bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020‒08‒09
sixty-four papers selected by
Kıvanç Görgülü
Technical University of Munich


  1. Proc Natl Acad Sci U S A. 2020 Aug 05. pii: 202002200. [Epub ahead of print]
    Heberle FA, Doktorova M, Scott HL, Skinkle AD, Waxham MN, Levental I.
      The nanoscale organization of biological membranes into structurally and compositionally distinct lateral domains is believed to be central to membrane function. The nature of this organization has remained elusive due to a lack of methods to directly probe nanoscopic membrane features. We show here that cryogenic electron microscopy (cryo-EM) can be used to directly image coexisting nanoscopic domains in synthetic and bioderived membranes without extrinsic probes. Analyzing a series of single-component liposomes composed of synthetic lipids of varying chain lengths, we demonstrate that cryo-EM can distinguish bilayer thickness differences as small as 0.5 Å, comparable to the resolution of small-angle scattering methods. Simulated images from computational models reveal that features in cryo-EM images result from a complex interplay between the atomic distribution normal to the plane of the bilayer and imaging parameters. Simulations of phase-separated bilayers were used to predict two sources of contrast between coexisting ordered and disordered phases within a single liposome, namely differences in membrane thickness and molecular density. We observe both sources of contrast in biomimetic membranes composed of saturated lipids, unsaturated lipids, and cholesterol. When extended to isolated mammalian plasma membranes, cryo-EM reveals similar nanoscale lateral heterogeneities. The methods reported here for direct, probe-free imaging of nanodomains in unperturbed membranes open new avenues for investigation of nanoscopic membrane organization.
    Keywords:  GPMVs; cryo-EM; liquid-disordered; liquid-ordered; nanodomains
    DOI:  https://doi.org/10.1073/pnas.2002200117
  2. J Clin Invest. 2020 Aug 04. pii: 136760. [Epub ahead of print]
    Jiang H, Torphy RJ, Steiger K, Hongo H, Ritchie AJ, Kriegsmann M, Horst D, Umetsu SE, Joseph NM, McGregor K, Pishvaian MJ, Blais EM, Lu B, Li M, Hollingsworth M, Stashko C, Volmar K, Yeh JJ, Weaver VM, Wang ZJ, Tempero MA, Weichert W, Collisson EA.
      Desmoplasia describes the deposition of extensive extracellular matrix and defines primary pancreatic ductal adenocarcinoma (PDA). The acellular component of this stroma has been implicated in PDA pathogenesis and is being targeted therapeutically in clinical trials. By analyzing the stromal content of PDA samples from numerous annotated PDA data sets and correlating stromal content with both anatomic site and clinical outcome, we found PDA metastases in the liver, the primary cause of mortality to have less stroma, have higher tumor cellularity than primary tumors. Experimentally manipulating stromal matrix with an anti- lysyl oxidase like-2 (anti-LOXL2) antibody in syngeneic orthotopic PDA mouse models significantly decreased matrix content, led to lower tissue stiffness, lower contrast retention on computed tomography, and accelerated tumor growth, resulting in diminished overall survival. These studies suggest an important protective role of stroma in PDA and urge caution in clinically deploying stromal depletion strategies.
    Keywords:  Cancer; Extracellular matrix; Oncology
    DOI:  https://doi.org/10.1172/JCI136760
  3. Biomedicines. 2020 Aug 03. pii: E270. [Epub ahead of print]8(8):
    Reyes-Castellanos G, Masoud R, Carrier A.
      Cancer cells reprogram their metabolism to meet bioenergetics and biosynthetic demands. The first observation of metabolic reprogramming in cancer cells was made a century ago ("Warburg effect" or aerobic glycolysis), leading to the classical view that cancer metabolism relies on a glycolytic phenotype. There is now accumulating evidence that most cancers also rely on mitochondria to satisfy their metabolic needs. Indeed, the current view of cancer metabolism places mitochondria as key actors in all facets of cancer progression. Importantly, mitochondrial metabolism has become a very promising target in cancer therapy, including for refractory cancers such as Pancreatic Ductal AdenoCarcinoma (PDAC). In particular, mitochondrial oxidative phosphorylation (OXPHOS) is an important target in cancer therapy. Other therapeutic strategies include the targeting of glutamine and fatty acids metabolism, as well as the inhibition of the TriCarboxylic Acid (TCA) cycle intermediates. A better knowledge of how pancreatic cancer cells regulate mitochondrial metabolism will allow the identification of metabolic vulnerabilities and thus novel and more efficient therapeutic options for the benefit of each patient.
    Keywords:  OXPHOS; biguanides; cancer metabolism; energetic metabolism; metabolic heterogeneity; mitochondria; mitochondrial complex I; mitochondrial metabolism; pancreatic ductal adenocarcinoma; therapeutic strategy
    DOI:  https://doi.org/10.3390/biomedicines8080270
  4. Cell Metab. 2020 Jul 30. pii: S1550-4131(20)30367-3. [Epub ahead of print]
    van Gastel N, Spinelli JB, Sharda A, Schajnovitz A, Baryawno N, Rhee C, Oki T, Grace E, Soled HJ, Milosevic J, Sykes DB, Hsu PP, Vander Heiden MG, Vidoudez C, Trauger SA, Haigis MC, Scadden DT.
      Cancer relapse begins when malignant cells pass through the extreme metabolic bottleneck of stress from chemotherapy and the byproducts of the massive cell death in the surrounding region. In acute myeloid leukemia, complete remissions are common, but few are cured. We tracked leukemia cells in vivo, defined the moment of maximal response following chemotherapy, captured persisting cells, and conducted unbiased metabolomics, revealing a metabolite profile distinct from the pre-chemo growth or post-chemo relapse phase. Persisting cells used glutamine in a distinctive manner, preferentially fueling pyrimidine and glutathione generation, but not the mitochondrial tricarboxylic acid cycle. Notably, malignant cell pyrimidine synthesis also required aspartate provided by specific bone marrow stromal cells. Blunting glutamine metabolism or pyrimidine synthesis selected against residual leukemia-initiating cells and improved survival in leukemia mouse models and patient-derived xenografts. We propose that timed cell-intrinsic or niche-focused metabolic disruption can exploit a transient vulnerability and induce metabolic collapse in cancer cells to overcome chemoresistance.
    Keywords:  acute myeloid leukemia; aspartate; bone marrow niche; cell metabolism; chemotherapy; glutamine; mouse models; patient-derived xenografts; pyrimidine synthesis; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.009
  5. Nat Immunol. 2020 Aug 03.
    Yamazaki T, Kirchmair A, Sato A, Buqué A, Rybstein M, Petroni G, Bloy N, Finotello F, Stafford L, Navarro Manzano E, Ayala de la Peña F, García-Martínez E, Formenti SC, Trajanoski Z, Galluzzi L.
      Autophagy supports both cellular and organismal homeostasis. However, whether autophagy should be inhibited or activated for cancer therapy remains unclear. Deletion of essential autophagy genes increased the sensitivity of mouse mammary carcinoma cells to radiation therapy in vitro and in vivo (in immunocompetent syngeneic hosts). Autophagy-deficient cells secreted increased amounts of type I interferon (IFN), which could be limited by CGAS or STING knockdown, mitochondrial DNA depletion or mitochondrial outer membrane permeabilization blockage via BCL2 overexpression or BAX deletion. In vivo, irradiated autophagy-incompetent mammary tumors elicited robust immunity, leading to improved control of distant nonirradiated lesions via systemic type I IFN signaling. Finally, a genetic signature of autophagy had negative prognostic value in patients with breast cancer, inversely correlating with mitochondrial abundance, type I IFN signaling and effector immunity. As clinically useful autophagy inhibitors are elusive, our findings suggest that mitochondrial outer membrane permeabilization may represent a valid target for boosting radiation therapy immunogenicity in patients with breast cancer.
    DOI:  https://doi.org/10.1038/s41590-020-0751-0
  6. Nat Metab. 2020 Aug 03.
    Hargreaves M, Spriet LL.
      The continual supply of ATP to the fundamental cellular processes that underpin skeletal muscle contraction during exercise is essential for sports performance in events lasting seconds to several hours. Because the muscle stores of ATP are small, metabolic pathways must be activated to maintain the required rates of ATP resynthesis. These pathways include phosphocreatine and muscle glycogen breakdown, thus enabling substrate-level phosphorylation ('anaerobic') and oxidative phosphorylation by using reducing equivalents from carbohydrate and fat metabolism ('aerobic'). The relative contribution of these metabolic pathways is primarily determined by the intensity and duration of exercise. For most events at the Olympics, carbohydrate is the primary fuel for anaerobic and aerobic metabolism. Here, we provide an overview of exercise metabolism and the key regulatory mechanisms ensuring that ATP resynthesis is closely matched to the ATP demand of exercise. We also summarize various interventions that target muscle metabolism for ergogenic benefit in athletic events.
    DOI:  https://doi.org/10.1038/s42255-020-0251-4
  7. J Vis Exp. 2020 Jul 17.
    Lambert LJ, Romero C, Sheffler DJ, Celeridad M, Cosford NDP, Tautz L.
      The Src-homology 2 (SH2) domain-containing phosphatase 2 (SHP2), encoded by the PTPN11 proto-oncogene, is a key mediator of receptor tyrosine kinase (RTK)-driven cell signaling, promoting cell survival and proliferation. In addition, SHP2 is recruited by immune check point receptors to inhibit B and T cell activation. Aberrant SHP2 function has been implicated in the development, progression, and metastasis of many cancers. Indeed, small molecule SHP2 inhibitors have recently entered clinical trials for the treatment of solid tumors with Ras/Raf/ERK pathway activation, including tumors with some oncogenic Ras mutations. However, the current class of SHP2 inhibitors is not effective against the SHP2 oncogenic variants that occur frequently in leukemias, and the development of specific small molecules that target oncogenic SHP2 is the subject of current research. A common problem with most drug discovery campaigns involving cytosolic proteins like SHP2 is that the primary assays that drive chemical discovery are often in vitro assays that do not report the cellular target engagement of candidate compounds. To provide a platform for measuring cellular target engagement, we developed both wild-type and mutant SHP2 cellular thermal shift assays. These assays reliably detect target engagement of SHP2 inhibitors in cells. Here, we provide a comprehensive protocol of this assay, which provides a valuable tool for the assessment and characterization of SHP2 inhibitors.
    DOI:  https://doi.org/10.3791/61457
  8. J Clin Invest. 2020 Aug 04. pii: 137553. [Epub ahead of print]
    Yuen VW, Wong CC.
