Advertisement
Cell
This journal offers authors two options (open access or subscription) to publish research

Mar 04, 2021

Volume 184Issue 5p1123-1394
Open Archive
On the cover: The transition from water to land is a key milestone in vertebrate evolution. In this issue, Wang et al. (1362–1376) report a 40 Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, and Bi et al. (1377–1391) report the genomes of four basal ray-finned fishes, including bichir (Polypterus senegalus), American paddlefish (Polyodon spathula), bowfin (Amia calva), and alligator gar (Atractosteus spatula). Using the genomes of these extant fish species, both studies uncover the ancestral genetic codes that are crucial for the evolutionary innovations that occurred during the vertebrate water-to-land transition. The cover image represents the early divergent bony fish species with their genomes sequenced and analyzed to shed light on evolution of terrestrial vertebrates. Artwork by SciStories LLC....
On the cover: The transition from water to land is a key milestone in vertebrate evolution. In this issue, Wang et al. (1362–1376) report a 40 Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, and Bi et al. (1377–1391) report the genomes of four basal ray-finned fishes, including bichir (Polypterus senegalus), American paddlefish (Polyodon spathula), bowfin (Amia calva), and alligator gar (Atractosteus spatula). Using the genomes of these extant fish species, both studies uncover the ancestral genetic codes that are crucial for the evolutionary innovations that occurred during the vertebrate water-to-land transition. The cover image represents the early divergent bony fish species with their genomes sequenced and analyzed to shed light on evolution of terrestrial vertebrates. Artwork by SciStories LLC.

Leading Edge

Obituary

  • Kathryn Anderson (1952–2020)

    • Zhirong Bao,
    • Mary K. Baylies,
    • Anna-Katerina Hadjantonakis,
    • Danwei Huangfu,
    • Maria Jasin,
    • Alexandra L. Joyner,
    • Elizabeth Lacy,
    • Eric C. Lai,
    • Lorenz Studer,
    • Thomas Vierbuchen,
    • Jennifer A. Zallen
    On November 30, 2020, we lost the brilliant, generous, and forward-thinking leader who founded and chaired the Developmental Biology Program at the Sloan Kettering Institute from 2002 to 2019. Kathryn Anderson was an extraordinary scientist who made landmark discoveries at every stage of her career (Figure 1). Her work transformed our understanding of mechanisms of embryonic patterning in Drosophila and mammals, and her insights into the diverse roles of the Toll/NF-κB and Hedgehog pathways have had a broad impact on biology and medicine.

Commentary

  • Public health actions to control new SARS-CoV-2 variants

    • Nathan D. Grubaugh,
    • Emma B. Hodcroft,
    • Joseph R. Fauver,
    • Alexandra L. Phelan,
    • Muge Cevik
    Recent reports suggest that some SARS-CoV-2 genetic variants, such as B.1.1.7, might be more transmissible and are quickly spreading around the world. As the emergence of more transmissible variants could exacerbate the pandemic, we provide public health guidance for increased surveillance and measures to reduce community transmission.

Previews

  • Precision genome editing heralds rapid de novo domestication for new crops

    • Xin-Guang Zhu,
    • Jian-Kang Zhu
    The de novo domestication has the potential to rapidly capitalize on desirable traits of wild plants. In this issue of Cell, Yu et al. report a route of de novo domestication of an allotetraploid rice, heralding the creation of a novel staple food crop to support global food security.
  • How to make a better T cell: in vivo CRISPR screens have some answers

    • Matteo Villa,
    • Michal A. Stanczak,
    • Erika L. Pearce
    Understanding what regulates CD8+ T cell responses is key to effectively harnessing these cells in human disease. In this issue of Cell, Huang et al. and Chen et al. use in vivo CRISPR screens to discover novel regulators of CD8+ T cell immunity to engineer a more efficacious response against cancer and infections.
  • Bone resorption goes green

