bims-pideca 2021-02-28 papers

on Class IA PI3K signalling in development and cancer

Issue of 2021‒02‒28
twenty-four papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth.
mTORC1 activity is supported by spatial association with focal adhesions.
Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition.
Cell Populations Expressing Stemness-Associated Markers in Vascular Anomalies.
Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.
The delta isoform of PI3K predominates in chronic myelomonocytic leukemia and can be targeted effectively with umbralisib and ruxolitinib.
P110α and P110δ catalytic subunits of PI3 kinase regulate lysophosphatidylcholine-induced TRPC6 externalization.
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities.
In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions.
Attenuating PI3K/Akt- mTOR pathway reduces dihydrosphingosine 1 phosphate mediated collagen synthesis and hypertrophy in primary cardiac cells.
CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition.
Renal angiomyolipoma and tuberous sclerosis complex: long-term safety and efficacy outcomes of Everolimus therapy.
A Quantitative Paradigm for Decision-Making in Precision Oncology.
The NCI Genomic Data Commons.
Uniform genomic data analysis in the NCI Genomic Data Commons.
A Bama miniature pig model of monoallelic TSC1 mutation for human tuberous sclerosis complex.
Re-defining synthetic lethality by phenotypic profiling for precision oncology.
T cell circuits that sense antigen density with an ultrasensitive threshold.
Monitoring Phosphoinositide Fluxes and Effectors During Leukocyte Chemotaxis and Phagocytosis.
Quantifying information accumulation encoded in the dynamics of biochemical signaling.
Variability within rare cell states enables multiple paths toward drug resistance.
The SWELL1-LRRC8 complex regulates endothelial AKT-eNOS signaling and vascular function.
Alpelisib for the treatment of PIK3CA-mutated, hormone receptor-positive, HER2-negative metastatic breast cancer.

Cell Metab. 2021 Feb 17. pii: S1550-4131(21)00057-7. [Epub ahead of print]

Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth.

Abigail S Krall, Peter J Mullen, Felicia Surjono, Milica Momcilovic, Ernst W Schmid, Christopher J Halbrook, Apisadaporn Thambundit, Steven D Mittelman, Costas A Lyssiotis, David B Shackelford, Simon R V Knott, Heather R Christofk.

  Mitochondrial respiration is critical for cell proliferation. In addition to producing ATP, respiration generates biosynthetic precursors, such as aspartate, an essential substrate for nucleotide synthesis. Here, we show that in addition to depleting intracellular aspartate, electron transport chain (ETC) inhibition depletes aspartate-derived asparagine, increases ATF4 levels, and impairs mTOR complex I (mTORC1) activity. Exogenous asparagine restores proliferation, ATF4 and mTORC1 activities, and mTORC1-dependent nucleotide synthesis in the context of ETC inhibition, suggesting that asparagine communicates active respiration to ATF4 and mTORC1. Finally, we show that combination of the ETC inhibitor metformin, which limits tumor asparagine synthesis, and either asparaginase or dietary asparagine restriction, which limit tumor asparagine consumption, effectively impairs tumor growth in multiple mouse models of cancer. Because environmental asparagine is sufficient to restore tumor growth in the context of respiration impairment, our findings suggest that asparagine synthesis is a fundamental purpose of tumor mitochondrial respiration, which can be harnessed for therapeutic benefit to cancer patients.

Keywords:  asparaginase; asparagine; cancer metabolism; cancer treatment; dietary restriction; metformin; respiration

DOI:  https://doi.org/10.1016/j.cmet.2021.02.001
J Cell Biol. 2021 May 03. pii: e202004010. [Epub ahead of print]220(5):

mTORC1 activity is supported by spatial association with focal adhesions.

Yoana Rabanal-Ruiz, Adam Byron, Alexander Wirth, Ralitsa Madsen, Lucia Sedlackova, Graeme Hewitt, Glyn Nelson, Julian Stingele, Jimi C Wills, Tong Zhang, André Zeug, Reinhard Fässler, Bart Vanhaesebroeck, Oliver D K Maddocks, Evgeni Ponimaskin, Bernadette Carroll, Viktor I Korolchuk.

The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogenic and stress signals to control growth and metabolism. Activation of mTORC1 by amino acids and growth factors involves recruitment of the complex to the lysosomal membrane and is further supported by lysosome distribution to the cell periphery. Here, we show that translocation of lysosomes toward the cell periphery brings mTORC1 into proximity with focal adhesions (FAs). We demonstrate that FAs constitute discrete plasma membrane hubs mediating growth factor signaling and amino acid input into the cell. FAs, as well as the translocation of lysosome-bound mTORC1 to their vicinity, contribute to both peripheral and intracellular mTORC1 activity. Conversely, lysosomal distribution to the cell periphery is dispensable for the activation of mTORC1 constitutively targeted to FAs. This study advances our understanding of spatial mTORC1 regulation by demonstrating that the localization of mTORC1 to FAs is both necessary and sufficient for its activation by growth-promoting stimuli.

DOI: https://doi.org/10.1083/jcb.202004010
Clin Cancer Res. 2021 Feb 22. pii: clincanres.CCR-20-3872-A.2020. [Epub ahead of print]

Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition.

