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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 161,564 papers from 674,550 authors.

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in category cell biology

7,188 results found. For more information, click each entry to expand.

1: The SARS-CoV-2 Spike protein disrupts human cardiac pericytes function through CD147-receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease
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Posted 21 Dec 2020

The SARS-CoV-2 Spike protein disrupts human cardiac pericytes function through CD147-receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease
45,182 downloads bioRxiv cell biology

Elisa Avolio, Michele Carrabba, Rachel Milligan, Maia Kavanagh Williamson, Antonio P Beltrami, Kapil Gupta, Karen T Elvers, Monica Gamez, Rebecca Foster, Kathleen Gillespie, Fergus Hamilton, David Arnold, Imre Berger, Massimo Caputo, Andrew D Davidson, Darryl Hill, Paolo Madeddu

Severe coronavirus disease 2019 (COVID-19) manifests as a life-threatening microvascular syndrome. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses the Spike (S) protein to engage with its receptors and infect host cells. To date, it is still not known whether heart vascular pericytes (PCs) are infected by SARS-CoV-2, and if the S protein alone provokes PC dysfunction. Here, we aimed to investigate the effects of the S protein on primary human cardiac PC signalling and function. Results show, for the first time, that cardiac PCs are not permissive to SARS-CoV-2 infection in vitro, whilst a recombinant S protein alone elicits functional alterations in PCs. This was documented as: (1) increased migration, (2) reduced ability to support endothelial cell (EC) network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm, and (4) production of pro-apoptotic factors responsible for EC death. Next, adopting a blocking strategy against the S protein receptors angiotensin-converting enzyme 2 (ACE2) and CD147, we discovered that the S protein stimulates the phosphorylation/activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) through the CD147 receptor, but not ACE2, in PCs. The neutralisation of CD147, either using a blocking antibody or mRNA silencing, reduced ERK1/2 activation and rescued PC function in the presence of the S protein. In conclusion, our findings suggest that circulating S protein prompts vascular PC dysfunction, potentially contributing to establishing microvascular injury in organs distant from the site of infection. This mechanism may have clinical and therapeutic implications.

2: SARS-CoV-2 Requires Cholesterol for Viral Entry and Pathological Syncytia Formation
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Posted 14 Dec 2020

SARS-CoV-2 Requires Cholesterol for Viral Entry and Pathological Syncytia Formation
20,565 downloads bioRxiv cell biology

David W. Sanders, Chanelle C. Jumper, Paul J. Ackerman, Dan Bracha, Anita Donlic, Hahn Kim, Devin Kenney, Ivan Castello-Serrano, Saori Suzuki, Tomokazu Tamura, Alexander H. Tavares, Mohsan Saeed, Alex S. Holehouse, Alexander Ploss, Ilya Levental, Florian Douam, Robert F. Padera, Bruce D. Levy, Clifford P Brangwynne

Many enveloped viruses induce multinucleated cells (syncytia), reflective of membrane fusion events caused by the same machinery that underlies viral entry. These syncytia are thought to facilitate replication and evasion of the host immune response. Here, we report that co-culture of human cells expressing the receptor ACE2 with cells expressing SARS-CoV-2 spike, results in synapse-like intercellular contacts that initiate cell-cell fusion, producing syncytia resembling those we identify in lungs of COVID-19 patients. To assess the mechanism of spike/ACE2-driven membrane fusion, we developed a microscopy-based, cell-cell fusion assay to screen ~6000 drugs and >30 spike variants. Together with cell biological and biophysical approaches, the screen reveals an essential role for membrane cholesterol in spike-mediated fusion, which extends to replication-competent SARS-CoV-2 isolates. Our findings provide a molecular basis for positive outcomes reported in COVID-19 patients taking statins, and suggest new strategies for therapeutics targeting the membrane of SARS-CoV-2 and other fusogenic viruses.

