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Table of Contents

March 2023 | Volume 6, No. 3

Research Articles

  • Ectopic CH60 mediates HAPLN1-induced cell survival signaling in multiple myeloma
    Open Access
    Ectopic CH60 mediates HAPLN1-induced cell survival signaling in multiple myeloma

    Debayan De Bakshi, Yu-Chia Chen, Shelly M Wuerzberger-Davis, Min Ma, Bayley J Waters, Lingjun Li, Aussie Suzuki, Shigeki Miyamoto

    Debayan De Bakshi ... Shigeki Miyamoto

    Published 13 December 2022

    This study defines ectopic mitochondrial chaperonin 60 (CH60) on the multiple myeloma cell surface as a HAPLN1 matrikine receptor that signals via TLR4 to induce NF-κB signaling and drug resistance.

  • Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae
    Open Access
    Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

    Richard G Dorrell, Alan Kuo, Zoltan Füssy, Elisabeth H Richardson, Asaf Salamov, Nikola Zarevski, Nastasia J Freyria, Federico M Ibarbalz, Jerry Jenkins, Juan Jose Pierella Karlusich, Andrei Stecca Steindorff, Robyn E Edgar, Lori Handley, Kathleen Lail, Anna Lipzen, Vincent Lombard, John McFarlane, Charlotte Nef, Anna MG Novák Vanclová, Yi Peng, Chris Plott, Marianne Potvin, Fabio Rocha Jimenez Vieira, Kerrie Barry, Colomban de Vargas, Bernard Henrissat, Eric Pelletier, Jeremy Schmutz, Patrick Wincker, Joel B Dacks, Chris Bowler, Igor V Grigoriev, Connie Lovejoy

    Richard G Dorrell ... Connie Lovejoy

    Published 15 December 2022

    The Arctic Ocean stands apart from other oceans. Using multiple genomes and transcriptomes from cultured and environmental sources, we found distinct genetic modifications in Arctic microalgae consistent with biogeographically constrained trait selectivity as an adaptive force in algal evolution.

  • Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria
    Open Access
    Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria

    Nimmy Francis, Malaya R Behera, Kathiresan Natarajan, Rakesh S Laishram

    Nimmy Francis ... Rakesh S Laishram

    Published 19 December 2022

    We show a tyrosine phosphorylation–controlled poly(A) polymerase I polyadenylation activity regulated stress response mechanism in bacteria that is distinct and operates downstream of the primary stress regulator RpoS.

  • Integrin ligands block mechanical signal transduction in baroreceptors
    Open Access
    Integrin ligands block mechanical signal transduction in baroreceptors

    Haiyan Zhao, Ping Liu, Xu Zha, Sitao Zhang, Jiaqi Cao, Hua Wei, Meili Wang, Haixia Huang, Wei Wang

    Haiyan Zhao ... Wei Wang

    Published 20 December 2022

    The binding of integrins to specific sequences in extracellular matrix forms the mechanical coupling to transfer stretch applied on the vascular wall to the baroreceptors.

  • Integrin β1/FAK/SRC signal pathway is involved in autism spectrum disorder in <em>Tspan7</em> knockout rats
    Open Access
    Integrin β1/FAK/SRC signal pathway is involved in autism spectrum disorder in Tspan7 knockout rats

    Shuo Pang, Zhuohui Luo, Wei Dong, Shan Gao, Wei Chen, Ning Liu, Xu Zhang, Xiang Gao, Jing Li, Kai Gao, Xudong Shi, Feifei Guan, Li Zhang, Lianfeng Zhang

    Shuo Pang ... Lianfeng Zhang

    Published 20 December 2022

    TSPAN7 knockout causes ASD-like phenotypes in rats through the integrin β1/FAK/SRC signal pathway, which provides novel insights into the role of TSPAN7 in psychiatric diseases, highlighting SRC as a potential target.

  • Branch point strength controls species-specific <em>CAMK2B</em> alternative splicing and regulates LTP
    Open Access
    Branch point strength controls species-specific CAMK2B alternative splicing and regulates LTP

    Andreas Franz, A Ioana Weber, Marco Preußner, Nicole Dimos, Alexander Stumpf, Yanlong Ji, Laura Moreno-Velasquez, Anne Voigt, Frederic Schulz, Alexander Neumann, Benno Kuropka, Ralf Kühn, Henning Urlaub, Dietmar Schmitz, Markus C Wahl, Florian Heyd

    Andreas Franz ... Florian Heyd

    Published 21 December 2022

    A mechanism that contributes to species-specific alternative splicing leading to increased coding capacity of primate genomes is presented and functionality for CamK2β splicing addressed.

