bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–06–13
twenty-one papers selected by
Ralitsa Radostinova Madsen, University College London
  1. PRMT5-mediated arginine methylation activates AKT kinase to govern tumorigenesis.
  2. Mutational Landscape of PI3K-AKT-mTOR Pathway in Breast Cancer: Implications for Targeted Therapeutics.
  3. The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane.
  4. Combined inhibition of DDR1 and CDK4/6 induces synergistic effects in ER-positive, HER2-negative breast cancer with PIK3CA/AKT1 mutations.
  5. Targeting the SHP2 phosphatase promotes vascular damage and inhibition of tumor growth.
  6. Alpelisib-Induced Diabetic Ketoacidosis: A Case Report and Review of Literature.
  7. Boosting immune surveillance by low-dose PI3K inhibitor facilitates early intervention of breast cancer.
  8. Epithelial cell plasticity: breaking boundaries and changing landscapes.
  9. Rhabdomyosarcoma: How Advanced Molecular Methods Are Shaping the Diagnostic and Therapeutic Paradigm.
  10. Brain insulin signalling in metabolic homeostasis and disease.
  11. "Modulating Phosphoinositide Profiles as a Roadmap for Treatment in Acute Myeloid Leukemia".
  12. Roles for growth factors and mutations in metastatic dissemination.
  13. Random errors in protein synthesis activate an age-dependent program of muscle atrophy in mice.
  14. Effect of PIK3CA variants on glioma-related epilepsy and response to treatment.
  15. Transgenic mouse models of breast cancer.
  16. Universal principles of lineage architecture and stem cell identity in renewing tissues.
  17. Accurate genomic variant detection in single cells with primary template-directed amplification.
  18. CRISPR-Cas9 can cause chromothripsis.
  19. Metabolic decisions in development and disease.
  20. PFC mTOR signaling as a biological signature for cognitive deficits in bipolar disorder without psychosis.
  21. GTTs and ITTs in mice: simple tests, complex answers.
  1. Nat Commun. 2021 06 08. 12(1): 3444
    PRMT5-mediated arginine methylation activates AKT kinase to govern tumorigenesis.
    Shasha Yin, Liu Liu, Charles Brobbey, Viswanathan Palanisamy, Lauren E Ball, Shaun K Olsen, Michael C Ostrowski, Wenjian Gan.
      AKT is involved in a number of key cellular processes including cell proliferation, apoptosis and metabolism. Hyperactivation of AKT is associated with many pathological conditions, particularly cancers. Emerging evidence indicates that arginine methylation is involved in modulating AKT signaling pathway. However, whether and how arginine methylation directly regulates AKT kinase activity remain unknown. Here we report that protein arginine methyltransferase 5 (PRMT5), but not other PRMTs, promotes AKT activation by catalyzing symmetric dimethylation of AKT1 at arginine 391 (R391). Mechanistically, AKT1-R391 methylation cooperates with phosphatidylinositol 3,4,5 trisphosphate (PIP3) to relieve the pleckstrin homology (PH)-in conformation, leading to AKT1 membrane translocation and subsequent activation by phosphoinositide-dependent kinase-1 (PDK1) and the mechanistic target of rapamycin complex 2 (mTORC2). As a result, deficiency in AKT1-R391 methylation significantly suppresses AKT1 kinase activity and tumorigenesis. Lastly, we show that PRMT5 inhibitor synergizes with AKT inhibitor or chemotherapeutic drugs to enhance cell death. Altogether, our study suggests that R391 methylation is an important step for AKT activation and its oncogenic function.
    DOI:  https://doi.org/10.1038/s41467-021-23833-2
  2. J Cancer. 2021 ;12(14): 4408-4417
    Mutational Landscape of PI3K-AKT-mTOR Pathway in Breast Cancer: Implications for Targeted Therapeutics.