3: Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract
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Posted 31 Mar 2020

Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract
13,710 downloads bioRxiv cell biology

Joan C. Smith, Erin L. Sausville, Vishruth Girish, Monet Lou Yuan, Kristen M. John, Jason M. Sheltzer

The factors mediating fatal SARS-CoV-2 infections are poorly understood. Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Using single-cell sequencing data, we demonstrate that ACE2 is expressed in a subset of secretory cells in the respiratory tract. Chronic smoke exposure triggers the expansion of this cell population and a concomitant increase in ACE2 expression. In contrast, quitting smoking decreases the abundance of these secretory cells and reduces ACE2 levels. Finally, we demonstrate that ACE2 expression is responsive to inflammatory signaling and can be upregulated by viral infections or interferon treatment. Taken together, these results may partially explain why smokers are particularly susceptible to severe SARS-CoV-2 infections. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination. ### Competing Interest Statement J.C.S. is a co-founder of Meliora Therapeutics and is an employee of Google, Inc. This work was performed outside of her affiliation with Google and used no proprietary knowledge or materials from Google. J.M.S. has received consulting fees from Ono Pharmaceuticals, is a member of the Advisory Board of Tyra Biosciences, and is a co-founder of Meliora Therapeutics.

4: Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris
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Posted 20 Dec 2017

Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris
13,611 downloads bioRxiv cell biology

Nicholas Schaum, Jim Karkanias, Norma F. Neff, Andrew P May, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis, Joshua Batson, Olga Botvinnik, Michelle B Chen, Steven Chen, Foad Green, Robert Jones, Ashley Maynard, Lolita Penland, Rene V Sit, Geoffrey M. Stanley, James T. Webber, Fabio Zanini, Ankit S. Baghel, Isaac Bakerman, Ishita Bansal, Daniela Berdnik, Biter Bilen, Douglas Brownfield, Corey Cain, Min Cho, Giana Cirolia, Stephanie D Conley, Aaron Demers, Kubilay Demir, Antoine de Morree, Tessa Divita, Haley du Bois, Laughing Bear Torrez Dulgeroff, Hamid Ebadi, F. Hernan Espinoza, Matt Fish, Qiang Gan, Benson M. George, Astrid Gillich, Geraldine Genetiano, Xueying Gu, Gunsagar Singh Gulati, Yan Hang, Shayan Hosseinzadeh, Albin Huang, Tal Iram, Taichi Isobe, Feather Ives, Kevin S Kao, Guruswamy Karnam, Aaron M Kershner, Bernhard Kiss, William Kong, Maya E. Kumar, Jonathan Lam, Davis P Lee, Song E Lee, Guang Li, Qingyun Li, Ling Liu, Annie Lo, Wan-Jin Lu, Anoop Manjunath, Kaia L. May, Oliver L. May, Marina McKay, Ross J Metzger, Marco Mignardi, Dullei Min, Ahmad N. Nabhan, Katharine M Ng, Joseph Noh, Rasika Patkar, Weng Chuan Peng, Robert Puccinelli, Eric J. Rulifson, Shaheen S Sikandar, Rahul Sinha, Krzysztof Szade, Weilun Tan, Cristina Tato, Krissie Tellez, Kyle Joseph Travaglini, Carolina Tropini, Lucas Waldburger, Linda J. van Weele, Michael N. Wosczyna, Jinyi Xiang, Soso Xue, Justin Youngyunpipatkul, Macy E Zardeneta, Fan Zhang, Lu Zhou, Paola Castro, Derek Croote, Joseph DeRisi, Angela Pisco, Bernhard M. Kiss, Christin S Kuo, Benoit Lehallier, Patricia K. Nguyen, Serena Y. Tan, Bruce M. Wang, Hanadie Yousef, Philip A Beachy, Charles K. F. Chan, Kerwyn Casey Huang, Kenneth Weinberg, Sean Wu, Ben A. Barres, Michael F Clarke, Seung K Kim, Mark A Krasnow, Norma Neff, Roeland Nusse, Thomas A. Rando, Justin Sonnenburg, Irving L. Weissman, Sean M. Wu

We have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, revealing gene expression in poorly characterized cell populations and allowing for direct and controlled comparison of gene expression in cell types shared between tissues, such as T-lymphocytes and endothelial cells from distinct anatomical locations. Two distinct technical approaches were used for most tissues: one approach, microfluidic droplet-based 3-end counting, enabled the survey of thousands of cells at relatively low coverage, while the other, FACS-based full length transcript analysis, enabled characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

5: Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms
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Posted 08 Jan 2018

Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms
13,264 downloads bioRxiv cell biology

Tsung-Li Liu, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, T. W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, E. M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution without inducing undue stress on either. We combined lattice light sheet microscopy with two-channel adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages, and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.

