bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–08–29
twenty-two papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Alkaline intracellular pHi (pHi) activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation.
  2. Disorders Related to PI3Kδ Hyperactivation: Characterizing the Clinical and Immunological Features of Activated PI3-Kinase Delta Syndromes.
  3. Primary cilia and lipid raft dynamics.
  4. Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation.
  5. Differential roles of FOXO transcription factors on insulin action in brown and white adipose tissue.
  6. Primary ciliary signaling: links with the cell cycle.
  7. Novel Paracrine Action of Endothelium Enhances Glucose Uptake in Muscle and Fat.
  8. PI3-Kinase p110α Deficiency Modulates T Cell Homeostasis and Function and Attenuates Experimental Allergic Encephalitis in Mature Mice.
  9. PI3K in T Cell Adhesion and Trafficking.
  10. Development of multiplex digital PCR assays for the detection of PIK3CA mutations in the plasma of metastatic breast cancer patients.
  11. Genetic reduction of mTOR extends lifespan in a mouse model of Hutchinson-Gilford Progeria syndrome.
  12. Insulin signaling establishes a developmental trajectory of adipose regulatory T cells.
  13. The mutational landscape of human somatic and germline cells.
  14. Extensive phylogenies of human development inferred from somatic mutations.
  15. Structured elements drive extensive circular RNA translation.
  16. Co-targeting CDK4/6 and AKT with endocrine therapy prevents progression in CDK4/6 inhibitor and endocrine therapy-resistant breast cancer.
  17. Metabolic plasticity drives development during mammalian embryogenesis.
  18. An overview of the insulin signaling pathway in model organisms Drosophila melanogaster and Caenorhabditis elegans.
  19. Cancer immunotherapy with PI3K and PD-1 dual-blockade via optimal modulation of T cell activation signal.
  20. Insulin Receptor Isoforms Differently Regulate Cell Proliferation and Apoptosis in the Ligand-Occupied and Unoccupied State.
  21. PTENα functions as an immune suppressor and promotes immune resistance in PTEN-mutant cancer.
  22. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.
  1. J Biol Chem. 2021 Aug 18. pii: S0021-9258(21)00903-0. [Epub ahead of print] 101100
    Alkaline intracellular pHi (pHi) activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation.
    D Kazyken, S I Lentz, D C Fingar.
      mTOR complex 2 (mTORC2) signaling controls cell metabolism, promotes cell survival, and contributes to tumorigenesis, yet its upstream regulation remains poorly defined. While considerable evidence supports the prevailing view that amino acids activate mTOR complex 1 (mTORC1) but not mTORC2, several studies reported paradoxical activation of mTORC2 signaling by amino acids. We noted that after amino acid starvation of cells in culture, addition of an amino acid solution increased mTORC2 signaling. Interestingly, we found the pH of the amino acid solution to be alkaline, ∼pH 10. These observations led us to discover and demonstrate here that alkaline intracellular pH (pHi) represents a previously unknown activator of mTORC2. Using a fluorescent pH-sensitive dye (cSNARF1-AM) coupled with live-cell imaging, we demonstrate that culturing cells in media at alkaline pH induces a rapid rise in pHi, which increases mTORC2 catalytic activity and downstream signaling to the pro-growth and -survival kinase Akt. Alkaline pHi also activates AMPK, a canonical sensor of energetic stress. Functionally, alkaline pHi attenuates mTOR- and AMPK-mediated apoptosis caused by growth factor withdrawal. Collectively, these findings reveal that alkaline pHi increases mTORC2- and AMPK-mediated signaling to promote cell survival during conditions of growth factor limitation, analogous to the demonstrated ability of energetic stress to activate AMPK-mTORC2 and promote cell survival. As elevated pHi represents an under-appreciated hallmark of cancer cells, we propose that alkaline pHi stress sensing by AMPK-mTORC2 may contribute to tumorigenesis by enabling cancer cells at the core of a growing tumor to evade apoptosis and survive.
    Keywords:  AMPK; Akt; intracellular pH (pHi); mTORC2
    DOI:  https://doi.org/10.1016/j.jbc.2021.101100
  2. Front Pediatr. 2021 ;9 702872
    Disorders Related to PI3Kδ Hyperactivation: Characterizing the Clinical and Immunological Features of Activated PI3-Kinase Delta Syndromes.
    Vyanka Redenbaugh, Tanya Coulter.
