bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒03‒14
seventy-two papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth.
  2. Pancreatic cancer is suppressed by fibroblast-derived collagen I.
  3. eIF2B conformation and assembly state regulates the integrated stress response.
  4. Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8+ T cells during the primary immune response.
  5. SMAD4 loss limits the vulnerability of pancreatic cancer cells to complex I inhibition via promotion of mitophagy.
  6. Transplanted hepatocytes rescue mice in acetaminophen-induced acute liver failure through paracrine signals for hepatic ATM and STAT3 pathways.
  7. Acetyl-CoA and Metabolite Fluxes Regulate White Adipose Tissue Expansion.
  8. Protein sequence design by conformational landscape optimization.
  9. Control of mitosis, inflammation, and cell motility by limited leakage of lysosomes.
  10. Targeting mitochondrial iron metabolism suppresses tumor growth and metastasis by inducing mitochondrial dysfunction and mitophagy.
  11. Autophagy and organelle homeostasis in cancer.
  12. Critical Phenomena in Plasma Membrane Organization and Function.
  13. Progenitor-like characteristics in a subgroup of UCP1+ cells within white adipose tissue.
  14. DNA methylation-based age clocks: from age prediction to age reversion.
  15. Friendly mediates membrane depolarization-induced mitophagy in Arabidopsis.
  16. Matrix-driven changes in metabolism support cytoskeletal activity to promote cell migration.
  17. Metabolic ROS Signaling: To Immunity and Beyond.
  18. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities.
  19. Mt-Keima detects PINK1-PRKN mitophagy in vivo with greater sensitivity than mito-QC.
  20. Reflux of Endoplasmic Reticulum proteins to the cytosol inactivates tumor suppressors.
  21. Mechanical Regulation of Transcription: Recent Advances.
  22. Membrane bending by protein phase separation.
  23. Blockade of 6-phosphogluconate dehydrogenase generates CD8+ effector T cells with enhanced anti-tumor function.
  24. CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor cells and T cells.
  25. Mitochondrial bioenergetic pathways in blood leukocyte transcriptome decrease after intensive weight loss but are rescued following weight regain in female physique athletes.
  26. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression.
  27. Intersection of immunometabolism and immunosenescence during aging.
  28. MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.
  29. Decoding the physical principles of two-component biomolecular phase separation.
  30. Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
  31. Balancing ER-Mitochondrial Ca2+ Fluxes in Health and Disease.
  32. KRAS mutation in pancreatic cancer.
  33. Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency.
  34. Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptake.
  35. Extra-cellular matrix in multicellular aggregates acts as a pressure sensor controlling cell proliferation and motility.
  36. NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation.
  37. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma.
  38. Autophagy in inflammation, infection, and immunometabolism.
  39. Drp1 is required for AgRP neuronal activity and feeding.
  40. Molecular switch architecture determines response properties of signaling pathways.
  41. mTORC1 couples cyst(e)ine availability with GPX4 protein synthesis and ferroptosis regulation.
  42. Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.
  43. The melanocortin pathway and energy homeostasis: From discovery to obesity therapy.
  44. Analyzing Melanoma Cell Oxygen Consumption and Extracellular Acidification Rates Using Seahorse Technology.
  45. Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors.
  46. Organotypic platform for studying cancer cell metastasis.
  47. c-Src facilitates tumorigenesis by phosphorylating and activating G6PD.
  48. Injury-mediated stiffening persistently activates muscle stem cells through YAP and TAZ mechanotransduction.
  49. KRAS G12C inhibition and innate immune targeting.
  50. Transcriptional analysis of islets of Langerhans from organ donors of different ages.
  51. Adhesion strength and contractility enable metastatic cells to become adurotactic.
  52. Association of Ablative Radiation Therapy With Survival Among Patients With Inoperable Pancreatic Cancer.
  53. Pancreatitis severity in mice with impaired CFTR function but pancreatic sufficiency is mediated via ductal and inflammatory cells-Not acinar cells.
  54. ROS-dependent HIF1α activation under forced lipid catabolism entails glycolysis and mitophagy as mediators of higher proliferation rate in cervical cancer cells.
  55. Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases.
  56. Senolytics: Potential for Alleviating Diabetes and Its Complications.
  57. Adapting the proteostasis capacity to sustain brain healthspan.
  58. Cooperative binding between distant transcription factors is a hallmark of active enhancers.
  59. The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps.
  60. Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney.
  61. Prevalence of low protein intake in 80+ year-old community-dwelling adults and association with dietary patterns and modifiable risk factors- a cross-sectional study.
  62. Cellular aging beyond cellular senescence: Markers of senescence prior to cell cycle arrest in vitro and in vivo.
  63. Fat induces glucose metabolism in non-transformed liver cells and promotes liver tumorigenesis.
  64. Molecular mapping of interstitial lung disease reveals a phenotypically distinct senescent basal epithelial cell population.
  65. Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines.
  66. A gene expression signature associated with ''K-Ras addiction'' reveals regulators of EMT and tumor cell survival.
  67. Silencing of LRRFIP1 enhances the sensitivity of gemcitabine in pancreatic cancer cells by activating JNK/c-Jun signaling.
  68. Matters of data openness and KapWeb, a web tool of multi-cancer survival analysis for cancer survivors.
  69. Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering.
  70. Cysteine-based crosslinking approach for characterization of oligomeric pore-forming proteins in the mitochondrial membranes.
  71. Exploiting the MUC5AC Antigen for Noninvasive Identification of Pancreatic Cancer.
  72. Two decades of research toward the treatment of locally advanced and metastatic pancreatic cancer: Remarkable effort and limited gain.
  1. Nat Cell Biol. 2021 Mar 08.
    Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth.
    Suprit Gupta, Julian Yano, Vincent Mercier, Htet Htwe Htwe, Hijai R Shin, Gilles Rademaker, Zeynep Cakir, Thomas Ituarte, Kwun W Wen, Grace E Kim, Roberto Zoncu, Aurélien Roux, David W Dawson, Rushika M Perera.
      Lysosomes must maintain the integrity of their limiting membrane to ensure efficient fusion with incoming organelles and degradation of substrates within their lumen. Pancreatic cancer cells upregulate lysosomal biogenesis to enhance nutrient recycling and stress resistance, but it is unknown whether dedicated programmes for maintaining the integrity of the lysosome membrane facilitate pancreatic cancer growth. Using proteomic-based organelle profiling, we identify the Ferlin family plasma membrane repair factor Myoferlin as selectively and highly enriched on the membrane of pancreatic cancer lysosomes. Mechanistically, lysosomal localization of Myoferlin is necessary and sufficient for the maintenance of lysosome health and provides an early acting protective system against membrane damage that is independent of the endosomal sorting complex required for transport (ESCRT)-mediated repair network. Myoferlin is upregulated in human pancreatic cancer, predicts poor survival and its ablation severely impairs lysosome function and tumour growth in vivo. Thus, retargeting of plasma membrane repair factors enhances the pro-oncogenic activities of the lysosome.
    DOI:  https://doi.org/10.1038/s41556-021-00644-7
  2. Cancer Cell. 2021 Mar 05. pii: S1535-6108(21)00119-7. [Epub ahead of print]
    Pancreatic cancer is suppressed by fibroblast-derived collagen I.
    Chris D Madsen.
      Clinical implementation of anti-stromal therapies in pancreatic cancer has been delayed by unanticipated tumor-restraining properties of the desmoplastic stroma. In confronting these challenges, Chen et al. demonstrate in this issue of Cancer Cell that fibroblast-specific deletion of collagen I, in the background of oncogenic Kras-induced spontaneous murine pancreatic ductal adenocarcinoma, enhances immune suppression and accelerates progression of disease.
    DOI:  https://doi.org/10.1016/j.ccell.2021.02.017
  3. Elife. 2021 Mar 10. pii: e65703. [Epub ahead of print]10
    eIF2B conformation and assembly state regulates the integrated stress response.
    Michael Schoof, Morgane Boone, Lan Wang, Rosalie Lawrence, Adam Frost, Peter Walter.
      The integrated stress response (ISR) is activated by phosphorylation of the translation initiation factor eIF2 in response to various stress conditions. Phosphorylated eIF2 (eIF2-P) inhibits eIF2's nucleotide exchange factor eIF2B, a two-fold symmetric heterodecamer assembled from subcomplexes. Here, we monitor and manipulate eIF2B assembly in vitro and in vivo. In the absence of eIF2B's α-subunit, the ISR is induced because unassembled eIF2B tetramer subcomplexes accumulate in cells. Upon addition of the small-molecule ISR inhibitor ISRIB, eIF2B tetramers assemble into active octamers. Surprisingly, ISRIB inhibits the ISR even in the context of fully assembled eIF2B decamers, revealing allosteric communication between the physically distant eIF2, eIF2-P, and ISRIB binding sites. Cryo-EM structures suggest a rocking motion in eIF2B that couples these binding sites. eIF2-P binding converts eIF2B decamers into 'conjoined tetramers' with diminished substrate binding and enzymatic activity. Canonical eIF2-P-driven ISR activation thus arises due to this change in eIF2B's conformational state.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.65703
  4. Immunity. 2021 Mar 06. pii: S1074-7613(21)00084-4. [Epub ahead of print]
    Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8+ T cells during the primary immune response.
    Lauren S Levine, Kamir J Hiam-Galvez, Diana M Marquez, Iliana Tenvooren, Matthew Z Madden, Diana C Contreras, Debolanle O Dahunsi, Jonathan M Irish, Olalekan O Oluwole, Jeffrey C Rathmell, Matthew H Spitzer.
      Memory T cells are thought to rely on oxidative phosphorylation and short-lived effector T cells on glycolysis. Here, we investigated how T cells arrive at these states during an immune response. To understand the metabolic state of rare, early-activated T cells, we adapted mass cytometry to quantify metabolic regulators at single-cell resolution in parallel with cell signaling, proliferation, and effector function. We interrogated CD8+ T cell activation in vitro and in response to Listeria monocytogenes infection in vivo. This approach revealed a distinct metabolic state in early-activated T cells characterized by maximal expression of glycolytic and oxidative metabolic proteins. Cells in this transient state were most abundant 5 days post-infection before rapidly decreasing metabolic protein expression. Analogous findings were observed in chimeric antigen receptor (CAR) T cells interrogated longitudinally in advanced lymphoma patients. Our study demonstrates the utility of single-cell metabolic analysis by mass cytometry to identify metabolic adaptations of immune cell populations in vivo and provides a resource for investigations of metabolic regulation of immune responses across a variety of applications.
    Keywords:  CD8 T cell; T cell activation; immunometabolism; mass cytometry
    DOI:  https://doi.org/10.1016/j.immuni.2021.02.018
  5. Oncogene. 2021 Mar 08.
    SMAD4 loss limits the vulnerability of pancreatic cancer cells to complex I inhibition via promotion of mitophagy.
    Zuzana Ezrova, Zuzana Nahacka, Jan Stursa, Lukas Werner, Erik Vlcak, Petra Kralova Viziova, Michael V Berridge, Radislav Sedlacek, Renata Zobalova, Jakub Rohlena, Stepana Boukalova, Jiri Neuzil.
      Pancreatic cancer is one of the deadliest forms of cancer, which is attributed to lack of effective treatment options and drug resistance. Mitochondrial inhibitors have emerged as a promising class of anticancer drugs, and several inhibitors of the electron transport chain (ETC) are being clinically evaluated. We hypothesized that resistance to ETC inhibitors from the biguanide class could be induced by inactivation of SMAD4, an important tumor suppressor involved in transforming growth factor β (TGFβ) signaling, and associated with altered mitochondrial activity. Here we show that, paradoxically, both TGFβ-treatment and the loss of SMAD4, a downstream member of TGFβ signaling cascade, induce resistance to biguanides, decrease mitochondrial respiration, and fragment the mitochondrial network. Mechanistically, the resistance of SMAD4-deficient cells is mediated by increased mitophagic flux driven by MAPK/ERK signaling, whereas TGFβ-induced resistance is autophagy-independent and linked to epithelial-to-mesenchymal transition (EMT). Interestingly, mitochondria-targeted tamoxifen, a complex I inhibitor under clinical trial, overcomes resistance mediated by SMAD4-deficiency or TGFβ signaling. Our data point to differential mechanisms underlying the resistance to treatment in PDAC arising from TGFβ signaling and SMAD4 loss, respectively. The findings will help the development of mitochondria-targeted therapy for pancreatic cancer patients with SMAD4 as a plausible predictive marker.
    DOI:  https://doi.org/10.1038/s41388-021-01726-4
  6. FASEB J. 2021 Apr;35(4): e21471
    Transplanted hepatocytes rescue mice in acetaminophen-induced acute liver failure through paracrine signals for hepatic ATM and STAT3 pathways.
    Preeti Viswanathan, Yogeshwar Sharma, Fadi-Luc Jaber, Tatyana Tchaikovskaya, Sanjeev Gupta.
      Acute liver failure constitutes a devastating condition that needs novel cell and molecular therapies. To elicit synergisms in cell types of therapeutic interest, we studied hepatocytes and liver sinusoidal endothelial in mice with acetaminophen-induced acute liver failure. The context of regenerative signals was examined by transplants in peritoneal cavity because it possesses considerable capacity and allows soluble signals to enter the systemic circulation. Whereas transplanted hepatocytes and liver sinusoidal endothelial cells engrafted in peritoneal cavity, only the former could rescue mice in liver failure by improving injury outcomes, activating hepatic DNA damage repair, and inducing liver regeneration. The cytokines secreted by donor hepatocytes or liver sinusoidal endothelial cells differed and in hepatocytes from mice undergoing acetaminophen toxicity major cytokines were even rendered deficient (eg, G-CSF, VEGF, and others). Significantly, recapitulating hepatotoxicity-related DNA damage response in cultured cells identified impairments in ATM and JAK/STAT3 intersections since replacing cytokines produced less from injured hepatocytes restored these pathways to avoid acetaminophen hepatotoxicity. Similarly, hepatocyte transplantation in acute liver failure restored ATM and JAK/STAT3 pathways to advance DNA damage/repair and liver regeneration. The unexpected identification of novel hepatic G-CSF receptor expression following injury allowed paradigmatic studies of G-CSF supplementation to confirm the centrality of this paracrine ATM and STAT3 intersection. Remarkably, DNA damage/repair and hepatic regeneration directed by G-CSF concerned rebalancing of regulatory gene networks overseeing inflammation, metabolism, and cell viability. We conclude that healthy donor hepatocytes offer templates for generating specialized cell types to replace metabolic functions and regenerative factors in liver failure.
