bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2020–11–22
nineteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Unbiased in vivo preclinical evaluation of anticancer drugs identifies effective therapy for the treatment of pancreatic adenocarcinoma.
  2. ABHD5 suppresses cancer cell anabolism through lipolysis-dependent activation of the AMPK/mTORC1 pathway.
  3. Overgrowth Syndromes-Evaluation, Diagnosis, and Management.
  4. AdipoR1/AdipoR2 dual agonist recovers nonalcoholic steatohepatitis and related fibrosis via endoplasmic reticulum-mitochondria axis.
  5. Inverse sex-based expression profiles of PTEN and Klotho in mice.
  6. PI3K Inhibitors and Adverse Events: Optimizing Patient Care for the Treatment of Advanced Breast Cancer.
  7. The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages.
  8. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment.
  9. IQGAP1 binds AMPK and is required for maximum AMPK activation.
  10. Integration of Online Omics-Data Resources for Cancer Research.
  11. The E3 ubiquitin ligase Peli1 regulates the metabolic actions of mTORC1 to suppress antitumor T cell responses.
  12. Protein Prenylation Drives Discrete Signaling Programs for the Differentiation and Maintenance of Effector Treg Cells.
  13. Computationally predicting clinical drug combination efficacy with cancer cell line screens and independent drug action.
  14. High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures.
  15. IFITM3 Enhances PI3K Pathway Signaling to Promote B-cell Malignancies.
  16. The translational repressor 4E-BP1 regulates RRM2 levels and functions as a tumor suppressor in Ewing sarcoma tumors.
  17. Cell type-selective secretome profiling in vivo.
  18. Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development.
  19. Mutation bias within oncogene families is related to proliferation-specific codon usage.
  1. Proc Natl Acad Sci U S A. 2020 Nov 16. pii: 201920240. [Epub ahead of print]
    Unbiased in vivo preclinical evaluation of anticancer drugs identifies effective therapy for the treatment of pancreatic adenocarcinoma.
    Olivera Grbovic-Huezo, Kenneth L Pitter, Nicolas Lecomte, Joseph Saglimbeni, Gokce Askan, Matilda Holm, Jerry P Melchor, Rohit Chandwani, Suhasini Joshi, Caj Haglund, Christine A Iacobuzio-Donahue, Gabriela Chiosis, Tuomas Tammela, Steven D Leach.
      Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at an advanced stage, which limits surgical options and portends a dismal prognosis. Current oncologic PDAC therapies confer marginal benefit and, thus, a significant unmet clinical need exists for new therapeutic strategies. To identify effective PDAC therapies, we leveraged a syngeneic orthotopic PDAC transplant mouse model to perform a large-scale, in vivo screen of 16 single-agent and 41 two-drug targeted therapy combinations in mice. Among 57 drug conditions screened, combined inhibition of heat shock protein (Hsp)-90 and MEK was found to produce robust suppression of tumor growth, leading to an 80% increase in the survival of PDAC-bearing mice with no significant toxicity. Mechanistically, we observed that single-agent MEK inhibition led to compensatory activation of resistance pathways, including components of the PI3K/AKT/mTOR signaling axis, which was overcome with the addition of HSP90 inhibition. The combination of HSP90(i) + MEK(i) was also active in vitro in established human PDAC cell lines and in vivo in patient-derived organoid PDAC transplant models. These findings encourage the clinical development of HSP90(i) + MEK(i) combination therapy and highlight the power of clinically relevant in vivo model systems for identifying cancer therapies.
    Keywords:  HSP90; MEK; PDAC; pancreatic cancer; trametinib
    DOI:  https://doi.org/10.1073/pnas.1920240117
  2. J Biol Chem. 2020 Nov 20. pii: jbc.RA120.014682. [Epub ahead of print]
    ABHD5 suppresses cancer cell anabolism through lipolysis-dependent activation of the AMPK/mTORC1 pathway.