6: The Human Cell Atlas
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Posted 08 May 2017

The Human Cell Atlas
12,829 downloads bioRxiv cell biology

Aviv Regev, Sarah A. Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed S. Lein, Sten Linnarsson, Joakim Lundeberg, Partha Majumder, John Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe’er, Anthony Phillipakis, Chris P Ponting, Steve Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J.T. Stubbington, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, the Human Cell Atlas Meeting Participants

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body, by undertaking a Human Cell Atlas Project as an international collaborative effort. The aim would be to define all human cell types in terms of distinctive molecular profiles (e.g., gene expression) and connect this information with classical cellular descriptions (e.g., location and morphology). A comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, as well as provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas.

7: SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients
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Posted 25 Aug 2020

SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients
11,593 downloads bioRxiv cell biology

Juan A Perez-Bermejo, Serah Kang, Sarah J. Rockwood, Camille R. Simoneau, David A. Joy, Gokul N. Ramadoss, Ana C. Silva, Will R. Flanigan, Huihui Li, Ken Nakamura, Jeffrey D. Whitman, Melanie Ott, Bruce R Conklin, Todd C McDevitt

Although COVID-19 causes cardiac dysfunction in up to 25% of patients, its pathogenesis remains unclear. Exposure of human iPSC-derived heart cells to SARS-CoV-2 revealed productive infection and robust transcriptomic and morphological signatures of damage, particularly in cardiomyocytes. Transcriptomic disruption of structural proteins corroborated adverse morphologic features, which included a distinct pattern of myofibrillar fragmentation and numerous iPSC-cardiomyocytes lacking nuclear DNA. Human autopsy specimens from COVID-19 patients displayed similar sarcomeric disruption, as well as cardiomyocytes without DNA staining. These striking cytopathic features provide new insights into SARS-CoV-2 induced cardiac damage, offer a platform for discovery of potential therapeutics, and raise serious concerns about the long-term consequences of COVID-19. ### Competing Interest Statement B.R.C. is a founder of Tenaya Therapeutics (https://www.tenayatherapeutics.com/), a company focused on finding treatments for heart failure, including genetic cardiomyopathies. B.R.C. and T.C.M. hold equity in Tenaya.

8: Inter-homologue repair in fertilized human eggs?
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Posted 28 Aug 2017

Inter-homologue repair in fertilized human eggs?
10,432 downloads bioRxiv cell biology

Dieter Egli, Michael V. Zuccaro, Michal Kosicki, George McDonald Church, Allan Bradley, Maria Jasin

Many human diseases have an underlying genetic component. The development and application of methods to prevent the inheritance of damaging mutations through the human germline could have significant health benefits, and currently include preimplantation genetic diagnosis and carrier screening. Ma et al. take this a step further by attempting to remove a disease mutation from the human germline through gene editing (1). They assert the following advances: (i) the correction of a pathogenic gene mutation responsible for hypertrophic cardiomyopathy in human embryos using CRISPR-Cas9 and (ii) the avoidance of mosaicism in edited embryos. In the case of correction, the authors conclude that repair using the homologous chromosome was as or more frequent than mutagenic nonhomologous end-joining (NHEJ). Their conclusion is significant, if validated, because such a self-repair mechanism would allow gene correction without the introduction of a repair template. While the authors analyses relied on the failure to detect mutant alleles, here we suggest approaches to provide direct evidence for inter-homologue recombination and discuss other events consistent with the data. We also review the biological constraints on inter-homologue recombination in the early embryo. (1) Ma, H. et al. Correction of a pathogenic gene mutation in human embryos. Nature, doi:10.1038/nature23305 (2017).

9: Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)
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Posted 28 Sep 2015

Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)
10,089 downloads bioRxiv cell biology

Hitoshi Niwa

In January 2014, it was reported that strong external stimuli, such as a transient low-pH stressor, was capable of inducing the reprogramming of mammalian somatic cells, resulting in the generation of pluripotent cells (Obokata et al. 2014a, b). This cellular reprograming event was designated 'stimulus-triggered acquisition of pluripotency' (STAP) by the authors of these reports. However, after multiple instances of scientific misconduct in the handling and presentation of the data were brought to light, both reports were retracted. To investigate the actual scientific significance of the purported STAP phenomenon, we sought to repeat the original experiments based on the methods presented in the retracted manuscripts and other relevant information. As a result, we have concluded that the STAP phenomenon as described in the original studies is not reproducible.