    • Jameel Iqbal,
    • Mone Zaidi
    In this issue of Cell, McDonald et al. show that giant multinucleated, bone-resorbing osteoclasts dissolve into smaller cells, termed “osteopmorhs,” which re-form into osteoclasts at distal bone sites (McDonald et al., 2021). These findings overturn the long-standing premise that osteoclasts differentiate solely from hematopoietic precursors and undergo apoptosis after completing resorption.
  • A vicious cycle in atherosclerosis

    • Aldons J. Lusis
    Clonal hematopoiesis, defined as the presence of expanded somatic blood cell clones, is associated with about a doubling in the risk of coronary heart disease in humans. Heyde and colleagues now provide evidence that clonal hematopoiesis results largely from increased stem cell proliferation, which is, in turn, stimulated by atherosclerosis.

Perspective

  • An expanded universe of cancer targets

    • William C. Hahn,
    • Joel S. Bader,
    • Theodore P. Braun,
    • Andrea Califano,
    • Paul A. Clemons,
    • Brian J. Druker,
    • Andrew J. Ewald,
    • Haian Fu,
    • Subhashini Jagu,
    • Christopher J. Kemp,
    • William Kim,
    • Calvin J. Kuo,
    • Michael T. McManus,
    • Gordon B. Mills,
    • Xiulei Mo,
    • Nidhi Sahni,
    • Stuart L. Schreiber,
    • Jessica A. Talamas,
    • Pablo Tamayo,
    • Jeffrey W. Tyner,
    • Bridget K. Wagner,
    • William A. Weiss,
    • Daniela S. Gerhard
    • the Cancer Target Discovery and Development Network
    Members of the Cancer Target Discovery and Development Network synthesize recent insights into the different classes and characteristics of cancer therapeutic vulnerabilities.

Articles

  • A route to de novo domestication of wild allotetraploid rice

    • Hong Yu,
    • Tao Lin,
    • Xiangbing Meng,
    • Huilong Du,
    • Jingkun Zhang,
    • Guifu Liu,
    • Mingjiang Chen,
    • Yanhui Jing,
    • Liquan Kou,
    • Xiuxiu Li,
    • Qiang Gao,
    • Yan Liang,
    • Xiangdong Liu,
    • Zhilan Fan,
    • Yuntao Liang,
    • Zhukuan Cheng,
    • Mingsheng Chen,
    • Zhixi Tian,
    • Yonghong Wang,
    • Chengcai Chu,
    • Jianru Zuo,
    • Jianmin Wan,
    • Qian Qian,
    • Bin Han,
    • Andrea Zuccolo,
    • Rod A. Wing,
    • Caixia Gao,
    • Chengzhi Liang,
    • Jiayang Li
    Li and colleagues developed a breeding route to de novo domestication of wild allotetraploid rice that provides a rational strategy for creating novel crops and generated a series of allotetraploid rice lines edited in domestication-related and agronomically important genes.
  • Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