      Phosphoinositide-3-kinase δ (PI3Kδ) is found in immune cells and is part of the PI3K/AKT/mTOR/S6K signalling pathway essential to cell survival, growth and differentiation. Hyperactivation of PI3Kδ enzyme results in Activated PI3-kinase delta syndrome (APDS). This childhood onset, autosomal dominant, combined immunodeficiency, is caused by heterozygous gain of function (GOF) mutations in PIK3CD (encodes PI3Kδ catalytic subunit p110δ), mutations in PIK3R1 (encodes PI3Kδ regulatory subunit p85α) or LOF mutations in PTEN (terminates PI3Kδ signalling) leading to APDS1, APDS2 and APDS-Like (APDS-L), respectively. APDS was initially described in 2013 and over 285 cases have now been reported. Prompt diagnosis of APDS is beneficial as targeted pharmacological therapies such as sirolimus and potentially PI3Kδ inhibitors can be administered. In this review, we provide an update on the clinical and laboratory features of this primary immunodeficiency. We discuss the common manifestations such as sinopulmonary infections, bronchiectasis, lymphoproliferation, susceptibility to herpesvirus, malignancy, as well as more rare non-immune features such as short stature and neurodevelopmental abnormalities. Laboratory characteristics, such as antibody deficiency and B cell and T cell, phenotypes are also summarised.
    Keywords:  PI3 K; PIK3CD; PIK3R1; activated PI3K delta syndrome; phosphatase and tensin homolog
    DOI:  https://doi.org/10.3389/fped.2021.702872
  3. Open Biol. 2021 Aug;11(8): 210130
    Primary cilia and lipid raft dynamics.
    Yuhei Nishimura, Daishi Yamakawa, Katsunori Uchida, Takashi Shiromizu, Masatoshi Watanabe, Masaki Inagaki.
      Primary cilia, antenna-like structures of the plasma membrane, detect various extracellular cues and transduce signals into the cell to regulate a wide range of functions. Lipid rafts, plasma membrane microdomains enriched in cholesterol, sphingolipids and specific proteins, are also signalling hubs involved in a myriad of physiological functions. Although impairment of primary cilia and lipid rafts is associated with various diseases, the relationship between primary cilia and lipid rafts is poorly understood. Here, we review a newly discovered interaction between primary cilia and lipid raft dynamics that occurs during Akt signalling in adipogenesis. We also discuss the relationship between primary cilia and lipid raft-mediated Akt signalling in cancer biology. This review provides a novel perspective on primary cilia in the regulation of lipid raft dynamics.
    Keywords:  Akt; adipogenesis; cancer; lipid raft dynamics; primary cilia
    DOI:  https://doi.org/10.1098/rsob.210130
  4. Sci Adv. 2021 Aug;pii: eabj4282. [Epub ahead of print]7(35):
    Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation.
    Manoj K Rathinaswamy, Udit Dalwadi, Kaelin D Fleming, Carson Adams, Jordan T B Stariha, Els Pardon, Minkyung Baek, Oscar Vadas, Frank DiMaio, Jan Steyaert, Scott D Hansen, Calvin K Yip, John E Burke.
      The class IB phosphoinositide 3-kinase (PI3K), PI3Kγ, is a master regulator of immune cell function and a promising drug target for both cancer and inflammatory diseases. Critical to PI3Kγ function is the association of the p110γ catalytic subunit to either a p101 or p84 regulatory subunit, which mediates activation by G protein-coupled receptors. Here, we report the cryo-electron microscopy structure of a heterodimeric PI3Kγ complex, p110γ-p101. This structure reveals a unique assembly of catalytic and regulatory subunits that is distinct from other class I PI3K complexes. p101 mediates activation through its Gβγ-binding domain, recruiting the heterodimer to the membrane and allowing for engagement of a secondary Gβγ-binding site in p110γ. Mutations at the p110γ-p101 and p110γ-adaptor binding domain interfaces enhanced Gβγ activation. A nanobody that specifically binds to the p101-Gβγ interface blocks activation, providing a novel tool to study and target p110γ-p101-specific signaling events in vivo.
    DOI:  https://doi.org/10.1126/sciadv.abj4282
  5. J Clin Invest. 2021 Aug 24. pii: 143328. [Epub ahead of print]
    Differential roles of FOXO transcription factors on insulin action in brown and white adipose tissue.
    Erica P Homan, Bruna Brasil Brandao, Samir Softic, Abdelfattah El Ouaamari, Brian T O'Neill, Rohit N Kulkarni, Jason K Kim, C Ronald Kahn.
