bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–12–05
forty papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Clinical Development of AKT Inhibitors and Associated Predictive Biomarkers to Guide Patient Treatment in Cancer Medicine.
  2. Quantitative systems pharmacology model-based investigation of Adverse Gastrointestinal Events Associated with Prolonged Treatment with PI3-Kinase (PI3K) Inhibitors.
  3. Ipatasertib plus paclitaxel for PIK3CA/AKT1/PTEN-altered hormone receptor-positive HER2-negative advanced breast cancer: primary results from cohort B of the IPATunity130 randomized phase 3 trial.
  4. Emergence of mTOR mutation as an acquired resistance mechanism to AKT inhibition, and subsequent response to mTORC1/2 inhibition.
  5. Phospholipase C-related catalytically inactive protein acts as a positive regulator for insulin signalling in adipocytes.
  6. Design, Synthesis, and Evaluation of Potent, Selective, and Bioavailable AKT Kinase Degraders.
  7. Intracranial venous malformation masquerading as a meningioma in PI3KCA-related overgrowth spectrum disorder.
  8. Segmental undergrowth is associated with pathogenic variants in vascular malformation genes: A retrospective case-series study.
  9. Personalized phosphoproteomics identifies functional signaling.
  10. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.
  11. Dyrk1b promotes hepatic lipogenesis by bypassing canonical insulin signaling and directly activating mTORC2 in mice.
  12. ER+ Breast Cancer Mammosphere Formation and Analysis.
  13. Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kα in early and advanced HER2-positive breast cancer.
  14. Inhibition of cytoplasmic EZH2 induces antitumor activity through stabilization of the DLC1 tumor suppressor protein.
  15. Dysregulated phosphoinositide 3-kinase signaling in microglia: shaping chronic neuroinflammation.
  16. Serine catabolism generates liver NADPH and supports hepatic lipogenesis.
  17. Distinct contributions of partial and full EMT to breast cancer malignancy.
  18. Lysophosphatidic acid shifts metabolic and transcriptional landscapes to induce a distinct cellular state in human pluripotent stem cells.
  19. A DAP5/eIF3d alternate mRNA translation mechanism promotes differentiation and immune suppression by human regulatory T cells.
  20. Author-sourced capture of pathway knowledge in computable form using Biofactoid.
  21. Insulin at 100 years - is rebalancing its action key to fighting obesity-related disease?
  22. Deciphering cell signaling networks with massively multiplexed biosensor barcoding.
  23. RPS6 phosphorylation occurs to a greater extent in the periphery of human skeletal muscle fibers, near focal adhesions, after anabolic stimuli.
  24. Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.
  25. A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor.
  26. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.
  27. Cancer stem cells: advances in biology and clinical translation-a Keystone Symposia report.
  28. Amino acid deprivation induces AKT activation by inducing GCN2/ATF4/REDD1 axis.
  29. Quantitative analysis of tumour spheroid structure.
  30. Robotic high-throughput biomanufacturing and functional differentiation of human pluripotent stem cells.
  31. Role of mammalian target of rapamycin complex 2 in primary and secondary liver cancer.
  32. AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation.
  33. Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer.
  34. The dark proteome: translation from noncanonical open reading frames.
  35. Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers.
  36. Fumarate is a terminal electron acceptor in the mammalian electron transport chain.
  37. Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation.
  38. Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes.
  39. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks.
  40. How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification.
  1. Pharmgenomics Pers Med. 2021 ;14 1517-1535
    Clinical Development of AKT Inhibitors and Associated Predictive Biomarkers to Guide Patient Treatment in Cancer Medicine.
    Niamh Coleman, Justin T Moyers, Alice Harbery, Igor Vivanco, Timothy A Yap.
      The serine/threonine kinase AKT is a critical effector of the phosphoinositide 3-kinase (PI3K) signaling cascade and has a pivotal role in cell growth, proliferation, survival, and metabolism. AKT is one of the most commonly activated pathways in human cancer and dysregulation of AKT-dependent pathways is associated with the development and maintenance of a range of solid tumors. There are multiple small-molecule inhibitors targeting different components of the PI3K/AKT pathway currently at various stages of clinical development, in addition to new combination strategies aiming to boost the therapeutic efficacy of these drugs. Correlative and translational studies have been undertaken in the context of clinical trials investigating AKT inhibitors, however the identification of predictive biomarkers of response and resistance to AKT inhibition remains an unmet need. In this review, we discuss the biological function and activation of AKT, discuss its contribution to tumor development and progression, and review the efficacy and toxicity data from clinical trials, including both AKT inhibitor monotherapy and combination strategies with other agents. We also discuss the promise and challenges associated with the development of AKT inhibitors and associated predictive biomarkers of response and resistance.
    Keywords:  AKT; AKT inhibitor; PI3K; m-TOR
    DOI:  https://doi.org/10.2147/PGPM.S305068
  2. CPT Pharmacometrics Syst Pharmacol. 2021 Dec 01.
    Quantitative systems pharmacology model-based investigation of Adverse Gastrointestinal Events Associated with Prolonged Treatment with PI3-Kinase (PI3K) Inhibitors.
    Kapil Gadkar, Christina Friedrich, Vincent Hurez, Maria-Luisa Ruiz, Leslie Dickmann, Mohit Kumar Jolly, Leah Schutt, Jin Jin, Joseph A Ware, Saroja Ramanujan.
      Several PI3K inhibitors are in clinical development for the treatment of various forms of cancers, including pan-PI3K inhibitors targeting all four PI3K isoforms (α, β, γ, δ), and isoform-selective inhibitors. Diarrhea and Immune-mediated colitis are among the adverse events (AEs) observed with PI3K inhibition which limit the maximal tolerated dose. A quantitative systems pharmacology model was developed to investigate PI3K-inhibitor-induced colitis. The effects of individual PI3K isoforms on relevant cellular pathways were incorporated into a mechanistic representation of mucosal inflammation. A virtual clinical population captures the observed clinical variability in the onset timing and rates of diarrhea and colitis for 7 clinically-tested PI3K inhibitors. Model-based analysis suggests that colitis development is governed by both the inhibition of PI3Kδ, which drives T cell differentiation and proliferation, and PI3Kα, which regulates epithelial barrier integrity. Specifically, when PI3Kα is inhibited below a given threshold, epithelial barrier dysfunction precipitates an exaggerated T effector response due to PI3Kδ-inhibition, leading to risk of diarrhea and colitis. This synergy explains why the lowest diarrhea and colitis rates are seen with the weakest PI3Kδ inhibition (alpelisib), and higher rates are seen with strong PI3Kδ inhibition if PI3Kα is even mildly inhibited (e.g, idelalisib), whereas strong PI3Kδ inhibition in the absence of PI3Kα inhibition does not result in high colitis rates (umbralisib). Thus, the model-based analysis suggests that PI3Kα and δ inhibition play unique but synergistic roles in driving colitis. Finally, we explore if and how dose-regimen might influence colitis rates for molecules that inhibit both PI3Kα and PI3Kδ.
    DOI:  https://doi.org/10.1002/psp4.12749
  3. Breast Cancer Res Treat. 2021 Dec 03.
    Ipatasertib plus paclitaxel for PIK3CA/AKT1/PTEN-altered hormone receptor-positive HER2-negative advanced breast cancer: primary results from cohort B of the IPATunity130 randomized phase 3 trial.
    Nicholas Turner, Rebecca A Dent, Joyce O'Shaughnessy, Sung-Bae Kim, Steven J Isakoff, Carlos Barrios, Shigehira Saji, Igor Bondarenko, Zbigniew Nowecki, Qinshu Lian, Sarah-Jayne Reilly, Heather Hinton, Matthew J Wongchenko, Bruno Kovic, Aruna Mani, Mafalda Oliveira.