    Weikai Xiao, Guochun Zhang, Bo Chen, Xiaoqing Chen, Lingzhu Wen, Jianguo Lai, Xuerui Li, Min Li, Hao Liu, Jing Liu, Han Han-Zhang, Analyn Lizaso, Ning Liao.
      Background: Comprehensive analysis of PI3K-AKT-mTOR pathway gene alterations in breast cancer may be helpful for targeted therapy. Methods: We performed targeted sequencing using a panel of 520 cancer-related genes to investigate gene alterations in the PI3K-AKT-mTOR pathway from 589 consecutive Chinese women diagnosed with stage I-III breast cancer. Analyses of overall survival (OS) were performed using the publicly available clinical and genomic data from METABRIC. Results: PI3K-AKT-mTOR pathway gene alterations were detected in 62.6% (369/589) of our cohort. The most commonly altered genes were PIK3CA (45%), PTEN (7.5%), AKT1 (5.9 %), PIK3R1 (2.7%), and PIK3CG (2%). Four PIK3CA mutations (E545K, H1047R, E542K, and H1047L) were detected in all the breast cancer molecular subtypes. Seven PIK3CA mutations (E545G, E418_L422delinsV, E726K, E110del, G1049R, G118D, and D350G) were only detected in HR+ subtypes. Two PIK3CA mutations (C420R and N345K) were only detected in non-triple-negative subtypes. Most cases with PTEN mutation were HR+/HER2- subtype (77.3%), followed by triple-negative subtype (18.2%). In the METABRIC breast cancer dataset, no significant OS difference was observed between the PIK3CA-mutant and wild-type groups. However, patients with multiple PIK3CA mutations (mOS: 131 vs. 159 months, P= 0.029), or PIK3CA mutations located in the C2 domain had significantly shorter OS (mOS, 130 vs. 154 months, P=0.020) than those without the mutations. Conclusions: Our study reveals the heterogeneity in PI3K-AKT-mTOR pathway among the breast cancer molecular subtypes in our cohort. Moreover, the number and specific sites of PIK3CA mutations have distinct prognostic impact.
    Keywords:  Breast cancer; PI3K-AKT-mTOR pathway; gene alteration; molecular subtypes; prognosis
    DOI:  https://doi.org/10.7150/jca.52993
  3. iScience. 2021 May 21. 24(5): 102438
    The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane.
    Hyunbum Jang, Iris Nira Smith, Charis Eng, Ruth Nussinov.
      Tumor suppressor PTEN, the second most highly mutated protein in cancer, dephosphorylates signaling lipid PIP3 produced by PI3Ks. Excess PIP3 promotes cell proliferation. The mechanism at the membrane of this pivotal phosphatase is unknown hindering drug discovery. Exploiting explicit solvent simulations, we tracked full-length PTEN trafficking from the cytosol to the membrane. We observed its interaction with membranes composed of zwitterionic phosphatidylcholine, anionic phosphatidylserine, and phosphoinositides, including signaling lipids PIP2 and PIP3. We tracked its moving away from the zwitterionic and getting absorbed onto anionic membrane that harbors PIP3. We followed it localizing on microdomains enriched in signaling lipids, as PI3K does, and observed PIP3 allosterically unfolding the N-terminal PIP2 binding domain, positioning it favorably for the polybasic motif interaction with PIP2. Finally, we determined PTEN catalytic action at the membrane, all in line with experimental observations, deciphering the mechanisms of how PTEN anchors to the membrane and restrains cancer.
    Keywords:  Cancer; In Silico Biology; Structural Biology
    DOI:  https://doi.org/10.1016/j.isci.2021.102438
  4. Oncogene. 2021 Jun 09.
    Combined inhibition of DDR1 and CDK4/6 induces synergistic effects in ER-positive, HER2-negative breast cancer with PIK3CA/AKT1 mutations.