Eric B Haura, Hitendra S Solanki, Eric A Welsh, Bin Fang, Victoria Izumi, Lancia N F Darville, Brandon Stone, Ryan Franzese, Sandip Chavan, Fumi Kinose, Denis Imbody, John M Koomen, Uwe Rix.

PURPOSE: Covalent inhibitors of KRASG12C specifically target tumors driven by this form of mutant KRAS, yet early studies show that bypass signaling drives adaptive resistance. While several combination strategies have been shown to improve efficacy of KRASG12C inhibitors, underlying mechanisms and predictive strategies for patient enrichment are less clear.EXPERIMENTAL DESIGN: We performed mass spectrometry based phosphoproteomics analysis in KRASG12C cell lines after short term treatment with ARS-1620. To understand signaling diversity and cell-type specific markers, we compared proteome and phosphoproteomes of KRASG12C cells. Gene expression patterns of KRASG12C cell lines and lung tumor tissues were examined.
RESULTS: Our analysis suggests cell-type specific perturbation to ERBB2/3 signaling compensate for repressed ERK and AKT signaling following ARS-1620 treatment in epithelial cell type, and this subtype was also more responsive to co-inhibition of SHP2 and SOS1. Conversely, both high basal and feedback activation of FGFR or AXL signaling was identified in mesenchymal cells. Inhibition of FGFR signaling suppress feedback activation of ERK and mTOR, while AXL inhibition suppress PI3K pathway. In both cell lines and human lung cancer tissues with KRASG12C we observed high basal ERBB2/3 associated with epithelial gene signatures while higher basal FGFR1 and AXL was observed in cells/tumors with mesenchymal gene signatures.
CONCLUSIONS: Our phosphoproteomic study identified cell-type adaptive responses to KRASG12C inhibitors. Markers and targets associated with ERBB2/3 signaling in epithelial subtype and FGFR1/AXL signaling in mesenchymal subtype should be considered in patient enrichment schemes with KRASG12C inhibitors.

DOI: https://doi.org/10.1158/1078-0432.CCR-20-3872
Front Surg. 2020 ;7 610758

Cell Populations Expressing Stemness-Associated Markers in Vascular Anomalies.

Ethan J Kilmister, Lauren Hansen, Paul F Davis, Sean R R Hall, Swee T Tan.

  Treatment of vascular anomalies (VAs) is mostly empirical and, in many instances unsatisfactory, as the pathogeneses of these heterogeneous conditions remain largely unknown. There is emerging evidence of the presence of cell populations expressing stemness-associated markers within many types of vascular tumors and vascular malformations. The presence of these populations in VAs is supported, in part, by the observed clinical effect of the mTOR inhibitor, sirolimus, that regulates differentiation of embryonic stem cells (ESCs). The discovery of the central role of the renin-angiotensin system (RAS) in regulating stem cells in infantile hemangioma (IH) provides a plausible explanation for its spontaneous and accelerated involution induced by β-blockers and ACE inhibitors. Recent work on targeting IH stem cells by inhibiting the transcription factor SOX18 using the stereoisomer R(+) propranolol, independent of β-adrenergic blockade, opens up exciting opportunities for novel treatment of IH without the β-adrenergic blockade-related side effects. Gene mutations have been identified in several VAs, involving mainly the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways. Existing cancer therapies that target these pathways engenders the exciting possibility of repurposing these agents for challenging VAs, with early results demonstrating clinical efficacy. However, there are several shortcomings with this approach, including the treatment cost, side effects, emergence of treatment resistance and unknown long-term effects in young patients. The presence of populations expressing stemness-associated markers, including transcription factors involved in the generation of induced pluripotent stem cells (iPSCs), in different types of VAs, suggests the possible role of stem cell pathways in their pathogenesis. Components of the RAS are expressed by cell populations expressing stemness-associated markers in different types of VAs. The gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways interact with different components of the RAS, which may influence cell populations expressing stemness-associated markers within VAs. The potential of targeting these populations by manipulating the RAS using repurposed, low-cost and commonly available oral medications, warrants further investigation. This review presents the accumulating evidence demonstrating the presence of stemness-associated markers in VAs, their expression of the RAS, and their interaction with gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways, in the pathogenesis of VAs.

Keywords:  embryonic stem cells; gene mutations; induced pluripotent stem cells; renin-angiotensin system; stemness-associated markers; vascular anomalies; vascular malformation; vascular tumor

DOI:  https://doi.org/10.3389/fsurg.2020.610758
Nat Rev Endocrinol. 2021 Feb 24.

Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.

Pauline Morigny, Jeremie Boucher, Peter Arner, Dominique Langin.