      The liver has strong innate immunity to counteract pathogens from the gastrointestinal tract. During the development of liver cancer, which is typically driven by chronic inflammation, the composition and biological roles of the innate immune cells are extensively altered. Hypoxia is a common finding in all stages of liver cancer development. Hypoxia drives the stabilization of hypoxia-inducible factors (HIFs), which act as central regulators to dampen the innate immunity of liver cancer. HIF signaling in innate immune cells and liver cancer cells together favor the recruitment and maintenance of pro-tumorigenic immune cells and the inhibition of anti-tumorigenic immune cells, promoting immune evasion. HIFs represent attractive therapeutic targets to inhibit the formation of an immunosuppressive microenvironment and growth of liver cancer.
    DOI:  https://doi.org/10.1172/JCI137553
  9. Cell. 2020 Jul 31. pii: S0092-8674(20)30870-9. [Epub ahead of print]
    Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Samusik N, Goltsev Y, Nolan GP.
      Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ineffective tumor control will advance immunotherapies. We re-engineered co-detection by indexing (CODEX) for paraffin-embedded tissue microarrays, enabling simultaneous profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers. We identified nine conserved, distinct cellular neighborhoods (CNs)-a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+ T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating how complex biological processes, such as antitumoral immunity, occur through concerted actions of cells and spatial domains.
    Keywords:  CODEX; FFPE; antitumoral immunity; cellular neighborhoods; colorectal cancer; immune checkpoints; immune tumor microenvironment; multiplexed imaging; tertiary lymphoid structures; tissue architecture
    DOI:  https://doi.org/10.1016/j.cell.2020.07.005
  10. Proc Natl Acad Sci U S A. 2020 Aug 03. pii: 202005052. [Epub ahead of print]
    Shirazi F, Jones RJ, Singh RK, Zou J, Kuiatse I, Berkova Z, Wang H, Lee HC, Hong S, Dick L, Chattopadhyay N, Orlowski RZ.
      KRAS, NRAS, and BRAF mutations which activate p44/42 mitogen-activated protein kinase (MAPK) signaling are found in half of myeloma patients and contribute to proteasome inhibitor (PI) resistance, but the underlying mechanisms are not fully understood. We established myeloma cell lines expressing wild-type (WT), constitutively active (CA) (G12V/G13D/Q61H), or dominant-negative (DN) (S17N)-KRAS and -NRAS, or BRAF-V600E. Cells expressing CA mutants showed increased proteasome maturation protein (POMP) and nuclear factor (erythroid-derived 2)-like 2 (NRF2) expression. This correlated with an increase in catalytically active proteasome subunit β (PSMB)-8, PSMB9, and PSMB10, which occurred in an ETS transcription factor-dependent manner. Proteasome chymotrypsin-like, trypsin-like, and caspase-like activities were increased, and this enhanced capacity reduced PI sensitivity, while DN-KRAS and DN-NRAS did the opposite. Pharmacologic RAF or MAPK kinase (MEK) inhibitors decreased proteasome activity, and sensitized myeloma cells to PIs. CA-KRAS, CA-NRAS, and CA-BRAF down-regulated expression of endoplasmic reticulum (ER) stress proteins, and reduced unfolded protein response activation, while DN mutations increased both. Finally, a bortezomib (BTZ)/MEK inhibitor combination showed enhanced activity in vivo specifically in CA-NRAS models. Taken together, the data support the hypothesis that activating MAPK pathway mutations enhance PI resistance by increasing proteasome capacity, and provide a rationale for targeting such patients with PI/RAF or PI/MEK inhibitor combinations. Moreover, they argue these mutations promote myeloma survival by reducing cellular stress, thereby distancing plasma cells from the apoptotic threshold, potentially explaining their high frequency in myeloma.
    Keywords:  BRAF; KRAS; NRAF; proteasome capacity; proteasome inhibitor sensitivity
    DOI:  https://doi.org/10.1073/pnas.2005052117
  11. Cell Stress. 2020 Jul 13. 4(8): 199-215
    Kim H, Ronai ZA.
      Protein methyl transferases play critical roles in numerous regulatory pathways that underlie cancer development, progression and therapy-response. Here we discuss the function of PRMT5, a member of the nine-member PRMT family, in controlling oncogenic processes including tumor intrinsic, as well as extrinsic microenvironmental signaling pathways. We discuss PRMT5 effect on histone methylation and methylation of regulatory proteins including those involved in RNA splicing, cell cycle, cell death and metabolic signaling. In all, we highlight the importance of PRMT5 regulation and function in cancer, which provide the foundation for therapeutic modalities targeting PRMT5.
    Keywords:  MEP50; PRMT1; PRMT5; histone; methylation; methyltransferase; splicing; transcription
    DOI:  https://doi.org/10.15698/cst2020.08.228
  12. Elife. 2020 Aug 03. pii: e58828. [Epub ahead of print]9
    Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper W, Bennett EJ, Beckmann R, Green R.
      Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.58828
  13. Br J Cancer. 2020 Aug 03.
    Dunlop CR, Wallez Y, Johnson TI, Bernaldo de Quirós Fernández S, Durant ST, Cadogan EB, Lau A, Richards FM, Jodrell DI.
      BACKGROUND: Personalised medicine strategies may improve outcomes in pancreatic ductal adenocarcinoma (PDAC), but validation of predictive biomarkers is required. Having developed a clinical trial to assess the ATR inhibitor, AZD6738, in combination with gemcitabine (ATRi/gem), we investigated ATM loss as a predictive biomarker of response to ATRi/gem in PDAC.METHODS: Through kinase inhibition, siRNA depletion and CRISPR knockout of ATM, we assessed how ATM targeting affected the sensitivity of PDAC cells to ATRi/gem. Using flow cytometry, immunofluorescence and immunoblotting, we investigated how ATRi/gem synergise in ATM-proficient and ATM-deficient cells, before assessing the impact of ATM loss on ATRi/gem sensitivity in vivo.
    RESULTS: Complete loss of ATM function (through pharmacological inhibition or CRISPR knockout), but not siRNA depletion, sensitised to ATRi/gem. In ATM-deficient cells, ATRi/gem-induced replication catastrophe was augmented, while phospho-Chk2-T68 and phospho-KAP1-S824 persisted via DNA-PK activity. ATRi/gem caused growth delay in ATM-WT xenografts in NSG mice and induced regression in ATM-KO xenografts.
    CONCLUSIONS: ATM loss augments replication catastrophe-mediated cell death induced by ATRi/gem and may predict clinical responsiveness to this combination. ATM status should be carefully assessed in tumours from patients with PDAC, since distinction between ATM-low and ATM-null could be critical in maximising the success of clinical trials using ATM expression as a predictive biomarker.
    DOI:  https://doi.org/10.1038/s41416-020-1016-2
  14. Nat Cell Biol. 2020 Aug;22(8): 973-985
    Kumar S, Jain A, Choi SW, da Silva GPD, Allers L, Mudd MH, Peters RS, Anonsen JH, Rusten TE, Lazarou M, Deretic V.
      Autophagy is a homeostatic process with multiple functions in mammalian cells. Here, we show that mammalian Atg8 proteins (mAtg8s) and the autophagy regulator IRGM control TFEB, a transcriptional activator of the lysosomal system. IRGM directly interacted with TFEB and promoted the nuclear translocation of TFEB. An mAtg8 partner of IRGM, GABARAP, interacted with TFEB. Deletion of all mAtg8s or GABARAPs affected the global transcriptional response to starvation and downregulated subsets of TFEB targets. IRGM and GABARAPs countered the action of mTOR as a negative regulator of TFEB. This was suppressed by constitutively active RagB, an activator of mTOR. Infection of macrophages with the membrane-permeabilizing microbe Mycobacterium tuberculosis or infection of target cells by HIV elicited TFEB activation in an IRGM-dependent manner. Thus, IRGM and its interactors mAtg8s close a loop between the autophagosomal pathway and the control of lysosomal biogenesis by TFEB, thus ensuring coordinated activation of the two systems that eventually merge during autophagy.
    DOI:  https://doi.org/10.1038/s41556-020-0549-1
  15. EMBO Rep. 2020 Aug 05. e50912
    Yang X, Potts PR.
      SIRT1 is a NAD+ -dependent deacetylase that controls key metabolic and signaling pathways, including inactivating the p53 tumor suppressor. However, the mechanisms controlling SIRT1 enzymatic activity in the context of cancer are unclear. Here, we show that the previously undescribed CSAG2 protein is a direct activator of SIRT1. CSAG2 is normally restricted to expression in the male germline but is frequently re-activated in cancers. CSAG2 is necessary for cancer cell proliferation and promotes tumorigenesis in vivo. Biochemical studies revealed that CSAG2 directly binds to and stimulates SIRT1 activity toward multiple substrates. Importantly, CSAG2 enhances SIRT1-mediated deacetylation of p53, inhibits p53 transcriptional activity, and improves cell survival in response to genotoxic stress. Mechanistically, CSAG2 binds SIRT1 catalytic domain and promotes activity independent of altering substrate affinity. Together, our results identify a previously undescribed mechanism for SIRT1 activation in cancer cells and highlight unanticipated approaches to therapeutically modulate SIRT1.
    Keywords:  NAD+-dependent deacetylase; apoptosis; cancer-testis antigen; genotoxic stress; oncogene
    DOI:  https://doi.org/10.15252/embr.202050912
  16. Cancers (Basel). 2020 Aug 04. pii: E2154. [Epub ahead of print]12(8):
    Tang Y, Durand S, Dalle S, Caramel J.
      Transcription factors, extensively described for their role in epithelial-mesenchymal transition (EMT-TFs) in epithelial cells, also display essential functions in the melanocyte lineage. Recent evidence has shown specific expression patterns and functions of these EMT-TFs in neural crest-derived melanoma compared to carcinoma. Herein, we present an update of the specific roles of EMT-TFs in melanocyte differentiation and melanoma progression. As major regulators of phenotype switching between differentiated/proliferative and neural crest stem cell-like/invasive states, these factors appear as major drivers of intra-tumor heterogeneity and resistance to treatment in melanoma, which opens new avenues in terms of therapeutic targeting.
    Keywords:  EMT; ZEB2/ZEB1 switch; intra-tumor heterogeneity; melanocyte differentiation; melanoma development; neural-crest stem cells; phenotype switching; resistance to treatment; transcription factors
    DOI:  https://doi.org/10.3390/cancers12082154
  17. EMBO Rep. 2020 Aug 04. e50446
    Matafora V, Farris F, Restuccia U, Tamburri S, Martano G, Bernardelli C, Sofia A, Pisati F, Casagrande F, Lazzari L, Marsoni S, Bonoldi E, Bachi A.