    Keywords:  DNA damage response; cell therapy; granulocyte colony-stimulating factor; inflammation; liver sinusoidal endothelial cells
    DOI:  https://doi.org/10.1096/fj.202002421R
  7. Trends Endocrinol Metab. 2021 Mar 09. pii: S1043-2760(21)00043-6. [Epub ahead of print]
    Acetyl-CoA and Metabolite Fluxes Regulate White Adipose Tissue Expansion.
    Jessica B Felix, Aaron R Cox, Sean M Hartig.
      White adipose tissue (WAT) depends on coordinated regulation of transcriptional and metabolic pathways to respond to whole-body energy demands. We highlight metabolites that contribute to biosynthetic reactions for WAT expansion. Recent studies have precisely defined how byproducts of carbohydrate and lipid metabolism affect physiological and endocrine functions in adipocytes. We emphasize the critical emerging roles of short-chain fatty acids (SCFAs) and tricarboxylic acid (TCA) cycle metabolites that connect lipogenesis to WAT energy balance and endocrine functions. These insights address how adipocytes use small molecules generated from central carbon metabolism to measure responses to nutritional stress.
    Keywords:  adipose tissue; insulin; lipid metabolism; metabolite; microenvironment
    DOI:  https://doi.org/10.1016/j.tem.2021.02.008
  8. Proc Natl Acad Sci U S A. 2021 Mar 16. pii: e2017228118. [Epub ahead of print]118(11):
    Protein sequence design by conformational landscape optimization.
    Christoffer Norn, Basile I M Wicky, David Juergens, Sirui Liu, David Kim, Doug Tischer, Brian Koepnick, Ivan Anishchenko, , David Baker, Sergey Ovchinnikov.
      The protein design problem is to identify an amino acid sequence that folds to a desired structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as finding an amino acid sequence for which the desired structure is the lowest energy state. As this calculation involves not only all possible amino acid sequences but also, all possible structures, most current approaches focus instead on the more tractable problem of finding the lowest-energy amino acid sequence for the desired structure, often checking by protein structure prediction in a second step that the desired structure is indeed the lowest-energy conformation for the designed sequence, and typically discarding a large fraction of designed sequences for which this is not the case. Here, we show that by backpropagating gradients through the transform-restrained Rosetta (trRosetta) structure prediction network from the desired structure to the input amino acid sequence, we can directly optimize over all possible amino acid sequences and all possible structures in a single calculation. We find that trRosetta calculations, which consider the full conformational landscape, can be more effective than Rosetta single-point energy estimations in predicting folding and stability of de novo designed proteins. We compare sequence design by conformational landscape optimization with the standard energy-based sequence design methodology in Rosetta and show that the former can result in energy landscapes with fewer alternative energy minima. We show further that more funneled energy landscapes can be designed by combining the strengths of the two approaches: the low-resolution trRosetta model serves to disfavor alternative states, and the high-resolution Rosetta model serves to create a deep energy minimum at the design target structure.
    Keywords:  energy landscape; machine learning; protein design; sequence optimization; stability prediction
    DOI:  https://doi.org/10.1073/pnas.2017228118
  9. Curr Opin Cell Biol. 2021 Mar 05. pii: S0955-0674(21)00024-7. [Epub ahead of print]71 29-37
    Control of mitosis, inflammation, and cell motility by limited leakage of lysosomes.
    Jonathan Stahl-Meyer, Kamilla Stahl-Meyer, Marja Jäättelä.
      Lysosomal membrane permeabilization and subsequent leakage of lysosomal hydrolases into the cytosol are considered as the major hallmarks of evolutionarily conserved lysosome-dependent cell death. Contradicting this postulate, new sensitive methods that can detect a minimal lysosomal membrane damage have demonstrated that lysosomal leakage does not necessarily equal cell death. Notably, cells are not only able to survive minor lysosomal membrane permeabilization, but some of their normal functions actually depend on leaked lysosomal hydrolases. Here we discuss emerging data suggesting that spatially and temporally controlled lysosomal leakage delivers lysosomal hydrolases to specific subcellular sites of action and controls at least three essential cellular processes, namely mitotic chromosome segregation, inflammatory signaling, and cellular motility.
    Keywords:  Adhesion; Cathepsins; Chromosome segregation; Inflammation; Lysosomal membrane permeabilization; Lysosomal storage disorders; Lysosome; Mitosis; Motility; NLRP3 inflammasome
    DOI:  https://doi.org/10.1016/j.ceb.2021.02.003
  10. Cancer Res. 2021 Mar 08. pii: canres.1628.2020. [Epub ahead of print]
    Targeting mitochondrial iron metabolism suppresses tumor growth and metastasis by inducing mitochondrial dysfunction and mitophagy.
    Cristian Sandoval-Acuña, Natalia Torrealba, Veronika Tomkova, Sukanya Balkrishna Jadhav, Kristyna Blazkova, Ladislav Merta, Sandra Lettlova, Miroslava Kari Adamcová, Daniel Rosel, Jan Brábek, Jiri Neuzil, Jan Stursa, Lukas Werner, Jaroslav Truksa.
      Deferoxamine (DFO) represents a widely used iron chelator for the treatment of iron overload. Here we describe the use of mitochondrially targeted deferoxamine (mitoDFO) as a novel approach to preferentially target cancer cells. The agent showed marked cytostatic, cytotoxic, and migrastatic properties in vitro, and it significantly suppressed tumor growth and metastasis in vivo. The underlying molecular mechanisms included (I) impairment of [Fe-S] cluster/heme biogenesis, leading to destabilization and loss of activity of [Fe-S] cluster/heme containing enzymes, (II) inhibition of mitochondrial respiration leading to mitochondrial ROS production, resulting in dysfunctional mitochondria with markedly reduced supercomplexes, and (III) fragmentation of the mitochondrial network and induction of mitophagy. Mitochondrial targeting of DFO represents a way to deprive cancer cells of biologically active iron, which is incompatible with their proliferation and invasion, without disrupting systemic iron metabolism. Our findings highlight the importance of mitochondrial iron metabolism for cancer cells and demonstrate repurposing deferoxamine into an effective anti-cancer drug via mitochondrial targeting.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1628
  11. Dev Cell. 2021 Mar 02. pii: S1534-5807(21)00121-0. [Epub ahead of print]
    Autophagy and organelle homeostasis in cancer.
    Dannah R Miller, Andrew Thorburn.
      Beginning with the earliest studies of autophagy in cancer, there have been indications that autophagy can both promote and inhibit cancer growth and progression; autophagy regulation of organelle homeostasis is similarly complicated. In this review we discuss pro- and antitumor effects of organelle-targeted autophagy and how this contributes to several hallmarks of cancer, such as evading cell death, genomic instability, and altered metabolism. Typically, the removal of damaged or dysfunctional organelles prevents tumor development but can also aid in proliferation or drug resistance in established tumors. By better understanding how organelle-specific autophagy takes place and can be manipulated, it may be possible to go beyond the brute-force approach of trying to manipulate all autophagy in order to improve therapeutic targeting of this process in cancer.
    Keywords:  ER-phagy; autophagy; cancer; lysophagy; mitophagy
    DOI:  https://doi.org/10.1016/j.devcel.2021.02.010
  12. Annu Rev Phys Chem. 2020 Dec 01.
    Critical Phenomena in Plasma Membrane Organization and Function.
    Thomas R Shaw, Subhadip Ghosh, Sarah L Veatch.
      Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in modulating this heterogeneity. Various biophysical mechanisms rooted in the concept of liquid-liquid phase separation have been proposed to explain diverse experimental observations of heterogeneity in model and cell membranes with distinct but overlapping applicability. In this review, we focus on the evidence for and the consequences of the hypothesis that the plasma membrane is poised near an equilibrium miscibility critical point. Critical phenomena explain certain features of the heterogeneity observed in cells and model systems but also go beyond heterogeneity to predict other interesting phenomena, including responses to perturbations in membrane composition. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 20, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physchem-090419-115951
  13. Dev Cell. 2021 Mar 09. pii: S1534-5807(21)00158-1. [Epub ahead of print]
    Progenitor-like characteristics in a subgroup of UCP1+ cells within white adipose tissue.
    Jooman Park, Sunhye Shin, Lifeng Liu, Iffat Jahan, Sang-Ging Ong, Pingwen Xu, Daniel C Berry, Yuwei Jiang.
      Thermogenic beige fat found in white adipose tissue is a potential therapeutic target to curb the global obesity and diabetes epidemic. However, these inducible thermogenic beige adipocytes have been thought to be short-lived and to rapidly convert to "white-like" adipocytes after discontinuing stimuli. In this study, using effective labeling techniques and genetic mouse tools, we demonstrate that a subset of UCP1+ cells that exist within white adipose tissue are able to self-divide and contribute to new beige adipocyte recruitment in response to β3 stimuli. When these cells are depleted or their adipogenic capability is blocked, β3-induced beige adipocyte formation is impaired. We also identify a cell-cycle machinery of p21 and CDKN2A as a molecular basis of beige adipocyte regulation. Collectively, our findings provide new insights into the cellular and molecular mechanisms of beige adipocyte regulation and potential therapeutic opportunities to induce the beige phenotype and treat metabolic disease.
    Keywords:  CDKN2A; UCP1; beige adipocytes; cell-cycle regulators; obesity; p21
    DOI:  https://doi.org/10.1016/j.devcel.2021.02.018
  14. Ageing Res Rev. 2021 Mar 05. pii: S1568-1637(21)00061-1. [Epub ahead of print] 101314
    DNA methylation-based age clocks: from age prediction to age reversion.
    Rezvan Noroozi, Soudeh Ghafouri-Fard, Aleksandra Pisarek, Joanna Rudnicka, Magdalena Spólnicka, Wojciech Branicki, Mohammad Taheri, Ewelina Pośpiech.
      Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
    Keywords:  DNA methylation; biological age; epigenetic age; epigenetic age acceleration; epigenetic clocks; epigenetic reprogramming; phenotypic age
    DOI:  https://doi.org/10.1016/j.arr.2021.101314
  15. Curr Biol. 2021 Mar 05. pii: S0960-9822(21)00275-X. [Epub ahead of print]
    Friendly mediates membrane depolarization-induced mitophagy in Arabidopsis.
    Juncai Ma, Zizhen Liang, Jierui Zhao, Pengfei Wang, Wenlong Ma, Keith K Mai, Juan A Fernandez Andrade, Yonglun Zeng, Nenad Grujic, Liwen Jiang, Yasin Dagdas, Byung-Ho Kang.
      The oxidative environment within the mitochondria makes them particularly vulnerable to proteotoxic stress. To maintain a healthy mitochondrial network, eukaryotes have evolved multi-tiered quality control pathways. If the stress cannot be alleviated, defective mitochondria are selectively removed by autophagy via a process termed mitophagy. Despite significant advances in metazoans and yeast, in plants, the molecular underpinnings of mitophagy are largely unknown. Here, using time-lapse imaging, electron tomography, and biochemical assays, we show that uncoupler treatments cause loss of mitochondrial membrane potential and induce autophagy in Arabidopsis. The damaged mitochondria are selectively engulfed by autophagosomes that are labeled by ATG8 proteins in an ATG5-dependent manner. Friendly, a member of the clustered mitochondria protein family, is recruited to the damaged mitochondria to mediate mitophagy. In addition to the stress, mitophagy is also induced during de-etiolation, a major cellular transformation during photomorphogenesis that involves chloroplast biogenesis. De-etiolation-triggered mitophagy is involved in cotyledon greening, pointing toward an inter-organellar crosstalk mechanism. Altogether, our results demonstrate how plants employ mitophagy to recycle damaged mitochondria during stress and development.
    Keywords:  Arabidopsis; autophagy; clustered mitochondria protein; de-etiolation; electron tomography; mitochondria recycling; mitophagy; time-lapse live-cell imaging; uncoupler
    DOI:  https://doi.org/10.1016/j.cub.2021.02.034
  16. Biophys J. 2021 Mar 08. pii: S0006-3495(21)00206-X. [Epub ahead of print]
    Matrix-driven changes in metabolism support cytoskeletal activity to promote cell migration.
    Yusheng Wu, Matthew R Zanotelli, Jian Zhang, Cynthia A Reinhart-King.
      The microenvironment provides both active and passive mechanical cues that regulate cell morphology, adhesion, migration, and metabolism. While the cellular response to those mechanical cues often requires energy-intensive actin cytoskeletal remodeling and actomyosin contractility, it remains unclear how cells dynamically adapt their metabolic activity to altered mechanical cues to support migration. Here, we investigated the changes in cellular metabolic activity in response to different 2D and 3D microenvironmental conditions, and how these changes relate to cytoskeletal activity and migration. Utilizing collagen micropatterning on polyacrylamide gels, intracellular energy levels and oxidative phosphorylation were found to be correlated with cell elongation and spreading and necessary for membrane ruffling. To determine whether this relationship holds in more physiological 3D matrices, collagen matrices were used to show that intracellular energy state was also correlated with protrusive activity and increased with matrix density. Pharmacological inhibition of oxidative phosphorylation revealed that cancer cells rely on oxidative phosphorylation to meet the elevated energy requirements for protrusive activity and migration in denser matrices. Together, these findings suggest that mechanical regulation of cytoskeletal activity during spreading and migration by the physical microenvironment is driven by an altered metabolic profile.