    • Emma C. Thomson,
    • Laura E. Rosen,
    • James G. Shepherd,
    • Roberto Spreafico,
    • Ana da Silva Filipe,
    • Jason A. Wojcechowskyj,
    • Chris Davis,
    • Luca Piccoli,
    • David J. Pascall,
    • Josh Dillen,
    • Spyros Lytras,
    • Nadine Czudnochowski,
    • Rajiv Shah,
    • Marcel Meury,
    • Natasha Jesudason,
    • Anna De Marco,
    • Kathy Li,
    • Jessica Bassi,
    • Aine O’Toole,
    • Dora Pinto,
    • Rachel M. Colquhoun,
    • Katja Culap,
    • Ben Jackson,
    • Fabrizia Zatta,
    • Andrew Rambaut,
    • Stefano Jaconi,
    • Vattipally B. Sreenu,
    • Jay Nix,
    • Ivy Zhang,
    • Ruth F. Jarrett,
    • William G. Glass,
    • Martina Beltramello,
    • Kyriaki Nomikou,
    • Matteo Pizzuto,
    • Lily Tong,
    • Elisabetta Cameroni,
    • Tristan I. Croll,
    • Natasha Johnson,
    • Julia Di Iulio,
    • Arthur Wickenhagen,
    • Alessandro Ceschi,
    • Aoife M. Harbison,
    • Daniel Mair,
    • Paolo Ferrari,
    • Katherine Smollett,
    • Federica Sallusto,
    • Stephen Carmichael,
    • Christian Garzoni,
    • Jenna Nichols,
    • Massimo Galli,
    • Joseph Hughes,
    • Agostino Riva,
    • Antonia Ho,
    • Marco Schiuma,
    • Malcolm G. Semple,
    • Peter J.M. Openshaw,
    • Elisa Fadda,
    • J. Kenneth Baillie,
    • John D. Chodera,
    • The ISARIC4C Investigators,
    • the COVID-19 Genomics UK (COG-UK) Consortium,
    • Suzannah J. Rihn,
    • Samantha J. Lycett,
    • Herbert W. Virgin,
    • Amalio Telenti,
    • Davide Corti,
    • David L. Robertson,
    • Gyorgy Snell
    Epidemiological, clinical, molecular, and structural characterization of the N439K mutation in the SARS-CoV-2 spike receptor binding motif demonstrates that it results in similar viral fitness compared to wild-type while conferring resistance against some neutralizing monoclonal antibodies and reducing the activity of some polyclonal antibody responses.
  • Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

    • Philip J.M. Brouwer,
    • Mitch Brinkkemper,
    • Pauline Maisonnasse,
    • Nathalie Dereuddre-Bosquet,
    • Marloes Grobben,
    • Mathieu Claireaux,
    • Marlon de Gast,
    • Romain Marlin,
    • Virginie Chesnais,
    • Ségolène Diry,
    • Joel D. Allen,
    • Yasunori Watanabe,
    • Julia M. Giezen,
    • Gius Kerster,
    • Hannah L. Turner,
    • Karlijn van der Straten,
    • Cynthia A. van der Linden,
    • Yoann Aldon,
    • Thibaut Naninck,
    • Ilja Bontjer,
    • Judith A. Burger,
    • Meliawati Poniman,
    • Anna Z. Mykytyn,
    • Nisreen M.A. Okba,
    • Edith E. Schermer,
    • Marielle J. van Breemen,
    • Rashmi Ravichandran,
    • Tom G. Caniels,
    • Jelle van Schooten,
    • Nidhal Kahlaoui,
    • Vanessa Contreras,
    • Julien Lemaître,
    • Catherine Chapon,
    • Raphaël Ho Tsong Fang,
    • Julien Villaudy,
    • Kwinten Sliepen,
    • Yme U. van der Velden,
    • Bart L. Haagmans,
    • Godelieve J. de Bree,
    • Eric Ginoux,
    • Andrew B. Ward,
    • Max Crispin,
    • Neil P. King,
    • Sylvie van der Werf,
    • Marit J. van Gils,
    • Roger Le Grand,
    • Rogier W. Sanders
    Brouwer et al. present preclinical evidence in support of a COVID-19 vaccine candidate, designed as a self-assembling two-component protein nanoparticle displaying multiple copies of the SARS-CoV-2 spike protein, which induces strong neutralizing antibody responses and protects from high-dose SARS-CoV-2 challenge.
  • Maturation and persistence of the anti-SARS-CoV-2 memory B cell response

    • Aurélien Sokal,
    • Pascal Chappert,
    • Giovanna Barba-Spaeth,
    • Anais Roeser,
    • Slim Fourati,
    • Imane Azzaoui,
    • Alexis Vandenberghe,
    • Ignacio Fernandez,
    • Annalisa Meola,
    • Magali Bouvier-Alias,
    • Etienne Crickx,
    • Asma Beldi-Ferchiou,
    • Sophie Hue,
    • Laetitia Languille,
    • Marc Michel,
    • Samia Baloul,
    • France Noizat-Pirenne,
    • Marine Luka,
    • Jérôme Mégret,
    • Mickaël Ménager,
    • Jean-Michel Pawlotsky,
    • Simon Fillatreau,
    • Felix A. Rey,
    • Jean-Claude Weill,
    • Claude-Agnès Reynaud,
    • Matthieu Mahévas
    The B cell response against SARS-CoV-2 shows a temporal shift from an extrafollicular reaction that includes memory B cells against seasonal coronaviruses toward a germinal center-dependent memory response encoding (spike-specific) neutralizing antibodies.
  • Enteric helminth coinfection enhances host susceptibility to neurotropic flaviviruses via a tuft cell-IL-4 receptor signaling axis