In mammals, the white adipocyte is a cell type that is specialized for storage of energy (in the form of triacylglycerols) and for energy mobilization (as fatty acids). White adipocyte metabolism confers an essential role to adipose tissue in whole-body homeostasis. Dysfunction in white adipocyte metabolism is a cardinal event in the development of insulin resistance and associated disorders. This Review focuses on our current understanding of lipid and glucose metabolic pathways in the white adipocyte. We survey recent advances in humans on the importance of adipocyte hypertrophy and on the in vivo turnover of adipocytes and stored lipids. At the molecular level, the identification of novel regulators and of the interplay between metabolic pathways explains the fine-tuning between the anabolic and catabolic fates of fatty acids and glucose in different physiological states. We also examine the metabolic alterations involved in the genesis of obesity-associated metabolic disorders, lipodystrophic states, cancers and cancer-associated cachexia. New challenges include defining the heterogeneity of white adipocytes in different anatomical locations throughout the lifespan and investigating the importance of rhythmic processes. Targeting white fat metabolism offers opportunities for improved patient stratification and a wide, yet unexploited, range of therapeutic opportunities.

DOI: https://doi.org/10.1038/s41574-021-00471-8
Exp Hematol. 2021 Feb 19. pii: S0301-472X(21)00089-8. [Epub ahead of print]

The delta isoform of PI3K predominates in chronic myelomonocytic leukemia and can be targeted effectively with umbralisib and ruxolitinib.

Matthew T Villaume, M Pia Arrate, Haley E Ramsey, Kathryn I Sunthankar, Matthew T Jenkins, Tamara K Moyo, Brianna N Smith, Melissa A Fischer, Merrida A Childress, Agnieszka E Gorska, P Brent Ferrell, Michael R Savona.

  Chronic myelomonocytic leukemia (CMML) is a myelodysplastic syndrome/myeloproliferative neoplasm overlap syndrome characterized by monocytic proliferation in the presence of dysplastic bone marrow changes, inflammatory symptoms and propensity for transformation to AML, with a poor prognosis and limited treatment options. Unlike the α and β isoforms, the PI3K-δ signaling protein is predominantly expressed by hematopoietic cells and therefore has garnered interest as a potential target for the treatment of lymphomas and leukemias. We revealed a pattern of increased PIK3CD : PIK3CA ratio in monocytic M5 AML patients and cell lines and this ratio correlated with responsiveness to pharmacological PI3K-δ inhibition in vitro . As CMML is a disease defined by monocytic clonal proliferation, we tested the PI3K-δ inhibitor, umbralisib, as a single agent, and in combination with the JAK1/2 inhibitor, ruxolitinib in CMML. Our ex vivo experiments with primary CMML patient samples showed synergistic inhibition of viability and clonogenicity with this combination. Phospho-specific flow cytometry revealed that dual inhibition had the unique ability to decrease STAT5, ERK, AKT and S6 phosphorylation simultaneously, which offers a mechanistic hypothesis for the enhanced efficacy of the combination treatment. These preclinical data demonstrate promising activity by co-inhibition of PI3K-δ and JAK1/2 and support the use of ruxolitinib + umbralisib combination therapy in CMML under active clinical investigation.

Keywords:  Chronic myelomonocytic leukemia; JAK/STAT; PI3K

DOI:  https://doi.org/10.1016/j.exphem.2021.02.008
Am J Physiol Cell Physiol. 2021 Feb 24.

P110α and P110δ catalytic subunits of PI3 kinase regulate lysophosphatidylcholine-induced TRPC6 externalization.

Pinaki Chaudhuri, Andrew H Smith, Priya Putta, Linda M Graham, Michael A Rosenbaum.

  Lipid oxidation products, including lysophosphatidylcholine (lysoPC) inhibit endothelial cell (EC) migration in vitro and impair EC healing of arterial injuries in vivo, in part by activating phosphatidylinositol 3-kinase (PI3K), which increases the externalization of canonical transient receptor potential 6 (TRPC6) channels and the subsequent increase in intracellular calcium. Inhibition of PI3K is a potential method to decrease TRPC6 activation and restore migration, but PI3K is involved in multiple intracellular signaling pathways and has multiple downstream effectors. The goal of this study is to identify the specific p110 catalytic subunit isoforms responsible for lysoPC-induced TRPC6 externalization to identify a target for intervention while minimizing impact on alternative signaling pathways. Down-regulation of the p110α and p110δ isoforms, but not the p110β or p110γ isoforms, with small interfering RNA significantly decreased phosphatidylinositol (3,4,5)-trisphosphate production and TRPC6 externalization, and significantly improved EC migration in the presence of lysoPC. These results identify an additional role of p110α in EC and reveal for the first time a specific role of p110δ in EC, providing a foundation for subsequent in vivo studies to investigate the impact of p110 isoform inhibition on arterial healing after injury.

Keywords:  PI3-kinase; TRPC6; endothelial cell migration; p110a; p110d

DOI:  https://doi.org/10.1152/ajpcell.00425.2020
Nature. 2021 Feb;590(7847): 649-654

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.

Diana Mahdessian, Anthony J Cesnik, Christian Gnann, Frida Danielsson, Lovisa Stenström, Muhammad Arif, Cheng Zhang, Trang Le, Fredric Johansson, Rutger Shutten, Anna Bäckström, Ulrika Axelsson, Peter Thul, Nathan H Cho, Oana Carja, Mathias Uhlén, Adil Mardinoglu, Charlotte Stadler, Cecilia Lindskog, Burcu Ayoglu, Manuel D Leonetti, Fredrik Pontén, Devin P Sullivan, Emma Lundberg.