    Maryam Shariati, Kurt W Evans, Xiaofeng Zheng, Christopher A Bristow, Patrick Kwok-Shing Ng, Yasmeen Q Rizvi, Coya Tapia, Fei Yang, Alessandro Carugo, Timothy P Heffernan, Michael D Peoples, Debu Tripathy, Funda Meric-Bernstam.
      Molecular alterations in the PI3K/AKT pathway occur frequently in hormone receptor-positive breast tumors. Patients with ER-positive, HER2-negative metastatic breast cancer are often treated with CDK4/6 inhibitors such as palbociclib in combination with endocrine therapy. Although this is an effective regimen, most patients ultimately progress. The purpose of this study was identifying synthetic lethality partners that can enhance palbociclib's antitumor efficacy in the presence of PIK3CA/AKT1 mutations. We utilized a barcoded shRNA library to determine critical targets for survival in isogenic MCF7 cells with PIK3CA/AKT1 mutations. We demonstrated that the efficacy of palbociclib is reduced in the presence of PIK3CA/AKT1 mutations. We also identified that the downregulation of discoidin domain receptor 1 (DDR1) is synthetically lethal with palbociclib. DDR1 knockdown and DDR1 pharmacological inhibitor decreased cell growth and inhibited cell cycle progression in all cell lines, while enhanced the sensitivity of PIK3CA/AKT1 mutant cells to palbociclib. Combined treatment of palbociclib and 7rh further induced cell cycle arrest in PIK3CA/AKT1 mutant cell lines. In vivo, 7rh significantly enhanced palbociclib's antitumor efficacy. Our data indicates that DDR1 inhibition can augment cell cycle suppressive effect of palbociclib and could be effective strategy for targeted therapy of ER-positive, HER2-negative breast cancers with PI3K pathway activation.
    DOI:  https://doi.org/10.1038/s41388-021-01819-0
  5. EMBO Mol Med. 2021 Jun 08. e14089
    Targeting the SHP2 phosphatase promotes vascular damage and inhibition of tumor growth.
    Yuyi Wang, Ombretta Salvucci, Hidetaka Ohnuki, Andy D Tran, Taekyu Ha, Jing-Xin Feng, Michael DiPrima, Hyeongil Kwak, Dunrui Wang, Yanlin Yu, Michael Kruhlak, Giovanna Tosato.
      The tyrosine phosphatase SHP2 is oncogenic in cancers driven by receptor-tyrosine-kinases, and SHP2 inhibition reduces tumor growth. Here, we report that SHP2 is an essential promoter of endothelial cell survival and growth in the remodeling tumor vasculature. Using genetic and chemical approaches to inhibit SHP2 activity in endothelial cells, we show that SHP2 inhibits pro-apoptotic STAT3 and stimulates proliferative ERK1/2 signaling. Systemic SHP2 inhibition in mice bearing tumor types selected for SHP2-independent tumor cell growth promotes degeneration of the tumor vasculature and blood extravasation; reduces tumor vascularity and blood perfusion; and increases tumor necrosis. Reduction of tumor growth ensues, independent of SHP2 targeting in the tumor cells, blocking immune checkpoints, or recruiting macrophages. We also show that inhibiting the Angiopoietin/TIE2/AKT cascade magnifies the vascular and anti-tumor effects of SHP2 inhibition by blocking tumor endothelial AKT signaling, not a target of SHP2. Since the SHP2 and Ang2/TIE2 pathways are active in vascular endothelial cells of human melanoma and colon carcinoma, SHP2 inhibitors alone or with Ang2/TIE2 inhibitors hold promise to effectively target the tumor endothelium.
    Keywords:  SHP2; cancer; endothelial cells; tumor growth; tumor vasculature
    DOI:  https://doi.org/10.15252/emmm.202114089
  6. AACE Clin Case Rep. 2021 Mar-Apr;7(2):7(2): 127-131
    Alpelisib-Induced Diabetic Ketoacidosis: A Case Report and Review of Literature.
    Maritza Carrillo, Renil M Rodriguez, Christopher L Walsh, Megan Mcgarvey.