      Melanoma progression is generally associated with increased transcriptional activity mediated by the Yes-associated protein (YAP). Mechanical signals from the extracellular matrix are sensed by YAP, which then activates the expression of proliferative genes, promoting melanoma progression and drug resistance. Which extracellular signals induce mechanotransduction, and how this is mediated, is not completely understood. Here, using secretome analyses, we reveal the extracellular accumulation of amyloidogenic proteins, i.e. premelanosome protein (PMEL), in metastatic melanoma, together with proteins that assist amyloid maturation into fibrils. We also confirm the accumulation of amyloid-like aggregates, similar to those detected in Alzheimer disease, in metastatic cell lines, as well as in human melanoma biopsies. Mechanistically, beta-secretase 2 (BACE2) regulates the maturation of these aggregates, which in turn induce YAP activity. We also demonstrate that recombinant PMEL fibrils are sufficient to induce mechanotransduction, triggering YAP signaling. Finally, we demonstrate that BACE inhibition affects cell proliferation and increases drug sensitivity, highlighting the importance of amyloids for melanoma survival, and the use of beta-secretase inhibitors as potential therapeutic approach for metastatic melanoma.
    Keywords:  BACE2; amyloid; mechanosignaling; metastasis; secretome
    DOI:  https://doi.org/10.15252/embr.202050446
  18. Sci Adv. 2020 Jul;6(30): eaba3688
    Dhanwani R, Takahashi M, Mathews IT, Lenzi C, Romanov A, Watrous JD, Pieters B, Hedrick CC, Benedict CA, Linden J, Nilsson R, Jain M, Sharma S.
      Mechanisms linking immune sensing of DNA danger signals in the extracellular environment to innate pathways in the cytosol are poorly understood. Here, we identify a previously unidentified immune-metabolic axis by which cells respond to purine nucleosides and trigger a type I interferon-β (IFN-β) response. We find that depletion of ADA2, an ectoenzyme that catabolizes extracellular dAdo to dIno, or supplementation of dAdo or dIno stimulates IFN-β. Under conditions of reduced ADA2 enzyme activity, dAdo is transported into cells and undergoes catabolysis by the cytosolic isoenzyme ADA1, driving intracellular accumulation of dIno. dIno is a functional immunometabolite that interferes with the cellular methionine cycle by inhibiting SAM synthetase activity. Inhibition of SAM-dependent transmethylation drives epigenomic hypomethylation and overexpression of immune-stimulatory endogenous retroviral elements that engage cytosolic dsRNA sensors and induce IFN-β. We uncovered a previously unknown cellular signaling pathway that responds to extracellular DNA-derived metabolites, coupling nucleoside catabolism by adenosine deaminases to cellular IFN-β production.
    DOI:  https://doi.org/10.1126/sciadv.aba3688
  19. Immunity. 2020 Jul 30. pii: S1074-7613(20)30318-6. [Epub ahead of print]
    Li W, Qiu S, Chen J, Jiang S, Chen W, Jiang J, Wang F, Si W, Shu Y, Wei P, Fan G, Tian R, Wu H, Xu C, Wang H.
      Clinical evidence suggests that poor persistence of chimeric antigen receptor-T cells (CAR-T) in patients limits therapeutic efficacy. Here, we designed a CAR with recyclable capability to promote in vivo persistence and to sustain antitumor activity. We showed that the engagement of tumor antigens induced rapid ubiquitination of CARs, causing CAR downmodulation followed by lysosomal degradation. Blocking CAR ubiquitination by mutating all lysines in the CAR cytoplasmic domain (CARKR) markedly repressed CAR downmodulation by inhibiting lysosomal degradation while enhancing recycling of internalized CARs back to the cell surface. Upon encountering tumor antigens, CARKR-T cells ameliorated the loss of surface CARs, which promoted their long-term killing capacity. Moreover, CARKR-T cells containing 4-1BB signaling domains displayed elevated endosomal 4-1BB signaling that enhanced oxidative phosphorylation and promoted memory T cell differentiation, leading to superior persistence in vivo. Collectively, our study provides a straightforward strategy to optimize CAR-T antitumor efficacy by redirecting CAR trafficking.
    Keywords:  4-1BB; CAR; CAR-T; T cell persistence; degradation; downmodulation; endosomal signaling; internalization; relapse; ubiquitination
    DOI:  https://doi.org/10.1016/j.immuni.2020.07.011
  20. Elife. 2020 Aug 03. pii: e58659. [Epub ahead of print]9
    Gaertner B, van Heesch S, Schneider-Lunitz V, Schulz JF, Witte F, Blachut S, Nguyen S, Wong R, Matta I, Hübner N, Sander M.
      Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin+ cells, in a manner independent of the nearby TF FOXA2. One-by-one deletion of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.
    Keywords:  computational biology; developmental biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.58659
  21. Nat Immunol. 2020 Aug 03.
    Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Pinaud S, Nicholls A, Ros XR, Su J, Eldridge MD, Riedel A, Serrao EM, Rodewald HR, Mack M, Shields JD, Cohen ES, McKenzie ANJ, Goodwin RJA, Brindle KM, Marioni JC, Halim TYF.
      Metastasis constitutes the primary cause of cancer-related deaths, with the lung being a commonly affected organ. We found that activation of lung-resident group 2 innate lymphoid cells (ILC2s) orchestrated suppression of natural killer (NK) cell-mediated innate antitumor immunity, leading to increased lung metastases and mortality. Using multiple models of lung metastasis, we show that interleukin (IL)-33-dependent ILC2 activation in the lung is involved centrally in promoting tumor burden. ILC2-driven innate type 2 inflammation is accompanied by profound local suppression of interferon-γ production and cytotoxic function of lung NK cells. ILC2-dependent suppression of NK cells is elaborated via an innate regulatory mechanism, which is reliant on IL-5-induced lung eosinophilia, ultimately limiting the metabolic fitness of NK cells. Therapeutic targeting of IL-33 or IL-5 reversed NK cell suppression and alleviated cancer burden. Thus, we reveal an important function of IL-33 and ILC2s in promoting tumor metastasis via their capacity to suppress innate type 1 immunity.
    DOI:  https://doi.org/10.1038/s41590-020-0745-y
  22. Nat Rev Clin Oncol. 2020 Aug 05.
    Galluzzi L, Humeau J, Buqué A, Zitvogel L, Kroemer G.
      Conventional chemotherapeutics have been developed into clinically useful agents based on their ability to preferentially kill malignant cells, generally owing to their elevated proliferation rate. Nonetheless, the clinical activity of various chemotherapies is now known to involve the stimulation of anticancer immunity either by initiating the release of immunostimulatory molecules from dying cancer cells or by mediating off-target effects on immune cell populations. Understanding the precise immunological mechanisms that underlie the efficacy of chemotherapy has the potential not only to enable the identification of superior biomarkers of response but also to accelerate the development of synergistic combination regimens that enhance the clinical effectiveness of immune checkpoint inhibitors (ICIs) relative to their effectiveness as monotherapies. Indeed, accumulating evidence supports the clinical value of combining appropriately dosed chemotherapies with ICIs. In this Review, we discuss preclinical and clinical data on the immunostimulatory effects of conventional chemotherapeutics in the context of ICI-based immunotherapy.
    DOI:  https://doi.org/10.1038/s41571-020-0413-z
  23. Aging Cell. 2020 Aug 02. e13201
    Chu X, Wen J, Raju RP.
      Cellular senescence is a state of irreversible growth arrest. Short-term programmed senescence such as in embryonic development and slowly progressing senescence as in aging are both well described. However, acute senescence in living organisms is not well understood. We hypothesized that hemorrhagic shock injury (HI) caused by whole body hypoxia and nutrient deprivation, resulting in organ dysfunction due to severe blood loss, could lead to acute senescence in vivo. Our experiments, for the first time, demonstrate a rapidly emerged, senolytics-responsive, senescence-like response in the rat liver in less than five hr following hemorrhagic shock. We conclude that the senescence, or pseudosenescence, observed is necessary to maintain tissue homeostasis following the injury.
    Keywords:  acute senescence; aging; cell cycle; senescence-associated secretory phenotype
    DOI:  https://doi.org/10.1111/acel.13201
  24. Nat Metab. 2020 Aug 03.
    Zhang T, Bauer C, Newman AC, Uribe AH, Athineos D, Blyth K, Maddocks ODK.
      Cancer cells have high demands for non-essential amino acids (NEAAs), which are precursors for anabolic and antioxidant pathways that support cell survival and proliferation. It is well-established that cancer cells consume the NEAA cysteine, and that cysteine deprivation can induce cell death; however, the specific factors governing acute sensitivity to cysteine starvation are poorly characterized. Here, we show that that neither expression of enzymes for cysteine synthesis nor availability of the primary precursor methionine correlated with acute sensitivity to cysteine starvation. We observed a strong correlation between efflux of the methionine-derived metabolite methylthioadenosine (MTA) and sensitivity to cysteine starvation. MTA efflux results from genetic deletion of methylthioadenosine phosphorylase (MTAP), which is frequently deleted in cancers. We show that MTAP loss upregulates polyamine metabolism which, concurrently with cysteine withdrawal, promotes elevated reactive oxygen species and prevents cell survival. Our results reveal an unexplored metabolic weakness at the intersection of polyamine and cysteine metabolism.
    DOI:  https://doi.org/10.1038/s42255-020-0253-2
  25. Nat Commun. 2020 Aug 06. 11(1): 3912
    Khalsa JK, Cheng N, Keegan J, Chaudry A, Driver J, Bi WL, Lederer J, Shah K.
      Immunotherapy has emerged as a promising approach to treat cancer, however, its efficacy in highly malignant brain-tumors, glioblastomas (GBM), is limited. Here, we generate distinct imageable syngeneic mouse GBM-tumor models and utilize RNA-sequencing, CyTOF and correlative immunohistochemistry to assess immune-profiles in these models. We identify immunologically-inert and -active syngeneic-tumor types and show that inert tumors have an immune-suppressive phenotype with numerous exhausted CD8 T cells and resident macrophages; fewer eosinophils and SiglecF+ macrophages. To mimic the clinical-settings of first line of GBM-treatment, we show that tumor-resection invigorates an anti-tumor response via increasing T cells, activated microglia and SiglecF+ macrophages and decreasing resident macrophages. A comparative CyTOF analysis of resected-tumor samples from GBM-patients and mouse GBM-tumors show stark similarities in one of the mouse GBM-tumors tested. These findings guide informed choices for use of GBM models for immunotherapeutic interventions and offer a potential to facilitate immune-therapies in GBM patients.