       PURPOSE: PI3K/AKT pathway alterations are frequent in hormone receptor-positive (HR+) breast cancers. IPATunity130 Cohort B investigated ipatasertib-paclitaxel in PI3K pathway-mutant HR+ unresectable locally advanced/metastatic breast cancer (aBC).
    METHODS: Cohort B of the randomized, double-blind, placebo-controlled, phase 3 IPATunity130 trial enrolled patients with HR+ HER2-negative PIK3CA/AKT1/PTEN-altered measurable aBC who were considered inappropriate for endocrine-based therapy (demonstrated insensitivity to endocrine therapy or visceral crisis) and were candidates for taxane monotherapy. Patients with prior chemotherapy for aBC or relapse < 1 year since (neo)adjuvant chemotherapy were ineligible. Patients were randomized 2:1 to ipatasertib (400 mg, days 1-21) or placebo, plus paclitaxel (80 mg/m2, days 1, 8, 15), every 28 days until disease progression or unacceptable toxicity. The primary endpoint was investigator-assessed progression-free survival (PFS).
    RESULTS: Overall, 146 patients were randomized to ipatasertib-paclitaxel and 76 to placebo-paclitaxel. In both arms, median investigator-assessed PFS was 9.3 months (hazard ratio, 1.00, 95% CI 0.71-1.40) and the objective response rate was 47%. Median paclitaxel duration was 6.9 versus 8.8 months in the ipatasertib-paclitaxel versus placebo-paclitaxel arms, respectively; median ipatasertib/placebo duration was 8.0 versus 9.1 months, respectively. The most common grade ≥ 3 adverse events were diarrhea (12% with ipatasertib-paclitaxel vs 1% with placebo-paclitaxel), neutrophil count decreased (9% vs 7%), neutropenia (8% vs 9%), peripheral neuropathy (7% vs 3%), peripheral sensory neuropathy (3% vs 5%) and hypertension (1% vs 5%).
    CONCLUSION: Adding ipatasertib to paclitaxel did not improve efficacy in PIK3CA/AKT1/PTEN-altered HR+ HER2-negative aBC. The ipatasertib-paclitaxel safety profile was consistent with each agent's known adverse effects. Trial registration NCT03337724.
    Keywords:  First-line; HER2 negative; Hormone receptor positive; Ipatasertib; PI3K/AKT
    DOI:  https://doi.org/10.1007/s10549-021-06450-x
  4. NPJ Precis Oncol. 2021 Dec 01. 5(1): 99
    Emergence of mTOR mutation as an acquired resistance mechanism to AKT inhibition, and subsequent response to mTORC1/2 inhibition.
    Niamh Coleman, Vivek Subbiah, Shubham Pant, Keyur Patel, Sinchita Roy-Chowdhuri, Sireesha Yedururi, Amber Johnson, Timothy A Yap, Jordi Rodon, Kenna Shaw, Funda Meric-Bernstam.
      Acquired resistance to molecular targeted therapy is a significant challenge of the precision medicine era. The ability to understand these mechanisms of resistance may improve patient selection and allow for the development of rationally designed next-line or combination treatment strategies and improved patient outcomes. AKT is a critical effector of the phosphoinositide 3-kinase signaling cascade, one of the most commonly activated pathways in human cancer. Deregulation of signaling pathways, such as RAF/MEK/ERK are previously described mechanisms of resistance to AKT/PI3K inhibitors. Mutations in the mTOR gene, however, are exceedingly rare. We present a case of acquired mTOR resistance, following targeted AKT inhibition, and subsequent response to mTOR1/2 inhibitor in a patient with metastatic endometrial cancer, the first documented response to ATP-competitive mTOR inhibition in this setting. This case supports mTOR mutation as a mechanism of resistance, and underscores the importance of tumor molecular profiling, exemplifying precision medicine in action.
    DOI:  https://doi.org/10.1038/s41698-021-00240-w
  5. J Cell Sci. 2021 Dec 03. pii: jcs.258584. [Epub ahead of print]
    Phospholipase C-related catalytically inactive protein acts as a positive regulator for insulin signalling in adipocytes.
    Jing Gao, Akiko Mizokami, Hiroshi Takeuchi, Aonan Li, Fei Huang, Haruki Nagano, Takashi Kanematsu, Eijiro Jimi, Masato Hirata.
      Insulin signalling is tightly controlled by various factors, but the exact molecular mechanism remains incompletely understood. We previously reported that phospholipase C-related but catalytically inactive protein (PRIP) interacts with Akt, the central molecule in insulin signalling. Here, we investigated whether PRIP is involved in the regulation of insulin signalling in adipocytes. We found that insulin signalling including insulin-stimulated phosphorylation of the insulin receptor (IR), insulin receptor substrate-1 (IRS-1), Akt, and glucose uptake, were impaired in adipocytes from PRIP-knockout (KO) mice compared with those from wild-type (WT) mice. The amount of IR expressed on the cell-surface was decreased in PRIP-KO adipocytes. Immunoprecipitation assay showed that PRIP interacted with IR. The reduced cell-surface IR in PRIP-KO adipocytes was comparable with that in WT cells when Rab5 expression was silenced using specific siRNA. In contrast, the dephosphorylation of IRS-1 at serine residues, some of which were reported to be involved in the internalisation of IR, was impaired in cells from PRIP-KO mice. These results suggest that PRIP facilitates insulin signalling by modulating the internalisation of IR in adipocytes.
    Keywords:  Adipocyte; Insulin receptor; Insulin receptor substrate-1; Insulin resistance; Insulin signalling
    DOI:  https://doi.org/10.1242/jcs.258584
  6. J Med Chem. 2021 Dec 02.
    Design, Synthesis, and Evaluation of Potent, Selective, and Bioavailable AKT Kinase Degraders.
    Xufen Yu, Jia Xu, Ling Xie, Li Wang, Yudao Shen, Kaitlyn M Cahuzac, Xian Chen, Jing Liu, Ramon E Parsons, Jian Jin.
      The serine/threonine kinase AKT functions as a critical node of the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (m-TOR) signaling pathway. Aberrant activation and overexpression of AKT are strongly correlated with numerous human cancers. To date, only two AKT degraders with no structure-activity relationship (SAR) results have been reported. Through extensive SAR studies on various linkers, E3 ligase ligands, and AKT binding moieties, we identified two novel and potent AKT proteolysis targeting chimera (PROTAC) degraders: von Hippel-Lindau (VHL)-recruiting degrader 13 (MS98) and cereblon (CRBN)-recruiting degrader 25 (MS170). These two compounds selectively induced robust AKT protein degradation, inhibited downstream signaling, and suppressed cancer cell proliferation. Moreover, these two degraders exhibited good plasma exposure levels in mice through intraperitoneal injection. Overall, our comprehensive SAR studies led to the discovery of degraders 13 and 25, which are potentially useful chemical tools to investigate biological and pathogenic functions of AKT in vitro and in vivo.
    DOI:  https://doi.org/10.1021/acs.jmedchem.1c01476
  7. Am J Med Genet A. 2021 Dec 02.
    Intracranial venous malformation masquerading as a meningioma in PI3KCA-related overgrowth spectrum disorder.
    Aristotelis Filippidis, Hart Lidov, Alyaa Al-Ibraheemi, Alfred P See, Siddharth Srivastava, Darren B Orbach, Katie Pricola Fehnel.