10: Large field of view-spatially resolved transcriptomics at nanoscale resolution
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Posted 19 Jan 2021

Large field of view-spatially resolved transcriptomics at nanoscale resolution
10,016 downloads bioRxiv cell biology

Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Jin Yang, Wenjiao Li, Jiangshan Xu, Shijie Hao, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Feng Lin, Xiaoxuan Tang, Zhao Li, Yan Hong, Defeng Fu, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Zhifeng Wang, Zhaohui Wang, Yue Yuan, Giacomo Volpe, Carl Ward, Pura Munoz-Canoves, Jean Paul Thiery, Fuxiang Zhao, Mei Li, Haoyan Kuang, Ou Wang, Haorong Lu, Bo Wang, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J Cornall, Mathias Uhlen, Miguel A. Esteban, Yuxiang Li, Longqi Liu, Xun Xu, Jian Wang

High-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. Here, we have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we applied Stereo-seq to the adult mouse brain and sagittal sections of E11.5 and E16.5 mouse embryos. Thanks to its unique features and amenability to additional modifications, Stereo-seq can pave the way for the systematic spatially resolved-omics characterization of tissues and organisms.

11: The protein expression profile of ACE2 in human tissues
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Posted 03 Apr 2020

The protein expression profile of ACE2 in human tissues
9,651 downloads bioRxiv cell biology

Feria Hikmet, Loren Méar, Åsa Edvinsson, Patrick Micke, Mathias Uhlen, Cecilia Lindskog

The novel SARS-coronavirus 2 (SARS-CoV-2) poses a global challenge on healthcare and society. For understanding the susceptibility for SARS-CoV-2 infection, the cell type-specific expression of the host cell surface receptor is necessary. The key protein suggested to be involved in host cell entry is Angiotensin I converting enzyme 2 (ACE2). Here, we report the expression pattern of ACE2 across >150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitutes an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection. ### Competing Interest Statement The authors have declared no competing interest.

12: A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse
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Posted 08 Jun 2019

A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse
9,449 downloads bioRxiv cell biology

The Tabula Muris Consortium, Angela Oliveira Pisco, Aaron McGeever, Nicholas Schaum, Jim Karkanias, Norma F. Neff, Spyros Darmanis, Tony Wyss-Coray, Stephen R. Quake

Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death[1][1]. Despite rapid advances over recent years, many of the molecular and cellular processes which underlie progressive loss of healthy physiology are poorly understood[2][2]. To gain a better insight into these processes we have created a single cell transcriptomic atlas across the life span of Mus musculus which includes data from 23 tissues and organs. We discovered cell-specific changes occurring across multiple cell types and organs, as well as age related changes in the cellular composition of different organs. Using single-cell transcriptomic data we were able to assess cell type specific manifestations of different hallmarks of aging, such as senescence[3][3], genomic instability[4][4] and changes in the organism’s immune system[2][2]. This Tabula Muris Senis provides a wealth of new molecular information about how the most significant hallmarks of aging are reflected in a broad range of tissues and cell types. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4

13: Neuropilin-1 is a host factor for SARS-CoV-2 infection
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Posted 05 Jun 2020

Neuropilin-1 is a host factor for SARS-CoV-2 infection
9,186 downloads bioRxiv cell biology

James L Daly, Boris Simonetti, Carlos Antón-Plágaro, Maia Kavanagh Williamson, Deborah Shoemark, Lorena Simón-Gracia, Katja Klein, Michael Bauer, Reka Hollandi, Urs F Greber, Peter Horvath, Richard B. Sessions, Ari Helenius, Julian A Hiscox, Tambet Teesalu, David Matthews, Andrew D. D. Davidson, Peter J. Cullen, Yohei Yamauchi