    DOI:  https://doi.org/10.1038/s41467-020-17704-5
  26. J Immunol. 2020 Aug 05. pii: ji1901167. [Epub ahead of print]
    Solouki S, Huang W, Elmore J, Limper C, Huang F, August A.
      CD8+ T cells play a critical role in adaptive immunity, differentiating into CD8+ memory T cells that form the basis of protective cellular immunity. Vaccine efficacy is attributed to long-term protective immunity, and understanding the parameters that regulate development of CD8+ T cells is critical to the design of T cell-mediated vaccines. We show in this study using mouse models that two distinct parameters, TCR signal strength (regulated by the tyrosine kinase ITK) and Ag affinity, play important but separate roles in modulating the development of memory CD8+ T cells. Unexpectedly, our data reveal that reducing TCR signal strength along with reducing Ag affinity for the TCR leads to enhanced and accelerated development of CD8+ memory T cells. Additionally, TCR signal strength is able to regulate CD8+ T cell effector cytokine R production independent of TCR Ag affinity. Analysis of RNA-sequencing data reveals that genes for inflammatory cytokines/cytokine receptors are significantly altered upon changes in Ag affinity and TCR signal strength. Furthermore, our findings show that the inflammatory milieu is critical in regulating this TCR signal strength-mediated increase in memory development, as both CpG oligonucleotide treatment or cotransfer of wild-type and Itk-/- T cells eliminates the observed increase in memory cell formation. These findings suggest that TCR signal strength and Ag affinity independently contribute to CD8+ memory T cell development, which is modulated by inflammation, and suggest that manipulating TCR signal strength along with Ag affinity, may be used to tune the development of CD8+ memory T cells during vaccine development.
    DOI:  https://doi.org/10.4049/jimmunol.1901167
  27. J Lipid Res. 2020 Aug 04. pii: jlr.RA120000899. [Epub ahead of print]
    Hall Z, Wilson CH, Burkhart DL, Ashmore T, Evan GI, Griffin JL.
      Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related deaths. Whilst mutations in Kras and over-expression of Myc are commonly found in patients, the role of altered lipid metabolism in lung cancer and its interplay with oncogenic Myc is poorly understood. Here we use a transgenic mouse model of Kras-driven lung adenocarcinoma with reversible activation of Myc, in combination with surface analysis lipid profiling of lung tumours and transcriptomics, to study the effect of Myc activity on cholesterol homeostasis. Our findings reveal that activation of Myc leads to the accumulation of cholesteryl esters (CE), stored in lipid droplets. Subsequent Myc deactivation leads to further increases in CEs, in contrast to tumours in which Myc was never activated. Gene expression analysis linked cholesterol transport and storage pathways to Myc activity. Our results suggest that increased Myc activity is associated with increased cholesterol influx, reduced efflux and accumulation of CE-rich lipid droplets in lung tumours. Targeting cholesterol homeostasis is proposed as a promising avenue to explore for novel treatments of lung cancer, with diagnostic and stratification potential in human NSCLC.
    Keywords:  Cancer; Cholesterol; Lipidomics; Lung; Mass spectrometry; adenocarcinoma; cholesteryl ester; lipid metabolism; liquid extraction surface analysis; mass spectrometry
    DOI:  https://doi.org/10.1194/jlr.RA120000899
  28. Nat Immunol. 2020 Aug 03.
    Koliaraki V, Prados A, Armaka M, Kollias G.
      Mesenchymal cells are mesoderm-derived stromal cells that are best known for providing structural support to organs, synthesizing and remodeling the extracellular matrix (ECM) and regulating development, homeostasis and repair of tissues. Recent detailed mechanistic insights into the biology of fibroblastic mesenchymal cells have revealed they are also significantly involved in immune regulation, stem cell maintenance and blood vessel function. It is now becoming evident that these functions, when defective, drive the development of complex diseases, such as various immunopathologies, chronic inflammatory disease, tissue fibrosis and cancer. Here, we provide a concise overview of the contextual contribution of fibroblastic mesenchymal cells in physiology and disease and bring into focus emerging evidence for both their heterogeneity at the single-cell level and their tissue-specific, spatiotemporal functional diversity.
    DOI:  https://doi.org/10.1038/s41590-020-0741-2
  29. Sci Transl Med. 2020 Aug 05. pii: eaax8096. [Epub ahead of print]12(555):
    Zhou Z, Moore TM, Drew BG, Ribas V, Wanagat J, Civelek M, Segawa M, Wolf DM, Norheim F, Seldin MM, Strumwasser AR, Whitney KA, Lester E, Reddish BR, Vergnes L, Reue K, Rajbhandari P, Tontonoz P, Lee J, Mahata SK, Hewitt SC, Shirihai O, Gastonbury C, Small KS, Laakso M, Jensen J, Lee S, Drevon CA, Korach KS, Lusis AJ, Hevener AL.
      Obesity is heightened during aging, and although the estrogen receptor α (ERα) has been implicated in the prevention of obesity, its molecular actions in adipocytes remain inadequately understood. Here, we show that adipose tissue ESR1/Esr1 expression inversely associated with adiposity and positively associated with genes involved in mitochondrial metabolism and markers of metabolic health in 700 Finnish men and 100 strains of inbred mice from the UCLA Hybrid Mouse Diversity Panel. To determine the anti-obesity actions of ERα in fat, we selectively deleted Esr1 from white and brown adipocytes in mice. In white adipose tissue, Esr1 controlled oxidative metabolism by restraining the targeted elimination of mitochondria via the E3 ubiquitin ligase parkin. mtDNA content was elevated, and adipose tissue mass was reduced in adipose-selective parkin knockout mice. In brown fat centrally involved in body temperature maintenance, Esr1 was requisite for both mitochondrial remodeling by dynamin-related protein 1 (Drp1) and uncoupled respiration thermogenesis by uncoupled protein 1 (Ucp1). In both white and brown fat of female mice and adipocytes in culture, mitochondrial dysfunction in the context of Esr1 deletion was paralleled by a reduction in the expression of the mtDNA polymerase γ subunit Polg1 We identified Polg1 as an ERα target gene by showing that ERα binds the Polg1 promoter to control its expression in 3T3L1 adipocytes. These findings support strategies leveraging ERα action on mitochondrial function in adipocytes to combat obesity and metabolic dysfunction.
    DOI:  https://doi.org/10.1126/scitranslmed.aax8096
  30. Mol Oncol. 2020 Aug 03.
    Gerada C, Ryan KM.
      Autophagy is a cellular degradation and recycling system, which can interact with components of innate immune signalling pathways to enhance pathogen clearance, in both immune and non-immune cells. Whilst this interaction is often beneficial for pathogen clearance, it can have varying outcomes in regards to tumorigenesis. Autophagy and the innate immune response can have both pro- and anti-tumorigenic effects at different stages of tumorigenesis due to the plastic nature of the tumour microenvironment (TME). Although both of these components have been studied in isolation as potential therapeutic targets, there has been less research concerning the interaction between autophagy and the innate immune response within the TME. As the innate immune response is critical for the formation of an effective anti-tumour adaptive immune response, targeting autophagy pathways in both tumour cells and innate immune cells could enhance tumour clearance. Within tumour cells, autophagy pathways are intertwined with pattern recognition receptor (PRR), inflammatory and cell death pathways, and therefore can alter the immunogenicity of the TME and development of the anti-tumour immune response. In innate immune cells, autophagy components can have autophagy-independent roles in functional pathways, and therefore could be valuable targets for enhancing immune cell function in the TME and immunotherapy. This review highlights the individual importance of autophagy and the innate immune response to tumorigenesis, and also explains the complex interactions between these pathways in the TME.
    Keywords:  Autophagy; cancer; immunotherapy; innate immune response; tumor microenvironment
    DOI:  https://doi.org/10.1002/1878-0261.12774
  31. Nat Cell Biol. 2020 Aug;22(8): 947-959
    Mercier V, Larios J, Molinard G, Goujon A, Matile S, Gruenberg J, Roux A.
      The plasma membrane tension strongly affects cell surface processes, such as migration, endocytosis and signalling. However, it is not known whether the membrane tension of organelles regulates their functions, notably intracellular traffic. The endosomal sorting complexes required for transport (ESCRT)-III complex is the major membrane remodelling complex that drives intra-lumenal-vesicle (ILV) formation on endosomal membranes. Here we used a fluorescent membrane-tension probe to show that ESCRT-III subunits are recruited onto endosomal membranes when the membrane tension is reduced. We find that tension-dependent recruitment is associated with ESCRT-III polymerization and membrane deformation in vitro and correlates with increased ILV formation in ESCRT-III-decorated endosomes in vivo. Finally, we find that the endosomal membrane tension decreases when ILV formation is triggered by EGF under physiological conditions. These results indicate that membrane tension is a major regulator of ILV formation and endosome trafficking, leading us to conclude that membrane tension can control organelle functions.
    DOI:  https://doi.org/10.1038/s41556-020-0546-4
  32. Elife. 2020 Aug 07. pii: e57814. [Epub ahead of print]9
    Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM.
      Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial surface, the importance of this localization is unclear. As yeast switch to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. Our data point to this change in mitochondrial volume fraction increasing the localization of certain nuclear-encoded mRNAs to the surface of the mitochondria. We show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization.
    Keywords:  S. cerevisiae; cell biology; chromosomes; gene expression; mRNA localization; mitochondria; protein synthesis
    DOI:  https://doi.org/10.7554/eLife.57814
  33. Cell Metab. 2020 Aug 04. pii: S1550-4131(20)30368-5. [Epub ahead of print]32(2): 150-152
    Boutagy NE, Fowler JW, Sessa WC.
      The precise mechanisms of free fatty acid (FFA) uptake in the vascular endothelium are unclear. In this issue of Cell Metabolism, Ibrahim et al. (2020) discover that FFA uptake is partially mediated by a vectorial, ER-mitochondria link, in which mitochondrial ATP production is locally used for the acyl-CoA synthetase activity of the ER-located fatty acid transport protein 4.
    DOI:  https://doi.org/10.1016/j.cmet.2020.07.010
  34. Nat Metab. 2020 Aug 03.
    Murphy RM, Watt MJ, Febbraio MA.