       Objective: To report the first case of diabetic ketoacidosis (DKA) and its management in a patient with diet-controlled prediabetes and metastatic breast cancer treated with alpelisib, a PI3K (phosphatidylinosiotol-3-kinase) inhibitor.
    Methods: Literature on the topic is reviewed. The case is that of a 66-year-old female with diet-controlled prediabetes and metastatic breast carcinoma who had initiated alpelisib 2 weeks prior to being admitted for diabetic ketoacidosis.
    Results: Admission laboratory examination revealed a blood sugar of 1137 mg/dL, an anion gap of 25, large ketones in urine, and positive acetone in serum. The HbA1c level was 9.4% (79 mmol/mol) on admission, which had been 6.3% (45 mmol/mol) seven months earlier. She was discharged on subcutaneous insulin and instructed to discontinue alpelisib. Alpelisib was restarted 2 days later, which exacerbated her hyperglycemia within 24 hours. In the following months, her hyperglycemia was successfully managed with insulin and a SGLT 2 inhibitor. Unfortunately, her breast cancer progressed, ultimately leading to discontinuation of alpelisib. Blood sugar levels returned to a nondiabetic range upon discontinuation of alpelisib, and she is currently off all antihyperglycemic agents.
    Conclusion: Although PI3KCA inhibitors remain a promising drug in patients with metastatic breast cancer who have not responded to previous treatment, patients must be closely monitored for adverse effects such as hyperglycemia. Hyperglycemia could be a potentially limiting side effect of alpelisib. The optimal management of hyperglycemia induced by alpelisib warrants further research.
    Keywords:  Akt, protein kinase B; DKA; DKA, diabetic ketoacidosis; HbA1c, glycosylated hemoglobin; PI3K, phosphatidylinosiotol-3-kinase; SGLT2, sodium glucose cotransporter 2; alpelisib; oncology; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.aace.2020.11.028
  7. Am J Cancer Res. 2021 ;11(5): 2005-2024
    Boosting immune surveillance by low-dose PI3K inhibitor facilitates early intervention of breast cancer.
    Jinyang Wang, Yuan Zhang, Yi Xiao, Xiangliang Yuan, Ping Li, Xiao Wang, Yimin Duan, Victoria L Seewaldt, Dihua Yu.
      Prevention of estrogen receptor-negative (ER-) breast cancer is an unmet challenge, although tamoxifen and aromatase inhibitors can successfully decrease the incidence of ER-positive (ER+) breast cancer. PI3K pathway activation has been detected in tamoxifen-resistant ER- breast lesions of patients. Here, we further ratified that the PI3K pathway is significantly activated in premalignant ER- breast lesions compared with paired normal tissues of patients, which prompted our assessment of targeting PI3K on inhibition of ER- mammary tumor initiation and progression. Both genetic knockdown of PIK3CA or intervention with low-doses of a PI3K inhibitor (GDC-0941) prevented the dysplasia phenotype of semi-transformed human ER- mammary epithelial cells in 3-dimensional culture in vitro. Importantly, low-dose GDC-0941 treatment significantly delayed mammary tumor initiation in the MMTV-neu mouse model without exhibiting discernable adverse effects. Interestingly, increased CD8+/GZMB+ T-cells were detected in mammary tissue after GDC-0941 treatment, suggesting enhanced immune surveillance. Mechanistically, elevated expression of potent T-cell chemo-attractants, including CCL5 and CXCL10, were detected both in vitro and in vivo after GDC-0941 treatment. Furthermore, inhibition of PI3K significantly increased T-cell recruitment in a CCL5/CXCL10-dependent manner. In human ER- breast cancer, PI3K activation is correlated with significantly reduced CCL5, CXCL10 and CD8A expression, suggesting that the decreased CD8+ T-cell recruitment and escape of immune surveillance may contribute to ER- breast cancer development. In summary, our study indicates that low-dose PI3K inhibitor treatment may intervene early stage ER- breast cancer development by enhancing immune surveillance via CCL5/CXCL10.