    Keywords:  cell metabolism; cell migration; collagen density; micropatterns; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.bpj.2021.02.044
  17. Biochemistry (Mosc). 2020 Dec;85(12): 1650-1667
    Metabolic ROS Signaling: To Immunity and Beyond.
    A Y Andreyev, Y E Kushnareva, N N Starkova, A A Starkov.
      Metabolism is a critical determinant of immune cell functionality. Immunometabolism, by definition, is a multidisciplinary area of immunology research that integrates the knowledge of energy transduction mechanisms and biochemical pathways. An important concept in the field is metabolic switch, a transition of immune cells upon activation to preferential utilization of select catabolic pathways for their energy needs. Mitochondria are not inert in this process and contribute to the metabolic adaptation by different mechanisms which include increasing ATP production to match dynamic bioenergetic demands and serving as a signaling platform. The latter involves generation of reactive oxygen species (ROS), one of the most intensively studied mitochondrial processes. While the role of mitochondrial ROS in the context of oxidative stress is well established, ROS signaling in immunity is an emerging and quickly changing field. In this review, we discuss ROS signaling and immunometabolism concepts from the standpoint of bioenergetics. We also provide a critical insight into the methodology for ROS assessment, outlining current challenges in the field. Finally, based on our analysis of the literature data, we hypothesize that regulatory ROS production, as opposed to oxidative stress, is controlled by mitochondrial biogenesis rather than metabolic switches.
    DOI:  https://doi.org/10.1134/S0006297920120160
  18. Nat Cancer. 2021 Feb;2(2): 141-156
    Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities.
    Luciano Garofano, Simona Migliozzi, Young Taek Oh, Fulvio D'Angelo, Ryan D Najac, Aram Ko, Brulinda Frangaj, Francesca Pia Caruso, Kai Yu, Jinzhou Yuan, Wenting Zhao, Anna Luisa Di Stefano, Franck Bielle, Tao Jiang, Peter Sims, Mario L Suvà, Fuchou Tang, Xiao-Dong Su, Michele Ceccarelli, Marc Sanson, Anna Lasorella, Antonio Iavarone.
      The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and therapeutic vulnerabilities. A computational approach for unbiased identification of core biological traits of single cells and bulk tumors uncovered four tumor cell states and GBM subtypes distributed along neurodevelopmental and metabolic axes, classified as proliferative/progenitor, neuronal, mitochondrial and glycolytic/plurimetabolic. Each subtype was enriched with biologically coherent multiomic features. Mitochondrial GBM was associated with the most favorable clinical outcome. It relied exclusively on oxidative phosphorylation for energy production, whereas the glycolytic/plurimetabolic subtype was sustained by aerobic glycolysis and amino acid and lipid metabolism. Deletion of the glucose-proton symporter SLC45A1 was the truncal alteration most significantly associated with mitochondrial GBM, and the reintroduction of SLC45A1 in mitochondrial glioma cells induced acidification and loss of fitness. Mitochondrial, but not glycolytic/plurimetabolic, GBM exhibited marked vulnerability to inhibitors of oxidative phosphorylation. The pathway-based classification of GBM informs survival and enables precision targeting of cancer metabolism.
    DOI:  https://doi.org/10.1038/s43018-020-00159-4
  19. Autophagy. 2021 Mar 08. 1-10
    Mt-Keima detects PINK1-PRKN mitophagy in vivo with greater sensitivity than mito-QC.
    Yi-Ting Liu, Danielle A Sliter, Mario K Shammas, Xiaoping Huang, Chunxin Wang, Hannah Calvelli, Dragan S Maric, Derek P Narendra.
      PINK1 and PRKN, which cause Parkinson disease when mutated, form a quality control mitophagy pathway that is well-characterized in cultured cells. The extent to which the PINK1-PRKN pathway contributes to mitophagy in vivo, however, is controversial. This is due in large part to conflicting results from studies using one of two mitophagy reporters: mt-Keima or mito-QC. Studies using mt-Keima have generally detected PINK1-PRKN mitophagy in vivo, whereas those using mito-QC generally have not. Here, we directly compared the performance of mito-QC and mt-Keima in cell culture and in mice subjected to a PINK1-PRKN activating stress. We found that mito-QC was less sensitive than mt-Keima for mitophagy, and that this difference was more pronounced for PINK1-PRKN mitophagy. These findings suggest that mito-QC's poor sensitivity may account for conflicting reports of PINK1-PRKN mitophagy in vivo and caution against using mito-QC as a reporter for PINK1-PRKN mitophagy.
    Keywords:  Autophagy; PARK2; PARKIN; Parkinson; degradation; disease; mitochondria; neurodegeneration; organelle
    DOI:  https://doi.org/10.1080/15548627.2021.1896924
  20. EMBO Rep. 2021 Mar 12. e51412
    Reflux of Endoplasmic Reticulum proteins to the cytosol inactivates tumor suppressors.
    Daria Sicari, Federica G Centonze, Raphael Pineau, Pierre-Jean Le Reste, Luc Negroni, Sophie Chat, M Aiman Mohtar, Daniel Thomas, Reynald Gillet, Ted Hupp, Eric Chevet, Aeid Igbaria.
      In the past decades, many studies reported the presence of endoplasmic reticulum (ER)-resident proteins in the cytosol. However, the mechanisms by which these proteins relocate and whether they exert cytosolic functions remain unknown. We find that a subset of ER luminal proteins accumulates in the cytosol of glioblastoma cells isolated from mouse and human tumors. In cultured cells, ER protein reflux to the cytosol occurs upon ER proteostasis perturbation. Using the ER luminal protein anterior gradient 2 (AGR2) as a proof of concept, we tested whether the refluxed proteins gain new functions in the cytosol. We find that refluxed, cytosolic AGR2 binds and inhibits the tumor suppressor p53. These data suggest that ER reflux constitutes an ER surveillance mechanism to relieve the ER from its contents upon stress, providing a selective advantage to tumor cells through gain-of-cytosolic functions-a phenomenon we name ER to Cytosol Signaling (ERCYS).
    Keywords:  ER stress; ERAD; cancer; endoplasmic reticulum; reflux
    DOI:  https://doi.org/10.15252/embr.202051412
  21. Trends Cell Biol. 2021 Mar 09. pii: S0962-8924(21)00033-7. [Epub ahead of print]
    Mechanical Regulation of Transcription: Recent Advances.
    Kaustubh Wagh, Momoko Ishikawa, David A Garcia, Diana A Stavreva, Arpita Upadhyaya, Gordon L Hager.
      Mechanotransduction is the ability of a cell to sense mechanical cues from its microenvironment and convert them into biochemical signals to elicit adaptive transcriptional and other cellular responses. Here, we describe recent advances in the field of mechanical regulation of transcription, highlight mechanical regulation of the epigenome as a key novel aspect of mechanotransduction, and describe recent technological advances that could further elucidate the link between mechanical stimuli and gene expression. In this review, we emphasize the importance of mechanotransduction as one of the governing principles of cancer progression, underscoring the need to conduct further studies of the molecular mechanisms involved in sensing mechanical cues and coordinating transcriptional responses.
    Keywords:  3D culture; chromatin architecture; genomics; light microscopy; mechanosensing; transcription
    DOI:  https://doi.org/10.1016/j.tcb.2021.02.008
  22. Proc Natl Acad Sci U S A. 2021 Mar 16. pii: e2017435118. [Epub ahead of print]118(11):
    Membrane bending by protein phase separation.
    Feng Yuan, Haleh Alimohamadi, Brandon Bakka, Andrea N Trementozzi, Kasey J Day, Nicolas L Fawzi, Padmini Rangamani, Jeanne C Stachowiak.
      Membrane bending is a ubiquitous cellular process that is required for membrane traffic, cell motility, organelle biogenesis, and cell division. Proteins that bind to membranes using specific structural features, such as wedge-like amphipathic helices and crescent-shaped scaffolds, are thought to be the primary drivers of membrane bending. However, many membrane-binding proteins have substantial regions of intrinsic disorder which lack a stable three-dimensional structure. Interestingly, many of these disordered domains have recently been found to form networks stabilized by weak, multivalent contacts, leading to assembly of protein liquid phases on membrane surfaces. Here we ask how membrane-associated protein liquids impact membrane curvature. We find that protein phase separation on the surfaces of synthetic and cell-derived membrane vesicles creates a substantial compressive stress in the plane of the membrane. This stress drives the membrane to bend inward, creating protein-lined membrane tubules. A simple mechanical model of this process accurately predicts the experimentally measured relationship between the rigidity of the membrane and the diameter of the membrane tubules. Discovery of this mechanism, which may be relevant to a broad range of cellular protrusions, illustrates that membrane remodeling is not exclusive to structured scaffolds but can also be driven by the rapidly emerging class of liquid-like protein networks that assemble at membranes.
    Keywords:  membrane biophysics; membrane curvature; protein phase separation
    DOI:  https://doi.org/10.1073/pnas.2017435118
  23. Cell Rep. 2021 Mar 09. pii: S2211-1247(21)00145-5. [Epub ahead of print]34(10): 108831
    Blockade of 6-phosphogluconate dehydrogenase generates CD8+ effector T cells with enhanced anti-tumor function.
    Saeed Daneshmandi, Teresa Cassel, Penghui Lin, Richard M Higashi, Gerburg M Wulf, Vassiliki A Boussiotis, Teresa W-M Fan, Pankaj Seth.
      Although T cell expansion depends on glycolysis, T effector cell differentiation requires signaling via the production of reactive oxygen species (ROS). Because the pentose phosphate pathway (PPP) regulates ROS by generating nicotinamide adenine dinucleotide phosphate (NADPH), we examined how PPP blockade affects T cell differentiation and function. Here, we show that genetic ablation or pharmacologic inhibition of the PPP enzyme 6-phosphogluconate dehydrogenase (6PGD) in the oxidative PPP results in the generation of superior CD8+ T effector cells. These cells have gene signatures and immunogenic markers of effector phenotype and show potent anti-tumor functions both in vitro and in vivo. In these cells, metabolic reprogramming occurs along with increased mitochondrial ROS and activated antioxidation machinery to balance ROS production against oxidative damage. Our findings reveal a role of 6PGD as a checkpoint for T cell effector differentiation/survival and evidence for 6PGD as an attractive metabolic target to improve tumor immunotherapy.
    Keywords:  6PGD; effector T cells; metabolism; pentose phosphate pathway; reactive oxygen species; tumor immunotherapy
    DOI:  https://doi.org/10.1016/j.celrep.2021.108831
  24. Cancer Discov. 2021 Mar 11. pii: candisc.1144.2020. [Epub ahead of print]
    CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor cells and T cells.
    Sushil Kumar, Zexian Zeng, Archis Bagati, Rong En Tay, Lionel A Sanz, Stella R Hartono, Yoshinaga Ito, Fieda Abderazzaq, Elodie Hatchi, Peng Jiang, Adam N R Cartwright, Olamide Olawoyin, Nathan D Mathewson, Jason W Pyrdol, Mamie Z Li, John G Doench, Matthew A Booker, Michael Y Tolstorukov, Stephen J Elledge, Frederic Chedin, X Shirley Liu, Kai W Wucherpfennig.
      A number of cancer drugs activate innate immune pathways in tumor cells but unfortunately also compromise anti-tumor immune function. We discovered that inhibition of Carm1, an epigenetic enzyme and co-transcriptional activator, elicited beneficial anti-tumor activity in both cytotoxic T cells and tumor cells. In T cells, Carm1 inactivation substantially enhanced their anti-tumor function and preserved memory-like populations required for sustained anti-tumor immunity. In tumor cells, Carm1 inactivation induced a potent type 1 interferon response that sensitized resistant tumors to cytotoxic T cells. Substantially increased numbers of dendritic cells, CD8 T cells and NK cells were present in Carm1-deficient tumors, and infiltrating CD8 T cells expressed low levels of exhaustion markers. Targeting of Carm1 with a small molecule elicited potent anti-tumor immunity and sensitized resistant tumors to checkpoint blockade. Targeting of this co-transcriptional regulator thus offers an opportunity to enhance immune function while simultaneously sensitizing resistant tumor cells to immune attack.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1144
  25. FASEB J. 2021 Apr;35(4): e21484
    Mitochondrial bioenergetic pathways in blood leukocyte transcriptome decrease after intensive weight loss but are rescued following weight regain in female physique athletes.
    Heikki V Sarin, Eija Pirinen, Kirsi H Pietiläinen, Ville Isola, Keijo Häkkinen, Markus Perola, Juha J Hulmi.
      Prolonged periods of energy deficit leading to weight loss induce metabolic adaptations resulting in reduced energy expenditure, but the mechanisms for energy conservation are incompletely understood. We examined 42 healthy athletic females (age 27.5 ± 4.0 years, body mass index 23.4 ± 1.7 kg/m2 ) who volunteered into either a group dieting for physique competition (n = 25) or a control group (n = 17). The diet group substantially reduced their energy intake and moderately increased exercise levels to induce loss of fat mass that was regained during a voluntary weight regain period. The control group maintained their typical lifestyle habits and body mass as instructed. From the diet group, fasting blood samples were drawn at baseline (PRE), after 4- to 5-month weight loss (PRE-MID), and after 4- to 5-month weight regain (MID-POST) as well as from the control group at similar intervals. Blood was analyzed to determine leukocyte transcriptome by RNA-Sequencing and serum metabolome by nuclear magnetic resonance (NMR) platform. The intensive weight loss period induced several metabolic adaptations, including a prominent suppression of transcriptomic signature for mitochondrial OXPHOS and ribosome biogenesis. The upstream regulator analysis suggested that this reprogramming of cellular energy metabolism may be mediated via AMPK/PGC1-α signaling and mTOR/eIF2 signaling-dependent pathways. Our findings show for the first time that prolonged energy deprivation induced modulation of mitochondrial metabolism can be observed through minimally invasive measures of leukocyte transcriptome and serum metabolome at systemic level, suggesting that adaptation to energy deficit is broader in humans than previously thought.