      Insulin and IGF-1 are essential for adipocyte differentiation and function. Mice lacking insulin and IGF-1 receptors in fat (FIGIRKO) exhibit complete loss of white and brown fat (WAT/BAT), glucose intolerance, insulin resistance, hepatosteatosis, and cold intolerance. To determine the role of FOXO transcription factors in the altered adipose phenotype, we generated FIGIRKO mice with fat-specific knockout of fat-expressed Foxos [Foxo1, Foxo3, Foxo4] (F-Quint KO). Unlike FIGIRKO mice, F-Quint KO mice had normal BAT, glucose tolerance, insulin-regulated hepatic glucose production, and cold tolerance. However, loss of FOXOs only partially rescued subcutaneous WAT and hepatosteatosis, did not rescue perigonadal WAT, or systemic insulin resistance, and led to even more marked hyperinsulinemia. Thus, FOXOs play different roles in insulin/IGF1 action in different adipose depots, being more important in BAT > subcutaneous WAT > visceral WAT. Disruption of FOXOs in fat also leads to a reversal of insulin resistance in liver, but not in skeletal muscle, and an exacerbation of hyperinsulinemia. Thus, adipose FOXOs play a unique role in regulating crosstalk between adipose depots, liver and β-cells.
    Keywords:  Adipose tissue; Endocrinology; Insulin signaling; Metabolism; Transcription
    DOI:  https://doi.org/10.1172/JCI143328
  6. Trends Cell Biol. 2021 Aug 19. pii: S0962-8924(21)00149-5. [Epub ahead of print]
    Primary ciliary signaling: links with the cell cycle.
    Kousuke Kasahara, Masaki Inagaki.
      Primary cilia are solitary, microtubule-based structures emanating from the surface of most vertebrate cells. Although it is understood that ciliary assembly and disassembly both depend upon and impact cell cycle progression, critical mechanistic details of these links remain unresolved. Accumulating evidence shows that the signaling pathways downstream of receptor tyrosine kinases and lysophosphatidic acid receptors control the dynamics of primary cilia. It has also become clear that primary cilia not only serve as signaling hubs but also regulate the composition of the surrounding membrane, which is likely to affect the response to growth factors. Here, we overview recent advances in understanding the interplay between primary cilia and the cell cycle, with a focus on growth factor signaling pathways.
    Keywords:  centrosome; lipid raft; lysophosphatidic acid; primary cilium; receptor tyrosine kinase
    DOI:  https://doi.org/10.1016/j.tcb.2021.07.009
  7. Circ Res. 2021 Aug 21.
    Novel Paracrine Action of Endothelium Enhances Glucose Uptake in Muscle and Fat.
    Hema Viswambharan, Nadira Yusupovna Yuldasheva, Helen Imrie, Katherine Bridge, Natalie Jayne Haywood, Anna Skromna, Karen E Hemmings, Emily Ruth Clark, V Kate Gatenby, Paul Cordell, Katie Simmons, Natallia Makava, Yilizila Abudushalamu, Naima Endesh, Jane Brown, Andrew Mn Walker, T Simon Futers, Karen E Porter, Richard M Cubbon, Khalid M Naseem, Ajay M Shah, David J Beech, Stephen Wheatcroft, Mark T Kearney, Piruthivi Sukumar.
      Rationale: A hallmark of type 2 diabetes is insulin resistance, which leads to increased endothelial cell production of superoxide and a simultaneous reduction in availability of the vasoprotective signalling radical, nitric oxide (NO). We recently demonstrated in preclinical models that type 2 diabetes simultaneously causes resistance to insulin like growth factor-1 (IGF-1) mediated glucose lowering and endothelial NO release. Objective: To examine the effect of insulin and IGF-1 resistance specifically in endothelial cells in vivo. Methods and Results: We generated mice expressing mutant IGF-1 receptors (mIGF-1R), which form non-functioning hybrid receptors with native insulin receptors (IR) and IGF-1R, directed to endothelial cells under control of the Tie2 promoter-enhancer. Despite endothelial cell insulin and IGF-1 resistance, mutant IGF-1R endothelial cell over-expressing mice (mIGFREO) had enhanced insulin and IGF-1 mediated systemic glucose disposal, lower fasting free fatty acids and triglycerides. In hyperinsulinaemic-euglycaemic clamp studies, mIGFREO had increased glucose disposal and increased glucose uptake into muscle and fat, in response to insulin. mIGFREO had increased NADPH oxidase 4 (Nox4) expression due to reduced expression of the microRNA, miR-25. Consistent with increased Nox4, mIGFREO endothelial cells generated increased hydrogen peroxide (H2O2), with no increase in superoxide. Treatment with catalase, a dismutase restored insulin tolerance to wild type levels in mIGFREO. Conclusions: Combined insulin and IGF-1 resistance restricted to the endothelium leads to a potentially favourable adaptation in contrast to pure insulin resistance, with increased Nox4-derived H2O2 generation mediating enhanced whole-body insulin sensitivity.