    Keywords:  ER- breast cancer; PI3K/Akt; immune surveillance; prevention
  8. EMBO Rep. 2021 Jun 06. e51921
    Epithelial cell plasticity: breaking boundaries and changing landscapes.
    Aleksandra Tata, Ryan D Chow, Purushothama Rao Tata.
      Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize "shape-shifting" mechanisms whereby they alter their form and function at a tissue-wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of "tissue logic" principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the "syntax" of plasticity-i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues-and how these processes can be manipulated for developing novel cancer therapeutics.
    Keywords:  cell plasticity; metaplasia; nearest developmental neighbor; transdifferentiation; transitional zones
    DOI:  https://doi.org/10.15252/embr.202051921
  9. Pediatr Dev Pathol. 2021 Jun 09. 10935266211013621
    Rhabdomyosarcoma: How Advanced Molecular Methods Are Shaping the Diagnostic and Therapeutic Paradigm.
    Petros Giannikopoulos, David M Parham.
      For the past 40 years, progress in rhabdomyosarcoma (RMS) has been focused on understanding its molecular basis and characterizing the mutations that drive its tumorigenesis and progression. Genetic predisposition to RMS has allowed discovery of key genetic pathways and driver mutations. Subclassification of RMS into embryonal (ERMS) and alveolar (ARMS) subtypes has shifted from histology to PAX-FOXO1 fusion status, and new driver mutations have been found in spindle cell RMS. Comprehensive molecular profiling leveraging genome-scale next-generation sequencing (NGS) indicates that the RAS/RAF/PI3K axis is mutated in the majority of ERMS and modulated by downstream effects of PAX-FOXO1 fusions in ARMS. Because of the continued poor outcome of high-risk RMS, a variety of molecular targets have been or are now being tested in current or recent therapy trials. New techniques such as single cell sequencing, spatial multi-omics, and CRISPR/Cas9 genome editing offer potential for further discovery, but a need for clinically annotated specimens persists.
    Keywords:  genetics; genomic studies; precision medicine; rhabdomyosarcoma; therapy
    DOI:  https://doi.org/10.1177/10935266211013621
  10. Nat Rev Endocrinol. 2021 Jun 09.
    Brain insulin signalling in metabolic homeostasis and disease.
    Thomas Scherer, Kenichi Sakamoto, Christoph Buettner.
      Insulin signalling in the central nervous system regulates energy homeostasis by controlling metabolism in several organs and by coordinating organ crosstalk. Studies performed in rodents, non-human primates and humans over more than five decades using intracerebroventricular, direct hypothalamic or intranasal application of insulin provide evidence that brain insulin action might reduce food intake and, more importantly, regulates energy homeostasis by orchestrating nutrient partitioning. This Review discusses the metabolic pathways that are under the control of brain insulin action and explains how brain insulin resistance contributes to metabolic disease in obesity, the metabolic syndrome and type 2 diabetes mellitus.
    DOI:  https://doi.org/10.1038/s41574-021-00498-x
  11. Front Oncol. 2021 ;11 678824
    "Modulating Phosphoinositide Profiles as a Roadmap for Treatment in Acute Myeloid Leukemia".
    Stefano Ratti, Camilla Evangelisti, Sara Mongiorgi, Alessia De Stefano, Antonietta Fazio, Francesca Bonomini, Matilde Y Follo, Irene Faenza, Lucia Manzoli, Bhavwanti Sheth, Magdalena C Vidalle, Scott T Kimber, Nullin Divecha, Lucio Cocco, Roberta Fiume.