  • An isoform-specific function of Cdc42 in regulating mammalian Exo70 during axon formation
    Open Access
    An isoform-specific function of Cdc42 in regulating mammalian Exo70 during axon formation

    Priyadarshini Ravindran, Andreas W Püschel

    Priyadarshini Ravindran ... Andreas W Püschel

    Published 21 December 2022

    The brain-specific isoform of the GTPase Cdc42 is shown to promote axon formation by interacting with the exocyst tethering complex and increasing exocytosis downstream of its activator Arhgef7.

  • Loss of surface transport is a main cellular pathomechanism of CRB2 variants causing podocytopathies
    Open Access
    Loss of surface transport is a main cellular pathomechanism of CRB2 variants causing podocytopathies

    Annika Möller-Kerutt, Birgit Schönhoff, Yvonne Rellmann, Britta George, Daniela Anne Braun, Hermann Pavenstädt, Thomas Weide

    Annika Möller-Kerutt ... Thomas Weide

    Published 22 December 2022

    CRB2 is an essential protein of the renal filtration barrier. This study reports the development of an in vitro assay, suitable to investigate the pathogenic potential of known and novel, so far uncharacterized CRB2 variants.

  • Unconventional interactions of the TRPV4 ion channel with beta-adrenergic receptor ligands
    Open Access
    Unconventional interactions of the TRPV4 ion channel with beta-adrenergic receptor ligands

    Miguel Benítez-Angeles, Emmanuel Juárez-González, Ariela Vergara-Jaque, Itzel Llorente, Gisela Rangel-Yescas, Stéphanie C Thébault, Marcia Hiriart, León D Islas, Tamara Rosenbaum

    Miguel Benítez-Angeles ... Tamara Rosenbaum

    Published 22 December 2022

    The transient receptor potential vanilloid (TRPV4) ion channel is important for respiratory function. Here, it is shown that TRPV4 is inhibited by bronchodilators widely used in diseases such as asthma.

  • De novo discovery of traits co-occurring with chronic obstructive pulmonary disease
    Open Access
    De novo discovery of traits co-occurring with chronic obstructive pulmonary disease

    Evgeniia Golovina, Tayaza Fadason, Rachel K Jaros, Haribalan Kumar, Joyce John, Kelly Burrowes, Merryn Tawhai, Justin M O’Sullivan

    Evgeniia Golovina ... Justin M O’Sullivan

    Published 27 December 2022

    This paper integrates different levels of biological information to identify shared genetic and biological pathways underlying the diverse clinical presentations of COPD. Thus, it identifies a collection of genetic variants and genes that may aid COPD patient stratification and treatment.

  • Mutation-agnostic RNA interference with engineered replacement rescues <em>Tmc1</em>-related hearing loss
    Open Access
    Mutation-agnostic RNA interference with engineered replacement rescues Tmc1-related hearing loss

    Yoichiro Iwasa, Miles J Klimara, Hidekane Yoshimura, William D Walls, Ryotaro Omichi, Cody A West, Seiji B Shibata, Paul T Ranum, Richard JH Smith

    Yoichiro Iwasa ... Richard JH Smith

    Published 27 December 2022

    Mutation-agnostic RNA interference with concomitant, knockdown-resistant gene replacement, results in robust auditory brainstem response and cochlear hair cell preservation in the murine model of TMC1-related autosomal dominant hearing loss.

  • Kindlin2 enables EphB/ephrinB bi-directional signaling to support vascular development
    Open Access
    Kindlin2 enables EphB/ephrinB bi-directional signaling to support vascular development

    Wenqing Li, Lai Wen, Bhavisha Rathod, Anne-Claude Gingras, Klaus Ley, Ho-Sup Lee

    Wenqing Li ... Ho-Sup Lee

    Published 27 December 2022

    Kindlin2 supports EphB4/ephrinB2 bi-directional signaling functions by associating with a highly conserved NIYY motif in the ephrinB2 cytoplasmic tail to promote ephrinB2 clustering and EphB4 activation, thereby enabling arteriovenous segregation during embryonic development.