    Guohua Chen, Guoli Zhou, Aaron Lotvola, James G Granneman, Jian Wang.
      ABHD5 is an essential coactivator of ATGL, the rate-limiting triglyceride (TG) lipase in many cell types. Importantly, ABHD5 also functions as a tumor suppressor, and ABHD5 mRNA expression levels correlate with patient survival for several cancers. Nevertheless, the mechanisms involved in ABHD5-dependent tumor suppression are not known. We found that overexpression of ABHD5 induces cell-cycle arrest at the G1 phase and causes growth retardation in a panel of prostate cancer cells. Transcriptomic profiling and biochemical analysis revealed that genetic or pharmacological activation of lipolysis by ABHD5 potently inhibits mTORC1 signaling, leading to a significant downregulation of protein synthesis. Mechanistically, we found that ABHD5 elevates intracellular AMP content, which activates AMPK, leading to inhibition of mTORC1. Interestingly, ABHD5-dependent suppression of mTORC1 was abrogated by pharmacological inhibition of DGAT1 or DGAT2, isoenzymes that re-esterify fatty acids in a process that consumes ATP. Collectively, this study maps out a novel molecular pathway crucial for limiting cancer cell proliferation, in which ABHD5-mediated lipolysis creates an energy-consuming futile cycle between TG hydrolysis and resynthesis, leading to inhibition of mTORC1 and cancer cell growth arrest.
    Keywords:  lipid signaling; lipolysis; metabolic regulation; tumor cell biology; tumor metabolism
    DOI:  https://doi.org/10.1074/jbc.RA120.014682
  3. Front Pediatr. 2020 ;8 574857
    Overgrowth Syndromes-Evaluation, Diagnosis, and Management.
    Joshua Manor, Seema R Lalani.
      Abnormally excessive growth results from perturbation of a complex interplay of genetic, epigenetic, and hormonal factors that orchestrate human growth. Overgrowth syndromes generally present with inherent health concerns and, in some instances, an increased risk of tumor predisposition that necessitate prompt diagnosis and appropriate referral. In this review, we introduce some of the more common overgrowth syndromes, along with their molecular mechanisms, diagnostics, and medical complications for improved recognition and management of patients affected with these disorders.
    Keywords:  Beckwith-Wiedemann; PIK3CA; Proteus Syndrome; Pten; Simpson-Golabi-Behmel; Sotos; Weaver; overgrowth
    DOI:  https://doi.org/10.3389/fped.2020.574857
  4. Nat Commun. 2020 11 16. 11(1): 5807
    AdipoR1/AdipoR2 dual agonist recovers nonalcoholic steatohepatitis and related fibrosis via endoplasmic reticulum-mitochondria axis.
    Hongjiao Xu, Qian Zhao, Nazi Song, Zhibin Yan, Runfeng Lin, Shuohan Wu, Lili Jiang, Sihua Hong, Junqiu Xie, Huihao Zhou, Rui Wang, Xianxing Jiang.
      Chronic nonalcoholic steatohepatitis (NASH) is a metabolic disorder that often leads to liver fibrosis, a condition with limited therapy options. Adiponectin is an adipocytokine that regulates glucose and lipid metabolism via binding to its receptors AdipoR1 and AdipoR2, and AdipoRs signaling is reported to enhance fatty acid oxidation and glucose uptake. Here, we synthesize and report an adiponectin-based agonist JT003, which potently improves insulin resistance in high fat diet induced NASH mice and suppresses hepatic stellate cells (HSCs) activation in CCl4 induced liver fibrosis. Mechanistic studies indicate that JT003 simultaneously stimulates AdipoR1- and AdipoR2- mediated signaling pathways as well as the PI3K-Akt pathway. Moreover, JT003 treatment significantly improves ER-mitochondrial axis function, which contributes to the reduced HSCs activation. Thus, the AdipoR1/AdipoR2 dual agonist improves both NASH and fibrosis in mice models, which provides the pharmacological and biological foundation for developing AdipoRs-based therapeutic agents on liver fibrosis.