      Polyphosphoinositides (PPIns) and their modulating enzymes are involved in regulating many important cellular functions including proliferation, differentiation or gene expression, and their deregulation is involved in human diseases such as metabolic syndromes, neurodegenerative disorders and cancer, including Acute Myeloid Leukemia (AML). Given that PPIns regulating enzymes are highly druggable targets, several studies have recently highlighted the potential of targeting them in AML. For instance many inhibitors targeting the PI3K pathway are in various stages of clinical development and more recently other novel enzymes such as PIP4K2A have been implicated as AML targets. PPIns have distinct subcellular organelle profiles, in part driven by the specific localisation of enzymes that metabolise them. In particular, in the nucleus, PPIns are regulated in response to various extracellular and intracellular pathways and interact with specific nuclear proteins to control epigenetic cell state. While AML does not normally manifest with as many mutations as other cancers, it does appear in large part to be a disease of dysregulation of epigenetic signalling and many novel therapeutics are aimed at reprogramming AML cells toward a differentiated cell state or to one that is responsive to alternative successful but limited AML therapies such as ATRA. Here, we propose that by combining bioinformatic analysis with inhibition of PPIns pathways, especially within the nucleus, we might discover new combination therapies aimed at reprogramming transcriptional output to attenuate uncontrolled AML cell growth. Furthermore, we outline how different part of a PPIns signalling unit might be targeted to control selective outputs that might engender more specific and therefore less toxic inhibitory outcomes.
    Keywords:  AML; PI3K; PIP4K; PLCB1; bioinformatic; epigenetic; phosphoinositides; transdifferentiation
    DOI:  https://doi.org/10.3389/fonc.2021.678824
  12. Biochem Soc Trans. 2021 Jun 08. pii: BST20210048. [Epub ahead of print]
    Roles for growth factors and mutations in metastatic dissemination.
    Nishanth Belugali Nataraj, Ilaria Marrocco, Yosef Yarden.
      Cancer is initiated largely by specific cohorts of genetic aberrations, which are generated by mutagens and often mimic active growth factor receptors, or downstream effectors. Once initiated cells outgrow and attract blood vessels, a multi-step process, called metastasis, disseminates cancer cells primarily through vascular routes. The major steps of the metastatic cascade comprise intravasation into blood vessels, circulation as single or collectives of cells, and eventual colonization of distant organs. Herein, we consider metastasis as a multi-step process that seized principles and molecular players employed by physiological processes, such as tissue regeneration and migration of neural crest progenitors. Our discussion contrasts the irreversible nature of mutagenesis, which establishes primary tumors, and the reversible epigenetic processes (e.g. epithelial-mesenchymal transition) underlying the establishment of micro-metastases and secondary tumors. Interestingly, analyses of sequencing data from untreated metastases inferred depletion of putative driver mutations among metastases, in line with the pivotal role played by growth factors and epigenetic processes in metastasis. Conceivably, driver mutations may not confer the same advantage in the microenvironment of the primary tumor and of the colonization site, hence phenotypic plasticity rather than rigid cellular states hardwired by mutations becomes advantageous during metastasis. We review the latest reported examples of growth factors harnessed by the metastatic cascade, with the goal of identifying opportunities for anti-metastasis interventions. In summary, because the overwhelming majority of cancer-associated deaths are caused by metastatic disease, understanding the complexity of metastasis, especially the roles played by growth factors, is vital for preventing, diagnosing and treating metastasis.
    Keywords:  epithelial-to-mesenchymal transition; growth factors; metastasis; mutation; tumor microenvironments; wound healing
    DOI:  https://doi.org/10.1042/BST20210048
  13. Commun Biol. 2021 Jun 08. 4(1): 703
    Random errors in protein synthesis activate an age-dependent program of muscle atrophy in mice.
    James Moore, Rashid Akbergenov, Martina Nigri, Patricia Isnard-Petit, Amandine Grimm, Petra Seebeck, Lisa Restelli, Stephan Frank, Anne Eckert, Kader Thiam, David P Wolfer, Dimitri Shcherbakov, Erik C Böttger.