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.319517
  8. Int J Mol Sci. 2021 Aug 13. pii: 8698. [Epub ahead of print]22(16):
    PI3-Kinase p110α Deficiency Modulates T Cell Homeostasis and Function and Attenuates Experimental Allergic Encephalitis in Mature Mice.
    José M Rojo, María Montes-Casado, Laura Aragoneses-Fenoll, Gloria Ojeda, Umberto Dianzani, Pilar Portolés.
      Class I phosphoinositide 3-kinases (PI3K) are involved in the development of normal and autoimmune responses, including Experimental Autoimmune Encephalomyelitis (EAE), a mouse model for human multiple sclerosis (MS). Here, the role of the ubiquitously expressed class IA PI3K p110α catalytic subunits in EAE has been analyzed using a model of Cre/flox mediated T cell specific deletion of p110α catalytic chain (p110αΔT). Comparison of two month-old (young) and six month-old (mature) p110αΔT mice and their wild type (WT) counterparts indicated loss of spleen CD4+ T cells that increased with age, indicating a role of p110α in their homeostasis. In contrast, CD4+ T regulatory (Treg) cells were enhanced in mature p110αΔT mice when compared to WT mice. Since Myelin Oligodendrocyte Glycoprotein (MOG) peptide-induced EAE is dependent on, or mediated by CD4+ T cells and CD4+ T cell-derived cytokines and controlled by Treg cells, development of EAE in young and mature WT or p110αΔT mice was analyzed. EAE clinical symptoms and disease scores in six month p110αΔT mice were significantly lower than those of mature WT, or young WT and p110αΔT mice. Furthermore, ex vivo antigen activation of lymph node cells from MOG immunized mature p110αΔT mice induced significantly lower levels of IFN-γ and IL-17A than young p110αΔT or young and mature WT mice. Other cytokines including IL-2, IL-10 or TNF-α showed no significant differences between p110αΔT and WT mature mice. Our data show a lower incidence of MOG-induced EAE in mature p110αΔT mice linked to altered T cell homeostasis and lower secretion of inflammatory cytokines.
    Keywords:  CD4+ T-lymphocytes; CD4+ Treg; autoimmune experimental encephalomyelitis; multiple sclerosis; phosphatidylinositol 3-kinases
    DOI:  https://doi.org/10.3390/ijms22168698
  9. Front Immunol. 2021 ;12 708908
    PI3K in T Cell Adhesion and Trafficking.
    Kristoffer H Johansen, Dominic P Golec, Julie H Thomsen, Pamela L Schwartzberg, Klaus Okkenhaug.
      PI3K signalling is required for activation, differentiation, and trafficking of T cells. PI3Kδ, the dominant PI3K isoform in T cells, has been extensively characterised using PI3Kδ mutant mouse models and PI3K inhibitors. Furthermore, characterisation of patients with Activated PI3K Delta Syndrome (APDS) and mouse models with hyperactive PI3Kδ have shed light on how increased PI3Kδ activity affects T cell functions. An important function of PI3Kδ is that it acts downstream of TCR stimulation to activate the major T cell integrin, LFA-1, which controls transendothelial migration of T cells as well as their interaction with antigen-presenting cells. PI3Kδ also suppresses the cell surface expression of CD62L and CCR7 which controls the migration of T cells across high endothelial venules in the lymph nodes and S1PR1 which controls lymph node egress. Therefore, PI3Kδ can control both entry and exit of T cells from lymph nodes as well as the recruitment to and retention of T cells within inflamed tissues. This review will focus on the regulation of adhesion receptors by PI3Kδ and how this contributes to T cell trafficking and localisation. These findings are relevant for our understanding of how PI3Kδ inhibitors may affect T cell redistribution and function.
    Keywords:  CCR7; CD62L; LFA-1; PI3K; adhesion; integrin; trafficking
    DOI:  https://doi.org/10.3389/fimmu.2021.708908
  10. Sci Rep. 2021 Aug 27. 11(1): 17316
    Development of multiplex digital PCR assays for the detection of PIK3CA mutations in the plasma of metastatic breast cancer patients.