SARS-CoV-2 is the causative agent of COVID-19, a coronavirus disease that has infected more than 6.6 million people and caused over 390,000 deaths worldwide. The Spike (S) protein of the virus forms projections on the virion surface responsible for host cell attachment and penetration. This viral glycoprotein is synthesized as a precursor in infected cells and, to be active, must be cleaved to two associated polypeptides: S1 and S2. For SARS-CoV-2 the cleavage is catalysed by furin, a host cell protease, which cleaves the S protein precursor at a specific sequence motif that generates a polybasic Arg-Arg-Ala-Arg (RRAR) C-terminal sequence on S1. This sequence motif conforms to the C-end rule (CendR), which means that the C-terminal sequence may allow the protein to associate with cell surface neuropilin-1 (NRP1) and neuropilin-2 (NRP2) receptors. Here we demonstrate using immunoprecipitation, site-specific mutagenesis, structural modelling, and antibody blockade that, in addition to engaging the known receptor ACE2, S1 can bind to NRP1 through the canonical CendR mechanism. This interaction enhances infection by SARS-CoV-2 in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection, and provides a therapeutic target for COVID-19. ### Competing Interest Statement The authors have declared no competing interest.

14: Atlas of Subcellular RNA Localization Revealed by APEX-seq
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Posted 26 Oct 2018

Atlas of Subcellular RNA Localization Revealed by APEX-seq
9,178 downloads bioRxiv cell biology

Furqan M. Fazal, Shuo Han, Pornchai Kaewsapsak, Kevin R Parker, Jin Xu, Alistair N Boettiger, Howard Y. Chang, Alice Y. Ting

We introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

15: CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
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Posted 24 Jun 2019

CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes
8,783 downloads bioRxiv cell biology

Mirjana Efremova, Miquel Vento-Tormo, Sarah A. Teichmann, Roser Vento-Tormo

Cell-cell communication mediated by receptor-ligand complexes is crucial for coordinating diverse biological processes, such as development, differentiation and responses to infection. In order to understand how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions. Our repository takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, the procedures for inferring cell-cell communication networks from scRNA-seq data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v2.0 is a novel version of our resource that incorporates additional functionalities to allow users to introduce new interacting molecules and reduce the time and resources needed to interrogate large datasets. CellPhoneDB v2.0 is publicly available at https://github.com/Teichlab/cellphonedb and as a user-friendly web interface at http://www.cellphonedb.org/. In our protocol, we demonstrate how to reveal meaningful biological discoveries from CellPhoneDB v2.0 using published data sets.

16: Mitochondria Are Physiologically Maintained At Close To 50 °C
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Posted 02 May 2017

Mitochondria Are Physiologically Maintained At Close To 50 °C
7,850 downloads bioRxiv cell biology

Dominique Chrétien, Paule Bénit, Hyung-Ho Ha, Susanne Keipert, Riyad El-Khoury, Young-Tae Chang, Martin Jastroch, Howard T. Jacobs, Pierre Rustin, Malgorzata Rak

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, while a noticeable proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 C, mitochondria were more than 10 C warmer when the respiratory chain was fully functional, both in HEK293cells and primary skin fibroblasts. This differential was abolished in cells lacking mitochondrial DNA or by respiratory inhibitors, but preserved or enhanced by expressing thermogenic enzymes such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at, or slightly above, 50 C. Our study prompts a re-examination of the literature on mitochondria, taking account of the inferred high temperature.

17: Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease
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Posted 05 Aug 2019

Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease
7,778 downloads bioRxiv cell biology

Richard John Wheeler, Hyun O Lee, Ina Poser, Arun Pal, Thom Doeleman, Satoshi Kishigami, Sukhleen Kour, Eric Nathaniel Anderson, Lara Marrone, Anastasia C. Murthy, Marcus Jahnel, Xiaojie Zhang, Edgar Boczek, Anatol Fritsch, Nicolas L Fawzi, Jared Sterneckert, Udai Pandey, Della C. David, Benjamin G. Davis, Andrew Baldwin, Andreas Hermann, Marc Bickle, Simon Alberti, Anthony A. Hyman

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with few avenues for treatment. Many proteins implicated in ALS associate with stress granules, which are examples of liquid-like compartments formed by phase separation. Aberrant phase transition of stress granules has been implicated in disease, suggesting that modulation of phase transitions could be a possible therapeutic route. Here, we combine cell-based and protein-based screens to show that lipoamide, and its related compound lipoic acid, reduce the propensity of stress granule proteins to aggregate in vitro . More significantly, they also prevented aggregation of proteins over the life time of Caenorhabditis elegans . Observations that they prevent dieback of ALS patient-derived (FUS mutant) motor neuron axons in culture and recover motor defects in Drosophila melanogaster expressing FUS mutants suggest plausibility as effective therapeutics. Our results suggest that altering phase behaviour of stress granule proteins in the cytoplasm could be a novel route to treat ALS.