The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.

DOI: https://doi.org/10.1038/s41586-021-03232-9
Nat Metab. 2021 Feb;3(2): 228-243

Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities.

Lam O Huang, Alexander Rauch, Eugenia Mazzaferro, Michael Preuss, Stefania Carobbio, Cigdem S Bayrak, Nathalie Chami, Zhe Wang, Ursula M Schick, Nancy Yang, Yuval Itan, Antonio Vidal-Puig, Marcel den Hoed, Susanne Mandrup, Tuomas O Kilpeläinen, Ruth J F Loos.

Obesity is a major risk factor for cardiometabolic diseases. Nevertheless, a substantial proportion of individuals with obesity do not suffer cardiometabolic comorbidities. The mechanisms that uncouple adiposity from its cardiometabolic complications are not fully understood. Here, we identify 62 loci of which the same allele is significantly associated with both higher adiposity and lower cardiometabolic risk. Functional analyses show that the 62 loci are enriched for genes expressed in adipose tissue, and for regulatory variants that influence nearby genes that affect adipocyte differentiation. Genes prioritized in each locus support a key role of fat distribution (FAM13A, IRS1 and PPARG) and adipocyte function (ALDH2, CCDC92, DNAH10, ESR1, FAM13A, MTOR, PIK3R1 and VEGFB). Several additional mechanisms are involved as well, such as insulin-glucose signalling (ADCY5, ARAP1, CREBBP, FAM13A, MTOR, PEPD, RAC1 and SH2B3), energy expenditure and fatty acid oxidation (IGF2BP2), browning of white adipose tissue (CSK, VEGFA, VEGFB and SLC22A3) and inflammation (SH2B3, DAGLB and ADCY9). Some of these genes may represent therapeutic targets to reduce cardiometabolic risk linked to excess adiposity.

DOI: https://doi.org/10.1038/s42255-021-00346-2
Cell. 2021 Feb 22. pii: S0092-8674(21)00171-9. [Epub ahead of print]

In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions.

Hongling Huang, Peipei Zhou, Jun Wei, Lingyun Long, Hao Shi, Yogesh Dhungana, Nicole M Chapman, Guotong Fu, Jordy Saravia, Jana L Raynor, Shaofeng Liu, Gustavo Palacios, Yong-Dong Wang, Chenxi Qian, Jiyang Yu, Hongbo Chi.

  How early events in effector T cell (TEFF) subsets tune memory T cell (TMEM) responses remains incompletely understood. Here, we systematically investigated metabolic factors in fate determination of TEFF and TMEM cells using in vivo pooled CRISPR screening, focusing on negative regulators of TMEM responses. We found that amino acid transporters Slc7a1 and Slc38a2 dampened the magnitude of TMEM differentiation, in part through modulating mTORC1 signaling. By integrating genetic and systems approaches, we identified cellular and metabolic heterogeneity among TEFF cells, with terminal effector differentiation associated with establishment of metabolic quiescence and exit from the cell cycle. Importantly, Pofut1 (protein-O-fucosyltransferase-1) linked GDP-fucose availability to downstream Notch-Rbpj signaling, and perturbation of this nutrient signaling axis blocked terminal effector differentiation but drove context-dependent TEFF proliferation and TMEM development. Our study establishes that nutrient uptake and signaling are key determinants of T cell fate and shape the quantity and quality of TMEM responses.

Keywords:  GDP-fucose; Notch; T cell memory; cell cycle exit; immunometabolism; in vivo pooled CRISPR screening; metabolic heterogeneity; nutrient signaling; systems immunology; terminal effector cell

DOI:  https://doi.org/10.1016/j.cell.2021.02.021
Int J Biochem Cell Biol. 2021 Feb 17. pii: S1357-2725(21)00036-4. [Epub ahead of print] 105952

Attenuating PI3K/Akt- mTOR pathway reduces dihydrosphingosine 1 phosphate mediated collagen synthesis and hypertrophy in primary cardiac cells.

Ruth R Magaye, Feby Savira, Yue Hua, Xin Xiong, Li Huang, Christopher Reid, Bernard L Flynn, David Kaye, Danny Liew, Bing H Wang.