    Keywords:  diet; exercise; leukocytes; oxidative phosphorylation; ribosomes
    DOI:  https://doi.org/10.1096/fj.202002029R
  26. Autophagy. 2021 Mar 08. 1-19
    Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression.
    Sara E Hanley, Stephen D Willis, Katrina F Cooper.
      Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
    Keywords:  Atg17; Gle1; Ssn2/Med13; autophagy; selective autophagy; transcriptional regulators
    DOI:  https://doi.org/10.1080/15548627.2021.1877934
  27. Curr Opin Pharmacol. 2021 Mar 05. pii: S1471-4892(21)00004-7. [Epub ahead of print]57 107-116
    Intersection of immunometabolism and immunosenescence during aging.
    Kyoo-A Lee, Paul D Robbins, Christina D Camell.
      Aging is associated with the highest risk for morbidity and mortality to chronic or metabolic diseases, which are present in 50% of the elderly. Improving metabolic and immune function of the elderly would improve quality of life and reduce the risk for all other diseases. Tissue-resident macrophages and the NLRP3 inflammasome are established drivers of inflammaging and metabolic dysfunction. Energy-sensing signaling pathways connect sterile and metabolic inflammation with cellular senescence and tissue dysfunction. We discuss recent advances in the immunometabolism field. Common themes revealed by recent publications include the alterations in metabolic signaling (SIRTUIN, AMPK, or mTOR pathways) in aged immune cells, the impact of senescence on inflammaging and tissue dysfunction, and the age-related changes in metabolic tissues, especially adipose tissue, as an immunological organ. Promising gerotherapeutics are candidates to broadly target nutrient and energy sensing, inflammatory and senescence pathways, and have potential to improve healthspan and treat age-related diseases.
    Keywords:  AMPK-mTOR pathway; Adipose tissue; Aging; Immunometabolism; Inflammaging; Macrophage; NAD metabolism; NLRP3 inflammasome; SIRTUIN pathway
    DOI:  https://doi.org/10.1016/j.coph.2021.01.003
  28. Genomics Proteomics Bioinformatics. 2021 Mar 04. pii: S1672-0229(21)00057-7. [Epub ahead of print]
    MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.
    Guangyu Wang, Bo Xia, Man Zhou, Jie Lv, Dongyu Zhao, Yanqiang Li, Yiwen Bu, Xin Wang, John P Cooke, Qi Cao, Min Gyu Lee, Lili Zhang, Kaifu Chen.
      Numerous studies of relationship between epigenomic features have focused on their strong correlation across the genome, likely because such relationship can be easily identified by many established methods for correlation analysis. However, two features with little correlation may still colocalize at many genomic sites to implement important functions. There is no bioinformatic tool for researchers to specifically identify such feature pairs. Here, we develop a method to identify feature pairs in which two features have maximal colocalization but minimal correlation (MACMIC) across the genome. By MACMIC analysis of 3385 feature pairs in 15 cell types, we reveal a dual role of CCCTC-binding factor (CTCF) in epigenetic regulation of cell identity genes. Although super-enhancers are associated with activation of target genes, only a subset of super-enhancers colocalized with CTCF regulate cell identity genes. At super-enhancers colocalized with CTCF, CTCF is required for the active marker H3K27ac in cell types requiring the activation, and also required for the repressive marker H3K27me3 in other cell types requiring repression. Our work demonstrates the biological utility of the MACMIC analysis and reveals a key role for CTCF in epigenetic regulation of cell identity. The code for MACMIC is available at the website GitHub, https://github.com/bxia888/MACMIC.
    Keywords:  CCCTC-binding factor; H3K27ac; H3K27me3; Mutual information; correlation
    DOI:  https://doi.org/10.1016/j.gpb.2020.10.008
  29. Elife. 2021 Mar 11. pii: e62403. [Epub ahead of print]10
    Decoding the physical principles of two-component biomolecular phase separation.
    Yaojun Zhang, Bin Xu, Benjamin G Weiner, Yigal Meir, Ned S Wingreen.
      Cells possess a multiplicity of non-membrane-bound compartments, which form via liquid-liquid phase separation. These condensates assemble and dissolve as needed to enable central cellular functions. One important class of condensates is those composed of two associating polymer species that form one-to-one specific bonds. What are the physical principles that underlie phase separation in such systems? To address this question, we employed coarse-grained molecular dynamics simulations to examine how the phase boundaries depend on polymer valence, stoichiometry, and binding strength. We discovered a striking phenomenon - for sufficiently strong binding, phase separation is suppressed at rational polymer stoichiometries, which we termed the magic-ratio effect. We further developed an analytical dimer-gel theory that confirmed the magic-ratio effect and disentangled the individual roles of polymer properties in shaping the phase diagram. Our work provides new insights into the factors controlling the phase diagrams of biomolecular condensates, with implications for natural and synthetic systems.
    Keywords:  associative polymers; biomolecular condensates; molecular dynamics simulations; none; phase separation; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.62403
  30. Cancer Cell. 2021 Mar 10. pii: S1535-6108(21)00117-3. [Epub ahead of print]
    Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
    Kevin Bi, Meng Xiao He, Ziad Bakouny, Abhay Kanodia, Sara Napolitano, Jingyi Wu, Grace Grimaldi, David A Braun, Michael S Cuoco, Angie Mayorga, Laura DelloStritto, Gabrielle Bouchard, John Steinharter, Alok K Tewari, Natalie I Vokes, Erin Shannon, Maxine Sun, Jihye Park, Steven L Chang, Bradley A McGregor, Rizwan Haq, Thomas Denize, Sabina Signoretti, Jennifer L Guerriero, Sébastien Vigneau, Orit Rozenblatt-Rosen, Asaf Rotem, Aviv Regev, Toni K Choueiri, Eliezer M Van Allen.
      Immune checkpoint blockade (ICB) results in durable disease control in a subset of patients with advanced renal cell carcinoma (RCC), but mechanisms driving resistance are poorly understood. We characterize the single-cell transcriptomes of cancer and immune cells from metastatic RCC patients before or after ICB exposure. In responders, subsets of cytotoxic T cells express higher levels of co-inhibitory receptors and effector molecules. Macrophages from treated biopsies shift toward pro-inflammatory states in response to an interferon-rich microenvironment but also upregulate immunosuppressive markers. In cancer cells, we identify bifurcation into two subpopulations differing in angiogenic signaling and upregulation of immunosuppressive programs after ICB. Expression signatures for cancer cell subpopulations and immune evasion are associated with PBRM1 mutation and survival in primary and ICB-treated advanced RCC. Our findings demonstrate that ICB remodels the RCC microenvironment and modifies the interplay between cancer and immune cell populations critical for understanding response and resistance to ICB.
    Keywords:  cancer; immunotherapy; kidney; resistance; single cell
    DOI:  https://doi.org/10.1016/j.ccell.2021.02.015
  31. Trends Cell Biol. 2021 Mar 04. pii: S0962-8924(21)00028-3. [Epub ahead of print]
    Balancing ER-Mitochondrial Ca2+ Fluxes in Health and Disease.
    Jens Loncke, Allen Kaasik, Ilya Bezprozvanny, Jan B Parys, Martijn Kerkhofs, Geert Bultynck.
      Organelles cooperate with each other to control cellular homeostasis and cell functions by forming close connections through membrane contact sites. Important contacts are present between the endoplasmic reticulum (ER), the main intracellular Ca2+-storage organelle, and the mitochondria, the organelle responsible not only for the majority of cellular ATP production but also for switching on cell death processes. Several Ca2+-transport systems focalize at these contact sites, thereby enabling the efficient transmission of Ca2+ signals from the ER toward mitochondria. This provides tight control of mitochondrial functions at the microdomain level. Here, we discuss how ER-mitochondrial Ca2+ transfers support cell function and how their dysregulation underlies, drives, or contributes to pathogenesis and pathophysiology, with a major focus on cancer and neurodegeneration but also with attention to other diseases such as diabetes and rare genetic diseases.
    Keywords:  Ca(2+) signaling; MAMs; cancer; contact sites; genetic diseases; neurodegeneration
    DOI:  https://doi.org/10.1016/j.tcb.2021.02.003
  32. Semin Oncol. 2021 Feb 23. pii: S0093-7754(21)00008-7. [Epub ahead of print]
    KRAS mutation in pancreatic cancer.
    Ji Luo.
      Pancreatic cancer is a recalcitrant cancer with one of the lowest 5-year survival rates. A hallmark of pancreatic cancer is the prevalence of oncogenic mutation in the KRAS gene. The KRAS oncogene plays a critical role in the initiation and maintenance of pancreatic tumors and its signaling network represents a major target for therapeutic intervention. A number of inhibitors have been developed against kinase effectors in various Ras signaling pathways. Their clinical activity, however, has been disappointing thus far. More recently, covalent inhibitors targeting the KRASG12C oncoprotein have been developed. These inhibitors showed promising activity in KRASG12C mutant pancreatic cancer in early clinical trials. This review will present an updated summary of our understanding of mutant KRAS function in pancreatic cancer and discuss therapeutic strategies that target oncogenic KRAS signaling in this disease.
    Keywords:  G12C; KRAS; MAPK pathway; Pancreatic cancer; Targeted therapy
    DOI:  https://doi.org/10.1053/j.seminoncol.2021.02.003
  33. EMBO J. 2021 Mar 09. e105776
    Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency.
    Andreas Lackner, Robert Sehlke, Marius Garmhausen, Giuliano Giuseppe Stirparo, Michelle Huth, Fabian Titz-Teixeira, Petra van der Lelij, Julia Ramesmayer, Henry F Thomas, Meryem Ralser, Laura Santini, Elena Galimberti, Mihail Sarov, A Francis Stewart, Austin Smith, Andreas Beyer, Martin Leeb.
      In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre- to post-implantation epiblast in utero. We identified 496 naïve state-associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.
    Keywords:  exit from naïve pluripotency; haploid ES cells; naïve to formative transition; signalling; systems biology
    DOI:  https://doi.org/10.15252/embj.2020105776
  34. Nat Metab. 2021 Mar 08.
    Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptake.
    Estifanos N Habtemichael, Don T Li, João Paulo Camporez, Xavier O Westergaard, Chloe I Sales, Xinran Liu, Francesc López-Giráldez, Stephen G DeVries, Hanbing Li, Diana M Ruiz, Kenny Y Wang, Bhavesh S Sayal, Sofia González Zapata, Pamela Dann, Stacey N Brown, Sandro Hirabara, Daniel F Vatner, Leigh Goedeke, William Philbrick, Gerald I Shulman, Jonathan S Bogan.
      TUG tethering proteins bind and sequester GLUT4 glucose transporters intracellularly, and insulin stimulates TUG cleavage to translocate GLUT4 to the cell surface and increase glucose uptake. This effect of insulin is independent of phosphatidylinositol 3-kinase, and its physiological relevance remains uncertain. Here we show that this TUG cleavage pathway regulates both insulin-stimulated glucose uptake in muscle and organism-level energy expenditure. Using mice with muscle-specific Tug (Aspscr1)-knockout and muscle-specific constitutive TUG cleavage, we show that, after GLUT4 release, the TUG C-terminal cleavage product enters the nucleus, binds peroxisome proliferator-activated receptor (PPAR)γ and its coactivator PGC-1α and regulates gene expression to promote lipid oxidation and thermogenesis. This pathway acts in muscle and adipose cells to upregulate sarcolipin and uncoupling protein 1 (UCP1), respectively. The PPARγ2 Pro12Ala polymorphism, which reduces diabetes risk, enhances TUG binding. The ATE1 arginyltransferase, which mediates a specific protein degradation pathway and controls thermogenesis, regulates the stability of the TUG product. We conclude that insulin-stimulated TUG cleavage coordinates whole-body energy expenditure with glucose uptake, that this mechanism might contribute to the thermic effect of food and that its attenuation could promote obesity.
    DOI:  https://doi.org/10.1038/s42255-021-00359-x
  35. Elife. 2021 Mar 11. pii: e63258. [Epub ahead of print]10
    Extra-cellular matrix in multicellular aggregates acts as a pressure sensor controlling cell proliferation and motility.
    Monika E Dolega, Sylvain Monnier, Benjamin Brunel, Jean-François Joanny, Pierre Recho, Giovanni Cappello.
      Imposed deformations play an important role in morphogenesis and tissue homeostasis, both in normal and pathological conditions. To perceive mechanical perturbations of different types and magnitudes, tissues need appropriate detectors, with a compliance that matches the perturbation amplitude. By comparing results of selective osmotic compressions of CT26 cells within multicellular aggregates and global aggregate compressions, we show that global compressions have a strong impact on the aggregates growth and internal cell motility, while selective compressions of same magnitude have almost no effect. Both compressions alter the volume of individual cells in the same way over a shor-timescale, but, by draining the water out of the extracellular matrix, the global one imposes a residual compressive mechanical stress on the cells over a long-timescale, while the selective one does not. We conclude that the extracellular matrix is as a sensor that mechanically regulates cell proliferation and migration in a 3D environment.
    Keywords:  mouse; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.63258
  36. Nat Chem Biol. 2021 Mar 08.
    NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation.
    Leonidas Emmanouilidis, Laura Esteban-Hofer, Fred F Damberger, Tebbe de Vries, Cristina K X Nguyen, Luis Fábregas Ibáñez, Simon Mergenthal, Enrico Klotzsch, Maxim Yulikov, Gunnar Jeschke, Frédéric H-T Allain.