    Julien Corné, Fanny Le Du, Véronique Quillien, Florence Godey, Lucie Robert, Héloïse Bourien, Angélique Brunot, Laurence Crouzet, Christophe Perrin, Claudia Lefeuvre-Plesse, Véronique Diéras, Thibault De la Motte Rouge.
      With the approval of new therapies targeting the PI3K pathway, the detection of PIK3CA mutations has become a key factor in treatment management for HR+/HER2- metastatic breast cancer (MBC). We developed multiplex digital PCR (dPCR) assays to detect and quantify PIK3CA mutations. A first screening assay allows the detection of 21 mutations, with a drop-off system targeting the 542-546 hotspot mutations combined with the simultaneous detection of N345K, C420R, H1047L and H1047R mutations. In the case of a positive result, a sequential strategy based on other assays that we have developped allows for precise mutation identification. Clinical validity was determined by analyzing plasma circulating free DNA (cfDNA) from 213 HR+/HER2- MBC samples, as well as DNA extracted from 97 available matched tumors from 89 patients. Our assays have shown reliable specificity, accuracy and reproducibility, with limits of blank of three and four droplets for the screening assay. Sixty-eight patients (32%) had at least one PIK3CA mutation detectable in their plasma, and we obtained 83.1% agreement between the cfDNA analysis and the corresponding tumors. The high sensitivity and robustness of these new dPCR assays make them well-suited for rapid and cost-effective detection of PIK3CA mutations in the plasma of MBC patients.
    DOI:  https://doi.org/10.1038/s41598-021-96644-6
  11. Aging Cell. 2021 Aug 28. e13457
    Genetic reduction of mTOR extends lifespan in a mouse model of Hutchinson-Gilford Progeria syndrome.
    Wayne A Cabral, Urraca L Tavarez, Indeevar Beeram, Diana Yeritsyan, Yoseph D Boku, Michael A Eckhaus, Ara Nazarian, Michael R Erdos, Francis S Collins.
      Hutchinson-Gilford progeria syndrome (HGPS) is a rare accelerated aging disorder most notably characterized by cardiovascular disease and premature death from myocardial infarction or stroke. The majority of cases are caused by a de novo single nucleotide mutation in the LMNA gene that activates a cryptic splice donor site, resulting in production of a toxic form of lamin A with a 50 amino acid internal deletion, termed progerin. We previously reported the generation of a transgenic murine model of progeria carrying a human BAC harboring the common mutation, G608G, which in the single-copy state develops features of HGPS that are limited to the vascular system. Here, we report the phenotype of mice bred to carry two copies of the BAC, which more completely recapitulate the phenotypic features of HGPS in skin, adipose, skeletal, and vascular tissues. We further show that genetic reduction of the mechanistic target of rapamycin (mTOR) significantly extends lifespan in these mice, providing a rationale for pharmacologic inhibition of the mTOR pathway in the treatment of HGPS.
    Keywords:  S6 Kinase; lamin A/C; laminopathies; mTOR; progeria
    DOI:  https://doi.org/10.1111/acel.13457
  12. Nat Immunol. 2021 09;22(9): 1175-1185
    Insulin signaling establishes a developmental trajectory of adipose regulatory T cells.
    Yangyang Li, Ying Lu, Shu-Hai Lin, Ning Li, Yichao Han, Qianru Huang, Yi Zhao, Feng Xie, Yixian Guo, Biaolong Deng, Andy Tsun, Juan Du, Dan Li, Joanne Sun, Guochao Shi, Fang Zheng, Xiao Su, Shengzhong Duan, Song Guo Zheng, Gang Wang, Xuemei Tong, Bin Li.
      Systematic characterizations of adipose regulatory T (Treg) cell subsets and their phenotypes remain uncommon. Using single-cell ATAC-sequencing and paired single-cell RNA and T cell receptor (TCR) sequencing to map mouse adipose Treg cells, we identified CD73hiST2lo and CD73loST2hi subsets with distinct clonal expansion patterns. Analysis of TCR-sharing data implied a state transition between CD73hiST2lo and CD73loST2hi subsets. Mechanistically, we revealed that insulin signaling occurs through a HIF-1α-Med23-PPAR-γ axis to drive the transition of CD73hiST2lo into a CD73loST2hi adipose Treg cell subset. Treg cells deficient in insulin receptor, HIF-1α or Med23 have decreased PPAR-γ expression that in turn promotes accumulation of CD73hiST2lo adipose Treg cells and physiological adenosine production to activate beige fat biogenesis. We therefore unveiled a developmental trajectory of adipose Treg cells and its dependence on insulin signaling. Our findings have implications for understanding the dynamics of adipose Treg cell subsets in aged and obese contexts.