      Gain of function PIK3CA pathogenic variants have been identified in overgrowth syndromes collectively termed "PIK3CA-related overgrowth spectrum" (PROS). There are no previously reported cases of cerebrovascular venous malformations in PROS syndromes, though somatic activating PIK3CA variants have been identified in extracranial venous malformation. This study was approved by the Institutional Review Boar at Boston Children's Hospital. A 14-year-old female mosaic for the de novo p.R108H pathogenic variant in the PIK3CA gene was found to have a large tumor involving the superior sagittal sinus with mass effect on the motor cortex most consistent with a parafalcine meningioma. She underwent surgical resection with pathology demonstrating a venous malformation. PIK3CA pathogenic variants have been identified in nonsyndromic extracranial venous and lymphatic malformations as well in brain tumors, including glioma and meningioma. However, PIK3CA variants have not previously been identified in purely intracranial venous malformations. This distinction is relevant to treatment decisions, given that mTOR inhibitors may provide an alternative option for noninvasive therapy in cases of suspected venous malformation.
    Keywords:  PIK3CA; PROS; venous malformation
    DOI:  https://doi.org/10.1002/ajmg.a.62570
  8. Clin Genet. 2021 Dec 01.
    Segmental undergrowth is associated with pathogenic variants in vascular malformation genes: A retrospective case-series study.
    Victor Martinez-Glez, Lara Rodriguez-Laguna, Vanesa Viana-Huete, Carolina García Torrijos, Begoña Hurtado, Pablo Lapunzina, Paloma Triana, Juan Carlos López-Gutiérrez.
      Segmental overgrowth has been widely described in patients with congenital vascular anomalies. However, segmental undergrowth has been poorly characterized, and no large series of patients have been published. We present the clinical and molecular characteristics a cohort of 37 patients with vascular malformations and segmental undergrowth. True undergrowth was only considered when the musculoskeletal system was involved to avoid confusion with other causes of segmental reduction, as in lipodystrophy or the long-term osteopenia seen in patients with Servelle-Martorell syndrome. Deep high-throughput sequencing was performed in tissue samples from 20 patients using a custom panel. We identified three groups: undergrowth associated with 1) venous, 2) capillary-venous, and 3) lymphatic-capillary-venous malformations. Congenital or early childhood onset undergrowth can occur with or without associated overgrowth. Different likely pathogenic or pathogenic variants were detected in 13 of 20 (65%) tissue samples in the PIK3CA, TEK, GNAQ, or GNA11 genes. In conclusion, the eponymous Servelle-Martorell syndrome should not be used as a synonym for undergrowth. Segmental undergrowth should be considered a characteristic associated with vascular malformations. Patients with PIK3CA variants show all different combinations of overgrowth and undergrowth. Thus, the term PROS (PIK3CA-Related Overgrowth Spectrum) does not cover the entire spectrum.
    Keywords:  GNA11; GNAQ; Overgrowth; PIK3CA; Somatic mosaicism; TEK; Undergrowth; Vascular malformations
    DOI:  https://doi.org/10.1111/cge.14095
  9. Nat Biotechnol. 2021 Dec 02.
    Personalized phosphoproteomics identifies functional signaling.
    Elise J Needham, Janne R Hingst, Benjamin L Parker, Kaitlin R Morrison, Guang Yang, Johan Onslev, Jonas M Kristensen, Kurt Højlund, Naomi X Y Ling, Jonathan S Oakhill, Erik A Richter, Bente Kiens, Janni Petersen, Christian Pehmøller, David E James, Jørgen F P Wojtaszewski, Sean J Humphrey.
      Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce 'personalized phosphoproteomics', a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.
    DOI:  https://doi.org/10.1038/s41587-021-01099-9
  10. Nat Genet. 2021 Dec 02.
    Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.
    Luz Garcia-Alonso, Louis-François Handfield, Kenny Roberts, Konstantina Nikolakopoulou, Ridma C Fernando, Lucy Gardner, Benjamin Woodhams, Anna Arutyunyan, Krzysztof Polanski, Regina Hoo, Carmen Sancho-Serra, Tong Li, Kwasi Kwakwa, Elizabeth Tuck, Valentina Lorenzi, Hassan Massalha, Martin Prete, Vitalii Kleshchevnikov, Aleksandra Tarkowska, Tarryn Porter, Cecilia Icoresi Mazzeo, Stijn van Dongen, Monika Dabrowska, Vasyl Vaskivskyi, Krishnaa T Mahbubani, Jong-Eun Park, Mercedes Jimenez-Linan, Lia Campos, Vladimir Yu Kiselev, Cecilia Lindskog, Paul Ayuk, Elena Prigmore, Michael R Stratton, Kourosh Saeb-Parsy, Ashley Moffett, Luiza Moore, Omer A Bayraktar, Sarah A Teichmann, Margherita Y Turco, Roser Vento-Tormo.
      The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.
    DOI:  https://doi.org/10.1038/s41588-021-00972-2
  11. J Clin Invest. 2021 Dec 02. pii: e153724. [Epub ahead of print]
    Dyrk1b promotes hepatic lipogenesis by bypassing canonical insulin signaling and directly activating mTORC2 in mice.
    Neha Bhat, Anand Narayanan, Mohsen Fathzadeh, Mario Kahn, Dongyan Zhang, Leigh Goedeke, Arpita Neogi, Rebecca L Cardone, Richard G Kibbey, Carlos Fernandez-Hernando, Henry N Ginsberg, Dhanpat Jain, Gerald Shulman, Arya Mani.
      Mutations in Dyrk1b are associated with metabolic syndrome and non-alcoholic fatty liver disease in humans. Our investigations showed that DYRK1B levels are increased in the liver of patients with non-alcoholic liver steatohepatitis (NASH) and in mice fed with a high fat/sucrose diet. Increasing Dyrk1b levels in the mouse liver enhanced de novo lipogenesis (DNL), fatty-acid uptake, and TAG secretion and caused NASH and hyperlipidemia. Conversely, knockdown of Dyrk1b was protective against high-calorie induced hepatic steatosis and fibrosis and hyperlipidemia. Mechanistically, Dyrk1b increased DNL by activating mTORC2 in a kinase independent fashion. Accordingly, the Dyrk1b-induced NASH was fully rescued when mTORC2 was genetically disrupted. The elevated DNL was associated with increased plasma membrane sn-1,2-diacylglyerol levels and increased PKCε-mediated IRKT1150 phosphorylation, which resulted in impaired activation of hepatic insulin signaling and reduced hepatic glycogen storage. These findings provide new insights into the mechanisms that underlie Dyrk1b-induced hepatic lipogenesis and hepatic insulin resistance and identify Dyrk1b as a therapeutic target for NASH and insulin resistance in the liver.
    Keywords:  Hepatology; Insulin signaling; Metabolism; Obesity; Protein kinases
    DOI:  https://doi.org/10.1172/JCI153724
  12. Methods Mol Biol. 2022 ;2422 233-245
    ER+ Breast Cancer Mammosphere Formation and Analysis.
    Ciera S Singleton, Leo Li-Ying Chan, Kelsey J McCulley, Sarah L Kessel, Luis Del Valle, Judy S Crabtree.
      Mammosphere formation assays are a popular and convenient technique in the study of breast cancer by providing an in vitro mechanism by which to study breast cancer stem cell (BCSC) contribution to tumorigenesis, as well as more closely mimicking the three-dimensional tumor microenvironment. In these assays, BCSCs are stimulated to proliferate in low adherence tissue culture dishes and the resulting mammospheres exhibit activation of stem cell-related signaling pathways. Here we describe the process for generating and analyzing mammospheres under varying conditions.
    Keywords:  Breast cancer stem cell; Mammosphere; Tissue culture; Tumor microenvironment
    DOI:  https://doi.org/10.1007/978-1-0716-1948-3_16
  13. Clin Transl Med. 2021 11;11(11): e589
    Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kα in early and advanced HER2-positive breast cancer.
    Lin-Wei Guo, Xiao-Guang Li, Yun-Song Yang, Xun-Xi Lu, Xiang-Chen Han, Guan-Tian Lang, Li Chen, Zhi-Ming Shao, Xin Hu.