      Many RNA-binding proteins undergo liquid-liquid phase separation, which underlies the formation of membraneless organelles, such as stress granules and P-bodies. Studies of the molecular mechanism of phase separation in vitro are hampered by the coalescence and sedimentation of organelle-sized droplets interacting with glass surfaces. Here, we demonstrate that liquid droplets of fused in sarcoma (FUS)-a protein found in cytoplasmic aggregates of amyotrophic lateral sclerosis and frontotemporal dementia patients-can be stabilized in vitro using an agarose hydrogel that acts as a cytoskeleton mimic. This allows their spectroscopic characterization by liquid-phase NMR and electron paramagnetic resonance spectroscopy. Protein signals from both dispersed and condensed phases can be observed simultaneously, and their respective proportions can be quantified precisely. Furthermore, the agarose hydrogel acts as a cryoprotectant during shock-freezing, which facilitates pulsed electron paramagnetic resonance measurements at cryogenic temperatures. Surprisingly, double electron-electron resonance measurements revealed a compaction of FUS in the condensed phase.
    DOI:  https://doi.org/10.1038/s41589-021-00752-3
  37. Cancer Cell. 2021 Mar 09. pii: S1535-6108(21)00115-X. [Epub ahead of print]
    Progressive immune dysfunction with advancing disease stage in renal cell carcinoma.
    David A Braun, Kelly Street, Kelly P Burke, David L Cookmeyer, Thomas Denize, Christina B Pedersen, Satyen H Gohil, Nicholas Schindler, Lucas Pomerance, Laure Hirsch, Ziad Bakouny, Yue Hou, Juliet Forman, Teddy Huang, Shuqiang Li, Ang Cui, Derin B Keskin, John Steinharter, Gabrielle Bouchard, Maxine Sun, Erica M Pimenta, Wenxin Xu, Kathleen M Mahoney, Bradley A McGregor, Michelle S Hirsch, Steven L Chang, Kenneth J Livak, David F McDermott, Sachet A Shukla, Lars R Olsen, Sabina Signoretti, Arlene H Sharpe, Rafael A Irizarry, Toni K Choueiri, Catherine J Wu.
      The tumor immune microenvironment plays a critical role in cancer progression and response to immunotherapy in clear cell renal cell carcinoma (ccRCC), yet the composition and phenotypic states of immune cells in this tumor are incompletely characterized. We performed single-cell RNA and T cell receptor sequencing on 164,722 individual cells from tumor and adjacent non-tumor tissue in patients with ccRCC across disease stages: early, locally advanced, and advanced/metastatic. Terminally exhausted CD8+ T cells were enriched in metastatic disease and were restricted in T cell receptor diversity. Within the myeloid compartment, pro-inflammatory macrophages were decreased, and suppressive M2-like macrophages were increased in advanced disease. Terminally exhausted CD8+ T cells and M2-like macrophages co-occurred in advanced disease and expressed ligands and receptors that support T cell dysfunction and M2-like polarization. This immune dysfunction circuit is associated with a worse prognosis in external cohorts and identifies potentially targetable immune inhibitory pathways in ccRCC.
    Keywords:  CD8 T cell exhaustion; cancer immunotherapy; cell-cell interaction; clear cell renal cell carcinoma; immune cell atlas; single-cell RNA sequencing; tumor-associated macrophages
    DOI:  https://doi.org/10.1016/j.ccell.2021.02.013
  38. Immunity. 2021 Mar 09. pii: S1074-7613(21)00041-8. [Epub ahead of print]54(3): 437-453
    Autophagy in inflammation, infection, and immunometabolism.
    Vojo Deretic.
      Autophagy is a quality-control, metabolic, and innate immunity process. Normative autophagy affects many cell types, including hematopoietic as well as non-hematopoietic, and promotes health in model organisms and humans. When autophagy is perturbed, this has repercussions on diseases with inflammatory components, including infections, autoimmunity and cancer, metabolic disorders, neurodegeneration, and cardiovascular and liver diseases. As a cytoplasmic degradative pathway, autophagy protects from exogenous hazards, including infection, and from endogenous sources of inflammation, including molecular aggregates and damaged organelles. The focus of this review is on the role of autophagy in inflammation, including type I interferon responses and inflammasome outputs, from molecules to immune cells. A special emphasis is given to the intersections of autophagy with innate immunity, immunometabolism, and functions of organelles such as mitochondria and lysosomes that act as innate immunity and immunometabolic signaling platforms.
    DOI:  https://doi.org/10.1016/j.immuni.2021.01.018
  39. Elife. 2021 Mar 09. pii: e64351. [Epub ahead of print]10
    Drp1 is required for AgRP neuronal activity and feeding.
    Sungho Jin, Nal Ae Yoon, Zhong-Wu Liu, Jae Eun Song, Tamas L Horvath, Jung Dae Kim, Sabrina Diano.
      The hypothalamic orexigenic Agouti-related peptide (AgRP)-expressing neurons are crucial for the regulation of whole-body energy homeostasis. Here, we show that fasting-induced AgRP neuronal activation is associated with dynamin-related peptide 1 (DRP1)-mediated mitochondrial fission and mitochondrial fatty acid utilization in AgRP neurons. In line with this, mice lacking Dnm1l in adult AgRP neurons (Drp1 cKO) show decreased fasting- or ghrelin-induced AgRP neuronal activity and feeding and exhibited a significant decrease in body weight, fat mass, and feeding accompanied by a significant increase in energy expenditure. In support of the role for mitochondrial fission and fatty acids oxidation, Drp1 cKO mice showed attenuated palmitic acid-induced mitochondrial respiration. Altogether, our data revealed that mitochondrial dynamics and fatty acids oxidation in hypothalamic AgRP neurons is a critical mechanism for AgRP neuronal function and body-weight regulation.
    Keywords:  AgRP; feeding; metabolism; mitochondria; mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.64351
  40. Proc Natl Acad Sci U S A. 2021 Mar 16. pii: e2013401118. [Epub ahead of print]118(11):
    Molecular switch architecture determines response properties of signaling pathways.
    Khem Raj Ghusinga, Roger D Jones, Alan M Jones, Timothy C Elston.
      Many intracellular signaling pathways are composed of molecular switches, proteins that transition between two states-on and off Typically, signaling is initiated when an external stimulus activates its cognate receptor that, in turn, causes downstream switches to transition from off to on using one of the following mechanisms: activation, in which the transition rate from the off state to the on state increases; derepression, in which the transition rate from the on state to the off state decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several operating principles for molecular switches. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to upstream fluctuations. We demonstrate that these operating principles also hold when the models are extended to include additional features, such as receptor removal, kinetic proofreading, and cascades of switches. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.
    Keywords:  activation; derepression; dose–response; noise; signaling pathways
    DOI:  https://doi.org/10.1073/pnas.2013401118
  41. Nat Commun. 2021 03 11. 12(1): 1589
    mTORC1 couples cyst(e)ine availability with GPX4 protein synthesis and ferroptosis regulation.
    Yilei Zhang, Robert V Swanda, Litong Nie, Xiaoguang Liu, Chao Wang, Hyemin Lee, Guang Lei, Chao Mao, Pranavi Koppula, Weijie Cheng, Jie Zhang, Zhenna Xiao, Li Zhuang, Bingliang Fang, Junjie Chen, Shu-Bing Qian, Boyi Gan.
      Glutathione peroxidase 4 (GPX4) utilizes glutathione (GSH) to detoxify lipid peroxidation and plays an essential role in inhibiting ferroptosis. As a selenoprotein, GPX4 protein synthesis is highly inefficient and energetically costly. How cells coordinate GPX4 synthesis with nutrient availability remains unclear. In this study, we perform integrated proteomic and functional analyses to reveal that SLC7A11-mediated cystine uptake promotes not only GSH synthesis, but also GPX4 protein synthesis. Mechanistically, we find that cyst(e)ine activates mechanistic/mammalian target of rapamycin complex 1 (mTORC1) and promotes GPX4 protein synthesis at least partly through the Rag-mTORC1-4EBP signaling axis. We show that pharmacologic inhibition of mTORC1 decreases GPX4 protein levels, sensitizes cancer cells to ferroptosis, and synergizes with ferroptosis inducers to suppress patient-derived xenograft tumor growth in vivo. Together, our results reveal a regulatory mechanism to coordinate GPX4 protein synthesis with cyst(e)ine availability and suggest using combinatorial therapy of mTORC1 inhibitors and ferroptosis inducers in cancer treatment.
    DOI:  https://doi.org/10.1038/s41467-021-21841-w
  42. Nat Commun. 2021 03 08. 12(1): 1510
    Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.
    Jussi Kupari, Dmitry Usoskin, Marc Parisien, Daohua Lou, Yizhou Hu, Michael Fatt, Peter Lönnerberg, Mats Spångberg, Bengt Eriksson, Nikolaos Barkas, Peter V Kharchenko, Karin Loré, Samar Khoury, Luda Diatchenko, Patrik Ernfors.
      Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.
    DOI:  https://doi.org/10.1038/s41467-021-21725-z
  43. Mol Metab. 2021 Mar 05. pii: S2212-8778(21)00046-6. [Epub ahead of print] 101206
    The melanocortin pathway and energy homeostasis: From discovery to obesity therapy.
    Giles S H Yeo, Daniela Herrera Moro Chao, Anna-Maria Siegert, Zoe M Koerperich, Mark D Ericson, Stephanie E Simonds, Courtney M Larson, Serge Luquet, Iain Clarke, Shubh Sharma, Karine Clément, Michael A Cowley, Carrie Haskell-Luevano, Lex Van Der Ploeg, Roger A H Adan.
      BACKGROUND: Over the past 20 years, insights from human and mouse genetics have illuminated the central role of the brain leptin-melanocortin pathway in the control of mammalian food intake, with genetic disruption resulting in extreme obesity, and more subtle polymorphic variation influencing the population distribution of body-weight. At the end of 2020, the Food & Drug Administration (FDA) approved setmelanotide, a melanocortin 4 receptor agonist, for use in individuals with severe obesity due to either pro-opiomelanocortin (POMC), proprotein convertase subtilisin/kexin type 1 (PCSK1) or leptin receptor (LEPR) deficiency.SCOPE OF REVIEW: Here, we will chart the history of the melanocortin pathway, explore its pharmacology, genetics and physiology, and tell the story of how a neuropeptidergic circuit managed to find its way to becoming an important druggable obesity target.
    CONCLUSIONS: Unravelling the genetics of the subset of severe obesity has revealed the importance of the melanocortin pathway in appetitive control; coupling this with studying the molecular pharmacology of compounds that bind the melanocortin receptors has brought a new drug to the market for obesity. This process provides a template of drug discovery for complex disorders, which in the case of setmelanotide took 25 years to go from a single gene to an approved drug.
    DOI:  https://doi.org/10.1016/j.molmet.2021.101206
  44. Methods Mol Biol. 2021 ;2265 81-89
    Analyzing Melanoma Cell Oxygen Consumption and Extracellular Acidification Rates Using Seahorse Technology.
    Ashley V Menk, Greg M Delgoffe.
      Cancer cells have deregulated metabolism that can contribute to the unique metabolic makeup of the tumor microenvironment. This can be variable between patients, and it is important to understand these differences since they potentially can affect therapy response. Here we discuss a method of processing and assaying metabolism from direct ex vivo murine and human tumor samples using seahorse extracellular flux analysis. This provides real-time profiling of oxidative versus glycolytic metabolism and can help infer the metabolic status of the tumor microenvironment.
    Keywords:  Extracellular flux; Glycolysis; Metabolism; Oxidative phosphorylation; Seahorse
    DOI:  https://doi.org/10.1007/978-1-0716-1205-7_6
  45. Nat Commun. 2021 03 09. 12(1): 1502
    Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors.
    Karsten Bach, Sara Pensa, Marija Zarocsinceva, Katarzyna Kania, Julie Stockis, Silvain Pinaud, Kyren A Lazarus, Mona Shehata, Bruno M Simões, Alice R Greenhalgh, Sacha J Howell, Robert B Clarke, Carlos Caldas, Timotheus Y F Halim, John C Marioni, Walid T Khaled.
      It is unclear how genetic aberrations impact the state of nascent tumour cells and their microenvironment. BRCA1 driven triple negative breast cancer (TNBC) has been shown to arise from luminal progenitors yet little is known about how BRCA1 loss-of-function (LOF) and concomitant mutations affect the luminal progenitor cell state. Here we demonstrate how time-resolved single-cell profiling of genetically engineered mouse models before tumour formation can address this challenge. We found that perturbing Brca1/p53 in luminal progenitors induces aberrant alveolar differentiation pre-malignancy accompanied by pro-tumourigenic changes in the immune compartment. Unlike alveolar differentiation during gestation, this process is cell autonomous and characterised by the dysregulation of transcription factors driving alveologenesis. Based on our data we propose a model where Brca1/p53 LOF inadvertently promotes a differentiation program hardwired in luminal progenitors, highlighting the deterministic role of the cell-of-origin and offering a potential explanation for the tissue specificity of BRCA1 tumours.
    DOI:  https://doi.org/10.1038/s41467-021-21783-3
  46. Exp Cell Res. 2021 Mar 04. pii: S0014-4827(21)00058-6. [Epub ahead of print]401(2): 112527
    Organotypic platform for studying cancer cell metastasis.
    Giulia Spennati, Lisa F Horowitz, David J McGarry, Dominika A Rudzka, Garett Armstrong, Michael F Olson, Albert Folch, Huabing Yin.
      Metastasis is the leading cause of mortality in cancer patients. To migrate to distant sites, cancer cells would need to adapt their behaviour in response to different tissue environments. Thus, it is essential to study this process in models that can closely replicate the tumour microenvironment. Here, we evaluate the use of organotypic liver and brain slices to study cancer metastasis. Morphological and viability parameters of the slices were monitored daily over 3 days in culture to assess their stability as a realistic 3D tissue platform for in vitro metastatic assays. Using these slices, we evaluated the invasion of MDA-MB-231 breast cancer cells and of a subpopulation that was selected for increased motility. We show that the more aggressive invasion of the selected cells likely resulted not only from their lower stiffness, but also from their lower adhesion to the surrounding tissue. Different invasion patterns in the brain and liver slices were observed for both subpopulations. Cells migrated faster in the brain slices (with an amoeboid-like mode) compared to in the liver slices (where they migrated with mesenchymal or collective migration-like modes). Inhibition of the Ras/MAPK/ERK pathway increased cell stiffness and adhesion forces, which resulted in reduced invasiveness. These results illustrate the potential for organotypic tissue slices to more closely mimic in vivo conditions during cancer cell metastasis than most in vitro models.