    DOI:  https://doi.org/10.1038/s41467-020-19668-y
  5. Sci Rep. 2020 Nov 19. 10(1): 20189
    Inverse sex-based expression profiles of PTEN and Klotho in mice.
    Natalia Prudente de Mello, Diana Zukas Andreotti, Ana Maria Orellana, Cristoforo Scavone, Elisa Mitiko Kawamoto.
      Sex differences are considered predictive factors in the development of several neurological diseases, which are also known to coincide with impaired phosphoinositide 3-kinase (PI3K)-AKT pathway activity, an essential signaling cascade involved in the control of several cellular functions such as autophagy and apoptosis. Here, under physiological conditions, we show important sex differences in the underlying balancing mechanisms that lead to similar AKT activity levels and autophagy and apoptosis processes in the two sexes. We demonstrate inverse sex-based expression of PTEN and Klotho, two important proteins that are known to negatively regulate the AKT pathway, and inverse sex-dependent levels of mTOR and FoxO3a activity. Taken together, our findings indicate that inverse sex-based regulation may be one of the underlying balancing mechanisms that differ between the sexes and a possible cause of sex-based autophagic and apoptotic responses to triggering situations that can lead to a sex-based predisposition to some neurological diseases.
    DOI:  https://doi.org/10.1038/s41598-020-77217-5
  6. Clin J Oncol Nurs. 2020 Dec 01. 24(6): 673-680
    PI3K Inhibitors and Adverse Events: Optimizing Patient Care for the Treatment of Advanced Breast Cancer.
    Sarah Donahue, Gretchen Santos Fulgencio.
       BACKGROUND: Excessive activation of the PI3K pathway has been associated with malignant transformation and resistance to treatment in various cancer types. Various PI3K inhibitors have been evaluated in phase 3 clinical trials; however, most have been associated with modest clinical improvement and poor tolerability. The safety profile of PI3K inhibitors poses new challenges in treatment monitoring and management of common adverse events (AEs).
    OBJECTIVES: The purpose of this article is to provide an overview of AEs associated with PI3K inhibitors, with a focus on alpelisib, as well as guidance on the prevention and management of AEs.
    METHODS: The literature and results from phase 3 trials evaluating the efficacy and safety of endocrine therapy plus PI3K inhibitors in patients with advanced breast cancer were reviewed.
    FINDINGS: AEs associated with PI3K inhibitors include hyperglycemia, diarrhea, nausea, rash, and decreased appetite. Prevention strategies are recommended to avoid the development or decrease the severity of these AEs. Patient education and multidisciplinary care are necessary for the optimal care of these patients.
    Keywords:  PI3K inhibitors; advanced breast cancer; adverse events; endocrine therapy
    DOI:  https://doi.org/10.1188/20.CJON.673-680
  7. Nat Metab. 2020 Nov 16.
    The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages.
    Julia S Brunner, Andrea Vogel, Alexander Lercher, Michael Caldera, Ana Korosec, Marlene Pühringer, Melanie Hofmann, Alexander Hajto, Markus Kieler, Lucia Quemada Garrido, Martina Kerndl, Mario Kuttke, Ildiko Mesteri, Maria W Górna, Marta Kulik, Paulina M Dominiak, Amanda E Brandon, Emma Estevez, Casey L Egan, Florian Gruber, Martina Schweiger, Jörg Menche, Andreas Bergthaler, Thomas Weichhart, Kristaps Klavins, Mark A Febbraio, Omar Sharif, Gernot Schabbauer.