      The coordination of nutrient sensing, delivery, uptake and utilization is essential for maintaining cellular, tissue and whole-body homeostasis. Such synchronization can be achieved only if metabolic information is communicated between the cells and tissues of the entire organism. During intense exercise, the metabolic demand of the body can increase approximately 100-fold. Thus, exercise is a physiological state in which intertissue communication is of paramount importance. In this Review, we discuss the physiological processes governing intertissue communication during exercise and the molecules mediating such cross-talk.
    DOI:  https://doi.org/10.1038/s42255-020-0258-x
  35. Cancer Manag Res. 2020 ;12 5597-5605
    Ni J, Zhang L.
      Cachexia is a multifactorial disease characterized by weight loss via skeletal muscle and adipose tissue loss, an imbalance in metabolic regulation, and reduced food intake. It is caused by factors of catabolism produced by tumors in the systemic circulation as well as physiological factors such as the imbalanced inflammatory activation, proteolysis, autophagy, and lipolysis that may occur with gastric, pancreatic, esophageal, lung cancer, liver, and bowel cancer. Cancer cachexia not only negatively affects the quality of life of patients with cancer but also reduces the effectiveness of anti-cancer chemotherapy and increases its toxicity, leading to increased cancer-related mortality and expenditure of medical resources. Currently, there are no effective medical interventions to completely reverse cachexia and no approved drugs. Adequate nutritional support is the main method of cachexia treatment, while drugs that target the inhibition of catabolism, cell damage, and excessive activation of inflammation are under study. This article reviews recent advances in the diagnosis, staging, and evaluation of cancer cachexia.
    Keywords:  cancer cachexia; disease staging; metabolic dysfunction
    DOI:  https://doi.org/10.2147/CMAR.S261585
  36. F1000Res. 2020 ;9 288
    Koblitz J, Schomburg D, Neumann-Schaal M.
      Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
    Keywords:  Data Visualization; Metabolic Maps; Metabolism; Omics Data; Pathways; SVG; Systems Biology
    DOI:  https://doi.org/10.12688/f1000research.23427.1
  37. Nat Rev Endocrinol. 2020 Aug 06.
    Geng L, Lam KSL, Xu A.
      Fibroblast growth factor 21 (FGF21) is a stress-inducible hormone that has important roles in regulating energy balance and glucose and lipid homeostasis through a heterodimeric receptor complex comprising FGF receptor 1 (FGFR1) and β-klotho. Administration of FGF21 to rodents or non-human primates causes considerable pharmacological benefits on a cluster of obesity-related metabolic complications, including a reduction in fat mass and alleviation of hyperglycaemia, insulin resistance, dyslipidaemia, cardiovascular disorders and non-alcoholic steatohepatitis (NASH). However, native FGF21 is unsuitable for clinical use owing to poor pharmacokinetic and biophysical properties. A large number of long-acting FGF21 analogues and agonistic monoclonal antibodies for the FGFR1-β-klotho receptor complexes have been developed. Several FGF21 analogues and mimetics have progressed to early phases of clinical trials in patients with obesity, type 2 diabetes mellitus and NASH. In these trials, the primary end points of glycaemic control have not been met, whereas substantial improvements were observed in dyslipidaemia, hepatic fat fractions and serum markers of liver fibrosis in patients with NASH. The complexity and divergence in pharmacology and pathophysiology of FGF21, interspecies variations in FGF21 biology, the possible existence of obesity-related FGF21 resistance and endogenous FGF21 inactivation enzymes represent major obstacles to clinical implementation of FGF21-based pharmacotherapies for metabolic diseases.
    DOI:  https://doi.org/10.1038/s41574-020-0386-0
  38. Elife. 2020 Aug 05. pii: e47318. [Epub ahead of print]9
    Vagne Q, Vrel JP, Sens P.
      The design principles dictating the spatio-temporal organisation of eukaryotic cells, and in particular the mechanisms controlling the self-organisation and dynamics of membrane-bound organelles such as the Golgi apparatus, remain elusive. Although this organelle was discovered 120 years ago, such basic questions as whether vesicular transport through the Golgi occurs in an anterograde (from entry to exit) or retrograde fashion are still strongly debated. Here, we address these issues by studying a quantitative model of organelle dynamics that includes: de-novo compartment generation, inter-compartment vesicular exchange, and biochemical conversion of membrane components. We show that anterograde or retrograde vesicular transports are asymptotic behaviors of a much richer dynamical system. Indeed, the structure and composition of cellular compartments and the directionality of vesicular exchange are intimately linked. They are emergent properties that can be tuned by varying the relative rates of vesicle budding, fusion and biochemical conversion.
    Keywords:  golgi apparatus; none; organelles; physics of living systems; self-organization; stochastic models
    DOI:  https://doi.org/10.7554/eLife.47318
  39. Cancer Res. 2020 Aug 01. 80(15): 3072-3073
    Kuijjer ML.
      One of the biggest challenges in cancer is predicting its initiation and course of progression. In this issue of Cancer Research, Rockne and colleagues use state transition theory to predict how peripheral mononuclear blood cells in mice transition from a healthy state to acute myeloid leukemia. They found that critical transcriptomic perturbations could predict initiation and progression of the disease. This is an important step toward accurately predicting cancer evolution, which may eventually facilitate early diagnosis of cancer and disease recurrence, and which could potentially inform on timing of therapeutic interventions.See related article by Rockne et al., 3157.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1878
  40. Autophagy. 2020 Aug 07.
    Kim S, Cho H, Hong SO, Oh SJ, Lee HJ, Cho E, Woo SR, Song JS, Chung JY, Son SW, Yoon SM, Jeon YM, Jeon S, Yee C, Lee KM, Hewitt SM, Kim JH, Song KH, Kim TW.
      Immune selection drives tumor cells to acquire refractory phenotypes. We previously demonstrated that cytotoxic T lymphocyte (CTL)-mediated immune pressure enriches NANOG+ tumor cells with stem-like and immune-refractory properties that make them resistant to CTLs. Here, we report that the emergence of refractory phenotypes is highly associated with an aberrant macroautophagic/autophagic state of the NANOG+ tumor cells and that the autophagic phenotype arises through transcriptional induction of MAP1LC3B/LC3B by NANOG. Furthermore, we found that upregulation of LC3B expression contributes to an increase in EGF secretion. The subsequent hyperactivation of EGFR-AKT signaling rendered NANOG+ tumor cells resistant to CTL killing. The NANOG-LC3B-p-EGFR axis was preserved across various types of human cancer and correlated negatively with the overall survival of cervical cancer patients. Inhibition of LC3B in immune-refractory tumor models rendered tumors susceptible to adoptive T-cell transfer, as well as PDCD1/PD-1 blockade, and led to successful, long-term control of the disease. Thus, our findings demonstrate a novel link among immune-resistance, stem-like phenotypes, and LC3B-mediated autophagic secretion in immune-refractory tumor cells, and implicate the LC3B-p-EGFR axis as a central molecular target for controlling NANOG+ immune-refractory cancer.
    Keywords:  EGFR; LC3B; MAP1LC3B; NANOG; cancer immunoediting; immune resistance; immunotherapy
    DOI:  https://doi.org/10.1080/15548627.2020.1805214
  41. Nat Metab. 2020 Aug 03.
    Klein Geltink RI, Edwards-Hicks J, Apostolova P, O'Sullivan D, Sanin DE, Patterson AE, Puleston DJ, Ligthart NAM, Buescher JM, Grzes KM, Kabat AM, Stanczak M, Curtis JD, Hässler F, Uhl FM, Fabri M, Zeiser R, Pearce EJ, Pearce EL.
      CD8+ effector T (TE) cell proliferation and cytokine production depends on enhanced glucose metabolism. However, circulating T cells continuously adapt to glucose fluctuations caused by diet and inter-organ metabolite exchange. Here we show that transient glucose restriction (TGR) in activated CD8+ TE cells metabolically primes effector functions and enhances tumour clearance in mice. Tumour-specific TGR CD8+ TE cells co-cultured with tumour spheroids in replete conditions display enhanced effector molecule expression, and adoptive transfer of these cells in a murine lymphoma model leads to greater numbers of immunologically functional circulating donor cells and complete tumour clearance. Mechanistically, TE cells treated with TGR undergo metabolic remodelling that, after glucose re-exposure, supports enhanced glucose uptake, increased carbon allocation to the pentose phosphate pathway (PPP) and a cellular redox shift towards a more reduced state-all indicators of a more anabolic programme to support their enhanced functionality. Thus, metabolic conditioning could be used to promote efficiency of T-cell products for adoptive cellular therapy.
    DOI:  https://doi.org/10.1038/s42255-020-0256-z
  42. Biochim Biophys Acta Mol Cell Res. 2020 Aug 04. pii: S0167-4889(20)30173-7. [Epub ahead of print] 118815
    Scrima R, Cela O, Agriesti F, Piccoli C, Tataranni T, Pacelli C, Mazzoccoli G, Capitanio N.
      Regulation of metabolism is emerging as a major output of circadian clock circuitry in mammals. Accordingly, mitochondrial oxidative metabolism undergoes both in vivo and in vitro daily oscillatory activities. In the present study we show that both glycolysis and mitochondrial oxygen consumption display a similar time-resolved rhythmic activity in synchronized HepG2 cell cultures, which translates in overall bioenergetic changes as documented by measurement of the ATP level. Treatment of synchronized cells with specific metabolic inhibitors unveiled pyruvate as a major source of reducing equivalents to the respiratory chain with its oxidation driven by the rhythmic (de)phosphorylation of pyruvate dehydrogenase. Further investigation enabled to causally link the autonomous cadenced mitochondrial respiration to a synchronous increase of the mitochondrial Ca2+. The rhythmic change of the mitochondrial respiration was dampened by inhibitors of the mitochondrial Ca2+ uniporter as well as of the ryanodine receptor Ca2+ channel or the ADPR cyclase, indicating that the mitochondrial Ca2+ influx originated from the ER store, likely at contact sites with the mitochondrial compartment. Notably, blockage of the mitochondrial Ca2+ influx resulted in deregulation of the expression of canonical clock genes such as BMALl1, CLOCK, NR1D1. All together our findings unveil a hitherto unexplored function of Ca2+-mediated signaling in time keeping the mitochondrial metabolism and in its feed-back modulation of the circadian clockwork.
    Keywords:  Circadian clock-genes; Inter-organelle communication; Mitochondria; Mitochondrial calcium signaling; Oxidative phosphorylation; Pyruvate dehydrogenase
    DOI:  https://doi.org/10.1016/j.bbamcr.2020.118815
  43. Autophagy. 2020 Aug 05.
    Cheng A, Tse KH, Chow HM, Gan Y, Song X, Ma F, Qian YXY, She W, Herrup K.