  • Trans-differentiation of trophoblast stem cells: implications in placental biology
    Open Access
    Trans-differentiation of trophoblast stem cells: implications in placental biology

    Madhurima Paul, Shreeta Chakraborty, Safirul Islam, Rupasri Ain

    Madhurima Paul ... Rupasri Ain

    Published 27 December 2022

    Formation of trophendothelial cells is associated with trophoblast differentiation and is regulated by HES1. Trophoblast differentiation–induced TRAIL secretion directs preferential demise of ECs located in their vicinity, aiding trophoblast vasculogenic mimicry.

  • Regulation of telomere silencing by the core histones–autophagy–Sir2 axis
    Open Access
    Regulation of telomere silencing by the core histones–autophagy–Sir2 axis

    Qianyun Mei, Qi Yu, Xin Li, Jianguo Chen, Xilan Yu

    Qianyun Mei ... Xilan Yu

    Published 30 December 2022

    This work reported that there is a global loss of core histones and progressively reduced telomere silencing during yeast chronological aging and uncovered the core histones-autophagy-Sir2 pathway that contributes to the aging-coupled loss of telomere silencing.

  • A SNX1–SNX2–VAPB partnership regulates endosomal membrane rewiring in response to nutritional stress
    Open Access
    A SNX1–SNX2–VAPB partnership regulates endosomal membrane rewiring in response to nutritional stress

    Juliane Da Graça, Juliette Charles, Morgane Djebar, Karla Alvarez-Valadez, Joëlle Botti, Etienne Morel

    Juliane Da Graça ... Etienne Morel

    Published 30 December 2022

    A specific SNX1-dependent endosome tubulation towards autophagosome biogenesis-associated regions of the ER is generated by nutrient deprivation and regulated by the SNX2/VAPB tethering complex.

  • <em>PACSIN2</em> as a modulator of autophagy and mercaptopurine cytotoxicity: mechanisms in lymphoid and intestinal cells
    Open Access
    PACSIN2 as a modulator of autophagy and mercaptopurine cytotoxicity: mechanisms in lymphoid and intestinal cells

    Giulia Zudeh, Raffaella Franca, Marianna Lucafò, Erik J Bonten, Matteo Bramuzzo, Riccardo Sgarra, Cristina Lagatolla, Martina Franzin, William E Evans, Giuliana Decorti, Gabriele Stocco

    Giulia Zudeh ... Gabriele Stocco

    Published 3 January 2023

    This study evaluates the role of PACSIN2 in autophagy modulation and its impact on mercaptopurine cytotoxicity in lymphoid and intestinal models.

  • Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells
    Open Access
    Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells

    Megan A Mahlke, Lior Lumerman, Peter Ly, Yael Nechemia-Arbely

    Megan A Mahlke ... Yael Nechemia-Arbely

    Published 3 January 2023

    Plasticity in the position of CENP-A enrichment and location of kinetochore recruitment between human cell lines is accompanied by precise CENP-A maintenance across the cell cycle to preserve unique epigenetic centromere identities among human cells.

  • An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing
    Open Access
    An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing

    Aftab Amin, Rentian Wu, Muhammad Ajmal Khan, Man Hei Cheung, Yanting Liang, Changdong Liu, Guang Zhu, Zhi-Ling Yu, Chun Liang

    Aftab Amin ... Chun Liang

    Published 4 January 2023

    Differential mutants confirmed Noc3’s separate roles in DNA replication and ribosome biogenesis, and an essential Noc3 dimerization cycle was found to mediate ORC dimerization in replication licensing.

  • SMN promotes mitochondrial metabolic maturation during myogenesis by regulating the MYOD-miRNA axis
    Open Access
    SMN promotes mitochondrial metabolic maturation during myogenesis by regulating the MYOD-miRNA axis

    Akihiro Ikenaka, Yohko Kitagawa, Michiko Yoshida, Chuang-Yu Lin, Akira Niwa, Tatsutoshi Nakahata, Megumu K Saito

    Akihiro Ikenaka ... Megumu K Saito

    Published 5 January 2023

    SMN contributes to muscle maturation by binding to the promoter regions of MYOD1 and miRNAs and regulating the expression of these molecules during myogenesis.

  • Lineage tracing reveals fate bias and transcriptional memory in human B cells
    Open Access
    Lineage tracing reveals fate bias and transcriptional memory in human B cells

    Michael Swift, Felix Horns, Stephen R Quake

    Michael Swift ... Stephen R Quake

    Published 13 January 2023

    We combined lineage tracing and single-cell transcriptomics to quantify the extent of cell-intrinsic fate bias in human B cells.