    Keywords:  3D microenvironment; Adhesion; Cell mechanics; Metastasis; Migration; Stiffness
    DOI:  https://doi.org/10.1016/j.yexcr.2021.112527
  47. Oncogene. 2021 Mar 08.
    c-Src facilitates tumorigenesis by phosphorylating and activating G6PD.
    Huanhuan Ma, Fengqiong Zhang, Lin Zhou, Tingyan Cao, Dachao Sun, Shixiong Wen, Jinpei Zhu, Zhaoqianyu Xiong, Ming-Tong Tsau, Mei-Ling Cheng, Li-Man Hung, Yanming Zhou, Qinxi Li.
      Glucose-6-phosphate dehydrogenase (G6PD) is the first and rate-limiting enzyme in pentose phosphate pathway (PPP), excessive activation of which has been considered to be involved in tumorigenesis. Here, we show that tyrosine kinase c-Src interacts with and phosphorylates G6PD at Tyr 112. This phosphorylation enhances catalytic activity of G6PD by dramatically decreasing its Km value and increasing its Kcat value for substrate glucose-6-phosphate. Activated G6PD therefore augments the PPP flux for NADPH and ribose-5-phosphate production which is required for detoxification of intracellular reactive oxygen species (ROS) and biosynthesis of cancer cells, and eventually contributes to tumorigenesis. Consistently, c-Src activation is closely correlated with tyrosine phosphorylation and activity of G6PD in clinical colorectal cancer samples. We thus uncover another aspect of c-Src in promoting cell proliferation and tumorigenesis, deepening our understanding of c-Src as a proto-oncogene.
    DOI:  https://doi.org/10.1038/s41388-021-01673-0
  48. Sci Adv. 2021 Mar;pii: eabe4501. [Epub ahead of print]7(11):
    Injury-mediated stiffening persistently activates muscle stem cells through YAP and TAZ mechanotransduction.
    Jason S Silver, K Arda Günay, Alicia A Cutler, Thomas O Vogler, Tobin E Brown, Bradley T Pawlikowski, Olivia J Bednarski, Kendra L Bannister, Cameron J Rogowski, Austin G Mckay, Frank W DelRio, Bradley B Olwin, Kristi S Anseth.
      The skeletal muscle microenvironment transiently remodels and stiffens after exercise and injury, as muscle ages, and in myopathic muscle; however, how these changes in stiffness affect resident muscle stem cells (MuSCs) remains understudied. Following muscle injury, muscle stiffness remained elevated after morphological regeneration was complete, accompanied by activated and proliferative MuSCs. To isolate the role of stiffness on MuSC behavior and determine the underlying mechanotransduction pathways, we cultured MuSCs on strain-promoted azide-alkyne cycloaddition hydrogels capable of in situ stiffening by secondary photocrosslinking of excess cyclooctynes. Using pre- to post-injury stiffness hydrogels, we found that elevated stiffness enhances migration and MuSC proliferation by localizing yes-associated protein 1 (YAP) and WW domain-containing transcription regulator 1 (WWTR1; TAZ) to the nucleus. Ablating YAP and TAZ in vivo promotes MuSC quiescence in postinjury muscle and prevents myofiber hypertrophy, demonstrating that persistent exposure to elevated stiffness activates mechanotransduction signaling maintaining activated and proliferating MuSCs.
    DOI:  https://doi.org/10.1126/sciadv.abe4501
  49. Expert Opin Ther Targets. 2021 Mar 11.
    KRAS G12C inhibition and innate immune targeting.
    Tetsuo Tani, Shunsuke Kitajima, Ella Conway, Erik Knelson, David Barbie.
      INTRODUCTION: KRAS mutations drive tumorigenesis by altering cell signaling and the tumor immune microenvironment. Recent studies have shown promise for KRAS-G12C covalent inhibitors, which are advancing rapidly through clinical trials. The sequencing and combination of these agents with other therapies including immune checkpoint blockade (ICB) will benefit from strategies that also address the immune microenvironment to improve durability of response.AREAS COVERED: This paper reviews KRAS signaling and discusses downstream effects on cytokine production and the tumor immune microenvironment. RAS targeted therapy is introduced and perspectives on therapeutic targeting of KRAS-G12C and its immunosuppressive tumor microenvironment are offered.
    EXPERT OPINION: The availability of KRAS-G12C covalent inhibitors raises hopes for targeting this pervasive oncogene and designing better therapeutic combinations to promote anti-tumor immunity. A comprehensive mechanistic understanding of KRAS immunosuppression is required in order to prioritize agents for clinical trials.
    Keywords:  IL-1β; KRAS; KRAS-G12C inhibitor; STING; cancer; oncogene; targeted therapies; tumorigenesis
    DOI:  https://doi.org/10.1080/14728222.2021.1902991
  50. PLoS One. 2021 ;16(3): e0247888
    Transcriptional analysis of islets of Langerhans from organ donors of different ages.
    Peter Seiron, Anton Stenwall, Anders Hedin, Louise Granlund, Jonathan Lou S Esguerra, Petr Volkov, Erik Renström, Olle Korsgren, Marcus Lundberg, Oskar Skog.
      Insulin secretion is impaired with increasing age. In this study, we aimed to determine whether aging induces specific transcriptional changes in human islets. Laser capture microdissection was used to extract pancreatic islet tissue from 37 deceased organ donors aged 1-81 years. The transcriptomes of the extracted islets were analysed using Ion AmpliSeq sequencing. 346 genes that co-vary significantly with age were found. There was an increased transcription of genes linked to senescence, and several aspects of the cell cycle machinery were downregulated with increasing age. We detected numerous genes not linked to aging in previous studies likely because earlier studies analysed islet cells isolated by enzymatic digestion which might affect the islet transcriptome. Among the novel genes demonstrated to correlate with age, we found an upregulation of SPP1 encoding osteopontin. In beta cells, osteopontin has been seen to be protective against both cytotoxicity and hyperglycaemia. In summary, we present a transcriptional profile of aging in human islets and identify genes that could affect disease course in diabetes.
    DOI:  https://doi.org/10.1371/journal.pone.0247888
  51. Cell Rep. 2021 Mar 09. pii: S2211-1247(21)00130-3. [Epub ahead of print]34(10): 108816
    Adhesion strength and contractility enable metastatic cells to become adurotactic.
    Benjamin Yeoman, Gabriel Shatkin, Pranjali Beri, Afsheen Banisadr, Parag Katira, Adam J Engler.
      Significant changes in cell stiffness, contractility, and adhesion, i.e., mechanotype, are observed during a variety of biological processes. Whether cell mechanics merely change as a side effect of or driver for biological processes is still unclear. Here, we sort genotypically similar metastatic cancer cells into strongly adherent (SA) versus weakly adherent (WA) phenotypes to study how contractility and adhesion differences alter the ability of cells to sense and respond to gradients in material stiffness. We observe that SA cells migrate up a stiffness gradient, or durotax, while WA cells largely ignore the gradient, i.e., adurotax. Biophysical modeling and experimental validation suggest that differences in cell migration and durotaxis between weakly and strongly adherent cells are driven by differences in intra-cellular actomyosin activity. These results provide a direct relationship between cell phenotype and durotaxis and suggest how, unlike other senescent cells, metastatic cancer cells navigate against stiffness gradients.
    Keywords:  acto-mysoin contractility; carcinoma; catch bonds; durotaxis; focal adhesions; metastasis
    DOI:  https://doi.org/10.1016/j.celrep.2021.108816
  52. JAMA Oncol. 2021 Mar 11.
    Association of Ablative Radiation Therapy With Survival Among Patients With Inoperable Pancreatic Cancer.
    Marsha Reyngold, Eileen M O'Reilly, Anna M Varghese, Megan Fiasconaro, Melissa Zinovoy, Paul B Romesser, Abraham Wu, Carla Hajj, John J Cuaron, Richard Tuli, Lara Hilal, Danny Khalil, Wungki Park, Ellen D Yorke, Zhigang Zhang, Kenneth H Yu, Christopher H Crane.
      Importance: Surgical resection has been considered the only curative option for patients with pancreatic cancer. Nonoperative local treatment options that can provide a similar benefit are needed. Emerging radiation techniques that address organ motion have enabled curative radiation doses to be given in patients with inoperable disease.Objective: To determine the association of hypofractionated ablative radiation therapy (A-RT) with survival for patients with locally advanced pancreatic cancer (LAPC) treated with a novel radiation planning and delivery technique.
    Design, Setting, and Participants: This cohort study included 119 consecutive patients treated with A-RT between June 2016 and February 2019 and enrolled in a prospectively maintained database. Patients were treated with a standardized technique within a large academic cancer center regional network. All patients with localized, unresectable, or medically inoperable pancreatic cancer with tumors of any size and less than 5 cm luminal abutment with the primary tumor were eligible.
    Interventions: Ablative RT (98 Gy biologically effective dose) was delivered using standard equipment. Respiratory gating, soft tissue image guidance, and selective adaptive planning were used to address organ motion and limit the dose to surrounding luminal organs.
    Main Outcomes and Measures: The primary outcome was overall survival (OS). Secondary outcomes included incidence of local progression and progression-free survival.
    Results: Between 2016 and 2019, 119 patients (59 men, median age 67 years) received A-RT, including 99 with T3/T4 and 53 with node-positive disease, with a median carbohydrate antigen 19-9 (CA19-9) level greater than 167 U/mL. Most (116 [97.5%]) received induction chemotherapy for a median of 4 months (0.5-18.4). Median OS from diagnosis and A-RT were 26.8 and 18.4 months, respectively. Respective 12- and 24-month OS from A-RT were 74% (95% CI, 66%-83%) and 38% (95% CI, 27%-52%). Twelve- and 24-month cumulative incidence of locoregional failure were 17.6% (95% CI, 10.4%-24.9%) and 32.8% (95% CI, 21.6%-44.1%), respectively. Postinduction CA19-9 decline was associated with improved locoregional control and survival. Grade 3 upper gastrointestinal bleeding occurred in 10 patients (8%) with no grade 4 to 5 events.
    Conclusions and Relevance: This cohort study of patients with inoperable LAPC found that A-RT following multiagent induction therapy for LAPC was associated with durable locoregional tumor control and favorable survival. Prospective randomized trials in patients with LAPC are warranted.
    DOI:  https://doi.org/10.1001/jamaoncol.2021.0057
  53. J Cell Mol Med. 2021 Mar 08.
    Pancreatitis severity in mice with impaired CFTR function but pancreatic sufficiency is mediated via ductal and inflammatory cells-Not acinar cells.
    Simon Trapp, Ali A Aghdassi, Juliane Glaubitz, Matthias Sendler, Frank Ulrich Weiss, Jens Peter Kühn, Marie-Luise Kromrey, Ujjwal M Mahajan, Petra Pallagi, Zoltán Rakonczay, Viktória Venglovecz, Markus M Lerch, Peter Hegyi, Julia Mayerle.
      Mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) are an established risk factor for cystic fibrosis (CF) and chronic pancreatitis. Whereas patients with CF usually develop complete exocrine pancreatic insufficiency, pancreatitis patients with CFTR mutations have mostly preserved exocrine pancreatic function. We therefore used a strain of transgenic mice with significant residual CFTR function (CFTRtm1HGU ) to induce pancreatitis experimentally by serial caerulein injections. Protease activation and necrosis were investigated in isolated acini, disease severity over 24h, pancreatic function by MRI, isolated duct stimulation and faecal chymotrypsin, and leucocyte function by ex vivo lipopolysaccharide (LPS) stimulation. Pancreatic and lung injury were more severe in CFTRtm1HGU but intrapancreatic trypsin and serum enzyme activities higher than in wild-type controls only at 8h, a time interval previously attributed to leucocyte infiltration. CCK-induced trypsin activation and necrosis in acini from CFTRtm1HGU did not differ from controls. Fluid and bicarbonate secretion were greatly impaired, whereas faecal chymotrypsin remained unchanged. LPS stimulation of splenocytes from CFTRtm1HGU resulted in increased INF-γ and IL-6, but decreased IL-10 secretion. CFTR mutations that preserve residual pancreatic function significantly increase the severity of experimental pancreatitis-mostly via impairing duct cell function and a shift towards a pro-inflammatory phenotype, not by rendering acinar cells more susceptible to pathological stimuli.
    Keywords:  CFTR; acute pancreatitis; ductal cells; inflammatory cells
    DOI:  https://doi.org/10.1111/jcmm.16404
  54. J Exp Clin Cancer Res. 2021 Mar 11. 40(1): 94
    ROS-dependent HIF1α activation under forced lipid catabolism entails glycolysis and mitophagy as mediators of higher proliferation rate in cervical cancer cells.
    Serena Castelli, Fabio Ciccarone, Daniela Tavian, Maria Rosa Ciriolo.
      BACKGROUND: In the last decades, the concept of metabolic rewiring as a cancer hallmark has been expanded beyond the "Warburg effect" and the importance of other metabolic routes, including lipid metabolism, has emerged. In cancer, lipids are not only a source of energy but are also required for the formation of membranes building blocks, signaling and post-translational modification of proteins. Since lipid metabolism contributes to the malignancy of cancer cells, it is an attractive target for therapeutic strategies.METHODS: Over-expression of the adipose triglyceride lipase (ATGL) was used to boost lipid catabolism in cervical cancer cells. The cervical cancer cell line HeLa was employed as the primary experimental model for all subsequent studies. The lipolytic activity of ATGL was mimicked by caproate, a short-chain fatty acid that is efficiently oxidized in mitochondria.