    • Pritesh Desai,
    • Hana Janova,
    • James P. White,
    • Glennys V. Reynoso,
    • Heather D. Hickman,
    • Megan T. Baldridge,
    • Joseph F. Urban Jr.,
    • Thaddeus S. Stappenbeck,
    • Larissa B. Thackray,
    • Michael S. Diamond
    Desai et al. show that the tuft cell/IL-4Rα circuit in the intestine can have detrimental consequences in the context of helminth and viral coinfection. Flavivirus infection of enteric neurons, in the setting of a type 2 immune response due to helminths, IL-25, or IL-4 signaling, impairs intestinal integrity and compromises host CD8+ T cell responses and survival.
  • Structures of HCMV Trimer reveal the basis for receptor recognition and cell entry

    • Marc Kschonsak,
    • Lionel Rougé,
    • Christopher P. Arthur,
    • Ho Hoangdung,
    • Nidhi Patel,
    • Ingrid Kim,
    • Matthew C. Johnson,
    • Edward Kraft,
    • Alexis L. Rohou,
    • Avinash Gill,
    • Nadia Martinez-Martin,
    • Jian Payandeh,
    • Claudio Ciferri
    Kschonsak et al. present cryo-EM structures of the HCMV herpesvirus gHgLgO glycoprotein Trimer bound to receptors PDGFRα and TGFβR3 and to broadly neutralizing antibodies. Their work reveals Trimer architecture and provides clues as to how the leading viral cause of congenital birth defects in humans can infect cells and be targeted for therapeutic or vaccine development.
  • In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions

    • Hongling Huang,
    • Peipei Zhou,
    • Jun Wei,
    • Lingyun Long,
    • Hao Shi,
    • Yogesh Dhungana,
    • Nicole M. Chapman,
    • Guotong Fu,
    • Jordy Saravia,
    • Jana L. Raynor,
    • Shaofeng Liu,
    • Gustavo Palacios,
    • Yong-Dong Wang,
    • Chenxi Qian,
    • Jiyang Yu,
    • Hongbo Chi
    Metabolic changes associated with amino acid transport and nutrient signaling regulate the fate of effector T cell populations and the generation of memory T cell responses.
  • In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

    • Zeyu Chen,
    • Eri Arai,
    • Omar Khan,
    • Zhen Zhang,
    • Shin Foong Ngiow,
    • Yuan He,
    • Hua Huang,
    • Sasikanth Manne,
    • Zhendong Cao,
    • Amy E. Baxter,
    • Zhangying Cai,
    • Elizabeth Freilich,
    • Mohammed A. Ali,
    • Josephine R. Giles,
    • Jennifer E. Wu,
    • Allison R. Greenplate,
    • Mohamed A. Hakeem,
    • Qingzhou Chen,
    • Makoto Kurachi,
    • Kito Nzingha,
    • Viktoriya Ekshyyan,
    • Divij Mathew,
    • Zhuoyu Wen,
    • Nancy A. Speck,
    • Alexis Battle,
    • Shelley L. Berger,
    • E. John Wherry,
    • Junwei Shi
    An in vivo T cell CRISPR screening platform identifies Fli1 as a factor modulating CD8+ T cell effector differentiation with limited effects on memory or exhaustion.
  • Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