      Adipose tissue macrophages (ATMs) display tremendous heterogeneity depending on signals in their local microenvironment and contribute to the pathogenesis of obesity. The phosphoinositide 3-kinase (PI3K) signalling pathway, antagonized by the phosphatase and tensin homologue (PTEN), is important for metabolic responses to obesity. We hypothesized that fluctuations in macrophage-intrinsic PI3K activity via PTEN could alter the trajectory of metabolic disease by driving distinct ATM populations. Using mice harbouring macrophage-specific PTEN deletion or bone marrow chimeras carrying additional PTEN copies, we demonstrate that sustained PI3K activity in macrophages preserves metabolic health in obesity by preventing lipotoxicity. Myeloid PI3K signalling promotes a beneficial ATM population characterized by lipid uptake, catabolism and high expression of the scavenger macrophage receptor with collagenous structure (MARCO). Dual MARCO and myeloid PTEN deficiencies prevent the generation of lipid-buffering ATMs, reversing the beneficial actions of elevated myeloid PI3K activity in metabolic disease. Thus, macrophage-intrinsic PI3K signalling boosts metabolic health by driving ATM programmes associated with MARCO-dependent lipid uptake.
    DOI:  https://doi.org/10.1038/s42255-020-00311-5
  8. Cancer Cell. 2020 Nov 16. pii: S1535-6108(20)30546-8. [Epub ahead of print]
    Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment.
    David A Wheeler, Naoko Takebe, Toshinori Hinoue, Katherine A Hoadley, Maria F Cardenas, Alina M Hamilton, Peter W Laird, Linghua Wang, Adrienne Johnson, Ninad Dewal, Vincent Miller, David Piñeyro, Manuel Castro de Moura, Manel Esteller, Hui Shen, Jean Claude Zenklusen, Roy Tarnuzzer, Lisa M McShane, James V Tricoli, Paul M Williams, Irina Lubensky, Geraldine O'Sullivan-Coyne, Elise C Kohn, Richard F Little, Jeffrey White, Shakun Malik, Lyndsay Harris, Carol Weil, Alice P Chen, Chris Karlovich, Brian Rodgers, Lalitha Shankar, Paula Jacobs, Tracy Nolan, Jianhong Hu, Donna M Muzny, Harshavardhan Doddapaneni, Viktoriya Korchina, Julie Gastier-Foster, Jay Bowen, Kristen Leraas, Elijah F Edmondson, James H Doroshow, Barbara A Conley, S Percy Ivy, Louis M Staudt.
      A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
    Keywords:  DNA methylation analysis; DNA repair mechanisms; N of 1 experiment; RNA sequencing; combination cancer therapy; exceptional response to therapy; integrating molecular and clinical data; multi-platform genomic analyses; precision cancer medicine; rare mutations; synthetic lethality; whole-exome sequencing
    DOI:  https://doi.org/10.1016/j.ccell.2020.10.015
  9. J Biol Chem. 2020 Nov 15. pii: jbc.RA120.016193. [Epub ahead of print]
    IQGAP1 binds AMPK and is required for maximum AMPK activation.
    Andrew C Hedman, Zhigang Li, Laëtitia Gorisse, Swetha Parvathaneni, Chase J Morgan, David B Sacks.
      AMP-activated protein kinase (AMPK) is a fundamental component of a protein kinase cascade that is an energy sensor. AMPK maintains energy homeostasis in the cell by promoting catabolic and inhibiting anabolic pathways. Activation of AMPK requires phosphorylation by the liver kinase B1 or by the Ca2+ /calmodulin-dependent protein kinase kinase 2 (CaMKK2). The scaffold protein IQGAP1 regulates intracellular signaling pathways, such as the mitogen-activated protein kinase and AKT signaling cascades. Recent work implicates the participation of IQGAP1 in metabolic function, but the molecular mechanisms underlying these effects are poorly understood. Here, using several approaches including binding analysis with fusion proteins, siRNA-mediated gene silencing, RT-PCR, and knockout mice, we investigated whether IQGAP1 modulates AMPK signaling. In vitro analysis reveals that IQGAP1 binds directly to the α1 subunit of AMPK. In addition, we observed a direct interaction between IQGAP1 and CaMKK2, which is mediated by the IQ domain of IQGAP1. Both CaMKK2 and AMPK associate with IQGAP1 in cells. The ability of metformin and increased intracellular free Ca2+ concentrations to activate AMPK is reduced in cells lacking IQGAP1. Importantly, Ca2+-stimulated AMPK phosphorylation was rescued by re-expression of IQGAP1 in IQGAP1-null cell lines. Comparison of the fasting response in wild-type and IQGAP1-null mice revealed that transcriptional regulation of the gluconeogenesis genes PCK1 and G6PC and the fatty acid synthesis genes FASN and ACC1 is impaired in IQGAP1-null mice. Our data disclose a previously unidentified functional interaction between IQGAP1 and AMPK and suggest that IQGAP1 modulates AMPK signaling.