  Cardiac fibrosis and myocyte hypertrophy play contributory roles in the progression of diseases such as heart Failure (HF) through what is collectively termed cardiac remodelling. The phosphoinositide 3- kinase (PI3K), protein kinase B (Akt) and mammalian target for rapamycin (mTOR) signalling pathway (PI3K/Akt- mTOR) pathway is an important pathway in protein synthesis, cell growth, cell proliferation, and lipid metabolism. The sphingolipid, dihydrosphingosine 1 phosphate (dhS1P) has been shown to bind to high density lipids in plasma. Unlike its analog, spingosine 1 phosphate (S1P), the role of dhS1P in cardiac fibrosis is still being deciphered. This study was conducted to investigate the effect of dhS1P on PI3K/Akt signalling in primary cardiac fibroblasts and mycoytes. Our findings demonstrate that inhibiting PI3K reduced collagen synthesis in neonatal cardiac fibroblasts (NCFs), and hypertrophy in neonatal cardiac myocytes (NCMs) induced by dhS1P, in vitro. Reduced activation of the PI3K/Akt- mTOR signalling pathway led to impaired translation of fibrotic proteins such as collagen 1 (Coll1) and transforming growth factor β (TGFβ) and inhibited the transcription and translation of tissue inhibitor of matrix metalloproteinase 1 (TIMP1). PI3K inhibition also affected the S1P receptors and gene expression of enzymes such as the dihydroceramide delta 4 desaturase (DEGS1) and sphingosine kinase 1 (SK1) in the de novo sphingolipid pathway. While in myocytes, PI3K inhibition reduced myocyte hypertrophy induced by dhS1P by reducing skeletal muscle α- actin (αSKA), and reduced protein translation due to increased glycogen synthase kinase 3β (GSK3β) mRNA expression. Our findings show a relationship between the PI3K/Akt- mTOR signalling cascade and exogenous dhS1P induced collagen synthesis and myocyte hypertrophy in primary neonatal cardiac cells.

Keywords:  Cardiac remodelling; Dihydrosphingosine 1 Phosphate; Fibrosis; Hypertrophy; PI3K; Protein Kinase B/Akt; Sphingolipid; mTOR; ribosomal protein S6

DOI:  https://doi.org/10.1016/j.biocel.2021.105952
Cell Rep. 2021 Feb 23. pii: S2211-1247(21)00081-4. [Epub ahead of print]34(8): 108768

CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition.

Adele M Musicant, Kshitij Parag-Sharma, Weida Gong, Monideepa Sengupta, Arindam Chatterjee, Erin C Henry, Yi-Hsuan Tsai, Michele C Hayward, Siddharth Sheth, Renee Betancourt, Trevor G Hackman, Ricardo J Padilla, Joel S Parker, Jimena Giudice, Colin A Flaveny, David N Hayes, Antonio L Amelio.

  Mucoepidermoid carcinoma (MEC) is a life-threatening salivary gland cancer that is driven primarily by a transcriptional coactivator fusion composed of cyclic AMP-regulated transcriptional coactivator 1 (CRTC1) and mastermind-like 2 (MAML2). The mechanisms by which the chimeric CRTC1/MAML2 (C1/M2) oncoprotein rewires gene expression programs that promote tumorigenesis remain poorly understood. Here, we show that C1/M2 induces transcriptional activation of the non-canonical peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) splice variant PGC-1α4, which regulates peroxisome proliferator-activated receptor gamma (PPARγ)-mediated insulin-like growth factor 1 (IGF-1) expression. This mitogenic transcriptional circuitry is consistent across cell lines and primary tumors. C1/M2-positive tumors exhibit IGF-1 pathway activation, and small-molecule drug screens reveal that tumor cells harboring the fusion gene are selectively sensitive to IGF-1 receptor (IGF-1R) inhibition. Furthermore, this dependence on autocrine regulation of IGF-1 transcription renders MEC cells susceptible to PPARγ inhibition with inverse agonists. These results yield insights into the aberrant coregulatory functions of C1/M2 and identify a specific vulnerability that can be exploited for precision therapy.

Keywords:  CRTC1-MAML2; IGF-1 inhibitor; PPARGC1A, IGF-1; cancer; chromosomal translocation; gene fusion; oncogene; transcriptional co-activator

DOI:  https://doi.org/10.1016/j.celrep.2021.108768
Actas Urol Esp. 2021 Feb 23. pii: S0210-4806(20)30258-8. [Epub ahead of print]

Renal angiomyolipoma and tuberous sclerosis complex: long-term safety and efficacy outcomes of Everolimus therapy.

E Ruiz Guerrero, M J Ledo Cepero, A V Ojeda Claro, M Soto Delgado, J L Álvarez-Ossorio Fernández.

  INTRODUCTION: Renal angiomyolipoma is a frequent manifestation of Tuberous Sclerosis Complex (TSC), for which everolimus therapy has been recently established as a novel non-invasive therapeutic option. As there are limited real life and long-term data, the analysis of our experience provides added value in terms of safety and efficacy.MATERIAL AND METHODS: Descriptive analysis of our experience in patients with giant bilateral renal angiomyolipomas, in the context of TSC, treated with 10 mg oral everolimus daily, during a median of 71.5 months. We evaluated the following parameters: response rate and duration, reduction of kidney size and lesions, prevention of complications and presentation of toxicity and its cause.
RESULTS: We confirm the effectiveness of treatment in 4 young patients, with multiple, bilateral angiomyolipomas of a median of 12 (5-19) cm maximum diameter, from June 2013 to date, after continuous reduction in lesion size, a decrease of 30% of the volume in 75% at six months and 50% in half of the subjects at two years, still showing drug response. Absence of complications such as bleeding or glomerular filtration rate decline in the long term, with a favorable safety profile, without interruptions and with mild-moderate, non-cumulative adverse effects, mostly within the first year of treatment.
CONCLUSION: Everolimus is a safe and effective therapeutic option for renal angiomyolipoma and various manifestations of TSC, which has been reproduced in real life with six years of follow-up.