       BACKGROUND: Few studies have discussed the contradictory roles of mutated-PI3Kα in HER2-positive (HER2+) breast cancer. Thus, we characterised the adaptive roles of PI3Kα mutations among HER2+ tumour progression.
    METHODS: We conducted prospective clinical sequencing of 1923 Chinese breast cancer patients and illustrated the clinical significance of PIK3CA mutations in locally advanced and advanced HER2+ cohort. A high-throughput PIK3CA mutations-barcoding screen was performed to reveal impactful mutation sites in tumour growth and drug responses.
    RESULTS: PIK3CA mutations acted as a protective factor in treatment-naïve patients; however, advanced/locally advanced patients harbouring mutated-PI3Kα exhibited a higher progressive disease rate (100% vs. 15%, p = .000053) and a lower objective response rate (81.7% vs. 95.4%, p = .0008) in response to trastuzumab-based therapy. Meanwhile, patients exhibiting anti-HER2 resistance had a relatively high variant allele fraction (VAF) of PIK3CA mutations; we defined the VAF > 12.23% as a predictor of poor anti-HER2 neoadjuvant treatment efficacy. Pooled mutations screen revealed that specific PI3Kα mutation alleles mediated own biological effects. PIK3CA functional mutations suppressed the growth of HER2+ cells, but conferred anti-HER2 resistance, which can be reversed by the PI3Kα-specific inhibitor BYL719.
    CONCLUSIONS: We proposed adaptive treatment strategies that the mutated PIK3CA and amplified ERBB2 should be concomitantly inhibited when exposing to continuous anti-HER2 therapy, while the combination of anti-HER2 and anti-PI3Kα treatment was not essential for anti-HER2 treatment-naïve patients. These findings improve the understanding of genomics-guided treatment in the different progressions of HER2+ breast cancer.
    Keywords:  early and advanced HER2-positive breast cancer; library screening; prospective sequencing; shifty PI3Kα treatment strategy
    DOI:  https://doi.org/10.1002/ctm2.589
  14. Nat Commun. 2021 Dec 03. 12(1): 6941
    Inhibition of cytoplasmic EZH2 induces antitumor activity through stabilization of the DLC1 tumor suppressor protein.
    Brajendra K Tripathi, Meghan F Anderman, Disha Bhargava, Luciarita Boccuzzi, Xiaolan Qian, Dunrui Wang, Marian E Durkin, Alex G Papageorge, Fernando J de Miguel, Katerina Politi, Kylie J Walters, James H Doroshow, Douglas R Lowy.
      mRNA expression of the DLC1 tumor suppressor gene is downregulated in many lung cancers and their derived cell lines, with DLC1 protein levels being low or absent. Although the role of increased EZH2 methyltransferase in cancer is usually attributed to its histone methylation, we unexpectedly observed that post-translational destabilization of DLC1 protein is common and attributable to its methylation by cytoplasmic EZH2, leading to CUL-4A ubiquitin-dependent proteasomal degradation of DLC1. Furthermore, siRNA knockdown of KRAS in several lines increases DLC1 protein, associated with a drastic reduction in cytoplasmic EZH2. Pharmacologic inhibition of EZH2, CUL-4A, or the proteasome can increase the steady-state level of DLC1 protein, whose tumor suppressor activity is further increased by AKT and/or SRC kinase inhibitors, which reverse the direct phosphorylation of DLC1 by these kinases. These rational drug combinations induce potent tumor growth inhibition, with markers of apoptosis and senescence, that is highly dependent on DLC1 protein.
    DOI:  https://doi.org/10.1038/s41467-021-26993-3
  15. J Neuroinflammation. 2021 Nov 27. 18(1): 276
    Dysregulated phosphoinositide 3-kinase signaling in microglia: shaping chronic neuroinflammation.
    Erskine Chu, Richelle Mychasiuk, Margaret L Hibbs, Bridgette D Semple.
      Microglia are integral mediators of innate immunity within the mammalian central nervous system. Typical microglial responses are transient, intending to restore homeostasis by orchestrating the removal of pathogens and debris and the regeneration of damaged neurons. However, prolonged and persistent microglial activation can drive chronic neuroinflammation and is associated with neurodegenerative disease. Recent evidence has revealed that abnormalities in microglial signaling pathways involving phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT) may contribute to altered microglial activity and exacerbated neuroimmune responses. In this scoping review, the known and suspected roles of PI3K-AKT signaling in microglia, both during health and pathological states, will be examined, and the key microglial receptors that induce PI3K-AKT signaling in microglia will be described. Since aberrant signaling is correlated with neurodegenerative disease onset, the relationship between maladapted PI3K-AKT signaling and the development of neurodegenerative disease will also be explored. Finally, studies in which microglial PI3K-AKT signaling has been modulated will be highlighted, as this may prove to be a promising therapeutic approach for the future treatment of a range of neuroinflammatory conditions.
    Keywords:  AKT; Cell signaling; Glia; Innate immune system; Neurodegenerative diseases; PI3K
    DOI:  https://doi.org/10.1186/s12974-021-02325-6
  16. Nat Metab. 2021 Nov 29.
    Serine catabolism generates liver NADPH and supports hepatic lipogenesis.
    Zhaoyue Zhang, Tara TeSlaa, Xincheng Xu, Xianfeng Zeng, Lifeng Yang, Gang Xing, Gregory J Tesz, Michelle F Clasquin, Joshua D Rabinowitz.
      Carbohydrate can be converted into fat by de novo lipogenesis, a process upregulated in fatty liver disease. Chemically, de novo lipogenesis involves polymerization and reduction of acetyl-CoA, using NADPH as the electron donor. The feedstocks used to generate acetyl-CoA and NADPH in lipogenic tissues remain, however, unclear. Here we show using stable isotope tracing in mice that de novo lipogenesis in adipose is supported by glucose and its catabolism via the pentose phosphate pathway to make NADPH. The liver, in contrast, derives acetyl-CoA for lipogenesis from acetate and lactate, and NADPH from folate-mediated serine catabolism. Such NADPH generation involves the cytosolic serine pathway in liver running in the opposite direction to that observed in most tissues and tumours, with NADPH made by the SHMT1-MTHFD1-ALDH1L1 reaction sequence. SHMT inhibition decreases hepatic lipogenesis. Thus, liver folate metabolism is distinctively wired to support cytosolic NADPH production and lipogenesis. More generally, while the same enzymes are involved in fat synthesis in liver and adipose, different substrates are used, opening the door to tissue-specific pharmacological interventions.
    DOI:  https://doi.org/10.1038/s42255-021-00487-4
  17. Dev Cell. 2021 Nov 23. pii: S1534-5807(21)00891-1. [Epub ahead of print]
    Distinct contributions of partial and full EMT to breast cancer malignancy.
    Fabiana Lüönd, Nami Sugiyama, Ruben Bill, Laura Bornes, Carolina Hager, Fengyuan Tang, Natascha Santacroce, Christian Beisel, Robert Ivanek, Thomas Bürglin, Stefanie Tiede, Jacco van Rheenen, Gerhard Christofori.
      Epithelial-mesenchymal transition (EMT) is a transient, reversible process of cell de-differentiation where cancer cells transit between various stages of an EMT continuum, including epithelial, partial EMT, and mesenchymal cell states. We have employed Tamoxifen-inducible dual recombinase lineage tracing systems combined with live imaging and 5-cell RNA sequencing to track cancer cells undergoing partial or full EMT in the MMTV-PyMT mouse model of metastatic breast cancer. In primary tumors, cancer cells infrequently undergo EMT and mostly transition between epithelial and partial EMT states but rarely reach full EMT. Cells undergoing partial EMT contribute to lung metastasis and chemoresistance, whereas full EMT cells mostly retain a mesenchymal phenotype and fail to colonize the lungs. However, full EMT cancer cells are enriched in recurrent tumors upon chemotherapy. Hence, cancer cells in various stages of the EMT continuum differentially contribute to hallmarks of breast cancer malignancy, such as tumor invasion, metastasis, and chemoresistance.