    DOI:  https://doi.org/10.1038/s41590-021-01010-3
  13. Nature. 2021 Aug 25.
    The mutational landscape of human somatic and germline cells.
    Luiza Moore, Alex Cagan, Tim H H Coorens, Matthew D C Neville, Rashesh Sanghvi, Mathijs A Sanders, Thomas R W Oliver, Daniel Leongamornlert, Peter Ellis, Ayesha Noorani, Thomas J Mitchell, Timothy M Butler, Yvette Hooks, Anne Y Warren, Mette Jorgensen, Kevin J Dawson, Andrew Menzies, Laura O'Neill, Calli Latimer, Mabel Teng, Ruben van Boxtel, Christine A Iacobuzio-Donahue, Inigo Martincorena, Rakesh Heer, Peter J Campbell, Rebecca C Fitzgerald, Michael R Stratton, Raheleh Rahbari.
      Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.
    DOI:  https://doi.org/10.1038/s41586-021-03822-7
  14. Nature. 2021 Aug 25.
    Extensive phylogenies of human development inferred from somatic mutations.
    Tim H H Coorens, Luiza Moore, Philip S Robinson, Rashesh Sanghvi, Joseph Christopher, James Hewinson, Moritz J Przybilla, Andrew R J Lawson, Michael Spencer Chapman, Alex Cagan, Thomas R W Oliver, Matthew D C Neville, Yvette Hooks, Ayesha Noorani, Thomas J Mitchell, Rebecca C Fitzgerald, Peter J Campbell, Iñigo Martincorena, Raheleh Rahbari, Michael R Stratton.
      Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
    DOI:  https://doi.org/10.1038/s41586-021-03790-y
  15. Mol Cell. 2021 Aug 19. pii: S1097-2765(21)00626-2. [Epub ahead of print]
    Structured elements drive extensive circular RNA translation.
    Chun-Kan Chen, Ran Cheng, Janos Demeter, Jin Chen, Shira Weingarten-Gabbay, Lihua Jiang, Michael P Snyder, Jonathan S Weissman, Eran Segal, Peter K Jackson, Howard Y Chang.
      The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
    Keywords:  18S complementarity; FGFR1; cap-independent translation; circFGFR1p; circRNA-encoded protein; circular RNA; internal ribosome entry site; structured RNA element
    DOI:  https://doi.org/10.1016/j.molcel.2021.07.042
  16. Nat Commun. 2021 08 25. 12(1): 5112
    Co-targeting CDK4/6 and AKT with endocrine therapy prevents progression in CDK4/6 inhibitor and endocrine therapy-resistant breast cancer.
    Carla L Alves, Sidse Ehmsen, Mikkel G Terp, Neil Portman, Martina Tuttolomondo, Odd L Gammelgaard, Monique F Hundebøl, Kamila Kaminska, Lene E Johansen, Martin Bak, Gabriella Honeth, Ana Bosch, Elgene Lim, Henrik J Ditzel.
      CDK4/6 inhibitors (CDK4/6i) combined with endocrine therapy have shown impressive efficacy in estrogen receptor-positive advanced breast cancer. However, most patients will eventually experience disease progression on this combination, underscoring the need for effective subsequent treatments or better initial therapies. Here, we show that triple inhibition with fulvestrant, CDK4/6i and AKT inhibitor (AKTi) durably impairs growth of breast cancer cells, prevents progression and reduces metastasis of tumor xenografts resistant to CDK4/6i-fulvestrant combination or fulvestrant alone. Importantly, switching from combined fulvestrant and CDK4/6i upon resistance to dual combination with AKTi and fulvestrant does not prevent tumor progression. Furthermore, triple combination with AKTi significantly inhibits growth of patient-derived xenografts resistant to combined CDK4/6i and fulvestrant. Finally, high phospho-AKT levels in metastasis of breast cancer patients treated with a combination of CDK4/6i and endocrine therapy correlates with shorter progression-free survival. Our findings support the clinical development of ER, CDK4/6 and AKT co-targeting strategies following progression on CDK4/6i and endocrine therapy combination, and in tumors exhibiting high phospho-AKT levels, which are associated with worse clinical outcome.
