization and regulation.

DOI: https://doi.org/10.1101/cshperspect.a036152
Nat Commun. 2019 Oct 24. 10(1): 4845

High-performance chemical- and light-inducible recombinases in mammalian cells and mice.

Benjamin H Weinberg, Jang Hwan Cho, Yash Agarwal, N T Hang Pham, Leidy D Caraballo, Maciej Walkosz, Charina Ortega, Micaela Trexler, Nathan Tague, Billy Law, William K J Benman, Justin Letendre, Jacob Beal, Wilson W Wong.

Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.

DOI: https://doi.org/10.1038/s41467-019-12800-7