      Random errors in protein synthesis are prevalent and ubiquitous, yet their effect on organismal health has remained enigmatic for over five decades. Here, we studied whether mice carrying the ribosomal ambiguity (ram) mutation Rps2-A226Y, recently shown to increase the inborn error rate of mammalian translation, if at all viable, present any specific, possibly aging-related, phenotype. We introduced Rps2-A226Y using a Cre/loxP strategy. Resulting transgenic mice were mosaic and showed a muscle-related phenotype with reduced grip strength. Analysis of gene expression in skeletal muscle using RNA-Seq revealed transcriptomic changes occurring in an age-dependent manner, involving an interplay of PGC1α, FOXO3, mTOR, and glucocorticoids as key signaling pathways, and finally resulting in activation of a muscle atrophy program. Our results highlight the relevance of translation accuracy, and show how disturbances thereof may contribute to age-related pathologies.
    DOI:  https://doi.org/10.1038/s42003-021-02204-z
  14. Epilepsy Res. 2021 Jun 02. pii: S0920-1211(21)00134-0. [Epub ahead of print]175 106681
    Effect of PIK3CA variants on glioma-related epilepsy and response to treatment.
    Steven Tobochnik, William Pisano, Emily Lapinskas, Keith L Ligon, Jong Woo Lee.
      Upregulation of the PI3K/AKT/mTOR pathway has been implicated in glioma-related epileptogenesis. In this retrospective analysis, epilepsy characteristics and response to treatment were evaluated in patients with gliomas harboring somatic mutation variants in PIK3CA. A cohort of 134 patients with 150 PIK3CA variants was extracted from previously validated databases. Patients with the hotspot H1047R, R88Q, E542K, and G118D variants comprised a subset (n = 41) for epilepsy phenotyping. In multivariate analysis, the presence of H1047R (n = 15) was associated with worse seizure control (p = 0.026). These results support preclinical findings and suggest that glioma PIK3CA variation may have promise as a biomarker for epilepsy severity and response to treatment.
    Keywords:  Epilepsy; Focal seizure; Glioma; PIK3CA; Somatic mutation
    DOI:  https://doi.org/10.1016/j.eplepsyres.2021.106681
  15. Cancer Lett. 2021 Jun 06. pii: S0304-3835(21)00251-2. [Epub ahead of print]516 73-83
    Transgenic mouse models of breast cancer.
    Angelina T Regua, Austin Arrigo, Daniel Doheny, Grace L Wong, Hui-Wen Lo.
      Transgenic breast cancer mouse models are critical tools for preclinical studies of human breast cancer. Genetic editing of the murine mammary gland allows for modeling of abnormal genetic events frequently found in human breast cancers. Genetically engineered mouse models (GEMMs) of breast cancer employ tissue-specific genetic manipulation for tumorigenic induction within the mammary tissue. Under the transcriptional control of mammary-specific promoters, transgenic mouse models can simulate spontaneous mammary tumorigenesis by expressing one or more putative oncogenes, such as MYC, HRAS, and PIK3CA. Alternatively, the Cre-Lox system allows for tissue-specific deletion of tumor suppressors, such as p53, Rb1, and Brca1, or specific knock-in of putative oncogenes. Thus, GEMMs can be designed to implement one or more genetic events to induce mammary tumorigenesis. Features of GEMMs, such as age of transgene expression, breeding quality, tumor latency, histopathological characteristics, and propensity for local and distant metastasis, are variable and strain-dependent. This review aims to summarize currently available transgenic breast cancer mouse models that undergo spontaneous mammary tumorigenesis upon genetic manipulation, their varying characteristics, and their individual genetic manipulations that model aberrant signaling events observed in human breast cancers.
    Keywords:  Breast cancer; Knockout mice; Mammary gland; Mouse models; Transgenic mice; Tumorigenesis
    DOI:  https://doi.org/10.1016/j.canlet.2021.05.027
  16. Development. 2021 Jun 01. pii: dev194399. [Epub ahead of print]148(11):
    Universal principles of lineage architecture and stem cell identity in renewing tissues.