    DOI:  https://doi.org/10.1038/s41467-021-25422-9
  17. Dev Cell. 2021 Aug 23. pii: S1534-5807(21)00603-1. [Epub ahead of print]56(16): 2329-2347.e6
    Metabolic plasticity drives development during mammalian embryogenesis.
    Mark S Sharpley, Fangtao Chi, Johanna Ten Hoeve, Utpal Banerjee.
      Mammalian preimplantation embryos follow a stereotypic pattern of development from zygotes to blastocysts. Here, we use labeled nutrient isotopologue analysis of small numbers of embryos to track downstream metabolites. Combined with transcriptomic analysis, we assess the capacity of the embryo to reprogram its metabolism through development. Early embryonic metabolism is rigid in its nutrient requirements, sensitive to reductive stress and has a marked disequilibrium between two halves of the TCA cycle. Later, loss of maternal LDHB and transcription of zygotic products favors increased activity of bioenergetic shuttles, fatty-acid oxidation and equilibration of the TCA cycle. As metabolic plasticity peaks, blastocysts can develop without external nutrients. Normal developmental metabolism of the early embryo is distinct from cancer metabolism. However, similarities emerge upon reductive stress. Increased metabolic plasticity with maturation is due to changes in redox control mechanisms and to transcriptional reprogramming of later-stage embryos during homeostasis or upon adaptation to environmental changes.
    Keywords:  MYC; NAD+/NADH; developmental metabolism; embryo; metabolic plasticity; metabolic reprogramming; preimplantation; redox; reductive stress; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.devcel.2021.07.020
  18. Peptides. 2021 Aug 24. pii: S0196-9781(21)00148-0. [Epub ahead of print] 170640
    An overview of the insulin signaling pathway in model organisms Drosophila melanogaster and Caenorhabditis elegans.
    Sanaz G Biglou, William G Bendena, Ian Chin-Sang.
      The insulin/insulin-like growth factor signaling pathway is an evolutionary conserved pathway across metazoans and is required for development, metabolism and behavior. This pathway is associated with various human metabolic disorders and cancers. Thus, model organisms including Drosophila melanogaster and Caenorhabditis elegans provide excellent opportunities to examine the structure and function of this pathway and its influence on cellular metabolism and proliferation. In this review, we will provide an overview of human insulin and the human insulin signaling pathway and explore the recent discoveries in model organisms Drosophila melanogaster and Caenorhabditis elegans. Our review will provide information regarding the various insulin-like peptides in model organisms as well as the conserved functions of insulin signaling pathways. Further investigation of the insulin signaling pathway in model organisms could provide a promising opportunity to develop novel therapies for various metabolic disorders and insulin-mediated cancers.
    Keywords:  Aging; Genetics; Growth; Insulin receptor; Insulin signaling; Peptide
    DOI:  https://doi.org/10.1016/j.peptides.2021.170640
  19. J Immunother Cancer. 2021 Aug;pii: e002279. [Epub ahead of print]9(8):
    Cancer immunotherapy with PI3K and PD-1 dual-blockade via optimal modulation of T cell activation signal.
    Sho Isoyama, Shigeyuki Mori, Daisuke Sugiyama, Yasuhiro Kojima, Yasuko Tada, Kohei Shitara, Kunihiko Hinohara, Shingo Dan, Hiroyoshi Nishikawa.
       BACKGROUND: Immune checkpoint blockade (ICB) induces durable clinical responses in patients with various types of cancer. However, its limited clinical efficacy requires the development of better approaches. In addition to immune checkpoint molecules, tumor-infiltrating immunosuppressive cells including regulatory T cells (Tregs) play crucial roles in the immune suppressive tumor microenvironment. While phosphatidylinositol 3-kinase (PI3K) inhibition as a Treg-targeted treatment has been implicated in animal models, its effects on human Tregs and on the potential impairment of effector T cells are required to be clarified for successful cancer immunotherapy.
    METHODS: The impact of a selective-PI3K inhibitor ZSTK474 with or without anti-programmed cell death 1 (PD-1) monoclonal antibody on Tregs and CD8+ T cells were examined with in vivo animal models and in vitro experiments with antigen specific and non-specific fashions using peripheral blood from healthy individuals and cancer patients. Phenotypes and functions of Tregs and effector T cells were examined with comprehensive gene and protein expression assays.