    Keywords:  EMT; EMT continuum; breast cancer; collective cell migration; dual recombinase; lineage tracing; metastasis; mouse models; therapy resistance
    DOI:  https://doi.org/10.1016/j.devcel.2021.11.006
  18. Cell Rep. 2021 Nov 30. pii: S2211-1247(21)01549-7. [Epub ahead of print]37(9): 110063
    Lysophosphatidic acid shifts metabolic and transcriptional landscapes to induce a distinct cellular state in human pluripotent stem cells.
    Faxiang Xu, Chunhao Deng, Zhili Ren, Liangyu Sun, Ya Meng, Weiwei Liu, Jianbo Wan, Guokai Chen.
      Pluripotent stem cells (PSCs) can be maintained in a continuum of cellular states with distinct features. Exogenous lipid supplements can relieve the dependence on de novo lipogenesis and shift global metabolism. However, it is largely unexplored how specific lipid components regulate metabolism and subsequently the pluripotency state. In this study, we report that the metabolic landscape of human PSCs (hPSCs) is shifted by signaling lipid lysophosphatidic acid (LPA), which naturally exists. LPA leads to a distinctive transcriptome profile that is not associated with de novo lipogenesis. Although exogenous lipids such as cholesterol, common free fatty acids, and LPA can affect cellular metabolism, they are not necessary for maintaining primed pluripotency. Instead, LPA induces distinct and reversible phenotypes in cell cycle, morphology, and mitochondria. This study reveals a distinct primed state that could be used to alter cell physiology in hPSCs for basic research and stem cell applications.
    Keywords:  LPA; cellular state; hPSC; lipid; metabolism; mitochondria; pluripotency; transcriptome
    DOI:  https://doi.org/10.1016/j.celrep.2021.110063
  19. Nat Commun. 2021 Nov 30. 12(1): 6979
    A DAP5/eIF3d alternate mRNA translation mechanism promotes differentiation and immune suppression by human regulatory T cells.
    Viviana Volta, Sandra Pérez-Baos, Columba de la Parra, Olga Katsara, Amanda Ernlund, Sophie Dornbaum, Robert J Schneider.
      Regulatory T cells (Treg cells) inhibit effector T cells and maintain immune system homeostasis. Treg cell maturation in peripheral sites requires inhibition of protein kinase mTORC1 and TGF-beta-1 (TGF-beta). While Treg cell maturation requires protein synthesis, mTORC1 inhibition downregulates it, leaving unanswered how Treg cells achieve essential mRNA translation for development and immune suppression activity. Using human CD4+ T cells differentiated in culture and genome-wide transcription and translation profiling, here we report that TGF-beta transcriptionally reprograms naive T cells to express Treg cell differentiation and immune suppression mRNAs, while mTORC1 inhibition impairs translation of T cell mRNAs but not those induced by TGF-beta. Rather than canonical mTORC1/eIF4E/eIF4G translation, Treg cell mRNAs utilize the eIF4G homolog DAP5 and initiation factor eIF3d in a non-canonical translation mechanism that requires cap-dependent binding by eIF3d directed by Treg cell mRNA 5' noncoding regions. Silencing DAP5 in isolated human naive CD4+ T cells impairs their differentiation into Treg cells. Treg cell differentiation is mediated by mTORC1 downregulation and TGF-beta transcriptional reprogramming that establishes a DAP5/eIF3d-selective mechanism of mRNA translation.
    DOI:  https://doi.org/10.1038/s41467-021-27087-w
  20. Elife. 2021 Dec 03. pii: e68292. [Epub ahead of print]10
    Author-sourced capture of pathway knowledge in computable form using Biofactoid.
    Jeffrey V Wong, Max Franz, Metin Can Siper, Dylan Fong, Funda Durupinar, Christian Dallago, Augustin Luna, John M Giorgi, Igor Rodchenkov, Özgün Babur, John A Bachman, Benjamin Gyori, Emek Demir, Gary D Bader, Chris Sander.
      Making the knowledge contained in scientific papers machine-readable and formally computable would allow researchers to take full advantage of this information by enabling integration with other knowledge sources to support data analysis and interpretation. Here we describe Biofactoid, a web-based platform that allows scientists to specify networks of interactions between genes, their products, and chemical compounds, and then translates this information into a representation suitable for computational analysis, search and discovery. We also report the results of a pilot study to encourage the wide adoption of Biofactoid by the scientific community.
    Keywords:  computational biology; genetics; genomics; none; systems biology
    DOI:  https://doi.org/10.7554/eLife.68292
  21. Dis Model Mech. 2021 Nov 01. pii: dmm049340. [Epub ahead of print]14(11):
    Insulin at 100 years - is rebalancing its action key to fighting obesity-related disease?
    Gemma V Brierley, Robert K Semple.
      One hundred years ago, insulin was purified and administered to people with diabetes to lower blood glucose, suppress ketogenesis and save lives. A century later, insulin resistance (IR) lies at the heart of the obesity-related disease pandemic. Multiple observations attest that IR syndrome is an amalgamation of gain and loss of insulin action, suggesting that IR is a misnomer. This misapprehension is reinforced by shortcomings in common model systems and is particularly pronounced for the tissue growth disorders associated with IR. It is necessary to move away from conceptualisation of IR as a pure state of impaired insulin action and to appreciate that, in the long term, insulin can harm as well as cure. The mixed state of gain and loss of insulin action, and its relationship to perturbed insulin-like growth factor (IGF) action, should be interrogated more fully in models recapitulating human disease. Only then may the potential of rebalancing insulin action, rather than simply increasing global insulin signalling, finally be appreciated.
    DOI:  https://doi.org/10.1242/dmm.049340
  22. Cell. 2021 Nov 18. pii: S0092-8674(21)01320-9. [Epub ahead of print]
    Deciphering cell signaling networks with massively multiplexed biosensor barcoding.
    Jr-Ming Yang, Wei-Yu Chi, Jessica Liang, Saki Takayanagi, Pablo A Iglesias, Chuan-Hsiang Huang.
      Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.
    Keywords:  KRAS; adaptation; barcode; cell non-autonomous effect; fluorescent biosensor; live cell imaging; machine learning; multiplexing; receptor tyrosine kinase; signaling network
    DOI:  https://doi.org/10.1016/j.cell.2021.11.005
  23. Am J Physiol Cell Physiol. 2021 Dec 01.
    RPS6 phosphorylation occurs to a greater extent in the periphery of human skeletal muscle fibers, near focal adhesions, after anabolic stimuli.
    Nathan Hodson, Michael Mazzulla, Maksym N H Holowaty, Dinesh Kumbhare, Daniel R Moore.