    Keywords:  AMP-activated kinase (AMPK); IQGAP1; calcium; calmodulin (CaM); cell signaling; homeostasis; metabolic regulation; metformin; protein-protein interaction; scaffold protein; signaling
    DOI:  https://doi.org/10.1074/jbc.RA120.016193
  10. Front Genet. 2020 ;11 578345
    Integration of Online Omics-Data Resources for Cancer Research.
    Tonmoy Das, Geoffroy Andrieux, Musaddeque Ahmed, Sajib Chakraborty.
      The manifestations of cancerous phenotypes necessitate alterations at different levels of information-flow from genome to proteome. The molecular alterations at different information processing levels serve as the basis for the cancer phenotype to emerge. To understand the underlying mechanisms that drive the acquisition of cancer hallmarks it is required to interrogate cancer cells using multiple levels of information flow represented by different omics - such as genomics, epigenomics, transcriptomics, and proteomics. The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to integrate the omics-data in a biologically meaningful manner. The plethora of cancer-specific online omics-data resources, if able to be integrated efficiently and systematically, may facilitate the generation of new biological insights for cancer research. In this review, we provide a comprehensive overview of the online single- and multi-omics resources that are dedicated to cancer. We catalog various online omics-data resources such as The Cancer Genome Atlas (TCGA) along with various TCGA-associated data portals and tools for multi-omics analysis and visualization, the International Cancer Genome Consortium (ICGC), Catalogue of Somatic Mutations in Cancer (COSMIC), The Pathology Atlas, Gene Expression Omnibus (GEO), and PRoteomics IDEntifications (PRIDE). By comparing the strengths and limitations of the respective online resources, we aim to highlight the current biological and technological challenges and possible strategies to overcome these challenges. We outline the available schemes for the integration of the multi-omics dimensions for stratifying cancer patients and biomarker prediction based on the integrated molecular-signatures of cancer. Finally, we propose the multi-omics driven systems-biology approaches to realize the potential of precision onco-medicine as the future of cancer research. We believe this systematic review will encourage scientists and clinicians worldwide to utilize the online resources to explore and integrate the available omics datasets that may provide a window of opportunity to generate new biological insights and contribute to the advancement of the field of cancer research.
    Keywords:  cancer; data-integration; multi-omics; proteogenomic analysis; systems biology
    DOI:  https://doi.org/10.3389/fgene.2020.578345
  11. EMBO J. 2020 Nov 20. e104532
    The E3 ubiquitin ligase Peli1 regulates the metabolic actions of mTORC1 to suppress antitumor T cell responses.
    Chun-Jung Ko, Lingyun Zhang, Zuliang Jie, Lele Zhu, Xiaofei Zhou, Xiaoping Xie, Tianxiao Gao, Jin-Young Yang, Xuhong Cheng, Shao-Cong Sun.
