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Table of Contents

June 2021 | Volume 4, No. 6

Research Articles

  • CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
    Open Access
    CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data

    Almut Lütge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D Robinson

    Almut Lütge ... Mark D Robinson

    Published 23 March 2021

    A systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.

  • Cancer-associated cells release citrate to support tumour metastatic progression
    Open Access
    Cancer-associated cells release citrate to support tumour metastatic progression

    Konstantin Drexler, Katharina M Schmidt, Katrin Jordan, Marianne Federlin, Vladimir M Milenkovic, Gerhard Liebisch, Anna Artati, Christian Schmidl, Gregor Madej, Janina Tokarz, Alexander Cecil, Wolfgang Jagla, Silke Haerteis, Thiha Aung, Christine Wagner, Maria Kolodziejczyk, Stefanie Heinke, Evan H Stanton, Barbara Schwertner, Dania Riegel, Christian H Wetzel, Wolfgang Buchalla, Martin Proescholdt, Christoph A Klein, Mark Berneburg, Hans J Schlitt, Thomas Brabletz, Christine Ziegler, Eric K Parkinson, Andreas Gaumann, Edward K Geissler, Jerzy Adamski, Sebastian Haferkamp, Maria E Mycielska

    Konstantin Drexler ... Maria E Mycielska

    Published 23 March 2021

    Cancer-associated stroma is recruited by cancer cells to synthesise and release citrate necessary to support metastatic progression of the disease.

  • DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteria
    Open Access
    DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteria

    Barbara Killy, Barbara Bodendorfer, Jörg Mages, Kristina Ritter, Jonathan Schreiber, Christoph Hölscher, Katharina Pracht, Arif Ekici, Hans-Martin Jäck, Roland Lang

    Barbara Killy ... Roland Lang

    Published 26 March 2021

    Lack of miRNA biosynthesis in DGCR8-deficient macrophages did not block macrophage differentiation but caused overshooting type I IFN responses to mycobacterial glycolipids.

  • RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes
    Open Access
    RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes

    Julieta Rivosecchi, Daniel Jost, Laetitia Vachez, François DR Gautier, Pascal Bernard, Vincent Vanoosthuyse

    Julieta Rivosecchi ... Vincent Vanoosthuyse

    Published 26 March 2021

    Using both experiments and mathematical modelling, the authors show that RNA polymerase backtracking contributes to the accumulation of condensin in the termination zone of active genes.

  • Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages
    Open Access
    Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages

    Samantha B Kemp, Nina G Steele, Eileen S Carpenter, Katelyn L Donahue, Grace G Bushnell, Aaron H Morris, Stephanie The, Sophia M Orbach, Veerin R Sirihorachai, Zeribe C Nwosu, Carlos Espinoza, Fatima Lima, Kristee Brown, Alexander A Girgis, Valerie Gunchick, Yaqing Zhang, Costas A Lyssiotis, Timothy L Frankel, Filip Bednar, Arvind Rao, Vaibhav Sahai, Lonnie D Shea, Howard C Crawford, Marina Pasca di Magliano

    Samantha B Kemp ... Marina Pasca di Magliano

    Published 29 March 2021

    This study uses biomaterial scaffolds to identify a macrophage gene signature defined by high expression of C1qa, C1qb, and Trem2 that is elevated systemically in mouse and human pancreatic cancer.

  • The AXL-PYK2-PKCα axis as a nexus of stemness circuits in TNBC
    Open Access
    The AXL-PYK2-PKCα axis as a nexus of stemness circuits in TNBC

    Lohit Khera, Yaron Vinik, Flavio Maina, Sima Lev

    Lohit Khera ... Sima Lev

    Published 30 March 2021

    A clinically relevant AXL-PYK2-PKCα axis where PYK2 and PKCα act as signaling nodes and functionally cooperate to converge stemness promoting pathways and regulate Oct4 and Nanog pluripotent TFs.

  • Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cells
    Open Access
    Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cells

    Jone Michelena, Stefania Pellegrino, Vincent Spegg, Matthias Altmeyer

    Jone Michelena ... Matthias Altmeyer

    Published 2 April 2021

    This study demonstrates how single cell normalization to genome size provides insight into genome function, here in the context of DNA double-strand break repair by 53BP1 versus BRCA1–BARD1.

  • Mitochondrial Aurora kinase A induces mitophagy by interacting with MAP1LC3 and Prohibitin 2
    Open Access
    Mitochondrial Aurora kinase A induces mitophagy by interacting with MAP1LC3 and Prohibitin 2

    Giulia Bertolin, Marie-Clotilde Alves-Guerra, Angélique Cheron, Agnès Burel, Claude Prigent, Roland Le Borgne, Marc Tramier

    Giulia Bertolin ... Marc Tramier

    Published 5 April 2021

    The multifunctional Ser/Thr kinase AURKA uses the Inner Mitochondrial Membrane receptor PHB2 and MAP1LC3 as a signalling platform to orchestrate the elimination of dysfunctional mitochondria.

  • Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza
    Open Access
    Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza

    Ayako Ohno, Nobuo Maita, Takanori Tabata, Hikaru Nagano, Kyohei Arita, Mariko Ariyoshi, Takayuki Uchida, Reiko Nakao, Anayt Ulla, Kosuke Sugiura, Koji Kishimoto, Shigetada Teshima-Kondo, Yuushi Okumura, Takeshi Nikawa

    Ayako Ohno ... Takeshi Nikawa

    Published 5 April 2021

    The structure of extracellular domain of MSPL and inhibitor complex helps to understand the TTSP functions, including TMPRSS2, and provides the insights of the infection of influenza and SARS-CoV.

  • In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
    Open Access
    In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood

    Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fatima Smagulova

    Louis Legoff ... Fatima Smagulova

    Published 9 April 2021

    In utero exposure to chlordecone affects chromatin and leads to activation of retroelements. This study shows the changes induced by chlordecone in human umbilical cord blood and blood-derived cell line.

  • NF-κB inhibition in keratinocytes causes RIPK1-mediated necroptosis and skin inflammation
    Open Access
    NF-κB inhibition in keratinocytes causes RIPK1-mediated necroptosis and skin inflammation

    Snehlata Kumari, Trieu-My Van, Daniela Preukschat, Hannah Schuenke, Marijana Basic, André Bleich, Ulf Klein, Manolis Pasparakis

    Snehlata Kumari ... Manolis Pasparakis

    Published 15 April 2021

    TNFR1 was found to cause skin inflammation in mice with epidermal keratinocyte-specific ablation of IKK2 or of both the NF-kB subunits RelA and cRel by triggering RIPK1-dependent, RIPK3-MLKL–mediated necroptosis of keratinocytes.

  • Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokines
    Open Access
    Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokines

    Jennifer S Stancill, Moujtaba Y Kasmani, Achia Khatun, Weiguo Cui, John A Corbett

    Jennifer S Stancill ... John A Corbett

    Published 21 April 2021

    Single-cell RNA-seq was used to show that islet endocrine cells respond to acute cytokine exposure with an increase in the expression of protective genes and the absence of apoptotic gene expression.

  • Fast but not furious: a streamlined selection method for genome-edited cells
    Open Access
    Fast but not furious: a streamlined selection method for genome-edited cells

    Haribaskar Ramachandran, Soraia Martins, Zacharias Kontarakis, Jean Krutmann, Andrea Rossi

    Haribaskar Ramachandran ... Andrea Rossi

    Published 26 April 2021

    Magnetic-activated genome-edited cell sorting (MAGECS) allows a fast and easy generation of genetically modified cells.

  • On the relation of gene essentiality to intron structure: a computational and deep learning approach
    Open Access
    On the relation of gene essentiality to intron structure: a computational and deep learning approach

    Ethan Schonfeld, Edward Vendrow, Joshua Vendrow, Elan Schonfeld

    Ethan Schonfeld ... Elan Schonfeld

    Published 27 April 2021

    A deep learning classifier predicts gene essentiality by intron sequence. A unique set of intron features of essential genes was found and its importance demonstrated by a high-performing classifier.

  • Cell-free expression of the outer membrane protein OprF of <em>Pseudomonas aeruginosa</em> for vaccine purposes
    Open Access
    Cell-free expression of the outer membrane protein OprF of Pseudomonas aeruginosa for vaccine purposes

    Géraldine Mayeux, Landry Gayet, Lavinia Liguori, Marine Odier, Donald K Martin, Sandra Cortès, Béatrice Schaack, Jean-Luc Lenormand

    Géraldine Mayeux ... Jean-Luc Lenormand

    Published 10 May 2021

    Production of recombinant proteoliposomes containing OprF from P. aeruginosa promotes the active open conformation of the porin exposing native epitopes. These OprF proteoliposomes were used as vaccines to protect mice against a P. aeruginosa acute pulmonary infection model.

Resource

  • Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation
    Open Access
    Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation

    Rachel E Heap, José Luis Marín-Rubio, Julien Peltier, Tiaan Heunis, Abeer Dannoura, Adam Moore, Matthias Trost

    Rachel E Heap ... Matthias Trost

    Published 14 April 2021

    L929 cell supernatant is commonly used to differentiate murine macrophages from bone marrow. The supernatant and its effect on macrophage phenotype was characterised by proteomics and the authors identified novel immunoregulatory proteins.

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Volume 4, No. 6
June 2021
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