      Following anabolic stimuli (mechanical loading and/or amino acid provision) the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of protein synthesis, translocates toward the cell periphery. However, it is unknown if mTORC1-mediated phosphorylation events occur in these peripheral regions or prior to translocation (i.e. in central regions). We therefore aimed to determine the cellular location of a mTORC1-mediated phosphorylation event, RPS6Ser240/244, in human skeletal muscle following anabolic stimuli. Fourteen young, healthy males either ingested a protein-carbohydrate beverage (0.25g/kg protein, 0.75g/kg carbohydrate) alone (n=7;23±5yrs;76.8±3.6kg;13.6±3.8%BF, FED) or following a whole-body resistance exercise bout (n=7;22±2yrs;78.1±3.6kg;12.2±4.9%BF, EXFED). Vastus lateralis muscle biopsies were obtained at rest (PRE) and 120 and 300min following anabolic stimuli. RPS6Ser240/244 phosphorylation measured by immunofluorescent staining or immunoblot was positively correlated (r=0.76, p<0.001). Peripheral staining intensity of p-RPS6Ser240/244 increased above PRE in both FED and EXFED at 120min (~54% and ~138% respectively, p<0.05) but was greater in EXFED at both post-stimuli time points (p<0.05). The peripheral-central ratio of p-RPS6240/244 staining displayed a similar pattern, even when corrected for total RPS6 distribution, suggesting RPS6 phosphorylation occurs to a greater extent in the periphery of fibers. Moreover, p-RPS6Ser240/244 intensity within paxillin-positive regions, a marker of focal adhesion complexes, was elevated at 120min irrespective of stimulus (p=0.006) before returning to PRE at 300min. These data confirm that RPS6Ser240/244 phosphorylation occurs in the region of human muscle fibers to which mTOR translocates following anabolic stimuli and identifies focal adhesion complexes as a potential site of mTORC1 regulation in vivo.
    Keywords:  Focal Adhesions; RPS6; Resistance Exercise; Skeletal muscle; mTOR
    DOI:  https://doi.org/10.1152/ajpcell.00357.2021
  24. Sci Signal. 2021 Nov 30. 14(711): eabc4520
    Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.
    April Lo, Kristin Holmes, Shriya Kamlapurkar, Filip Mundt, Sitapriya Moorthi, Iris Fung, Shaunt Fereshetian, Jacqueline Watson, Steven A Carr, Philipp Mertins, Alice H Berger.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/scisignal.abc4520
  25. Elife. 2021 Nov 30. pii: e73218. [Epub ahead of print]10
    A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor.
    Yongjian Huang, Jana Ognjenovic, Deepti Karandur, Kate Miller, Alan Merk, Sriram Subramaniam, John Kuriyan.
      The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that couples the binding of extracellular ligands, such as EGF and transforming growth factor-α (TGF-α), to the initiation of intracellular signaling pathways. EGFR binds to EGF and TGF-α with similar affinity, but generates different signals from these ligands. To address the mechanistic basis of this phenomenon, we have carried out cryo-EM analyses of human EGFR bound to EGF and TGF-α. We show that the extracellular module adopts an ensemble of dimeric conformations when bound to either EGF or TGF-α. The two extreme states of this ensemble represent distinct ligand-bound quaternary structures in which the membrane-proximal tips of the extracellular module are either juxtaposed or separated. EGF and TGF-α differ in their ability to maintain the conformation with the membrane-proximal tips of the extracellular module separated, and this conformation is stabilized preferentially by an oncogenic EGFR mutation. Close proximity of the transmembrane helices at the junction with the extracellular module has been associated previously with increased EGFR activity. Our results show how EGFR can couple the binding of different ligands to differential modulation of this proximity, thereby suggesting a molecular mechanism for the generation of ligand-sensitive differential outputs in this receptor family.
    Keywords:  biochemistry; chemical biology; human; molecular biophysics; structural biology
    DOI:  https://doi.org/10.7554/eLife.73218
  26. Mol Cell. 2021 Nov 22. pii: S1097-2765(21)00956-4. [Epub ahead of print]
    Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.
    Sophie Trefely, Katharina Huber, Joyce Liu, Michael Noji, Stephanie Stransky, Jay Singh, Mary T Doan, Claudia D Lovell, Eliana von Krusenstiern, Helen Jiang, Anna Bostwick, Hannah L Pepper, Luke Izzo, Steven Zhao, Jimmy P Xu, Kenneth C Bedi, J Eduardo Rame, Juliane G Bogner-Strauss, Clementina Mesaros, Simone Sidoli, Kathryn E Wellen, Nathaniel W Snyder.
      Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
    Keywords:  acyl-CoA; branched chain amino acids; histone; internal standard; isoleucine; matrix effects; metabolomics; mitochondria; nucleus; propionylation; subcellular
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.006
  27. Ann N Y Acad Sci. 2021 Nov 30.
    Cancer stem cells: advances in biology and clinical translation-a Keystone Symposia report.
    Jennifer Cable, Duanqing Pei, Lola M Reid, Xin Wei Wang, Sonam Bhatia, Panagiotis Karras, Jan Joseph Melenhorst, Markus Grompe, Justin D Lathia, Erwei Song, Calvin J Kuo, Ning Zhang, Richard M White, Stephanie Ky Ma, Lichun Ma, Y Rebecca Chin, Michael M Shen, Irene Oi Lin Ng, Klaus H Kaestner, Lei Zhou, Shaheen Sikandar, Clemens A Schmitt, Wei Guo, Carmen Chak-Lui Wong, Junfang Ji, Dean G Tang, Anna Dubrovska, Chunzhang Yang, Wolf R Wiedemeyer, Irving L Weissman.
      The test for the cancer stem cell (CSC) hypothesis is to find a target expressed on all, and only CSCs in a patient tumor, then eliminate all cells with that target that eliminates the cancer. That test has not yet been achieved, but CSC diagnostics and targets found on CSCs and some other cells have resulted in a few clinically relevant therapies. However, it has become apparent that eliminating the subset of tumor cells characterized by self-renewal properties is essential for long-term tumor control. CSCs are able to regenerate and initiate tumor growth, recapitulating the heterogeneity present in the tumor before treatment. As great progress has been made in identifying and elucidating the biology of CSCs as well as their interactions with the tumor microenvironment, the time seems ripe for novel therapeutic strategies that target CSCs to find clinical applicability. On May 19-21, 2021, researchers in cancer stem cells met virtually for the Keystone eSymposium "Cancer Stem Cells: Advances in Biology and Clinical Translation" to discuss recent advances in the understanding of CSCs as well as clinical efforts to target these populations.
    Keywords:  cancer stem cell; hepatocellular carcinoma; organoids; pluripotent; progenitors; stemness; tumor heterogeneity; tumorigenesis
    DOI:  https://doi.org/10.1111/nyas.14719
  28. Cell Death Dis. 2021 Dec 03. 12(12): 1127
    Amino acid deprivation induces AKT activation by inducing GCN2/ATF4/REDD1 axis.
    Hyeon-Ok Jin, Sung-Eun Hong, Ji-Young Kim, Se-Kyeong Jang, In-Chul Park.
      Amino acid availability is sensed by various signaling molecules, including general control nonderepressible 2 (GCN2) and mechanistic target of rapamycin complex 1 (mTORC1). However, it is unclear how these sensors are associated with cancer cell survival under low amino acid availability. In the present study, we investigated AKT activation in non-small cell lung cancer (NSCLC) cells deprived of each one of 20 amino acids. Among the 20 amino acids, deprivation of glutamine, arginine, methionine, and lysine induced AKT activation. AKT activation was induced by GCN2/ATF4/REDD1 axis-mediated mTORC2 activation under amino acid deprivation. In CRISPR-Cas9-mediated REDD1-knockout cells, AKT activation was not induced by amino acid deprivation, indicating that REDD1 plays a major role in AKT activation under amino acid deprivation. Knockout of REDD1 sensitized cells cultured under glutamine deprivation conditions to radiotherapy. Taken together, GCN2/ATF4/REDD1 axis induced by amino acid deprivation promotes cell survival signal, which might be a potential target for cancer therapy.
    DOI:  https://doi.org/10.1038/s41419-021-04417-w
  29. Elife. 2021 Nov 29. pii: e73020. [Epub ahead of print]10
    Quantitative analysis of tumour spheroid structure.
    Alexander P Browning, Jesse A Sharp, Ryan J Murphy, Gency Gunasingh, Brodie Lawson, Kevin Burrage, Nikolas K Haass, Matthew Simpson.