      Metabolic fitness of T cells is crucial for immune responses against infections and tumorigenesis. Both the T cell receptor (TCR) signal and environmental cues contribute to the induction of T cell metabolic reprogramming, but the underlying mechanism is incompletely understood. Here, we identified the E3 ubiquitin ligase Peli1 as an important regulator of T cell metabolism and antitumor immunity. Peli1 ablation profoundly promotes tumor rejection, associated with increased tumor-infiltrating CD4 and CD8 T cells. The Peli1-deficient T cells display markedly stronger metabolic activities, particularly glycolysis, than wild-type T cells. Peli1 controls the activation of a metabolic kinase, mTORC1, stimulated by both the TCR signal and growth factors, and this function of Peli1 is mediated through regulation of the mTORC1-inhibitory proteins, TSC1 and TSC2. Peli1 mediates non-degradative ubiquitination of TSC1, thereby promoting TSC1-TSC2 dimerization and TSC2 stabilization. These results establish Peli1 as a novel regulator of mTORC1 and downstream mTORC1-mediated actions on T cell metabolism and antitumor immunity.
    Keywords:  Peli1; T cell metabolism; antitumor immunity; mTORC1; ubiquitination
    DOI:  https://doi.org/10.15252/embj.2020104532
  12. Cell Metab. 2020 Nov 11. pii: S1550-4131(20)30591-X. [Epub ahead of print]
    Protein Prenylation Drives Discrete Signaling Programs for the Differentiation and Maintenance of Effector Treg Cells.
    Wei Su, Nicole M Chapman, Jun Wei, Hu Zeng, Yogesh Dhungana, Hao Shi, Jordy Saravia, Peipei Zhou, Lingyun Long, Sherri Rankin, Anil Kc, Peter Vogel, Hongbo Chi.
      Effector regulatory T (eTreg) cells are essential for immune tolerance and depend upon T cell receptor (TCR) signals for generation. The immunometabolic signaling mechanisms that promote the differentiation and maintenance of eTreg cells remain unclear. Here, we show that isoprenoid-dependent posttranslational lipid modifications dictate eTreg cell accumulation and function by intersecting with TCR-induced intracellular signaling. We find that isoprenoids are essential for activated Treg cell suppressive activity, and Treg cell-specific deletion of the respective farnesylation- and geranylgeranylation-promoting enzymes Fntb or Pggt1b leads to the development of fatal autoimmunity, associated with reduced eTreg cell accumulation. Mechanistically, Fntb promotes eTreg cell maintenance by regulating mTORC1 activity and ICOS expression. In contrast, Pggt1b acts as a rheostat of TCR-dependent transcriptional programming and Rac-mediated signaling for establishment of eTreg cell differentiation and immune tolerance. Therefore, our results identify bidirectional metabolic signaling, specifically between immunoreceptor signaling and metabolism-mediated posttranslational lipid modifications, for the differentiation and maintenance of eTreg cells.
    Keywords:  Fntb; Pggt1b; Treg cells; immunometabolism; mTOR; protein prenylation
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.022
  13. Nat Commun. 2020 11 17. 11(1): 5848
    Computationally predicting clinical drug combination efficacy with cancer cell line screens and independent drug action.
    Alexander Ling, R Stephanie Huang.
      Evidence has recently emerged that many clinical cancer drug combinations may derive their efficacy from independent drug action (IDA), where patients only receive benefit from the single most effective drug in a drug combination. Here we present IDACombo, an IDA based method to predict the efficacy of drug combinations using monotherapy data from high-throughput cancer cell line screens. We show that IDACombo predictions closely agree with measured drug combination efficacies both in vitro (Pearson's correlation = 0.93 when comparing predicted efficacies to measured efficacies for >5000 combinations) and in a systematically selected set of clinical trials (accuracy > 84% for predicting statistically significant improvements in patient outcomes for 26 first line therapy trials). Finally, we demonstrate how IDACombo can be used to systematically prioritize combinations for development in specific cancer settings, providing a framework for quickly translating existing monotherapy cell line data into clinically meaningful predictions of drug combination efficacy.