    RESULTS: Here, we provide evidence of the association between boosted lipid catabolism and the increased proliferation and migration capability of cervical cancer cells. These pro-tumoral effects were ascribed to the reactive oxygen species (ROS)-mediated induction of hypoxia-inducible factor-1α (HIF1α) triggered by the increased mitochondrial fatty acids (FAs) oxidation. HIF1α activation increases glycolytic flux and lactate production, promoting cell proliferation. At the same time, HIF1α increases protein and mRNA levels of its known target BCL2 and adenovirus E1B 19-kDa-interacting protein 3 (BNIP3), which in turn activates mitophagy as a pro-survival process, as demonstrated by the induction of apoptosis upon inhibition of mitophagy. These effects were mimicked by the short-chain fatty acid caproate, confirming that forcing lipid catabolism results in HIF1α induction.
    CONCLUSIONS: Boosting lipid catabolism by ATGL over-expression has a pro-tumor role in cervical cancer cells, dependent on ROS production and HIF1α induction. Together with the bioinformatics evidence of the correlation of ATGL activity with the aggressiveness of cervical cancer cells, our data suggest that ATGL could be a promising prognostic marker for cervical cancer and highlight the need of further investigations on the role of this lipase in cancer cells. This evidence could be exploited to develop new personalized therapy, based on the functionality of the antioxidant equipment of cancer cells, considering that ROS content could affect ATGL role.
    Keywords:  ATGL; HIF1α; Lipid catabolism; Mitophagy; Pseudo-hypoxia; ROS
    DOI:  https://doi.org/10.1186/s13046-021-01887-w
  55. Genetics. 2021 Mar 03. 217(1): 1-19
    Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases.
    Christopher M Hickey, Carolyn Breckel, Mengwen Zhang, William C Theune, Mark Hochstrasser.
      Intracellular proteolysis by the ubiquitin-proteasome system regulates numerous processes and contributes to protein quality control (PQC) in all eukaryotes. Covalent attachment of ubiquitin to other proteins is specified by the many ubiquitin ligases (E3s) expressed in cells. Here we determine the E3s in Saccharomyces cerevisiae that function in degradation of proteins bearing various PQC degradation signals (degrons). The E3 Ubr1 can function redundantly with several E3s, including nuclear-localized San1, endoplasmic reticulum/nuclear membrane-embedded Doa10, and chromatin-associated Slx5/Slx8. Notably, multiple degrons are targeted by more ubiquitylation pathways if directed to the nucleus. Degrons initially assigned as exclusive substrates of Doa10 were targeted by Doa10, San1, and Ubr1 when directed to the nucleus. By contrast, very short hydrophobic degrons-typical targets of San1-are shown here to be targeted by Ubr1 and/or San1, but not Doa10. Thus, distinct types of PQC substrates are differentially recognized by the ubiquitin system in a compartment-specific manner. In human cells, a representative short hydrophobic degron appended to the C-terminus of GFP-reduced protein levels compared with GFP alone, consistent with a recent study that found numerous natural hydrophobic C-termini of human proteins can act as degrons. We also report results of bioinformatic analyses of potential human C-terminal degrons, which reveal that most peptide substrates of Cullin-RING ligases (CRLs) are of low hydrophobicity, consistent with previous data showing CRLs target degrons with specific sequences. These studies expand our understanding of PQC in yeast and human cells, including the distinct but overlapping PQC E3 substrate specificity of the cytoplasm and nucleus.
    Keywords:  degron; proteasome; protein degradation; protein quality control; ubiquitin
    DOI:  https://doi.org/10.1093/genetics/iyaa031
  56. Endocrinology. 2021 Mar 11. pii: bqab058. [Epub ahead of print]
    Senolytics: Potential for Alleviating Diabetes and Its Complications.
    Allyson K Palmer, Tamar Tchkonia, James L Kirkland.
      Therapeutics that target cellular senescence, including novel "senolytic" compounds, hold significant promise for treating or preventing obesity-induced metabolic dysfunction, type 2 diabetes, and the multiple complications of diabetes and obesity. Senolytics selectively clear senescent cells, which accumulate with aging and obesity and represent a fundamental mechanism of aging that contributes to metabolic dysfunction and diabetes pathogenesis. In addition to improving metabolic function, targeting senescent cells holds promise as a preventative strategy to reduce incidence and severity of diabetes complications. The intermittent administration schedule utilized for senolytic therapy may confer benefits in terms of improving adherence and limiting adverse effects. It is necessary to design effective clinical trials that will safely translate discoveries from preclinical models into human studies that may pave the way for a novel therapeutic class for treating obesity, diabetes, and their complications. In this review, we outline what is known regarding the role of cellular senescence in the pathogenesis of type 2 diabetes and its complications, present evidence from preclinical models that targeting cellular senescence is beneficial, review senolytic drugs, and outline the features of clinical trials investigating the role of targeting senescent cells for diabetes.
    Keywords:  aging; cellular senescence; diabetes complications; diabetes mellitus
    DOI:  https://doi.org/10.1210/endocr/bqab058
  57. Cell. 2021 Mar 01. pii: S0092-8674(21)00157-4. [Epub ahead of print]
    Adapting the proteostasis capacity to sustain brain healthspan.
    Claudio Hetz.
      Sustaining neuronal proteostasis during the course of our life is a central aspect required for brain function. The dynamic nature of synaptic composition and abundance is a requisite to drive cognitive and motor processes involving a tight control of many aspects of protein biosynthesis and degradation. Through the concerted action of specialized stress sensors, the proteostasis network monitors and limits the accumulation of damaged, misfolded, or aggregated proteins. These stress pathways signal to the cytosol and nucleus to reprogram gene expression, enabling adaptive programs to recover cell function. During aging, the activity of the proteostasis network declines, which may increase the risk of accumulating abnormal protein aggregates, a hallmark of most neurodegenerative diseases. Here, I discuss emerging concepts illustrating the functional significance of adaptive signaling pathways to normal brain physiology and their contribution to age-related disorders. Pharmacological and gene therapy strategies to intervene and boost proteostasis are expected to extend brain healthspan and ameliorate disease states.
    Keywords:  ▪▪▪
    DOI:  https://doi.org/10.1016/j.cell.2021.02.007
  58. Mol Cell. 2021 Mar 05. pii: S1097-2765(21)00100-3. [Epub ahead of print]
    Cooperative binding between distant transcription factors is a hallmark of active enhancers.
    Satyanarayan Rao, Kami Ahmad, Srinivas Ramachandran.
      Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent of TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. Enrichment of short micrococcal nuclease (MNase)-protected DNA segments indicates that the majority of enhancers harbor two or more TF-binding sites, and we uncover protected fragments that correspond to co-bound sites in thousands of enhancers. From the analysis of co-binding, we find that cooperativity dominates TF binding in vivo at the majority of active enhancers. Cooperativity is highest between sites spaced 50 bp apart, indicating that cooperativity occurs without apparent protein-protein interactions. Our findings suggest nucleosomes promoting cooperativity because co-binding may effectively clear nucleosomes and promote enhancer function.
    Keywords:  chromatin dynamics; enhancer; enhancer cooperativity; nucleosome; transcription factor
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.014
  59. Sci Signal. 2021 Mar 09. pii: eaax7942. [Epub ahead of print]14(673):
    The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps.
    Falko Apel, Liudmila Andreeva, Lorenz Sebastian Knackstedt, Robert Streeck, Christian Karl Frese, Christian Goosmann, Karl-Peter Hopfner, Arturo Zychlinsky.
      Neutrophil extracellular traps (NETs) are structures consisting of chromatin and antimicrobial molecules that are released by neutrophils during a form of regulated cell death called NETosis. NETs trap invading pathogens, promote coagulation, and activate myeloid cells to produce type I interferons (IFNs), proinflammatory cytokines that regulate the immune system. Here, we showed that macrophages and other myeloid cells phagocytosed NETs. Once in phagosomes, NETs translocated to the cytosol, where the DNA backbones of these structures activated the innate immune sensor cyclic GMP-AMP synthase (cGAS) and induced type I IFN production. The NET-associated serine protease neutrophil elastase (NE) mediated the activation of this pathway. We showed that NET induction in mice treated with the lectin concanavalin A, a model of autoimmune hepatitis, resulted in cGAS-dependent stimulation of an IFN response, suggesting that NETs activated cGAS in vivo. Thus, our findings suggest that cGAS is a sensor of NETs, mediating immune cell activation during infection.
    DOI:  https://doi.org/10.1126/scisignal.aax7942
  60. Elife. 2021 Mar 09. pii: e62585. [Epub ahead of print]10
    Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney.
    Yuka Takemon, Joel M Chick, Isabela Gerdes Gyuricza, Daniel A Skelly, Olivier Devuyst, Steven P Gygi, Gary A Churchill, Ron Korstanje.
      Little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand these changes, we measured mRNA and protein levels in genetically diverse mice at different ages. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.
    Keywords:  computational biology; mouse; systems biology
    DOI:  https://doi.org/10.7554/eLife.62585
  61. Br J Nutr. 2021 Mar 08. 1-29
    Prevalence of low protein intake in 80+ year-old community-dwelling adults and association with dietary patterns and modifiable risk factors- a cross-sectional study.
    Sussi F Buhl, Anne M Beck, Britt Christensen, Gry Kock, Eleanor Boyle, Paolo Caserotti.
      Low protein intake may accelerate age-related loss of lean mass and physical function. We investigated prevalence of low protein intake (<1.0 g/kg/day) and the associations between dietary patterns, key modifiable risk factors and low protein intake in self-reliant community-dwelling adults ≥ 80 years. This cross-sectional study consisted of two home-visits. Data collection consisted of physical measurements (physical function, weight, height, physical activity) and self-report of nutritional intake (4-day food records), appetite, eating symptoms, dysphagia, dental status, medical conditions, pain and living status. Binary analyses were performed to compare participants with low and normal protein intake. Multiple logistic regression analyses were performed to investigate associations between low protein intake, dietary patterns and modifiable risk factors adjusted for age, sex, BMI-categories and diseases. N=126 were included in the study from January 2017 to August 2018. Prevalence of low protein intake was 54%. A greater day-to-day variation in protein intake was associated with low protein intake (adjusted OR 2.5 CI: 1.14-5.48). Participants with low protein intake had a higher prevalence of nausea, diarrhoea and mouth dryness. Reduced appetite, mouth dryness and pain increased odds of low protein intake (adjusted OR 3.06 CI: 1.23-7.63, OR 3.41 CI:1.51-7.7, OR 1.54 CI:1.00-2.36, respectively). There was a high prevalence of low protein intake in community-dwelling adults ≥ 80-years. Day-to-day variability, reduced appetite, mouth dryness and pain may be potentially modifiable risk factors. Targeting dietary patterns and risk factors in primary prevention strategies may be important to improve intake of protein and minimise risk of physical frailty.
    Keywords:  Eating symptoms; Loss of physical function; Older adults; Physical Frailty; Primary Prevention; Protein malnutrition
    DOI:  https://doi.org/10.1017/S0007114521000799
  62. Aging Cell. 2021 Mar 12. e13338
    Cellular aging beyond cellular senescence: Markers of senescence prior to cell cycle arrest in vitro and in vivo.
    Mikolaj Ogrodnik.
      The field of research on cellular senescence experienced a rapid expansion from being primarily focused on in vitro aspects of aging to the vast territories of animal and clinical research. Cellular senescence is defined by a set of markers, many of which are present and accumulate in a gradual manner prior to senescence induction or are found outside of the context of cellular senescence. These markers are now used to measure the impact of cellular senescence on aging and disease as well as outcomes of anti-senescence interventions, many of which are at the stage of clinical trials. It is thus of primary importance to discuss their specificity as well as their role in the establishment of senescence. Here, the presence and role of senescence markers are described in cells prior to cell cycle arrest, especially in the context of replicative aging and in vivo conditions. Specifically, this review article seeks to describe the process of "cellular aging": the progression of internal changes occurring in primary cells leading to the induction of cellular senescence and culminating in cell death. Phenotypic changes associated with aging prior to senescence induction will be characterized, as well as their effect on the induction of cell senescence and the final fate of cells reviewed. Using published datasets on assessments of senescence markers in vivo, it will be described how disparities between quantifications can be explained by the concept of cellular aging. Finally, throughout the article the applicational value of broadening cellular senescence paradigm will be discussed.
    Keywords:  aging; cellular senescence; evolutionary biology; molecular biology of aging; molecular damage; theories of aging; wound healing
    DOI:  https://doi.org/10.1111/acel.13338
  63. Cancer Res. 2021 Mar 09. pii: canres.1954.2020. [Epub ahead of print]
    Fat induces glucose metabolism in non-transformed liver cells and promotes liver tumorigenesis.
    Lindsay A Broadfield, João André Gonçalves Duarte, Roberta Schmieder, Dorien Broekaert, Koen Veys, Mélanie Planque, Kim Vriens, Yasuaki Karasawa, Francesco Napolitano, Suguru Fujita, Masashi Fujii, Miki Eto, Bryan Holvoet, Roman Vangoitsenhoven, Juan Fernandez-Garcia, Joke Van Elsen, Jonas Dehairs, Jia Zeng, James Dooley, Rebeca Alba Rubio, Jos van Pelt, Thomas G P Grünewald, Adrian Liston, Chantal Mathieu, Christophe M Deroose, Johannes V Swinnen, Diether Lambrechts, Diego di Bernardo, Shinya Kuroda, Katrien De Bock, Sarah-Maria Fendt.