    RESULTS: Improved antitumor effects by the PI3K inhibitor in combination with ICB, particularly PD-1 blockade, were observed in mice and humans. Although administration of the PI3K inhibitor at higher doses impaired activation of CD8+ T cells as well as Tregs, the optimization (doses and timing) of this combination treatment selectively decreased intratumoral Tregs, resulting in increased tumor antigen-specific CD8+ T cells in the treated mice. Moreover, on the administration of the PI3K inhibitor with the optimal dose for selectively deleting Tregs, PI3K signaling was inhibited not only in Tregs but also in activated CD8+ T cells, leading to the enhanced generation of tumor antigen-specific memory CD8+ T cells which contributed to durable antitumor immunity. These opposing outcomes between Tregs and CD8+ T cells were attributed to the high degree of dependence on T cell signaling in the former but not in the latter.
    CONCLUSIONS: PI3K inhibitor in the combination with ICB with the optimized protocol fine-tuned T cell activation signaling for antitumor immunity via decreasing Tregs and optimizing memory CD8+ T cell responses, illustrating a promising combination therapy.
    Keywords:  combination; drug therapy; immunologic memory; immunotherapy; tumor microenvironment
    DOI:  https://doi.org/10.1136/jitc-2020-002279
  20. Int J Mol Sci. 2021 Aug 13. pii: 8729. [Epub ahead of print]22(16):
    Insulin Receptor Isoforms Differently Regulate Cell Proliferation and Apoptosis in the Ligand-Occupied and Unoccupied State.
    Michele Massimino, Laura Sciacca, Nunziatina Laura Parrinello, Nunzio Massimo Scalisi, Antonino Belfiore, Riccardo Vigneri, Paolo Vigneri.
      The insulin receptor (IR) presents two isoforms (IR-A and IR-B) that differ for the α-subunit C-terminal. Both isoforms are expressed in all human cells albeit in different proportions, yet their functional properties-when bound or unbound to insulin-are not well characterized. From a cell model deprived of the Insulin-like Growth Factor 1 Receptor (IGF1-R) we therefore generated cells exhibiting no IR (R-shIR cells), or only human IR-A (R-shIR-A), or exclusively human IR-B (R-shIR-B) and we studied the specific effect of the two isoforms on cell proliferation and cell apoptosis. In the absence of insulin both IR-A and IR-B similarly inhibited proliferation but IR-B was 2-3 fold more effective than IR-A in reducing resistance to etoposide-induced DNA damage. In the presence of insulin, IR-A and IR-B promoted proliferation with the former significantly more effective than the latter at increasing insulin concentrations. Moreover, only insulin-bound IR-A, but not IR-B, protected cells from etoposide-induced cytotoxicity. In conclusion, IR isoforms have different effects on cell proliferation and survival. When unoccupied, IR-A, which is predominantly expressed in undifferentiated and neoplastic cells, is less effective than IR-B in protecting cells from DNA damage. In the presence of insulin, particularly when present at high levels, IR-A provides a selective growth advantage.
    Keywords:  DNA damage; apoptosis; caspase 3; cell proliferation; insulin action; insulin receptor
    DOI:  https://doi.org/10.3390/ijms22168729
  21. Nat Commun. 2021 Aug 26. 12(1): 5147
    PTENα functions as an immune suppressor and promotes immune resistance in PTEN-mutant cancer.
    Yizhe Sun, Dan Lu, Yue Yin, Jia Song, Yang Liu, Wenyan Hao, Fang Qi, Guangze Zhang, Xin Zhang, Liang Liu, Zhiqiang Lin, Hui Liang, Xuyang Zhao, Yan Jin, Yuxin Yin.
      PTEN is frequently mutated in human cancers and PTEN mutants promote tumor progression and metastasis. PTEN mutations have been implicated in immune regulation, however, the underlying mechanism is largely unknown. Here, we report that PTENα, the isoform of PTEN, remains active in cancer bearing stop-gained PTEN mutations. Through counteraction of CD8+ T cell-mediated cytotoxicity, PTENα leads to T cell dysfunction and accelerates immune-resistant cancer progression. Clinical analysis further uncovers that PTENα-active mutations suppress host immune responses and result in poor prognosis in cancer as relative to PTENα-inactive mutations. Furthermore, germline deletion of Ptenα in mice increases cell susceptibility to immune attack through augmenting stress granule formation and limiting synthesis of peroxidases, leading to massive oxidative cell death and severe inflammatory damage. We propose that PTENα protects tumor from T cell killing and thus PTENα is a potential target in antitumor immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-021-25417-6
  22. Nat Commun. 2021 08 24. 12(1): 5086
    Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.
    NCI PDXNet Consortium
      Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.
    DOI:  https://doi.org/10.1038/s41467-021-25177-3
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