  • Secondary findings in a large Pakistani cohort tested with whole genome sequencing
    Open Access
    Secondary findings in a large Pakistani cohort tested with whole genome sequencing

    Aliaksandr Skrahin, Huma Arshad Cheema, Maqbool Hussain, Nuzhat Noureen Rana, Khalil Ur Rehman, Raman Kumar, Gabriela Oprea, Najim Ameziane, Arndt Rolfs, Volha Skrahina

    Aliaksandr Skrahin ... Volha Skrahina

    Published 12 January 2023

    Testing a large Pakistani cohort with whole genome sequencing, we concluded that in countries such as Pakistan, the list of ACMG secondary findings could be expanded.

  • Functional substitutions of amino acids that differ between GDF11 and GDF8 impact skeletal development and skeletal muscle
    Open Access
    Functional substitutions of amino acids that differ between GDF11 and GDF8 impact skeletal development and skeletal muscle

    John Lian, Ryan G Walker, Andrea D’Amico, Ana Vujic, Melanie J Mills, Kathleen A Messemer, Kourtney R Mendello, Jill M Goldstein, Krystynne A Leacock, Soraya Epp, Emma V Stimpfl, Thomas B Thompson, Amy J Wagers, Richard T Lee

    John Lian ... Richard T Lee

    Published 11 January 2023

    Replacement of amino acids unique to GDF11 and GDF8 into the native locus of the other ligand yields measurable, differential skeletal and muscle phenotypes, revealing distinct features between the ligands and a requirement for GDF11 in early-stage skeletal development.

  • Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome
    Open Access
    Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome

    James A Watson, Raphaël Pantier, Uma Jayachandran, Kashyap Chhatbar, Beatrice Alexander-Howden, Valdeko Kruusvee, Michal Prendecki, Adrian Bird, Atlanta G Cook

    James A Watson ... Atlanta G Cook

    Published 12 January 2023

    SALL4 recognises AT-rich DNA motifs via a pair of evolutionarily conserved zinc fingers, and mutations of residues critical for DNA binding are responsible for a rare developmental disorder.

  • An unconventional cancer-promoting function of methamphetamine in hepatocellular carcinoma
    Open Access
    An unconventional cancer-promoting function of methamphetamine in hepatocellular carcinoma

    Zizhen Si, GuanJun Yang, Xidi Wang, Zhaoying Yu, Qian Pang, Shuangshuang Zhang, Liyin Qian, Yuer Ruan, Jing Huang, Liu Yu

    Zizhen Si ... Liu Yu

    Published 20 January 2023

    METH use is associated with a higher incidence of hepatocellular carcinoma (HCC) in METH abusers and rehabilitees. METH exposure promotes HCC progression by ROS-mediated activation of the Ras/MEK/ERK signaling pathway. Clearance of ROS by NAC abolishes METH-induced HCC progression.

Resources

  • IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing
    Open Access
    IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing

    Kelren S Rodrigues, Luiz P Petroski, Paulo H Utumi, Adriano Ferrasa, Roberto H Herai

    Kelren S Rodrigues ... Roberto H Herai

    Published 6 January 2023

    The online atlas IARA is a curated and updated resource with genetic and molecular data on the biogenesis of human spliceosome machinery involved in RNA splicing.

  • Disease- and sex-specific differences in patients with heart valve disease: a proteome study
    Open Access
    Disease- and sex-specific differences in patients with heart valve disease: a proteome study

    Sarah Nordmeyer, Milena Kraus, Matthias Ziehm, Marieluise Kirchner, Marie Schafstedde, Marcus Kelm, Sylvia Niquet, Mariet Mathew Stephen, Istvan Baczko, Christoph Knosalla, Matthieu-P Schapranow, Gunnar Dittmar, Michael Gotthardt, Martin Falcke, Vera Regitz-Zagrosek, Titus Kuehne, Philipp Mertins

    Sarah Nordmeyer ... Philipp Mertins

    Published 10 January 2023

    Proteomics provide novel insights into molecular mechanisms and cardiac remodeling in heart failure because of pressure overload in aortic valve stenosis and volume overload in mitral valve regurgitation.

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Volume 6, No. 3
March 2023
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