Keywords:  Angiomiolipoma; Angiomyolipoma; Complejo esclerosis tuberosa; Everolimus; Safety; Seguridad; Tuberous Sclerosis Complex

DOI:  https://doi.org/10.1016/j.acuro.2020.11.004
Trends Cancer. 2021 Feb 23. pii: S2405-8033(21)00020-0. [Epub ahead of print]

A Quantitative Paradigm for Decision-Making in Precision Oncology.

Dalit Engelhardt, Franziska Michor.

  The complexity and variability of cancer progression necessitate a quantitative paradigm for therapeutic decision-making that is dynamic, personalized, and capable of identifying optimal treatment strategies for individual patients under substantial uncertainty. Here, we discuss the core components and challenges of such an approach and highlight the need for comprehensive longitudinal clinical and molecular data integration in its development. We describe the complementary and varied roles of mathematical modeling and machine learning in constructing dynamic optimal cancer treatment strategies and highlight the potential of reinforcement learning approaches in this endeavor.

Keywords:  machine learning; mathematical modeling; personalized medicine; treatment optimization

DOI:  https://doi.org/10.1016/j.trecan.2021.01.006
Nat Genet. 2021 Feb 22.

The NCI Genomic Data Commons.

Allison P Heath, Vincent Ferretti, Stuti Agrawal, Maksim An, James C Angelakos, Renuka Arya, Rosita Bajari, Bilal Baqar, Justin H B Barnowski, Jeffrey Burt, Ann Catton, Brandon F Chan, Fay Chu, Kim Cullion, Tanja Davidsen, Phuong-My Do, Christian Dompierre, Martin L Ferguson, Michael S Fitzsimons, Michael Ford, Miyuki Fukuma, Sharon Gaheen, Gajanan L Ganji, Tzintzuni I Garcia, Sameera S George, Daniela S Gerhard, Francois Gerthoffert, Fauzi Gomez, Kang Han, Kyle M Hernandez, Biju Issac, Richard Jackson, Mark A Jensen, Sid Joshi, Ajinkya Kadam, Aishmit Khurana, Kyle M J Kim, Victoria E Kraft, Shenglai Li, Tara M Lichtenberg, Janice Lodato, Laxmi Lolla, Plamen Martinov, Jeffrey A Mazzone, Daniel P Miller, Ian Miller, Joshua S Miller, Koji Miyauchi, Mark W Murphy, Thomas Nullet, Rowland O Ogwara, Francisco M Ortuño, Jesús Pedrosa, Phuong L Pham, Maxim Y Popov, James J Porter, Raymond Powell, Karl Rademacher, Colin P Reid, Samantha Rich, Bessie Rogel, Himanso Sahni, Jeremiah H Savage, Kyle A Schmitt, Trevar J Simmons, Joseph Sislow, Jonathan Spring, Lincoln Stein, Sean Sullivan, Yajing Tang, Mathangi Thiagarajan, Heather D Troyer, Chang Wang, Zhining Wang, Bedford L West, Alex Wilmer, Shane Wilson, Kaman Wu, William P Wysocki, Linda Xiang, Joseph T Yamada, Liming Yang, Christine Yu, Christina K Yung, Jean Claude Zenklusen, Junjun Zhang, Zhenyu Zhang, Yuanheng Zhao, Ariz Zubair, Louis M Staudt, Robert L Grossman.

DOI: https://doi.org/10.1038/s41588-021-00791-5
Nat Commun. 2021 02 22. 12(1): 1226

Uniform genomic data analysis in the NCI Genomic Data Commons.

Zhenyu Zhang, Kyle Hernandez, Jeremiah Savage, Shenglai Li, Dan Miller, Stuti Agrawal, Francisco Ortuno, Louis M Staudt, Allison Heath, Robert L Grossman.

The goal of the National Cancer Institute's (NCI's) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive ( https://gdc.cancer.gov/ ).

DOI: https://doi.org/10.1038/s41467-021-21254-9
J Genet Genomics. 2021 Jan 13. pii: S1673-8527(21)00001-1. [Epub ahead of print]

A Bama miniature pig model of monoallelic TSC1 mutation for human tuberous sclerosis complex.

Xiaoxue Li, Tingdong Hu, Jiying Liu, Bin Fang, Xue Geng, Qiang Xiong, Lining Zhang, Yong Jin, Xiaorui Liu, Lin Li, Ying Wang, Rongfeng Li, Xiaochun Bai, Haiyuan Yang, Yifan Dai.