    Philip Greulich, Ben D MacArthur, Cristina Parigini, Rubén J Sánchez-García.
      Adult tissues in multicellular organisms typically contain a variety of stem, progenitor and differentiated cell types arranged in a lineage hierarchy that regulates healthy tissue turnover. Lineage hierarchies in disparate tissues often exhibit common features, yet the general principles regulating their architecture are not known. Here, we provide a formal framework for understanding the relationship between cell molecular 'states' and cell 'types', based on the topology of admissible cell state trajectories. We show that a self-renewing cell type - if defined as suggested by this framework - must reside at the top of any homeostatic renewing lineage hierarchy, and only there. This architecture arises as a natural consequence of homeostasis, and indeed is the only possible way that lineage architectures can be constructed to support homeostasis in renewing tissues. Furthermore, under suitable feedback regulation, for example from the stem cell niche, we show that the property of 'stemness' is entirely determined by the cell environment, in accordance with the notion that stem cell identities are contextual and not determined by hard-wired, cell-intrinsic characteristics. This article has an associated 'The people behind the papers' interview.
    Keywords:  Cell state; Cell trajectories; Cell type; Self-renewal; Stem cell fate choice; Stem cell lineage
    DOI:  https://doi.org/10.1242/dev.194399
  17. Proc Natl Acad Sci U S A. 2021 Jun 15. pii: e2024176118. [Epub ahead of print]118(24):
    Accurate genomic variant detection in single cells with primary template-directed amplification.
    Veronica Gonzalez-Pena, Sivaraman Natarajan, Yuntao Xia, David Klein, Robert Carter, Yakun Pang, Bridget Shaner, Kavya Annu, Daniel Putnam, Wenan Chen, Jon Connelly, Shondra Pruett-Miller, Xiang Chen, John Easton, Charles Gawad.
      Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
    Keywords:  genome editing off-target; mutagenesis; single-cell sequencing; whole genome amplification
    DOI:  https://doi.org/10.1073/pnas.2024176118
  18. Nat Genet. 2021 Jun;53(6): 768-769
    CRISPR-Cas9 can cause chromothripsis.
    Fyodor D Urnov.
      
    DOI:  https://doi.org/10.1038/s41588-021-00881-4
  19. Development. 2021 Jun 01. pii: dev199609. [Epub ahead of print]148(11):
    Metabolic decisions in development and disease.
    Lluc Mosteiro, Hanaa Hariri, Jelle van den Ameele.
      The intimate relationships between cell fate and metabolism have long been recognized, but a mechanistic understanding of how metabolic pathways are dynamically regulated during development and disease, how they interact with signalling pathways, and how they affect differential gene expression is only emerging now. We summarize the key findings and the major themes that emerged from the virtual Keystone Symposium 'Metabolic Decisions in Development and Disease' held in March 2021.
    Keywords:  Cell fate; Development; Metabolic plasticity; Metabolism; Nutrition
    DOI:  https://doi.org/10.1242/dev.199609
  20. Cell Rep Med. 2021 May 18. 2(5): 100282
    PFC mTOR signaling as a biological signature for cognitive deficits in bipolar disorder without psychosis.
    Jelena Radulovic, Vilma Gabbay.
      Vanderplow et al.1 report decreased PFC Akt-mTOR signaling in males with bipolar disorder (BD) without psychosis compared with those with psychosis, possibly related to cognitive deficits. Understanding how cognition differs between these BD subtypes clinically and biologically remains a challenge.
    DOI:  https://doi.org/10.1016/j.xcrm.2021.100282
  21. Nat Metab. 2021 Jun 11.
    GTTs and ITTs in mice: simple tests, complex answers.
    Sam Virtue, Antonio Vidal-Puig.
      
    DOI:  https://doi.org/10.1038/s42255-021-00414-7
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