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Table of Contents

September 2023 | Volume 6, No. 9

Research Articles

  • Toxicity of <em>C9orf72</em>-associated dipeptide repeat peptides is modified by commonly used protein tags
    Open Access
    Toxicity of C9orf72-associated dipeptide repeat peptides is modified by commonly used protein tags

    Javier Morón-Oset, Lilly KS Fischer, Mireia Carcolé, Ashling Giblin, Pingze Zhang, Adrian M Isaacs, Sebastian Grönke, Linda Partridge

    Javier Morón-Oset ... Linda Partridge

    Published 12 June 2023

    Protein tags affect the toxicity of C9orf72-associated dipeptide repeat proteins and therefore should be avoided in preclinical models of C9orf72 ALS and FTD.

  • MiR-93-5p inhibits retinal neurons apoptosis by regulating PDCD4 in acute ocular hypertension model
    Open Access
    MiR-93-5p inhibits retinal neurons apoptosis by regulating PDCD4 in acute ocular hypertension model

    Cheng Tan, Wenjia Shi, Yun Zhang, Can Liu, Tu Hu, Dan Chen, Jufang Huang

    Cheng Tan ... Jufang Huang

    Published 12 June 2023

    It is found that miR-93-5p decreases retinal neuron apoptosis through suppressing PDCD4 in acute ocular hypertension model, which indicates miR-93-5p as a therapeutic target of glaucoma.

  • PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase
    Open Access
    PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase

    Avishek Ghosh, Aishwarya Venugopal, Dhananjay Shinde, Sanjeev Sharma, Meera Krishnan, Swarna Mathre, Harini Krishnan, Sankhanil Saha, Padinjat Raghu

    Avishek Ghosh ... Padinjat Raghu

    Published 14 June 2023

    PIP4K is a lipid kinase implicated in tumour growth, immune function, and metabolic regulation. This study shows that PIP4K regulates PI3P levels and autophagy, thereby controlling cell size in Drosophila salivary glands.

  • Hypoxia controls expression of kidney-pathogenic <em>MUC1</em> variants
    Open Access
    Hypoxia controls expression of kidney-pathogenic MUC1 variants

    Stephanie Naas, René Krüger, Karl Xaver Knaup, Julia Naas, Steffen Grampp, Mario Schiffer, Michael Wiesener, Johannes Schödel

    Stephanie Naas ... Johannes Schödel

    Published 14 June 2023

    Hypoxia or pharmacological treatment with novel HIF stabilizers promotes the expression of MUC1 genetic variants that predispose to the development of chronic kidney disease in renal tubular cells.

  • Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria
    Open Access
    Time-resolved proteomic analyses of senescence highlight metabolic rewiring of mitochondria

    Jun Yong Kim, Ilian Atanassov, Frederik Dethloff, Lara Kroczek, Thomas Langer

    Jun Yong Kim ... Thomas Langer

    Published 15 June 2023

    Time-resolved proteomic analyses of senescent fibroblasts reveal that nearly 40% of the analyzed mitochondrial proteome have changed upon induction of senescence. Our study highlights the rewiring of mitochondrial metabolism as a central feature among all changes in mitochondrial pathways of senescent cells.

  • Distant sequence regions of JBP1 contribute to J-DNA binding
    Open Access
    Distant sequence regions of JBP1 contribute to J-DNA binding

    Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick HN Celie, Daan P Geerke, Robbie P Joosten, Anastassis Perrakis

    Ida de Vries ... Anastassis Perrakis

    Published 16 June 2023

    Structural modeling and mutagenesis reveal that the N-terminus and DNA-binding domain of JBP1 recognize base-J, enabling replication of this epigenetic marker by JBP1’s thymidine hydroxylase domain.

  • Clec12a inhibits MSU-induced immune activation through lipid raft expulsion
    Open Access
    Clec12a inhibits MSU-induced immune activation through lipid raft expulsion

    Ying Xu, Dingka Song, Wei Wang, Shixin Li, Tongtao Yue, Tie Xia, Yan Shi

    Ying Xu ... Yan Shi

    Published 20 June 2023

    C type lection receptor Clec12a inhibits MSU induced Dendritic cell activation via its transmembrane domain rather than intracellular ITIM.