      ATM (ataxia telangiectasia mutated) protein is found associated with multiple organelles including synaptic vesicles, endosomes and lysosomes, often in cooperation with ATR (ataxia telangiectasia and Rad3 related). Mutation of the ATM gene results in ataxia-telangiectasia (A-T), an autosomal recessive disorder with defects in multiple organs including the nervous system. Precisely how ATM deficiency leads to the complex phenotypes of A-T, however, remains elusive. Here, we reported that part of the connection may lie in autophagy and lysosomal abnormalities. We found that ATM was degraded through the autophagy pathway, while ATR was processed by the proteasome. Autophagy and lysosomal trafficking were both abnormal in atm-/- neurons and the deficits impacted cellular functions such as synapse maintenance, neuronal survival and glucose uptake. Upregulated autophagic flux was observed in atm-/- lysosomes, associated with a more acidic pH. Significantly, we found that the ATP6V1A (ATPase, H+ transporting, lysosomal V1 subunit A) proton pump was an ATM kinase target. In atm-/- neurons, lysosomes showed enhanced retrograde transport and accumulated in the perinuclear regions. We attributed this change to an unexpected physical interaction between ATM and the retrograde transport motor protein, dynein. As a consequence, SLC2A4/GLUT4 (solute carrier family 4 [facilitated glucose transporter], member 4) translocation to the plasma membrane was inhibited and trafficking to the lysosomes was increased, leading to impaired glucose uptake capacity. Together, these data underscored the involvement of ATM in a variety of neuronal vesicular trafficking processes, offering new and therapeutically useful insights into the pathogenesis of A-T.
    Keywords:  SLC2A4/GLUT4; ataxia-telangiectasia; autophagy; lysosome; neurodegeneration; protein degradation; trafficking
    DOI:  https://doi.org/10.1080/15548627.2020.1805860
  44. JCI Insight. 2020 Aug 06. pii: 137869. [Epub ahead of print]5(15):
    Nokin MJ, Darbo E, Travert C, Drogat B, Lacouture A, San José S, Cabrera N, Turcq B, Prouzet-Mauleon V, Falcone M, Villanueva A, Wang H, Herfs M, Mosteiro M, Jänne PA, Pujol JL, Maraver A, Barbacid M, Nadal E, Santamaría D, Ambrogio C.
      Platinum-based chemotherapy in combination with immune-checkpoint inhibitors is the current standard of care for patients with advanced lung adenocarcinoma (LUAD). However, tumor progression evolves in most cases. Therefore, predictive biomarkers are needed for better patient stratification and for the identification of new therapeutic strategies, including enhancing the efficacy of chemotoxic agents. Here, we hypothesized that discoidin domain receptor 1 (DDR1) may be both a predictive factor for chemoresistance in patients with LUAD and a potential target positively selected in resistant cells. By using biopsies from patients with LUAD, KRAS-mutant LUAD cell lines, and in vivo genetically engineered KRAS-driven mouse models, we evaluated the role of DDR1 in the context of chemotherapy treatment. We found that DDR1 is upregulated during chemotherapy both in vitro and in vivo. Moreover, analysis of a cohort of patients with LUAD suggested that high DDR1 levels in pretreatment biopsies correlated with poor response to chemotherapy. Additionally, we showed that combining DDR1 inhibition with chemotherapy prompted a synergistic therapeutic effect and enhanced cell death of KRAS-mutant tumors in vivo. Collectively, this study suggests a potential role for DDR1 as both a predictive and prognostic biomarker, potentially improving the chemotherapy response of patients with LUAD.
    Keywords:  Drug therapy; Lung cancer; Molecular biology; Oncology; Therapeutics
    DOI:  https://doi.org/10.1172/jci.insight.137869
  45. Cancer Res. 2020 Aug 01. 80(15): 3070-3071
    Carpenter ES, Steele NG, Pasca di Magliano M.
      Pancreatic cancer is characterized by an extensive and complex microenvironment, and is resistant to both chemotherapy and immune checkpoint blockade. The study by Principe and colleagues in this issue of Cancer Research proposes a combinatorial approach based on targeting the very mechanisms of resistance to gemcitabine, a commonly used chemotherapeutic agent. The authors show that gemcitabine treatment causes profound changes in the pancreatic cancer microenvironment, including elevated TGFβ signaling and immune checkpoint expression, as well as increased antigen presentation in tumor cells. Accordingly, they show that the combination of chemotherapy, TGFβ signaling inhibition, and immune checkpoint blockade effectively restores antitumor immunity and results in a significant survival benefit.See related article by Principe et al., p. 3101.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1692
  46. Elife. 2020 Aug 07. pii: e60513. [Epub ahead of print]9
    Wang Y, Han Y, She J, Nguyen NX, Mootha VK, Bai XC, Jiang Y.
      Mitochondrial Ca2+ uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, MICU1 and MICU2, among which MCU and EMRE form a subcomplex and function as the conductive channel while MICU1 and MICU2 are EF-hand proteins that regulate the channel activity in a Ca2+ dependent manner. Here we present the EM structures of the human mitochondrial calcium uniporter holocomplex (uniplex) in the presence and absence of Ca2+, revealing distinct Ca2+ dependent assembly of the uniplex. Our structural observations suggest that Ca2+ changes the dimerization interaction between MICU1 and MICU2, which in turn determines how the MICU1-MICU2 subcomplex interacts with the MCU-EMRE channel and, consequently, changes the distribution of the uniplex assemblies between the blocked and unblocked states.
    Keywords:  biochemistry; chemical biology; human; molecular biophysics; structural biology
    DOI:  https://doi.org/10.7554/eLife.60513
  47. Anal Biochem. 2020 Jul 29. pii: S0003-2697(20)30409-7. [Epub ahead of print]606 113877
    Cao Z, Jose I, Glab J, Puthalakath H, Osellame LD, Hoogenraad NJ.
      Rapidly identifying cachexia-inducing factors that directly induce muscle wasting is an existing challenge. We developed two reporter cell lines that allow swift detection of such factors in blood from patients. C2C12 myoblasts were used for the establishment of reporter cells. A luciferase reporter gene, driven by promoters of wasting genes, Muscle RING-finger protein-1 (MuRF1) and Muscle Atrophy F-Box Protein (MAFbx/Atrogin-1) were used for the construction of reporter constructs. Increased expression of these genes in muscle tissue under wasting conditions was shown in vivo and in vitro. We found these reporter cell lines could detect factors associated with cancer cachexia, such as myostatin (Mstn), activin A, and TNF-α. We further investigated the capacity to directly detect a cachectic state using plasma samples from cachectic mice and cancer patients. Activation of the reporter cell lines was observed by the addition of plasma from mice with cancer cachexia and serum samples from patients with pancreatic or colorectal cancer. These results indicate that the reporter cell lines are competent as a tool for screening cachexia-inducing factors and potentially distinguishing a cachectic state induced by cancer.
    Keywords:  Cachexia-inducing factor; Cancer cachexia; Muscle wasting; Reporter
    DOI:  https://doi.org/10.1016/j.ab.2020.113877
  48. Nutrients. 2020 Aug 05. pii: E2338. [Epub ahead of print]12(8):
    White R, Nonis M, Pearson JF, Burgess E, Morrin HR, Pullar JM, Spencer E, Vissers MCM, Robinson BA, Dachs GU.
      Vitamin C (ascorbate) acts as an antioxidant and enzyme cofactor, and plays a vital role in human health. Vitamin C status can be affected by illness, with low levels being associated with disease due to accelerated turnover. However, robust data on the ascorbate status of patients with cancer are sparse. This study aimed to accurately measure ascorbate concentrations in plasma from patients with cancer, and determine associations with patient or tumor characteristics. We recruited 150 fasting patients with cancer (of 199 total recruited) from two cohorts, either prior to cancer surgery or during cancer chemo- or immunotherapy. A significant number of patients with cancer had inadequate plasma ascorbate concentrations. Low plasma status was more prevalent in patients undergoing cancer therapy. Ascorbate status was higher in women than in men, and exercising patients had higher levels than sedentary patients. Our study may prompt increased vigilance of ascorbate status in cancer patients.
    Keywords:  ascorbate; breast cancer; chemotherapy; colorectal cancer; exercise; immunotherapy; surgery
    DOI:  https://doi.org/10.3390/nu12082338
  49. Nat Genet. 2020 Aug 03.
    Mas-Ponte D, Supek F.
      Certain mutagens, including the APOBEC3 (A3) cytosine deaminase enzymes, can create multiple genetic changes in a single event. Activity of A3s results in striking 'mutation showers' occurring near DNA breakpoints; however, less is known about the mechanisms underlying the majority of A3 mutations. We classified the diverse patterns of clustered mutagenesis in tumor genomes, which identified a new A3 pattern: nonrecurrent, diffuse hypermutation (omikli). This mechanism occurs independently of the known focal hypermutation (kataegis), and is associated with activity of the DNA mismatch-repair pathway, which can provide the single-stranded DNA substrate needed by A3, and contributes to a substantial proportion of A3 mutations genome wide. Because mismatch repair is directed towards early-replicating, gene-rich chromosomal domains, A3 mutagenesis has a high propensity to generate impactful mutations, which exceeds that of other common carcinogens such as tobacco smoke and ultraviolet exposure. Cells direct their DNA repair capacity towards more important genomic regions; thus, carcinogens that subvert DNA repair can be remarkably potent.
    DOI:  https://doi.org/10.1038/s41588-020-0674-6
  50. J Hepatol. 2020 Jul 29. pii: S0168-8278(20)30489-X. [Epub ahead of print]
    Luo YD, Fang L, Yu HQ, Zhang J, Lin XT, Liu XY, Wu D, Li GX, Huang D, Zhang YJ, Chen S, Jiang Y, Shuai L, He Y, Zhang LD, Bie P, Xie CM.
      BACKGROUND AND AIMS: p53 mutations occur frequently in human hepatocellular carcinoma (HCC). Activation of the mammalian target of rapamycin (mTOR) pathway is also associated with HCC. However, it is still unknown whether these changes together initiate HCC and can be targeted as a potential therapeutic strategy.METHODS: We generated mouse models in which mTOR was hyperactivated by loss of tuberous sclerosis complex 1 (Tsc1) with or without p53 haplodeficiency. Primary cells were isolated from mouse livers. Oncogenic signaling was assessed in vitro and in vivo, with or without targeted inhibition of a single molecule or multiple molecules. Transcriptional profiling was used to identify biomarkers predictive of HCC. Human HCC materials were used to corroborate the findings from mouse models.