    DOI:  https://doi.org/10.1038/s41467-020-19563-6
  14. Elife. 2020 Nov 18. pii: e59445. [Epub ahead of print]9
    High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures.
    Kyaw Thu Minn, Yuheng C Fu, Shenghua He, Sabine Dietmann, Steven C George, Mark A Anastasio, Samantha A Morris, Lilianna Solnica-Krezel.
      During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells in radial arrangement. Using single-cell RNA sequencing and cross-species comparisons with mouse, cynomolgus monkey gastrulae, and post-implantation human embryos, we reveal that gastruloids contain cells transcriptionally similar to epiblast, ectoderm, mesoderm, endoderm, primordial germ cells, trophectoderm, and amnion. Upon gastruloid dissociation, single cells reseeded onto micro-discs were motile and aggregated with the same but segregated from distinct cell types. Ectodermal cells segregated from endodermal and extraembryonic but mixed with mesodermal cells. Our work demonstrates that the gastruloid system models primate-specific features of embryogenesis, and that gastruloid cells exhibit evolutionarily conserved sorting behaviors. This work generates a resource for transcriptomes of human extraembryonic and embryonic germ layers differentiated in a stereotyped arrangement.
    Keywords:  developmental biology; human; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.59445
  15. Cancer Discov. 2020 Nov 20.
    IFITM3 Enhances PI3K Pathway Signaling to Promote B-cell Malignancies.
      Pre-B cells in Ifitm3 -/- mice were less able to transform into B-cell cancers than in wild-type mice.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2020-168
  16. Oncogene. 2020 Nov 15.
    The translational repressor 4E-BP1 regulates RRM2 levels and functions as a tumor suppressor in Ewing sarcoma tumors.
    Kelli L Goss, Stacia L Koppenhafer, Torin Waters, William W Terry, Kuo-Kuang Wen, Meng Wu, Jason Ostergaard, Peter M Gordon, David J Gordon.
      Ribonucleotide reductase (RNR), which is a heterodimeric tetramer composed of RRM1 and RRM2 subunits, is the rate-limiting enzyme in the synthesis of deoxyribonucleoside triphosphates (dNTPs) and essential for both DNA replication and the repair of DNA damage. The activity of RNR is coordinated with the cell cycle and regulated by fluctuations in the level of the RRM2 subunit. Multiple cancer types, including Ewing sarcoma tumors, are sensitive to inhibitors of RNR or a reduction in the levels of either the RRM1 or RRM2 subunits of RNR. Here, we show that the expression of the RRM2 protein is dependent on active protein synthesis and that 4E-BP1, a repressor of cap-dependent protein translation, specifically regulates the level of the RRM2 protein. Furthermore, inhibition of mTORC1/2, but not mTORC1, activates 4E-BP1, inhibits protein synthesis, and reduces the level of the RRM2 protein in multiple sarcoma cell lines. This effect of mTORC1/2 inhibitors on protein synthesis and RRM2 levels was rescued in cell lines with the CRISPR/Cas9-mediated knockout of 4E-BP1. In addition, the inducible expression of a mutant 4E-BP1 protein that cannot be phosphorylated by mTOR blocked protein synthesis and inhibited the growth of Ewing sarcoma cells in vitro and in vivo in a xenograft. Overall, these results provide insight into the multifaceted regulation of RRM2 protein levels and identify a regulatory link between protein translation and DNA replication.
    DOI:  https://doi.org/10.1038/s41388-020-01552-0
  17. Nat Chem Biol. 2020 Nov 16.
    Cell type-selective secretome profiling in vivo.
    Wei Wei, Nicholas M Riley, Andrew C Yang, Joon T Kim, Stephanie M Terrell, Veronica L Li, Marta Garcia-Contreras, Carolyn R Bertozzi, Jonathan Z Long.