  • Differential roles of CTP synthetases CTPS1 and CTPS2 in cell proliferation
    Open Access
    Differential roles of CTP synthetases CTPS1 and CTPS2 in cell proliferation

    Norbert Minet, Anne-Claire Boschat, Rebecca Lane, David Laughton, Philip Beer, Hélène Asnagli, Claire Soudais, Tim Bourne, Alain Fischer, Emmanuel Martin, Sylvain Latour

    Norbert Minet ... Sylvain Latour

    Published 22 June 2023

    The CTP nucleotide is essential for cell proliferation. This study explores the respective contributions of CTP synthetases 1 and 2 in cell proliferation. Compared with CTPS2, CTPS1 is the main contributor in association with its higher enzymatic activity.

  • The linker histone H1–BRCA1 axis is a crucial mediator of replication fork stability
    Open Access
    The linker histone H1–BRCA1 axis is a crucial mediator of replication fork stability

    Meryem Ozgencil, Arlinda Dullovi, Romane Catherine Christiane Higos, Zuzana Hořejší, Roberto Bellelli

    Meryem Ozgencil ... Roberto Bellelli

    Published 26 June 2023

    The replication-dependent histones H1 interact with BRCA1 upon replication stress. Cells deficient for H1 fail to recruit BRCA1 to stalled replication forks and undergo fork resection and collapse.

  • Peripheral immune system modulates Purkinje cell degeneration in Niemann–Pick disease type C1
    Open Access
    Peripheral immune system modulates Purkinje cell degeneration in Niemann–Pick disease type C1

    Toru Yasuda, Toru Uchiyama, Nobuyuki Watanabe, Noriko Ito, Kazuhiko Nakabayashi, Hideki Mochizuki, Masafumi Onodera

    Toru Yasuda ... Masafumi Onodera

    Published 27 June 2023

    We demonstrate that peripheral immune cells are involved in the cerebral neuronal degeneration in Niemann–Pick disease type C1. Our work can contribute to a novel therapeutic strategy that can potentially be combined with the ongoing lipid reduction therapeutic efforts.

  • MAP4K4 regulates forces at cell–cell and cell–matrix adhesions to promote collective cell migration
    Open Access
    MAP4K4 regulates forces at cell–cell and cell–matrix adhesions to promote collective cell migration

    Lara Elis Alberici Delsin, Cédric Plutoni, Anna Clouvel, Sarah Keil, Léa Marpeaux, Lina Elouassouli, Adele Khavari, Allen J Ehrlicher, Gregory Emery

    Lara Elis Alberici Delsin ... Gregory Emery

    Published 27 June 2023

    Using A431 carcinoma cells, the study shows that MAP4K4 coordinates cluster migration by regulating forces and stability of focal adhesions and adherens junctions, promoting cytoskeleton rearrangements.

  • The mRNA decapping machinery targets <em>LBD3/ASL9</em> to mediate apical hook and lateral root development
    Open Access
    The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development

    Zhangli Zuo, Milena E Roux, Jonathan R Chevalier, Yasin F Dagdas, Takafumi Yamashino, Søren D Højgaard, Emilie Knight, Lars Østergaard, Eleazar Rodriguez, Morten Petersen

    Zhangli Zuo ... Morten Petersen

    Published 29 June 2023

    This study identifies LBD3/ASL9 as targets of mRNA decay machinery, and ASL9 contributes to apical hook and lateral root development, possibly through interfering with cytokinin/auxin responses.

  • AR activates YAP/TAZ differentially in prostate cancer
    Open Access
    AR activates YAP/TAZ differentially in prostate cancer

    Omar Salem, Siyang Jia, Bin-Zhi Qian, Carsten Gram Hansen

    Omar Salem ... Carsten Gram Hansen

    Published 29 June 2023

    We show YAP and TAZ are differentially activated upon androgen stimulation. Through genetic targeting of YAP, we show that YAP drives the ability for anchorage independent growth and find that YAP/TAZ is not essential for AR signalling.

  • β-Catenin regulates endocardial cushion growth by suppressing p21
    Open Access
    β-Catenin regulates endocardial cushion growth by suppressing p21

    Huahua Liu, Pengfei Lu, Shan He, Yuru Luo, Yuan Fang, Sonia Benkaci, Bingruo Wu, Yidong Wang, Bin Zhou

    Huahua Liu ... Bin Zhou

    Published 29 June 2023

    This work demonstrates that β-catenin–mediated suppression of p21 is essential for endocardial cushion formation, suggesting a potential role of β-catenin in the etiology of congenital heart defects.