      Tumour spheroids are common in vitro experimental models of avascular tumour growth. Compared with traditional two-dimensional culture, tumour spheroids more closely mimic the avascular tumour microenvironment where spatial differences in nutrient availability strongly influence growth. We show that spheroids initiated using significantly different numbers of cells grow to similar limiting sizes, suggesting that avascular tumours have a limiting structure; in agreement with untested predictions of classical mathematical models of tumour spheroids. We develop a novel mathematical and statistical framework to study the structure of tumour spheroids seeded from cells transduced with fluorescent cell cycle indicators, enabling us to discriminate between arrested and cycling cells and identify an arrested region. Our analysis shows that transient spheroid structure is independent of initial spheroid size, and the limiting structure can be independent of seeding density. Standard experimental protocols compare spheroid size as a function of time; however, our analysis suggests that comparing spheroid structure as a function of overall size produces results that are relatively insensitive to variability in spheroid size. Our experimental observations are made using two melanoma cell lines, but our modelling framework applies across a wide range of spheroid culture conditions and cell lines.
    Keywords:  cancer biology; computational biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.73020
  30. Stem Cell Reports. 2021 Nov 23. pii: S2213-6711(21)00585-3. [Epub ahead of print]
    Robotic high-throughput biomanufacturing and functional differentiation of human pluripotent stem cells.
    Carlos A Tristan, Pinar Ormanoglu, Jaroslav Slamecka, Claire Malley, Pei-Hsuan Chu, Vukasin M Jovanovic, Yeliz Gedik, Yogita Jethmalani, Charles Bonney, Elena Barnaeva, John Braisted, Sunil K Mallanna, Dorjbal Dorjsuren, Michael J Iannotti, Ty C Voss, Sam Michael, Anton Simeonov, Ilyas Singeç.
      Efficient translation of human induced pluripotent stem cells (hiPSCs) requires scalable cell manufacturing strategies for optimal self-renewal and functional differentiation. Traditional manual cell culture is variable and labor intensive, posing challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient- and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation and generated functional neurons, cardiomyocytes, and hepatocytes. To validate our approach, we compared robotic and manual cell culture operations and performed comprehensive molecular and cellular characterizations (e.g., single-cell transcriptomics, mass cytometry, metabolism, electrophysiology) to benchmark industrial-scale cell culture operations toward building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy.
    Keywords:  CEPT cocktail; biomanufacturing; cell differentiation; high-throughput; iPS cell; mass cytometry; robotic cell culture; single-cell transcriptomics; standardization
    DOI:  https://doi.org/10.1016/j.stemcr.2021.11.004
  31. World J Gastrointest Oncol. 2021 Nov 15. 13(11): 1632-1647
    Role of mammalian target of rapamycin complex 2 in primary and secondary liver cancer.
    Katharina Joechle, Jessica Guenzle, Claus Hellerbrand, Pavel Strnad, Thorsten Cramer, Ulf Peter Neumann, Sven Arke Lang.
      The mammalian target of rapamycin (mTOR) acts in two structurally and functionally distinct protein complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). Upon deregulation, activated mTOR signaling is associated with multiple processes involved in tumor growth and metastasis. Compared with mTORC1, much less is known about mTORC2 in cancer, mainly because of the unavailability of a selective inhibitor. However, existing data suggest that mTORC2 with its two distinct subunits Rictor and mSin1 might play a more important role than assumed so far. It is one of the key effectors of the PI3K/AKT/mTOR pathway and stimulates cell growth, cell survival, metabolism, and cytoskeletal organization. It is not only implicated in tumor progression, metastasis, and the tumor microenvironment but also in resistance to therapy. Rictor, the central subunit of mTORC2, was found to be upregulated in different kinds of cancers and is associated with advanced tumor stages and a bad prognosis. Moreover, AKT, the main downstream regulator of mTORC2/Rictor, is one of the most highly activated proteins in cancer. Primary and secondary liver cancer are major problems for current cancer therapy due to the lack of specific medical treatment, emphasizing the need for further therapeutic options. This review, therefore, summarizes the role of mTORC2/Rictor in cancer, with special focus on primary liver cancer but also on liver metastases.
    Keywords:  Cholangiocellular carcinoma; Hepatocellular carcinoma; Liver cancer; Liver metastases; Mammalian target of rapamycin; Mammalian target of rapamycin complex 2; Rictor
    DOI:  https://doi.org/10.4251/wjgo.v13.i11.1632
  32. Sci Transl Med. 2021 Dec;13(622): eabe3947
    AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation.
    Faten A Sayed, Lay Kodama, Li Fan, Gillian K Carling, Joe C Udeochu, David Le, Qingyun Li, Lu Zhou, Man Ying Wong, Rose Horowitz, Pearly Ye, Hansruedi Mathys, Minghui Wang, Xiang Niu, Linas Mazutis, Xueqiao Jiang, Xueting Wang, Fuying Gao, Matthew Brendel, Maria Telpoukhovskaia, Tara E Tracy, Georgia Frost, Yungui Zhou, Yaqiao Li, Yue Qiu, Zuolin Cheng, Guoqiang Yu, John Hardy, Giovanni Coppola, Fei Wang, Michael A DeTure, Bin Zhang, Lei Xie, John Q Trajnowski, Virginia M Y Lee, Shiaoching Gong, Subhash C Sinha, Dennis W Dickson, Wenjie Luo, Li Gan.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/scitranslmed.abe3947
  33. Nat Commun. 2021 Nov 29. 12(1): 6967
    Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer.
    Pauliina M Munne, Lahja Martikainen, Iiris Räty, Kia Bertula, Nonappa, Janika Ruuska, Hanna Ala-Hongisto, Aino Peura, Babette Hollmann, Lilya Euro, Kerim Yavuz, Linda Patrikainen, Maria Salmela, Juho Pokki, Mikko Kivento, Juho Väänänen, Tomi Suomi, Liina Nevalaita, Minna Mutka, Panu Kovanen, Marjut Leidenius, Tuomo Meretoja, Katja Hukkinen, Outi Monni, Jeroen Pouwels, Biswajyoti Sahu, Johanna Mattson, Heikki Joensuu, Päivi Heikkilä, Laura L Elo, Ciara Metcalfe, Melissa R Junttila, Olli Ikkala, Juha Klefström.
      Breast cancer is now globally the most frequent cancer and leading cause of women's death. Two thirds of breast cancers express the luminal estrogen receptor-positive (ERα + ) phenotype that is initially responsive to antihormonal therapies, but drug resistance emerges. A major barrier to the understanding of the ERα-pathway biology and therapeutic discoveries is the restricted repertoire of luminal ERα + breast cancer models. The ERα + phenotype is not stable in cultured cells for reasons not fully understood. We examine 400 patient-derived breast epithelial and breast cancer explant cultures (PDECs) grown in various three-dimensional matrix scaffolds, finding that ERα is primarily regulated by the matrix stiffness. Matrix stiffness upregulates the ERα signaling via stress-mediated p38 activation and H3K27me3-mediated epigenetic regulation. The finding that the matrix stiffness is a central cue to the ERα phenotype reveals a mechanobiological component in breast tissue hormonal signaling and enables the development of novel therapeutic interventions. Subject terms: ER-positive (ER + ), breast cancer, ex vivo model, preclinical model, PDEC, stiffness, p38 SAPK.
    DOI:  https://doi.org/10.1038/s41467-021-27220-9
  34. Trends Cell Biol. 2021 Nov 26. pii: S0962-8924(21)00226-9. [Epub ahead of print]
    The dark proteome: translation from noncanonical open reading frames.
    Bradley W Wright, Zixin Yi, Jonathan S Weissman, Jin Chen.