  Tuberous sclerosis complex (TSC) is a dominant genetic neurocutaneous syndrome characterized by multiple organ hamartomas. Although rodent models bearing a germline mutation in either TSC1 or TSC2 genes have been generated, they do not develop pathogenic lesions matching those seen in patients with TSC because of the significant differences between mice and humans, highlighting the need for an improved large animal model of TSC. Here, we successfully generated monoallelic TSC1-modified Bama miniature pigs using the CRISPR/Cas9 system along with somatic cell nuclear transfer (SCNT) technology. The expression of phosphorylated target ribosomal protein S6 was significantly enhanced in the piglets, indicating that disruption of a TSC1 allele activated the mechanistic target of rapamycin (mTOR) signaling pathway. Notably, differing from the mouse TSC models reported previously, the TSC1+/- Bama miniature pig developed cardiac rhabdomyoma and subependymal nodules, resembling the major clinical features that occur in patients with TSC. These TSC1+/- Bama miniature pigs could serve as valuable large animal models for further elucidation of the pathogenesis of TSC and the development of therapeutic strategies for TSC disease.

Keywords:  CRISPR/Cas9; Cardiac rhabdomyosarcoma; Subependymal nodules; TSC1; Tuberous sclerosis complex

DOI:  https://doi.org/10.1016/j.jgg.2020.11.005
Cell Chem Biol. 2021 Feb 16. pii: S2451-9456(21)00052-0. [Epub ahead of print]

Re-defining synthetic lethality by phenotypic profiling for precision oncology.

Yevhen Akimov, Tero Aittokallio.

  High-throughput functional and genomic screening techniques provide systematic means for phenotypic discovery. Using synthetic lethality (SL) as a paradigm for anticancer drug and target discovery, we describe how these screening technologies may offer new possibilities to identify therapeutically relevant and selective SL interactions by addressing some of the challenges that have made robust discovery of SL candidates difficult. We further introduce an extended concept of SL interaction, in which a simultaneous perturbation of two or more cellular components reduces cell viability more than expected by their individual effects, which we feel is highly befitting for anticancer applications. We also highlight the potential benefits and challenges related to computational quantification of synergistic interactions and cancer selectivity. Finally, we explore how tumoral heterogeneity can be exploited to find phenotype-specific SL interactions for precision oncology using high-throughput functional screening and the exciting opportunities these methods provide for the identification of subclonal SL interactions.

Keywords:  CRISPR screening; drug combinations; phenotypic screening; precision oncology; synergistic interactions; synthetic lethality

DOI:  https://doi.org/10.1016/j.chembiol.2021.01.026
Science. 2021 Feb 25. pii: eabc1855. [Epub ahead of print]

T cell circuits that sense antigen density with an ultrasensitive threshold.

Rogelio A Hernandez-Lopez, Wei Yu, Katelyn A Cabral, Olivia A Creasey, Maria Del Pilar Lopez Pazmino, Yurie Tonai, Arsenia De Guzman, Anna Mäkelä, Kalle Saksela, Zev J Gartner, Wendell A Lim.

Overexpressed tumor associated antigens (e.g., HER2 and epidermal growth factor receptor) are attractive targets for therapeutic T cells, but toxic "off-tumor" cross-reaction with normal tissues expressing low levels of target antigen can occur with Chimeric Antigen Receptor (CAR) T cells. Inspired by natural ultrasensitive response circuits, we engineered a two-step positive feedback circuit that allows T cells to discriminate targets based on a sigmoidal antigen density threshold. In this circuit, a low affinity synthetic Notch receptor for HER2 controls the expression of a high affinity CAR for HER2. Increasing HER2 density thus has cooperative effects on T cells-it both increases CAR expression and activation-leading to a sigmoidal response. T cells with this circuit show sharp discrimination between target cells expressing normal amounts of HER2 and cancer cells expressing 100-fold more HER2, both in vitro and in vivo.

DOI: https://doi.org/10.1126/science.abc1855
Front Cell Dev Biol. 2021 ;9 626136

Monitoring Phosphoinositide Fluxes and Effectors During Leukocyte Chemotaxis and Phagocytosis.

Fernando Montaño-Rendón, Sergio Grinstein, Glenn F W Walpole.

  The dynamic re-organization of cellular membranes in response to extracellular stimuli is fundamental to the cell physiology of myeloid and lymphoid cells of the immune system. In addition to maintaining cellular homeostatic functions, remodeling of the plasmalemma and endomembranes endow leukocytes with the potential to relay extracellular signals across their biological membranes to promote rolling adhesion and diapedesis, migration into the tissue parenchyma, and to ingest foreign particles and effete cells. Phosphoinositides, signaling lipids that control the interface of biological membranes with the external environment, are pivotal to this wealth of functions. Here, we highlight the complex metabolic transitions that occur to phosphoinositides during several stages of the leukocyte lifecycle, namely diapedesis, migration, and phagocytosis. We describe classical and recently developed tools that have aided our understanding of these complex lipids. Finally, major downstream effectors of inositides are highlighted including the cytoskeleton, emphasizing the importance of these rare lipids in immunity and disease.

Keywords:  chemotaxis; inositol lipids; lipid biosensors; lipid signaling; macrophage; neutrophil; phagocytosis; phosphoinositides

DOI:  https://doi.org/10.3389/fcell.2021.626136
Nat Commun. 2021 02 24. 12(1): 1272

Quantifying information accumulation encoded in the dynamics of biochemical signaling.