    RESULTS: p53 haploinsufficiency facilitates mTOR signaling via the Pten/PI3k/Akt axis, promoting HCC tumorigenesis and lung metastasis. Inhibition of PI3K/Akt reduced mTOR activity, which effectively enhanced the anticancer effort of an mTOR inhibitor. Abcc4 was found to be responsible for p53 haploinsufficiency- and Tsc1 loss-driven HCC tumorigenesis. Moreover, in clinical HCC samples, Abcc4 specifically identified an aggressive subtype. The mTOR inhibitor rapamycin significantly reduced hepatocarcinogenesis triggered by Tsc1 loss and p53 haploinsufficiency in vivo, as well as the biomarker Abcc4.
    CONCLUSIONS: Our data advance the current understanding of the activation of the Pten/PI3K/Akt/mTOR axis and its downstream target Abcc4 in hepatocarcinogenesis driven by p53 reduction and Tsc1 loss. Targeting mTOR, an unexpected vulnerability in p53 (haplo)deficiency HCC, can be exploited therapeutically to treat Abcc-4-positive HCC patients.
    Keywords:  Abcc4; PI3K/Akt; Pten; Tsc1/mTOR; hepatocellular carcinoma; p53; poor survival; rapamycin; sapanisertib
    DOI:  https://doi.org/10.1016/j.jhep.2020.07.036
  51. Sci Transl Med. 2020 Aug 05. pii: eaaz9746. [Epub ahead of print]12(555):
    Min J, Chin LK, Oh J, Landeros C, Vinegoni C, Lee J, Lee SJ, Park JY, Liu AQ, Castro CM, Lee H, Im H, Weissleder R.
      Rapid, automated, point-of-care cellular diagnosis of cancer remains difficult in remote settings due to lack of specialists and medical infrastructure. To address the need for same-day diagnosis, we developed an automated image cytometry system (CytoPAN) that allows rapid breast cancer diagnosis of scant cellular specimens obtained by fine needle aspiration (FNA) of palpable mass lesions. The system is devoid of moving parts for stable operations, harnesses optimized antibody kits for multiplexed analysis, and offers a user-friendly interface with automated analysis for rapid diagnoses. Through extensive optimization and validation using cell lines and mouse models, we established breast cancer diagnosis and receptor subtyping in 1 hour using as few as 50 harvested cells. In a prospective patient cohort study (n = 68), we showed that the diagnostic accuracy was 100% for cancer detection and the receptor subtyping accuracy was 96% for human epidermal growth factor receptor 2 and 93% for hormonal receptors (ER/PR), two key biomarkers associated with breast cancer. A combination of FNA and CytoPAN offers faster, less invasive cancer diagnoses than the current standard (core biopsy and histopathology). This approach should enable the ability to more rapidly diagnose breast cancer in global and remote settings.
    DOI:  https://doi.org/10.1126/scitranslmed.aaz9746
  52. Membranes (Basel). 2020 Aug 03. pii: E177. [Epub ahead of print]10(8):
    Lin XP, Mintern JD, Gleeson PA.
      Macropinocytosis is a unique pathway of endocytosis characterised by the nonspecific internalisation of large amounts of extracellular fluid, solutes and membrane in large endocytic vesicles known as macropinosomes. Macropinocytosis is important in a range of physiological processes, including antigen presentation, nutrient sensing, recycling of plasma proteins, migration and signalling. It has become apparent in recent years from the study of specialised cells that there are multiple pathways of macropinocytosis utilised by different cell types, and some of these pathways are triggered by different stimuli. Understanding the physiological function of macropinocytosis requires knowledge of the regulation and fate of the macropinocytosis pathways in a range of cell types. Here, we compare the mechanisms of macropinocytosis in different primary and immortalised cells, identify the gaps in knowledge in the field and discuss the potential approaches to analyse the function of macropinocytosis in vivo.
    Keywords:  amiloride; cancer cells; dendritic cells; endothelial cells; epithelial cells; macrophages; macropinocytosis; macropinosomes; membrane ruffling; microglia; neurons
    DOI:  https://doi.org/10.3390/membranes10080177
  53. J Biochem. 2020 Aug 03. pii: mvaa091. [Epub ahead of print]
    Zannino L, Casali C, Siciliani S, Biggiogera M.
      In the last decades it has become increasingly clear how the modulation of spatial organization of chromatin over time and through the cell cycle is closely connected to gene function regulation. Different physicochemical stimuli contribute to the realization of specific transcriptional programs and finally to a specific cellular phenotype. In this review, we aim to describe the current knowledge about the dynamics regulating the movements and the interactions of molecules within the nucleus and their impact on gene functions. In particular, taking into account that these forces exert their effect in a nuclear environment characterized by a high concentration of molecules, we will discuss the role of proteins and structures that regulate these movements and transduce physicochemical signals acting on the cell to the nucleus.
    Keywords:  Chromatin; Molecular crowding; Nuclear architecture; Nuclear physicochemical dynamics; Phase separation
    DOI:  https://doi.org/10.1093/jb/mvaa091
  54. Mol Metab. 2020 Jul 30. pii: S2212-8778(20)30131-9. [Epub ahead of print] 101057
    Avrahami D, Wang YJ, Schug J, Feleke E, Gao L, Liu C, Consortium HPAP, Naji A, Glaser B, Kaestner KH.
      OBJECTIVE: Dedifferentiation of pancreatic β-cells may reduce islet function in type 2 diabetes (T2D). However, the prevalence, plasticity and functional consequences of this cellular state remain unknown.METHODS: We employed single-cell RNAseq to detail the maturation program of α- and β-cells during human ontogeny. We also compared islets from non-diabetic and T2D individuals.
    RESULTS: Both α- and β-cells mature in part by repressing non-endocrine genes, however, α-cells retain hallmarks of an immature state, while β-cells attain a full β-cell specific gene expression program. In islets from T2D donors, both α- and β-cells have a less mature expression profile, de-repressing the juvenile genetic program and exocrine genes and increasing expression of exocytosis, inflammation and stress response signaling pathways. These changes are consistent with the increased proportion of β-cells displaying suboptimal function observed in T2D islets.
    CONCLUSIONS: These findings provide new insights into the molecular program underlying islet cell maturation during human ontogeny and the loss of transcriptomic maturity that occurs in islets of type 2 diabetics.
    Keywords:  Human islet; ontogeny; single cell RNAseq; type 2 diabetes; α-cell; β-cell
    DOI:  https://doi.org/10.1016/j.molmet.2020.101057
  55. Cell Stem Cell. 2020 Aug 06. pii: S1934-5909(20)30348-9. [Epub ahead of print]27(2): 192-194
    Li JH, Chen YY.
      Senescence is a critical factor in several diseases, yet senolytic therapies targeting senescent cells remain hindered by lack of specificity. In the June issue of Nature, Amor et al. (2020) develop chimeric antigen receptor (CAR)-T cells targeting uPAR, a novel senescent-cell marker, to treat liver adenocarcinoma and liver fibrosis.
    DOI:  https://doi.org/10.1016/j.stem.2020.07.010
  56. bioRxiv. 2020 Jul 29. pii: 2020.07.27.218115. [Epub ahead of print]
    Ghebremedhin A, Salam AB, Adu-Addai B, Noonan S, Stratton R, Ahmed MSU, Khantwal C, Martin GR, Lin H, Andrews C, Karanam B, Rudloff U, Lopez H, Jaynes J, Yates C.
      Activated M2 polarized macrophages are drivers of pulmonary fibrosis in several clinical scenarios such as Acute Respiratory Disease Syndrome (ARDS) and Idiopathic Pulmonary Fibrosis (IPF), through the production of inflammatory and fibrosis-inducing cytokines. In this study, we investigated the effect of targeting the CD206 receptor with a novel fragment of a Host Defense Peptide (HDP), RP-832c to decrease cytokines that cause fibrosis. RP-832c selectively binds to CD206 on M2 polarized bone marrow derived macrophages (BMDM) in vitro , resulting in a time-dependent decrease in CD206 expression, and a transient increase in M1 marker TNFα, which resolves over a 24hr period. To elucidate the antifibrotic effect of RP-832c, we used a murine model of bleomycin (BLM) -induced early-stage pulmonary fibrosis. RP-832c significantly reduced bleomycin-induced fibrosis in a dosage dependent manner, as well as decreased CD206, TGF-β1 and α-SMA expression in mouse lungs. Interestingly we did not observe any changes in the resident alveolar macrophage marker CD170 expression. Similarly, in an established model of lung fibrosis, RP-832c significantly decreased fibrosis in the lung, as well as significantly decreased inflammatory cytokines TNFα, IL-6, IL-10, INF-γ, CXCL1/2, and fibrosis markers TGF-β1 and MMP-13. In comparison with FDA approved drugs, Nintedanib and Pirfenidone, RP-832c exhibited a similar reduction in fibrosis compared to Pirfenidone, and to a greater extent than Nintedanib, with no apparent toxicities observed on body weight or blood chemistry. In summary, RP-832c is a potential agent to mitigate the overactivity of M2 macrophages in pathogenesis several pulmonary fibrotic diseases, including SARS-CoV-2 induced lung fibrosis.
    DOI:  https://doi.org/10.1101/2020.07.27.218115
  57. Cancer Treat Rev. 2020 Jul 22. pii: S0305-7372(20)30122-5. [Epub ahead of print]89 102084
    McNamara MG, Jacobs T, Lamarca A, Hubner RA, Valle JW, Amir E.
      Accurate identification of patients with solid tumors likely to respond to immunotherapy is crucial. Tumor mutational burden (TMB) measures the number of somatic mutations in a tumor and is an emerging prognostic and predictive biomarker for anti-programmed cell death (PD) 1/anti-PD-ligand 1 therapy and other immunotherapeutic agents. Tumor mutational burden is assessed optimally by whole exome sequencing, but next generation sequencing provides TMB estimates in a more timely and cost-effective manner. Blood-based measurement of TMB in plasma offers an alternative to the need for adequate tumor tissue for molecular testing, and has demonstrated the ability to identify patients who derive benefit from immunotherapy. Tumor mutational burden has diverse prognostic impact in different solid tumor types and also has a demonstrated role in predicting improved survival in patients receiving immunotherapy. There are challenges to TMB adoption into standard clinical practice, including variations in its definition, with the mutational number defining TMB-high appearing to vary across cancer types. The magnitude of TMB also varies across different tumor types, with the highest levels reported in melanoma and other skin cancers (where ultraviolet light is the dominant mutational process), followed by non-small cell lung cancer and other squamous carcinomas. Concerns regarding inter-laboratory and inter-platform variations in analysis methods have been raised, highlighting the need for standardization. Integration of other genomic or pathological biomarkers with TMB may increase its prognostic and predictive capabilities and validation of individual or combination models in prospective trials is warranted.