    • Nathan D. Mathewson,
    • Orr Ashenberg,
    • Itay Tirosh,
    • Simon Gritsch,
    • Elizabeth M. Perez,
    • Sascha Marx,
    • Livnat Jerby-Arnon,
    • Rony Chanoch-Myers,
    • Toshiro Hara,
    • Alyssa R. Richman,
    • Yoshinaga Ito,
    • Jason Pyrdol,
    • Mirco Friedrich,
    • Kathrin Schumann,
    • Michael J. Poitras,
    • Prafulla C. Gokhale,
    • L. Nicolas Gonzalez Castro,
    • Marni E. Shore,
    • Christine M. Hebert,
    • Brian Shaw,
    • Heather L. Cahill,
    • Matthew Drummond,
    • Wubing Zhang,
    • Olamide Olawoyin,
    • Hiroaki Wakimoto,
    • Orit Rozenblatt-Rosen,
    • Priscilla K. Brastianos,
    • X. Shirley Liu,
    • Pamela S. Jones,
    • Daniel P. Cahill,
    • Matthew P. Frosch,
    • David N. Louis,
    • Gordon J. Freeman,
    • Keith L. Ligon,
    • Alexander Marson,
    • E. Antonio Chiocca,
    • David A. Reardon,
    • Aviv Regev,
    • Mario L. Suvà,
    • Kai W. Wucherpfennig
    Single-cell analysis of tumor-infiltrating T cells in glioma patients identifies a T cell population co-expressing a cytotoxicity program and NK cell receptors. Mathewson et al. reveal the functional significance of NK cell receptors such as CD161 in inhibiting the anti-tumor function of T cells, highlighting their potential as targets for immunotherapy.
  • Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

    • Plinio C. Casarotto,
    • Mykhailo Girych,
    • Senem M. Fred,
    • Vera Kovaleva,
    • Rafael Moliner,
    • Giray Enkavi,
    • Caroline Biojone,
    • Cecilia Cannarozzo,
    • Madhusmita Pryiadrashini Sahu,
    • Katja Kaurinkoski,
    • Cecilia A. Brunello,
    • Anna Steinzeig,
    • Frederike Winkel,
    • Sudarshan Patil,
    • Stefan Vestring,
    • Tsvetan Serchov,
    • Cassiano R.A.F. Diniz,
    • Liina Laukkanen,
    • Iseline Cardon,
    • Hanna Antila,
    • Tomasz Rog,
    • Timo Petteri Piepponen,
    • Clive R. Bramham,
    • Claus Normann,
    • Sari E. Lauri,
    • Mart Saarma,
    • Ilpo Vattulainen,
    • Eero Castrén
    Direct binding of both typical and fast-acting antidepressants to the BDNF receptor TRKB accounts for cell biological and behavioral actions of antidepressants. This mechanism directly connects antidepressant action to neuronal plasticity and may explain the slow action of typical antidepressants.
  • RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination

    • Sijie Liu,
    • Yu Hua,
    • Jingna Wang,
    • Lingyan Li,
    • Junjie Yuan,
    • Bo Zhang,
    • Ziyang Wang,
    • Jianguo Ji,
    • Daochun Kong
    During homologous recombination (HR) and the HR-mediated repair of DNA double-strand breaks, RNA polymerase III synthesizes an RNA strand that transiently forms an RNA-DNA hybrid to protect the 3′ overhang from degradation.
  • Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption

    • Michelle M. McDonald,
    • Weng Hua Khoo,
    • Pei Ying Ng,
    • Ya Xiao,
    • Jad Zamerli,
    • Peter Thatcher,
    • Wunna Kyaw,
    • Karrnan Pathmanandavel,
    • Abigail K. Grootveld,
    • Imogen Moran,
    • Danyal Butt,
    • Akira Nguyen,
    • Alexander Corr,
    • Sean Warren,
    • Maté Biro,
    • Natalie C. Butterfield,
    • Siobhan E. Guilfoyle,
    • Davide Komla-Ebri,
    • Michael R.G. Dack,
    • Hannah F. Dewhurst,
    • John G. Logan,
    • Yongxiao Li,
    • Sindhu T. Mohanty,
    • Niall Byrne,
    • Rachael L. Terry,
    • Marija K. Simic,
    • Ryan Chai,
    • Julian M.W. Quinn,
    • Scott E. Youlten,
    • Jessica A. Pettitt,
    • David Abi-Hanna,
    • Rohit Jain,
    • Wolfgang Weninger,
    • Mischa Lundberg,
    • Shuting Sun,
    • Frank H. Ebetino,
    • Paul Timpson,
    • Woei Ming Lee,
    • Paul A. Baldock,
    • Michael J. Rogers,
    • Robert Brink,
    • Graham R. Williams,
    • J.H. Duncan Bassett,
    • John P. Kemp,
    • Nathan J. Pavlos,
    • Peter I. Croucher,
    • Tri Giang Phan
    Tracking osteoclasts during cycles of fission and fusion reveals a transcriptionally distinct “osteomorph” population that are fusion competent, motile, and capable of forming osteoclasts that resorb bone.

Theory

  • Increased stem cell proliferation in atherosclerosis accelerates clonal hematopoiesis

    • Alexander Heyde,
    • David Rohde,
    • Cameron S. McAlpine,
    • Shuang Zhang,
    • Friedrich F. Hoyer,
    • Jeffrey M. Gerold,
    • David Cheek,
    • Yoshiko Iwamoto,
    • Maximilian J. Schloss,
    • Katrien Vandoorne,
    • Oriol Iborra-Egea,
    • Christian Muñoz-Guijosa,
    • Antoni Bayes-Genis,
    • Johannes G. Reiter,
    • Morgan Craig,
    • Filip K. Swirski,
    • Matthias Nahrendorf,
    • Martin A. Nowak,
    • Kamila Naxerova
    Heyde et al. propose that clonal hematopoiesis can be a symptom rather than a cause of atherosclerosis, since this disease increases hematopoietic stem cell division, which results in accelerated somatic evolution.

Resources

  • African lungfish genome sheds light on the vertebrate water-to-land transition

    • Kun Wang,
    • Jun Wang,
    • Chenglong Zhu,
    • Liandong Yang,
    • Yandong Ren,
    • Jue Ruan,
    • Guangyi Fan,
    • Jiang Hu,
    • Wenjie Xu,
    • Xupeng Bi,
    • Youan Zhu,
    • Yue Song,
    • Huatao Chen,
    • Tiantian Ma,
    • Ruoping Zhao,
    • Haifeng Jiang,
    • Bin Zhang,
    • Chenguang Feng,
    • Yuan Yuan,
    • Xiaoni Gan,
    • Yongxin Li,
    • Honghui Zeng,
    • Qun Liu,
    • Yaolei Zhang,
    • Feng Shao,
    • Shijie Hao,
    • He Zhang,
    • Xun Xu,
    • Xin Liu,
    • Depeng Wang,
    • Min Zhu,
    • Guojie Zhang,
    • Wenming Zhao,
    • Qiang Qiu,
    • Shunping He,
    • Wen Wang
    Genome assembly and analysis of the massive African lungfish genome has shed light on genetic innovations required for the water-to-land transition
  • Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

    • Xupeng Bi,
    • Kun Wang,
    • Liandong Yang,
    • Hailin Pan,
    • Haifeng Jiang,
    • Qiwei Wei,
    • Miaoquan Fang,
    • Hao Yu,
    • Chenglong Zhu,
    • Yiran Cai,
    • Yuming He,
    • Xiaoni Gan,
    • Honghui Zeng,
    • Daqi Yu,
    • Youan Zhu,
    • Huifeng Jiang,
    • Qiang Qiu,
    • Huanming Yang,
    • Yong E. Zhang,
    • Wen Wang,
    • Min Zhu,
    • Shunping He,
    • Guojie Zhang
    Comparative analyses of divergent lineages of ray-finned fishes reveal that that these species exhibit mosaic genomic features that have facilitated the adaptive evolution of phenotypes that contributed to the water-to-land transition.

Corrections

Advertisement
Advertisement