      Secreted polypeptides are a fundamental axis of intercellular and endocrine communication. However, a global understanding of the composition and dynamics of cellular secretomes in intact mammalian organisms has been lacking. Here, we introduce a proximity biotinylation strategy that enables labeling, detection and enrichment of secreted polypeptides in a cell type-selective manner in mice. We generate a proteomic atlas of hepatocyte, myocyte, pericyte and myeloid cell secretomes by direct purification of biotinylated secreted proteins from blood plasma. Our secretome dataset validates known cell type-protein pairs, reveals secreted polypeptides that distinguish between cell types and identifies new cellular sources for classical plasma proteins. Lastly, we uncover a dynamic and previously undescribed nutrient-dependent reprogramming of the hepatocyte secretome characterized by the increased unconventional secretion of the cytosolic enzyme betaine-homocysteine S-methyltransferase (BHMT). This secretome profiling strategy enables dynamic and cell type-specific dissection of the plasma proteome and the secreted polypeptides that mediate intercellular signaling.
    DOI:  https://doi.org/10.1038/s41589-020-00698-y
  18. Dev Cell. 2020 Nov 13. pii: S1534-5807(20)30841-8. [Epub ahead of print]
    Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development.
    Sadie VanHorn, Samantha A Morris.
      Lineage tracing and fate mapping, overlapping yet distinct disciplines to follow cells and their progeny, have evolved rapidly over the last century. Lineage tracing aims to identify all progeny arising from an individual cell, placing them within a lineage hierarchy. The recent emergence of genomic technologies, such as single-cell and spatial transcriptomics, has fostered sophisticated new methods to reconstruct lineage relationships at high resolution. In contrast, fate maps, schematics showing which parts of the embryo will develop into which tissue, have remained relatively static since the 1970s. However, fate maps provide spatial information, often lost in lineage reconstruction, that can offer fundamental mechanistic insight into development. Here, we broadly review the origins of fate mapping and lineage tracing approaches. We focus on the most recent developments in lineage tracing, permitted by advances in single-cell genomics. Finally, we explore the current potential to leverage these new technologies to synthesize high-resolution fate maps and discuss their potential for interrogating development at new depths.
    Keywords:  fate mapping; lineage tracing; single-cell RNA sequencing; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.devcel.2020.10.021
  19. Proc Natl Acad Sci U S A. 2020 Nov 16. pii: 202016119. [Epub ahead of print]
    Mutation bias within oncogene families is related to proliferation-specific codon usage.
    Hannah Benisty, Marc Weber, Xavier Hernandez-Alias, Martin H Schaefer, Luis Serrano.
      It is well known that in cancer gene families some members are more frequently mutated in tumor samples than their family counterparts. A paradigmatic case of this phenomenon is KRAS from the RAS family. Different explanations have been proposed ranging from differential interaction with other proteins to preferential expression or localization. Interestingly, it has been described that despite the high amino acid identity between RAS family members, KRAS employs an intriguing differential codon usage. Here, we found that this phenomenon is not exclusive to the RAS family. Indeed, in the RAS family and other oncogene families with two or three members, the most prevalently mutated gene in tumor samples employs a differential codon usage that is characteristic of genes involved in proliferation. Prompted by these observations, we chose the RAS family to experimentally demonstrate that the translation efficiency of oncogenes that are preferentially mutated in tumor samples is increased in proliferative cells compared to quiescent cells. These results were further validated by assessing the translation efficiency of KRAS in cell lines that differ in their tRNA expression profile. These differences are related to the cell division rate of the studied cells and thus suggest an important role in context-specific oncogene expression regulation. Altogether, our study demonstrates that dynamic translation programs contribute to shaping the expression profiles of oncogenes. Therefore, we propose this codon bias as a regulatory layer to control cell context-specific expression and explain the differential prevalence of mutations in certain members of oncogene families.
    Keywords:  KRAS; codon usage; oncogene; tRNA; translation
    DOI:  https://doi.org/10.1073/pnas.2016119117
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