    Keywords:  Biomarkers; Immune checkpoint blockade; Next-generation sequencing; Predictive; Prognostic; Tumor mutational burden
    DOI:  https://doi.org/10.1016/j.ctrv.2020.102084
  58. Semin Immunopathol. 2020 Aug 05.
    Conte M, Martucci M, Chiariello A, Franceschi C, Salvioli S.
      A global reshaping of the immune responses occurs with ageing, indicated as immunosenescence, where mitochondria and mitochondrial metabolism play an important role. However, much less is known about the role of mitochondrial stress response in this reshaping and in particular of the molecules induced by such response, collectively indicated as mitokines. In this review, we summarize the current knowledge on the role of mitokines in modulating immune response and inflammation focusing on GDF15, FGF21 and humanin and their possible involvement in the chronic age-related low-grade inflammation dubbed inflammaging. Although many aspects of their biology are still controversial, available data suggest that these mitokines have an anti-inflammatory role and increase with age. Therefore, we hypothesize that they can be considered part of an adaptive and integrated immune-metabolic mechanism activated by mitochondrial dysfunction that acts within the framework of a larger anti-inflammatory network aimed at controlling both acute inflammation and inflammaging.
    Keywords:  Human ageing; Immunosenescence; Inflammaging; Mitochondrial metabolism; Mitokines
    DOI:  https://doi.org/10.1007/s00281-020-00813-0
  59. Sci Transl Med. 2020 Aug 05. pii: eaax8313. [Epub ahead of print]12(555):
    Lupo B, Sassi F, Pinnelli M, Galimi F, Zanella ER, Vurchio V, Migliardi G, Gagliardi PA, Puliafito A, Manganaro D, Luraghi P, Kragh M, Pedersen MW, Horak ID, Boccaccio C, Medico E, Primo L, Nichol D, Spiteri I, Heide T, Vatsiou A, Graham TA, Élez E, Argiles G, Nuciforo P, Sottoriva A, Dienstmann R, Pasini D, Grassi E, Isella C, Bertotti A, Trusolino L.
      Blockade of epidermal growth factor receptor (EGFR) causes tumor regression in some patients with metastatic colorectal cancer (mCRC). However, residual disease reservoirs typically remain even after maximal response to therapy, leading to relapse. Using patient-derived xenografts (PDXs), we observed that mCRC cells surviving EGFR inhibition exhibited gene expression patterns similar to those of a quiescent subpopulation of normal intestinal secretory precursors with Paneth cell characteristics. Compared with untreated tumors, these pseudodifferentiated tumor remnants had reduced expression of genes encoding EGFR-activating ligands, enhanced activity of human epidermal growth factor receptor 2 (HER2) and HER3, and persistent signaling along the phosphatidylinositol 3-kinase (PI3K) pathway. Clinically, properties of residual disease cells from the PDX models were detected in lingering tumors of responsive patients and in tumors of individuals who had experienced early recurrence. Mechanistically, residual tumor reprogramming after EGFR neutralization was mediated by inactivation of Yes-associated protein (YAP), a master regulator of intestinal epithelium recovery from injury. In preclinical trials, Pan-HER antibodies minimized residual disease, blunted PI3K signaling, and induced long-term tumor control after treatment discontinuation. We found that tolerance to EGFR inhibition is characterized by inactivation of an intrinsic lineage program that drives both regenerative signaling during intestinal repair and EGFR-dependent tumorigenesis. Thus, our results shed light on CRC lineage plasticity as an adaptive escape mechanism from EGFR-targeted therapy and suggest opportunities to preemptively target residual disease.
    DOI:  https://doi.org/10.1126/scitranslmed.aax8313
  60. Mol Cells. 2020 Aug 05.
    Song YC, Lee SE, Jin Y, Park HW, Chun KH, Lee HW.
      Recently, tumor microenvironment (TME) and its stromal constituents have provided profound insights into understanding alterations in tumor behavior. After each identification regarding the unique roles of TME compartments, non-malignant stromal cells are found to provide a sufficient tumorigenic niche for cancer cells. Of these TME constituents, adipocytes represent a dynamic population mediating endocrine effects to facilitate the crosstalk between cancer cells and distant organs, as well as the interplay with nearby tumor cells. To date, the prevalence of obesity has emphasized the significance of metabolic homeostasis along with adipose tissue (AT) inflammation, cancer incidence, and multiple pathological disorders. In this review, we summarized distinct characteristics of hypertrophic adipocytes and cancer to highlight the importance of an individual's metabolic health during cancer therapy. As AT undergoes inflammatory alterations inducing tissue remodeling, immune cell infiltration, and vascularization, these features directly influence the TME by favoring tumor progression. A comparison between inflammatory AT and progressing cancer could potentially provide crucial insights into delineating the complex communication network between uncontrolled hyperplastic tumors and their microenvironmental components. In turn, the comparison will unravel the underlying properties of dynamic tumor behavior, advocating possible therapeutic targets within TME constituents.
    Keywords:  adipose tissue; cancer-associated adipocyte; inflammation; obesity; tumor microenvironment
    DOI:  https://doi.org/10.14348/molcells.2020.0118
  61. Aging Cell. 2020 Aug 03. e13206
    Yang L, Lin X, Tang H, Fan Y, Zeng S, Jia L, Li Y, Shi Y, He S, Wang H, Hu Z, Gong X, Liang X, Yang Y, Liu X.
      Mammals' aging is correlated with the accumulation of somatic heteroplasmic mitochondrial DNA (mtDNA) mutations. Whether and how aging accumulated mtDNA mutations modulate fertility remains unknown. Here, we analyzed oocyte quality of young (≤30 years old) and elder (≥38 years old) female patients and show the elder group had lower blastocyst formation rate and more mtDNA point mutations in oocytes. To test the causal role of mtDNA point mutations on infertility, we used polymerase gamma (POLG) mutator mice. We show that mtDNA mutation levels inversely correlate with fertility, interestingly mainly affecting not male but female fertility. mtDNA mutations decrease female mice's fertility by reducing ovarian primordial and mature follicles. Mechanistically, accumulation of mtDNA mutations decreases fertility by impairing oocyte's NADH/NAD+ redox state, which could be rescued by nicotinamide mononucleotide treatment. For the first time, we answer the fundamental question of the causal effect of age-accumulated mtDNA mutations on fertility and its sex dependence, and show its distinct metabolic controlling mechanism.
    Keywords:  aging; fertility; mitochondria; mitochondrial DNA; nicotinamide mononucleotide
    DOI:  https://doi.org/10.1111/acel.13206
  62. Mol Cancer Ther. 2020 Aug 03. pii: molcanther.0161.2020. [Epub ahead of print]
    Riviere P, Goodman AM, Okamura R, Barkauskas DA, Whitchurch TJ, Lee S, Khalid N, Collier R, Marebiona M, Frampton GM, Fabrizio D, Sharabi AB, Kato S, Kurzrock R.
      Higher tumor mutational burden (TMB) has been correlated with response to checkpoint blockade immunotherapy. However, it is unclear whether TMB independently serves as a prognostic biomarker for outcomes in immunotherapy-naïve patients. Here we evaluated the relationship between TMB and overall survival in 1,415 immunotherapy-naïve patients with diverse advanced malignancies. TMB was studied both as a tiered variable (low ≤5 mutations/Mb, intermediate >5 and <20, high ≥20 and <50, and very high ≥50) and as a continuous variable. Interestingly, we observed a parabolic correlation between TMB and overall survival, where intermediate-range TMB correlated with decreased survival while low and very high TMB correlated with improved outcomes (median survival: 238, 174, 195, and 350 weeks for low, intermediate, high, and very high TMB respectively; multivariate p<0.01). This corresponded to a hazard ratio of 1.29 (95% confidence interval, 1.07-1.54; p < 0.01) for intermediate-range TMB on multivariable survival analysis correcting for known confounders including primary tumor of origin. These results demonstrate that TMB may have utility as a prognostic biomarker in immunotherapy-naïve patients, with a protective effect at higher TMBs, and that studies of survival in immunotherapy-treated patients may need to stratify or randomize by TMB in a non-linear fashion to account for this confounding.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-20-0161
  63. J Biol Chem. 2020 Aug 06. pii: jbc.RA120.013820. [Epub ahead of print]
    Ben C, Wu X, Takahashi-Kanemitsu A, Knight CT, Hayashi T, Hatakeyama M.
      In addition to acting as a transcriptional coactivator, YAP1 directly mediates translocalization of the pro-oncogenic phosphatase SHP2 from the cytoplasm to nucleus. In the cytoplasm, SHP2 potentiates RAS-ERK signaling, which promotes cell proliferation and cell motility, while in the nucleus, it mediates gene regulation. As a result, elucidating the details of SHP2 trafficking is important for understanding its biological roles, including in cancer. YAP1 comprises multiple splicing isoforms defined in part by the presence (as in YAP1-2γ) or absence (as in YAP1-2α) of a γ-segment encoded by exon 6 that disrupts a critical leucine zipper. While the disruptive segment is known to reduce coactivator function, it is unclear how this element impacts the physical and functional relationships between YAP1 and SHP2. To explore this question, we first demonstrated that YAP1-2γ cannot bind SHP2. Nevertheless, YAP1-2γ exhibits stronger mitogenic and motogenic activities than does YAP1-2α because the YAP1-2α-mediated delivery of SHP2 to the nucleus weakens cytoplasmic RAS-ERK signaling. However, YAP1-2γ confers less in vivo tumorigenicity than does YA1-2α by recruiting tumor-inhibitory macrophages. Mechanistically, YAP1-2γ transactivates and the YAP1-2α-SHP2 complex transrepresses the monocyte/macrophage chemoattractant CCL2. Thus, cell-intrinsic and cell-extrinsic pro-oncogenic YAP1 activities are inversely regulated by alternative splicing of exon 6. Notably, oncogenic KRAS downregulates the SRSF3 splicing factor that prevents exon 6 skipping, thereby creating a YAP1-2α-dominant situation that supports a "cold" immune microenvironment.
    Keywords:  CCL2; Hippo pathway; Ras protein; SHP2; YAP1; chemokine; differential splicing; spliceosome; trascription repression; tumor microenvironment
    DOI:  https://doi.org/10.1074/jbc.RA120.013820