18: Cellular and Molecular Probing of Intact Transparent Human Organs
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Posted 21 May 2019

Cellular and Molecular Probing of Intact Transparent Human Organs
7,001 downloads bioRxiv cell biology

Shan Zhao, Mihail Ivilinov Todorov, Ruiyao Cai, Hanno Steinke, Elisabeth Kemter, Eckhard Wolf, Jan Lipfert, Ingo Bechmann, Ali Ertürk

Optical tissue transparency permits cellular and molecular investigation of complex tissues in 3D, a fundamental need in biomedical sciences. Adult human organs are particularly challenging for this approach, owing to the accumulation of dense and sturdy molecules in decades-aged human tissues. Here, we introduce SHANEL method utilizing a new tissue permeabilization approach to clear and label stiff human organs. We used SHANEL to generate the first intact transparent adult human brain and kidney, and perform 3D histology using antibodies and dyes in centimeters depth. Thereby, we revealed structural details of the sclera, iris and suspensory ligament in the human eye, and the vessels and glomeruli in the human kidney. We also applied SHANEL on transgenic pig organs to map complex structures of EGFP expressing beta cells in >10 cm size pancreas. Overall, SHANEL is a robust and unbiased technology to chart the cellular and molecular architecture of intact large mammalian organs.

19: OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization
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Posted 29 Mar 2021

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization
6,707 downloads bioRxiv cell biology

Nathan H. Cho, Keith C Cheveralls, Andreas-David Brunner, Kibeom Kim, Andre C. Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y. Li, Hera Canaj, James Y.S. Kim, Edna M. Setwart, Christian Gnann, Frank McCarthy, Joana P. Cabrera, Rachel M. Brunetti, Bryant B. Chhun, Greg Dingle, Marco Y. Hein, Bo Huang, Shalin B. Mehta, Jonathan Weissman, Rafael Gomez-Sjoberg, Daniel N Itzhak, Loic Alain Royer, Matthias Mann, Manuel Leonetti

Elucidating the wiring diagram of the human cell is one of the central goals of the post-genomic era. Here, we integrate genome engineering, confocal imaging, mass spectrometry and data science to systematically map protein localization in live cells and protein interactions under endogenous expression conditions. For this, we generated a library of 1,311 CRISPR-edited cell lines harboring fluorescent tags that also serve as handles for affinity capture, and applied a new machine learning framework to encode the interaction and localization profiles of each protein. Our approach provides a data-driven description of the molecular and spatial networks that organize the human proteome. We show that unsupervised clustering of these networks delineates functional groups and facilitates biological discovery, while hierarchical analyses uncover the core features that template cellular architecture. Furthermore, we discover that localization signatures are remarkably predictive of protein function, and often contain enough information to identify molecular interactions. Paired with a fully interactive website (opencell.czbiohub.org), OpenCell is a resource for the quantitative cartography of human cellular organization.

20: CRISPR interference-based platform for multimodal genetic screens in human iPSC-derived neurons
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Posted 07 Jan 2019

CRISPR interference-based platform for multimodal genetic screens in human iPSC-derived neurons
6,429 downloads bioRxiv cell biology

Ruilin Tian, Mariam A Gachechiladze, Connor H Ludwig, Matthew T. Laurie, Jason Y Hong, Diane Nathaniel, Anika V Prabhu, Michael S Fernandopulle, Rajan Patel, Mehrnoosh Abshari, Michael E Ward, Martin Kampmann

CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. However, most previous CRISPR-based screens were conducted in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. First, a survival-based screen revealed neuron-specific essential genes and genes that improved neuronal survival upon knockdown. Second, a screen with a single-cell transcriptomic readout uncovered several examples of genes whose knockdown had strikingly cell-type specific consequences. Third, a longitudinal imaging screen detected distinct consequences of gene knockdown on neuronal morphology. Our results highlight the power of unbiased genetic screens in iPSC-derived differentiated cell types and provide a platform for systematic interrogation of normal and disease states of neurons.

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