      Hepatic fat accumulation is associated with diabetes and hepatocellular carcinoma (HCC). Here we characterize the metabolic response that high fat availability elicits in livers prior to disease development. After a short term on a high fat diet, otherwise healthy mice showed elevated hepatic glucose uptake and increased glucose contribution to serine and pyruvate carboxylase activity compared to control diet mice. This glucose phenotype occurred independently from transcriptional or proteomic programming, which identifies increased peroxisomal and lipid metabolism pathways. High fat diet-fed mice exhibited increased lactate production when challenged with glucose. Consistently, administration of an oral glucose bolus to healthy individuals revealed a correlation between waist circumference and lactate secretion in a human cohort. In vitro, palmitate exposure stimulated production of reactive oxygen species and subsequent glucose uptake and lactate secretion in hepatocytes and liver cancer cells. Furthermore, high fat diet enhanced the formation of HCC compared to control diet in mice exposed to a hepatic carcinogen. Regardless of the dietary background, all murine tumors showed similar alterations in glucose metabolism to those identified in fat exposed non-transformed mouse livers; however, particular lipid species were elevated in high fat diet tumor and non-tumor-bearing high fat diet liver tissue. These findings suggest that fat can induce glucose-mediated metabolic changes in non-transformed liver cells similar to those found in HCC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1954
  64. JCI Insight. 2021 Mar 11. pii: 143626. [Epub ahead of print]
    Molecular mapping of interstitial lung disease reveals a phenotypically distinct senescent basal epithelial cell population.
    Daryle J DePianto, Jason A Vander Heiden, Katrina B Morshead, Kai-Hui Sun, Zora Modrusan, Grace Teng, Paul J Wolters, Joseph R Arron.
      Compromised regenerative capacity of lung epithelial cells can lead to cellular senescence, which may precipitate fibrosis. While increased markers of senescence have been reported in idiopathic pulmonary fibrosis (IPF), the origin and identity of these senescent cells remain unclear, and tools to characterize context-specific cellular senescence in human lung are lacking. We observed that the senescent marker p16 is predominantly localized to bronchiolized epithelial structures in scarred regions of IPF and systemic sclerosis associated interstitial lung disease ILD (SSc-ILD) lung tissue, overlapping with the basal epithelial markers Keratin 5 and Keratin 17. Using in vitro models, we derived transcriptional signatures of senescence programming specific to different types of lung epithelial cells, and interrogated these signatures in a single-cell RNA-seq data set derived from control, IPF, and SSc-ILD lung tissue. We identified a population of basal epithelial cells defined by, and enriched for, markers of cellular senescence, and identified candidate markers specific to senescent basal epithelial cells in ILD that can enable future functional studies. Notably, gene expression of these cells significantly overlaps with terminally differentiating cells in stratified epithelia, where it is driven by p53 activation as part of the senescence program.
    Keywords:  Aging; Cellular senescence; Fibrosis; Pulmonology
    DOI:  https://doi.org/10.1172/jci.insight.143626
  65. Clin Epigenetics. 2021 Mar 06. 13(1): 49
    Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines.
    Suleyman Vural, Alida Palmisano, William C Reinhold, Yves Pommier, Beverly A Teicher, Julia Krushkal.
      BACKGROUND: Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents.RESULTS: We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation.
    CONCLUSIONS: Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.
    Keywords:  Cancer drug treatment; DNA methylation; Epigenetic analysis; Gene expression
    DOI:  https://doi.org/10.1186/s13148-021-01026-4
  66. Cancer Cell. 2021 Mar 08. pii: S1535-6108(21)00111-2. [Epub ahead of print]39(3): 441-442
    A gene expression signature associated with ''K-Ras addiction'' reveals regulators of EMT and tumor cell survival.
    Anurag Singh, Patricia Greninger, Daniel Rhodes, Louise Koopman, Sheila Violette, Nabeel Bardeesy, Jeff Settleman.
      
    DOI:  https://doi.org/10.1016/j.ccell.2021.02.009
  67. Pancreatology. 2021 Mar 03. pii: S1424-3903(21)00068-5. [Epub ahead of print]
    Silencing of LRRFIP1 enhances the sensitivity of gemcitabine in pancreatic cancer cells by activating JNK/c-Jun signaling.
    Shuhei Kawasaki, Hideo Ohtsuka, Yoshihiro Sato, Daisuke Douchi, Masaki Sato, Kyohei Ariake, Kunihiro Masuda, Koji Fukase, Masamichi Mizuma, Kei Nakagawa, Hiroki Hayashi, Takanori Morikawa, Fuyuhiko Motoi, Michiaki Unno.
      BACKGROUND: The epithelial-mesenchymal transition (EMT) in cancer cells has been shown to closely associate with the survival and drug resistance of cancer cells. We recently provided evidence that Wnt signal activator leucine-rich repeat in flightless-1-interacting protein 1 (LRRFIP1) regulates EMT in pancreatic cancer. LRRFIP1 silencing inhibits the translocation of β-catenin to the nucleus, which led to reverse EMT in cancer cells. It was suggested that LRRFIP1 was implicated in gemcitabine sensitivity by regulating EMT signaling.METHODS: Gemcitabine chemosensitivity was investigated in LRRFIP1-knockdown pancreatic cancer cells (PANC-1 and MIA Paca-2). In addition, the effects of LRRFIP1 knockdown on JNK/SAPK (stress activated-protein kinase) signaling and apoptosis were evaluated.
    RESULTS: LRRFIP1 silencing accelerates gemcitabine-induced caspase activity and cell death in pancreatic cancer cells. It was also revealed that gemcitabine-induced phosphorylation of c-Jun N-terminal kinase (JNK) and c-Jun were increased in LRRFIP1 knockdown cells. The activation of JNK/c-Jun in LRRFIP1-knockdown cells was significantly diminished by the inhibition of Rac activity. It was confirmed that the acquisition of gemcitabine sensitivity by LRRFIP1 silencing largely depends on the stimulation of JNK/SAPK (stress activated-protein kinase) signaling.
    CONCLUSIONS: Our findings suggest that reversing EMT and transient activation of JNK might be essential for the gemcitabine sensitivity in LRRFIP1 knockdown pancreatic cancer cells. Our discoveries highlight the potential role of LRRFIP1 in the chemosensitivity related to the regulation of EMT signaling.
    Keywords:  Gemcitabine; JNK; JNK/SAPK signal; LRRFIP1; Wnt signal; c-Jun
    DOI:  https://doi.org/10.1016/j.pan.2021.02.018
  68. Cancer Sci. 2021 Mar 10.
    Matters of data openness and KapWeb, a web tool of multi-cancer survival analysis for cancer survivors.
    Jason Lin, Yohko Nakamura, Haruo Mikami, Miho Kusakabe, Nobuhiro Saruki, Fumihiko Wakao, Hiroki Nagase.
      KapWeb is an interactive tool for the determination of cancer survival rates based on case outcomes compiled from more than half a million records from cancer registries all over Japan, and we believe that both the tool and the call for data openness and transparency are important.
    DOI:  https://doi.org/10.1111/cas.14788
  69. Nat Commun. 2021 03 11. 12(1): 1579
    Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering.
    Aaron Cravens, Osman K Jamil, Deze Kong, Jonathan T Sockolosky, Christina D Smolke.
      Random mutagenesis is a technique used to generate diversity and engineer biological systems. In vivo random mutagenesis generates diversity directly in a host organism, enabling applications such as lineage tracing, continuous evolution, and protein engineering. Here we describe TRIDENT (TaRgeted In vivo Diversification ENabled by T7 RNAP), a platform for targeted, continual, and inducible diversification at genes of interest at mutation rates one-million fold higher than natural genomic error rates. TRIDENT targets mutagenic enzymes to precise genetic loci by fusion to T7 RNA polymerase, resulting in mutation windows following a mutation targeting T7 promoter. Mutational diversity is tuned by DNA repair factors localized to sites of deaminase-driven mutation, enabling sustained mutation of all four DNA nucleotides at rates greater than 10-4 mutations per bp. We show TRIDENT can be applied to routine in vivo mutagenesis applications by evolving a red-shifted fluorescent protein and drug-resistant mutants of an essential enzyme.
    DOI:  https://doi.org/10.1038/s41467-021-21876-z
  70. Methods Enzymol. 2021 ;pii: S0076-6879(21)00045-8. [Epub ahead of print]649 371-396
    Cysteine-based crosslinking approach for characterization of oligomeric pore-forming proteins in the mitochondrial membranes.
    Zhi Zhang, Bo Huang, Xuejun C Zhang, Jialing Lin.
      Mitochondria are important not only to healthy but also dying cells. In particular, apoptotic cell death initiates when the mitochondrial outer membrane is permeabilized by Bax, a protein of the Bcl-2 family. Bax shares a structural fold with some α-helical bacterial pore-forming toxins before these proteins actively engage membranes. Despite decades of intensive research, the structures of the pores formed by these proteins are mostly unknown, mainly because the pores are assembled by different numbers of the proteins whose conformation and interaction are highly dynamic. Site-specific crosslinking of the pore-forming proteins in cellular membranes where the pores are assembled is a powerful approach to assess the biological pore structure, dynamics and function. In this chapter, we describe a cysteine-based site-specific crosslinking protocol for the Bax protein in the mitochondrial membrane. We discuss the expected results and the resulting structural-functional models for the pore-forming Bax oligomer, in comparison with other crosslinking approaches that have been used to study other mitochondrial protein complexes. At the end, we highlight the advantages of the crosslinking approaches as well as the limitations and alternative approaches.
    Keywords:  Bax; Cysteine-based protein crosslinking; Membrane; Mitochondria; Pore-forming protein
    DOI:  https://doi.org/10.1016/bs.mie.2021.01.023
  71. J Nucl Med. 2021 Mar 12. pii: jnumed.120.256776. [Epub ahead of print]
    Exploiting the MUC5AC Antigen for Noninvasive Identification of Pancreatic Cancer.
    Kelly E Henry, Travis Shaffer, Kyeara N Mack, Janine Ring, Anuja Ogirala, Susanne Klein-Scory, Christina Eilert-Micus, Wolff Schmiegel, Thilo Bracht, Barbara Sitek, Marguerite Clyne, Colm Reid, Bence Sipos, Jason S Lewis, Holger Kalthoff, Jan Grimm.
      Pancreatic cancer (PC) remains the 4th leading cause of cancer death; therefore, there is a clinically unmet need for novel therapeutics and diagnostic markers to treat this devastating disease. Physicians often rely on biopsy or CT for diagnosis, but more specific protein biomarkers are highly desired to assess the stage and severity of PC in a noninvasive manner. Serum biomarkers such as CA19.9 are of particular interest as they are commonly elevated in PC but have exhibited suboptimal performance in the clinic. MUC5AC has emerged as a useful serum biomarker that is specific for PC vs. inflammation. We developed RA96, an anti-MUC5AC antibody, to gauge its utility in PC diagnosis through immunohistochemical (IHC) analysis and whole-body PET in PC. Methods: In this study, extensive biochemical characterization determined MUC5AC as the antigen for RA96. We then determined the utility of RA96 for MUC5AC IHC on clinical PC and pre-clinical PC. Finally, we radiolabeled RA96 with zirconium-89 to assess its application as a whole-body PET radiotracer for MUC5AC quantification in PC. Results: Immunohistochemical staining with RA96 distinguished chronic pancreatitis (CP), PanIN, and varying grades of pancreatic ductal adenocarcinoma (PDAC) in clinical samples. [89Zr]Zr-DFO-RA96 was able to detect MUC5AC with high specificity in mice bearing capan-2 xenografts. Conclusion: Our study demonstrates that RA96 can differentiate between inflammation and PC, improving the fidelity of PC diagnosis. Our immuno-PET tracer [89Zr]Zr-DFO-RA96 shows specific detection of MUC5AC+ tumors in vivo, highlighting the utility of MUC5AC targeting for diagnosis of PC.
    Keywords:  Immuno-PET; MUC5AC; Molecular Imaging; Oncology: Pancreas; PET/CT; Pancreatic cancer; RA96; Zirconium-89
    DOI:  https://doi.org/10.2967/jnumed.120.256776
  72. Semin Oncol. 2021 Feb 10. pii: S0093-7754(21)00001-4. [Epub ahead of print]
    Two decades of research toward the treatment of locally advanced and metastatic pancreatic cancer: Remarkable effort and limited gain.
    Celine Yeh, Susan E Bates.
      Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy that is diagnosed at the locally advanced or metastatic stage in approximately 80% of cases. Relative to other tumor types, progress in the treatment of this disease has been painfully slow. While agents targeting DNA repair have proven successful in a subset of patients, the majority of PDACs do not exhibit validated molecular targets. Hence, conventional chemotherapy remains at the forefront of therapy for this disease. In this review, we study two decades of efforts to improve upon the gemcitabine backbone - 67 phase II and III trials enrolling 16,446 patients - that culminated in the approvals of gemcitabine/nab-paclitaxel (Gem/NabP) and FOLFIRINOX. Today, these remain gold standards for the first-line treatment of locally advanced unresectable and metastatic PDAC, while ongoing efforts focus on improving upon the Gem/NabP backbone. Because real world data often do not reflect the data of randomized controlled trials (RCTs), we also summarize the retrospective evidence comparing the efficacy of Gem/NabP and FOLFIRINOX in the first-line setting - 29 studies reporting a median overall survival of 10.7 and 9.1 months for FOLFIRINOX and Gem/NabP, respectively. These values are surprisingly comparable to those reported by the pivotal RCTs at 11.1 and 8.5 months. Finally, there is a paucity of RCT data regarding the efficacy of second-line therapy. Hence, we conclude this review by summarizing the data that ultimately demonstrate a small but significant survival benefit of second-line therapy with Gem/NabP or FOLFIRINOX. Collectively, these studies describe the long journey, the steady effort, and the myriad lessons to be learned from 20 years of PDAC trials to inform strategies for success in clinical trials moving forward.
    Keywords:  FOLFIRINOX; Gemcitabine; Metastatic pancreatic cancer; Nab-paclitaxel; Real-world data; Second-line therapy
    DOI:  https://doi.org/10.1053/j.seminoncol.2021.01.001
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