      Omics-based technologies have revolutionized our understanding of the coding potential of the genome. In particular, these studies revealed widespread unannotated open reading frames (ORFs) throughout genomes and that these regions have the potential to encode novel functional (micro-)proteins and/or hold regulatory roles. However, despite their genomic prevalence, relatively few of these noncanonical ORFs have been functionally characterized, likely in part due to their under-recognition by the broader scientific community. The few that have been investigated in detail have demonstrated their essentiality in critical and divergent biological processes. As such, here we aim to discuss recent advances in understanding the diversity of noncanonical ORFs and their roles, as well as detail biologically important examples within the context of the mammalian genome.
    Keywords:  CRISPR; microproteins; noncanonical ORFs; ribosome profiling; short ORFs; translation
    DOI:  https://doi.org/10.1016/j.tcb.2021.10.010
  35. Nat Commun. 2021 Dec 03. 12(1): 7051
    Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers.
    Solip Park, Fran Supek, Ben Lehner.
      The classic two-hit model posits that both alleles of a tumor suppressor gene (TSG) must be inactivated to cause cancer. In contrast, for some oncogenes and haploinsufficient TSGs, a single genetic alteration can suffice to increase tumor fitness. Here, by quantifying the interactions between mutations and copy number alterations (CNAs) across 10,000 tumors, we show that many cancer genes actually switch between acting as one-hit or two-hit drivers. Third order genetic interactions identify the causes of some of these switches in dominance and dosage sensitivity as mutations in other genes in the same biological pathway. The correct genetic model for a gene thus depends on the other mutations in a genome, with a second hit in the same gene or an alteration in a different gene in the same pathway sometimes representing alternative evolutionary paths to cancer.
    DOI:  https://doi.org/10.1038/s41467-021-27242-3
  36. Science. 2021 Dec 03. 374(6572): 1227-1237
    Fumarate is a terminal electron acceptor in the mammalian electron transport chain.
    Jessica B Spinelli, Paul C Rosen, Hans-Georg Sprenger, Anna M Puszynska, Jessica L Mann, Julian M Roessler, Andrew L Cangelosi, Antonia Henne, Kendall J Condon, Tong Zhang, Tenzin Kunchok, Caroline A Lewis, Navdeep S Chandel, David M Sabatini.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abi7495
  37. Dev Cell. 2021 Nov 24. pii: S1534-5807(21)00894-7. [Epub ahead of print]
    Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation.
    Holly Merta, Jake W Carrasquillo Rodríguez, Maya I Anjur-Dietrich, Tevis Vitale, Mitchell E Granade, Thurl E Harris, Daniel J Needleman, Shirin Bahmanyar.
      Failure to reorganize the endoplasmic reticulum (ER) in mitosis results in chromosome missegregation. Here, we show that accurate chromosome segregation in human cells requires cell cycle-regulated ER membrane production. Excess ER membranes increase the viscosity of the mitotic cytoplasm to physically restrict chromosome movements, which impedes the correction of mitotic errors leading to the formation of micronuclei. Mechanistically, we demonstrate that the protein phosphatase CTDNEP1 counteracts mTOR kinase to establish a dephosphorylated pool of the phosphatidic acid phosphatase lipin 1 in interphase. CTDNEP1 control of lipin 1 limits the synthesis of fatty acids for ER membrane biogenesis in interphase that then protects against chromosome missegregation in mitosis. Thus, regulation of ER size can dictate the biophysical properties of mitotic cells, providing an explanation for why ER reorganization is necessary for mitotic fidelity. Our data further suggest that dysregulated lipid metabolism is a potential source of aneuploidy in cancer cells.
    Keywords:  CTDNEP1; aneuploidy; lipid homeostasis; lipin; mTOR; medulloblastoma; micronuclei; mitosis; nuclear assembly
    DOI:  https://doi.org/10.1016/j.devcel.2021.11.009
  38. Elife. 2021 Dec 03. pii: e63129. [Epub ahead of print]10
    Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes.
    Michelina Kierzek, Parker E Deal, Evan W Miller, Shatanik Mukherjee, Dagmar Wachten, Arnd Baumann, U Benjamin Kaupp, Timo Strünker, Christoph Brenker.
      Fluorescent probes that change their spectral properties upon binding to small biomolecules, ions, or changes in the membrane potential (Vm) are invaluable tools to study cellular signaling pathways. Here, we introduce a novel technique for simultaneous recording of multiple probes at millisecond time resolution: frequency- and spectrally-tuned multiplexing (FASTM). Different from present multiplexing approaches, FASTM uses phase-sensitive signal detection, which renders various combinations of common probes for Vm and ions accessible for multiplexing. Using kinetic stopped-flow fluorimetry, we show that FASTM allows simultaneous recording of rapid changes in Ca2+, pH, Na+, and Vm with high sensitivity and minimal crosstalk. FASTM is also suited for multiplexing using single-cell microscopy and genetically-encoded FRET biosensors. Moreover, FASTM is compatible with opto-chemical tools to study signaling using light. Finally, we show that the exceptional time resolution of FASTM also allows resolving rapid chemical reactions. Altogether, FASTM opens new opportunities for interrogating cellular signaling.
    Keywords:  cell biology
    DOI:  https://doi.org/10.7554/eLife.63129
  39. PLoS Comput Biol. 2021 Nov 29. 17(11): e1009621
    HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks.
    Upinder S Bhalla.
      Signaling networks mediate many aspects of cellular function. The conventional, mechanistically motivated approach to modeling such networks is through mass-action chemistry, which maps directly to biological entities and facilitates experimental tests and predictions. However such models are complex, need many parameters, and are computationally costly. Here we introduce the HillTau form for signaling models. HillTau retains the direct mapping to biological observables, but it uses far fewer parameters, and is 100 to over 1000 times faster than ODE-based methods. In the HillTau formalism, the steady-state concentration of signaling molecules is approximated by the Hill equation, and the dynamics by a time-course tau. We demonstrate its use in implementing several biochemical motifs, including association, inhibition, feedforward and feedback inhibition, bistability, oscillations, and a synaptic switch obeying the BCM rule. The major use-cases for HillTau are system abstraction, model reduction, scaffolds for data-driven optimization, and fast approximations to complex cellular signaling.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009621
  40. Biochem Soc Trans. 2021 Dec 02. pii: BST20210135. [Epub ahead of print]
    How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification.
    Maria Mircea, Stefan Semrau.
      On its path from a fertilized egg to one of the many cell types in a multicellular organism, a cell turns the blank canvas of its early embryonic state into a molecular profile fine-tuned to achieve a vital organismal function. This remarkable transformation emerges from the interplay between dynamically changing external signals, the cell's internal, variable state, and tremendously complex molecular machinery; we are only beginning to understand. Recently developed single-cell omics techniques have started to provide an unprecedented, comprehensive view of the molecular changes during cell-type specification and promise to reveal the underlying gene regulatory mechanism. The exponentially increasing amount of quantitative molecular data being created at the moment is slated to inform predictive, mathematical models. Such models can suggest novel ways to manipulate cell types experimentally, which has important biomedical applications. This review is meant to give the reader a starting point to participate in this exciting phase of molecular developmental biology. We first introduce some of the principal molecular players involved in cell-type specification and discuss the important organizing ability of biomolecular condensates, which has been discovered recently. We then review some of the most important single-cell omics methods and relevant findings they produced. We devote special attention to the dynamics of the molecular changes and discuss methods to measure them, most importantly lineage tracing. Finally, we introduce a conceptual framework that connects all molecular agents in a mathematical model and helps us make sense of the experimental data.
    Keywords:  computational models; developmental biology; epigenomics; eukaryotic gene expression; transcriptomics
    DOI:  https://doi.org/10.1042/BST20210135
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