  • The NSL complex is required for piRNA production from telomeric clusters
    Open Access
    The NSL complex is required for piRNA production from telomeric clusters

    Shantanu S Iyer, Yidan Sun, Janine Seyfferth, Vinitha Manjunath, Maria Samata, Anastasios Alexiadis, Tanvi Kulkarni, Noel Gutierrez, Plamen Georgiev, Maria Shvedunova, Asifa Akhtar

    Shantanu S Iyer ... Asifa Akhtar

    Published 30 June 2023

    Germline knockdown of the NSL complex leads to transposon derepression, particularly of telomeric transposons. NSL2 binds promoters of telomeric transposons and its depletion leads to alterations in the chromatin state of multiple telomeric piRNA clusters.

  • ACE2-EGFR-MAPK signaling contributes to SARS-CoV-2 infection
    Open Access
    ACE2-EGFR-MAPK signaling contributes to SARS-CoV-2 infection

    Melanie Engler, Dan Albers, Pascal Von Maltitz, Rüdiger Groß, Jan Münch, Ion Cristian Cirstea

    Melanie Engler ... Ion Cristian Cirstea

    Published 4 July 2023

    SARS-CoV-2 activates the conserved EGFR-RAS-MAPK pathway through a novel mechanism that involves an ACE2-EGFR cross talk and pharmacological inhibition of the MAPK pathway is able to reduce viral infection.

  • Structural insights into CED-3 activation
    Open Access
    Structural insights into CED-3 activation

    Yini Li, Lu Tian, Ying Zhang, Yigong Shi

    Yini Li ... Yigong Shi

    Published 4 July 2023

    They report cryo-EM structures of CED-4 and three CED-4/CED-3 complexes with multiple oligomeric states. CARD–CARD interaction between CED-4 and CED-3 is essential for CED-3 activation and the newly reported dynamic organization of CED-4 regulates the onset of apoptosis.

  • Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes
    Open Access
    Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

    Xixi Zhang, Zimu Li, Yanjun Zhang, Yutong Liu, Jingjing Wang, Banghui Liu, Qiuluan Chen, Qian Wang, Lutang Fu, Peiyi Wang, Xiaolin Zhong, Liang Jin, Qihong Yan, Ling Chen, Jun He, Jincun Zhao, Xiaoli Xiong

    Xixi Zhang ... Xiaoli Xiong

    Published 4 July 2023

    SARS-CoV-1 spike protein is stabilized with engineered disulfide bonds, and cryo-EM imaging of these stabilized S-trimers reveals rare spike conformations.

  • Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20
    Open Access
    Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20

    Nicholas K Preiss, Yasmin Kamal, Owen M Wilkins, Chenyang Li, Fred W Kolling, Heidi W Trask, Young-Kwang Usherwood, Chao Cheng, Hildreth R Frost, Edward J Usherwood

    Nicholas K Preiss ... Edward J Usherwood

    Published 6 July 2023

    This work characterizes the transcriptional and epigenetic control of memory CD8 T cell differentiation by the BTB-ZF family transcription factor Zbtb20 using single cell RNA and ATAC sequencing and identifies direct genomic targets of Zbtb20 using CUT&RUN.

  • Differential roles of FOXC2 in the trabecular meshwork and Schlemm’s canal in glaucomatous pathology
    Open Access
    Differential roles of FOXC2 in the trabecular meshwork and Schlemm’s canal in glaucomatous pathology

    Naoto Ujiie, Pieter R Norden, Raymond Fang, Lisa Beckmann, Zhen Cai, Junghun Kweon, Ting Liu, Can Tan, Megan S Kuhn, W Daniel Stamer, Kazushi Aoto, Susan E Quaggin, Hao F Zhang, Tsutomu Kume

    Naoto Ujiie ... Tsutomu Kume

    Published 6 July 2023

    FOXC2 is required in the Schlemm’s canal endothelium and neural crest-derived trabecular meshwork cells for the morphogenesis and maintenance of Schlemm’s canal.

  • B-cell targeting with anti-CD38 daratumumab: implications for differentiation and memory responses
    Open Access
    B-cell targeting with anti-CD38 daratumumab: implications for differentiation and memory responses

    Dorit Verhoeven, Lucas Grinwis, Casper Marsman, Machiel H Jansen, T2B Consortium, Ester MM Van Leeuwen, Taco W Kuijpers

    Dorit Verhoeven ... Taco W Kuijpers

    Published 7 July 2023

    Daratumumab is an anti-CD38–targeting antibody that depletes plasma cells. This study shows that daratumumab also disturbs humoral immune responses beyond depletion only and may be used as therapeutic in B cell–mediated autoimmune diseases.

  • Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides
    Open Access
    Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

    Rubika Balendra, Igor Ruiz de los Mozos, Hana M Odeh, Idoia Glaria, Carmelo Milioto, Katherine M Wilson, Agnieszka M Ule, Martina Hallegger, Laura Masino, Stephen Martin, Rickie Patani, James Shorter, Jernej Ule, Adrian M Isaacs

    Rubika Balendra ... Adrian M Isaacs

    Published 12 July 2023

    C9orf72 poly(PR) binds to 558 RNAs in human cells, and the sequence GAAGA is enriched at its binding sites. Poly(PR) has nanomolar affinity for GAAGA RNA, and this RNA induces poly(PR) phase separation.

  • The pyruvate dehydrogenase complex regulates mitophagic trafficking and protein phosphorylation
    Open Access
    The pyruvate dehydrogenase complex regulates mitophagic trafficking and protein phosphorylation

    Panagiota Kolitsida, Vladimir Nolic, Jianwen Zhou, Michael Stumpe, Natalie M Niemi, Jörn Dengjel, Hagai Abeliovich

    Panagiota Kolitsida ... Hagai Abeliovich

    Published 13 July 2023

    Mutations in the PDC affect the phosphorylation and mitophagic trafficking of matrix proteins, through the novel regulation of associated kinases and a phosphatase. We suggest that this occurs by the direct allosteric regulation of the phosphatase and kinases by the PDC.

  • A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler
    Open Access
    A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler

    Leonhard A Karl, Lorenzo Galanti, Susanne CS Bantele, Felix Metzner, Barbara Šafarić, Lional Rajappa, Benjamin Foster, Vanessa Borges Pires, Priyanka Bansal, Erika Chacin, Jerôme Basquin, Karl E Duderstadt, Christoph F Kurat, Till Bartke, Karl-Peter Hopfner, Boris Pfander

    Leonhard A Karl ... Boris Pfander

    Published 19 July 2023

    Biochemical data suggest that the SAM-key domain of the budding yeast remodeler Fun30 is required for its nucleosome remodeling activity by regulating the catalytic ATPase.

  • Exploring the impact of dexamethasone on gene regulation in myeloma cells
    Open Access
    Exploring the impact of dexamethasone on gene regulation in myeloma cells

    Victor Bessonneau-Gaborit, Jonathan Cruard, Catherine Guerin-Charbonnel, Jennifer Derrien, Jean-Baptiste Alberge, Elise Douillard, Magali Devic, Sophie Deshayes, Loïc Campion, Frank Westermann, Phillipe Moreau, Carl Herrmann, Jérémie Bourdon, Florence Magrangeas, Stéphane Minvielle

    Victor Bessonneau-Gaborit ... Stéphane Minvielle

    Published 31 July 2023

    The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter–enhancer interactions and DNA loop stabilization.

Methods

  • A network embedding approach to identify active modules in biological interaction networks
    Open Access
    A network embedding approach to identify active modules in biological interaction networks

    Claude Pasquier, Vincent Guerlais, Denis Pallez, Raphaël Rapetti-Mauss, Olivier Soriani

    Claude Pasquier ... Olivier Soriani

    Published 20 June 2023

    This study proposes the AMINE method as a flexible and efficient approach to identify active modules from a data embedding combining gene expression and interaction data.

Reviews

  • Transducing compressive forces into cellular outputs in cancer and beyond
    Open Access
    Transducing compressive forces into cellular outputs in cancer and beyond

    Céline Schmitter, Mickaël Di-Luoffo, Julie Guillermet-Guibert

    Céline Schmitter ... Julie Guillermet-Guibert

    Published 26 June 2023

    The review identifies signaling and cell biology processes selectively induced by mechanical compressive forces on normal or pathological tissues such as tumors for the development of novel treatments.

Resources

  • Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
    Open Access
    Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

    Li-Chun Cheng, Xi Zhang, Sabyasachi Baboo, Julie A Nguyen, Salvador Martinez-Bartolomé, Esther Loose, Jolene Diedrich, John R Yates, Larry Gerace

    Li-Chun Cheng ... Larry Gerace

    Published 11 July 2023

    A cohort of low-abundance transmembrane proteins concentrated at the nuclear envelope has been identified, predicting diverse new functions for this membrane system.

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Volume 6, No. 9
September 2023
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