Ying Tang, Adewunmi Adelaja, Felix X-F Ye, Eric Deeds, Roy Wollman, Alexander Hoffmann.

Cellular responses to environmental changes are encoded in the complex temporal patterns of signaling proteins. However, quantifying the accumulation of information over time to direct cellular decision-making remains an unsolved challenge. This is, in part, due to the combinatorial explosion of possible configurations that need to be evaluated for information in time-course measurements. Here, we develop a quantitative framework, based on inferred trajectory probabilities, to calculate the mutual information encoded in signaling dynamics while accounting for cell-cell variability. We use it to understand NFκB transcriptional dynamics in response to different immune threats, and reveal that some threats are distinguished faster than others. Our analyses also suggest specific temporal phases during which information distinguishing threats becomes available to immune response genes; one specific phase could be mapped to the functionality of the IκBα negative feedback circuit. The framework is generally applicable to single-cell time series measurements, and enables understanding how temporal regulatory codes transmit information over time.

DOI: https://doi.org/10.1038/s41467-021-21562-0
Nat Biotechnol. 2021 Feb 22.

Variability within rare cell states enables multiple paths toward drug resistance.

Benjamin L Emert, Christopher J Cote, Eduardo A Torre, Ian P Dardani, Connie L Jiang, Naveen Jain, Sydney M Shaffer, Arjun Raj.

Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA fluorescence in situ hybridization to directly capture rare cells that give rise to cellular behaviors of interest. Applying Rewind to BRAFV600E melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ~1:1,000-1:10,000 cells) and relative persistence of MAP kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences among several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones after drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.

DOI: https://doi.org/10.1038/s41587-021-00837-3
Elife. 2021 Feb 25. pii: e61313. [Epub ahead of print]10

The SWELL1-LRRC8 complex regulates endothelial AKT-eNOS signaling and vascular function.

Ahmad F Alghanem, Javier Abello, Joshua M Maurer, Ashutosh Kumar, Chau My Ta, Susheel K Gunasekar, Urooj Fatima, Chen Kang, Litao Xie, Oluwaseun Adeola, Megan Riker, Macaulay Elliot-Hudson, Rachel A Minerath, Chad E Grueter, Robert F Mullins, Amber N Stratman, Rajan Sah.

  The endothelium responds to numerous chemical and mechanical factors in regulating vascular tone, blood pressure and blood flow. The endothelial volume regulatory anion channel (VRAC) has been proposed to be mechano-sensitive and thereby sense fluid flow and hydrostatic pressure to regulate vascular function. Here, we show that the Leucine Rich Repeat Containing Protein 8a, LRRC8A (SWELL1) is required for VRAC in human umbilical vein endothelial cells (HUVECs). Endothelial LRRC8A regulates AKT-eNOS signaling under basal, stretch and shear-flow stimulation, forms a GRB2-Cav1-eNOS signaling complex, and is required for endothelial cell alignment to laminar shear flow. Endothelium-restricted Lrrc8a KO mice develop hypertension in response to chronic angiotensin-II infusion and exhibit impaired retinal blood flow with both diffuse and focal blood vessel narrowing in the setting of Type 2 diabetes (T2D). These data demonstrate that LRRC8A regulates AKT-eNOS in endothelium and is required for maintaining vascular function, particularly in the setting of T2D.

Keywords:  cell biology; mouse

DOI:  https://doi.org/10.7554/eLife.61313
Expert Opin Pharmacother. 2021 Feb 24. 1-9

Alpelisib for the treatment of PIK3CA-mutated, hormone receptor-positive, HER2-negative metastatic breast cancer.

Fanny Leenhardt, Marie Alexandre, William Jacot.

  Introduction: Two-thirds of advanced breast cancers are hormone receptor (HR)-positive and human epidermal growth factor receptor 2 (HER2)-negative (HR+/HER2-). Gene mutations in PIK3CA, encoding the PI3K catalytic subunit alpha of phosphatidyl-inositol 3-kinase (PI3K), are a frequent event in this population and are implicated in hormone therapy resistance. Alpelisib is a PI3K-alpha inhibitor and is the first PI3K inhibitor approved, in association with fulvestrant, by the FDA and EMA, based on improved progression-free survival (PFS) versus fulvestrant alone in a randomized phase III trial in HR+/HER2-, PIK3CA-mutated tumors following progression on/after HT.Areas covered: The scientific rationale, preclinical development, pharmacokinetics, and clinical efficacy/safety of alpelisib-fulvestrant are summarized. The role of alpelisib in the clinical setting is discussed, referencing current therapeutic options and clinical challenges associated with alpelisib's safety profile.Expert opinion: Alpelisib is an option for patients with HR+/HER2-, PIK3CA-mutated tumors whose disease progressed during/after aromatase inhibitor treatment. The PFS benefit appears clinically significant over fulvestrant alone, with a 7.9 months, non-significant, improvement in overall survival. Its safety profile requires strict patient selection, mainly based on baseline glycemic status, and close monitoring.

Keywords:  Metastatic breast cancer; hormonotherapy; mutation; phosphatidylinositol 3-kinase

DOI:  https://doi.org/10.1080/14656566.2021.1873952