Leucine-Rich Repeat Containing 8A Contributes to the Expansion Of
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LRRC8A Regulates Hypotonicity-Induced NLRP3 Inflammasome Activation
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.146225; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. LRRC8A regulates hypotonicity-induced NLRP3 inflammasome activation Jack P. Green1*,#, Tessa Swanton1*, Lucy V. Morris1, Lina Y. El-Sharkawy2, James Cook1, Shi Yu1, James Beswick2, Antony Adamson3, Neil Humphreys3,4, Richard A. Bryce2, Sally Freeman2, Catherine Lawrence1,5, David Brough1,5,# 1Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK. 2Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK. 3Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK. 4Present address: EMBL-Rome, Epigenetics and Neurobiology Unit, Adriano Buzzati- Traverso Campus, Via Ramarini 32, 00015 Monterotondo (RM), Italy. 5Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK. * Contributed equally # To whom correspondence should be addressed: David Brough. Tel: +44 (0)161 275 5039; Email: [email protected] Jack Green. Tel +44 (0)161 306 0502; Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.146225; this version posted June 12, 2020. -
Abstracts Genome 10K & Genome Science 29 Aug - 1 Sept 2017 Norwich Research Park, Norwich, Uk
Genome 10K c ABSTRACTS GENOME 10K & GENOME SCIENCE 29 AUG - 1 SEPT 2017 NORWICH RESEARCH PARK, NORWICH, UK Genome 10K c 48 KEYNOTE SPEAKERS ............................................................................................................................... 1 Dr Adam Phillippy: Towards the gapless assembly of complete vertebrate genomes .................... 1 Prof Kathy Belov: Saving the Tasmanian devil from extinction ......................................................... 1 Prof Peter Holland: Homeobox genes and animal evolution: from duplication to divergence ........ 2 Dr Hilary Burton: Genomics in healthcare: the challenges of complexity .......................................... 2 INVITED SPEAKERS ................................................................................................................................. 3 Vertebrate Genomics ........................................................................................................................... 3 Alex Cagan: Comparative genomics of animal domestication .......................................................... 3 Plant Genomics .................................................................................................................................... 4 Ksenia Krasileva: Evolution of plant Immune receptors ..................................................................... 4 Andrea Harper: Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees ............................................................................................................ -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
The LRRC8A:C Heteromeric Channel Is a Cgamp Transporter and the Dominant
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted February 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells Lauren J. Lahey1,2, Xianlan Wen3, Rachel E. Mardjuki2,4, Volker Böhnert2,5, Christopher Ritchie2,5, Jacqueline A. Carozza2,4, Gaelen T. Hess2,6, Merritt Maduke3, Michael C. Bassik2,6, and Lingyin Li2,5,7,* 1Biophysics Program, 2Stanford ChEM-H, 3Department of Molecular and Cellular Physiology, 4Department of Chemistry, 5Department of Biochemistry, 6Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA. 7Lead Contact *Correspondence: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted February 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. SUMMARY Extracellular 2'3'-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import actiVity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient. cGAMP influences anion influx through VRAC, indicating it is likely a direct substrate of the channel. -
Selective Transport of Neurotransmitters and Modulators by Distinct Volume-Regulated LRRC8 Anion Channels Darius Lutter1,2,3, Florian Ullrich1,2, Jennifer C
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 1122-1133 doi:10.1242/jcs.196253 RESEARCH ARTICLE Selective transport of neurotransmitters and modulators by distinct volume-regulated LRRC8 anion channels Darius Lutter1,2,3, Florian Ullrich1,2, Jennifer C. Lueck1,2,3, Stefan Kempa2 and Thomas J. Jentsch1,2,4,* ABSTRACT volume regulation (Jentsch, 2016; Nilius et al., 1997; Pedersen In response to swelling, mammalian cells release chloride and et al., 2016). This plasma membrane channel, which appears to be organic osmolytes through volume-regulated anion channels expressed in all cells, is normally closed but can be activated by cell swelling or other cellular signaling cascades. In most cells, VRAC (VRACs). VRACs are heteromers of LRRC8A and other LRRC8 − isoforms (LRRC8B to LRRC8E), which are co-expressed in HEK293 opening leads to an efflux of Cl , which, together with an efflux of + + and most other cells. The spectrum of VRAC substrates and its K through independent K channels, lowers the intracellular dependence on particular LRRC8 isoforms remains largely unknown. osmolarity and, by secondarily driving water efflux, results in We show that, besides the osmolytes taurine and myo-inositol, regulatory volume decrease. Cell swelling also stimulates an efflux ‘ ’ myo LRRC8 channels transport the neurotransmitters glutamate, of organic osmolytes such as -inositol, taurine and glutamate. aspartate and γ-aminobutyric acid (GABA) and the co-activator It was controversial whether this release occurs through VRAC or D-serine. HEK293 cells engineered to express defined subsets of through a distinct channel named VSOAC (for volume-sensitive LRRC8 isoforms were used to elucidate the subunit-dependence organic osmolyte/anion channel) (Jackson and Strange, 1993; of transport. -
Evolution of the P53-MDM2 Pathway Emma Åberg1, Fulvio Saccoccia1, Manfred Grabherr1, Wai Ying Josefin Ore1, Per Jemth1* and Greta Hultqvist1,2*
Åberg et al. BMC Evolutionary Biology (2017) 17:177 DOI 10.1186/s12862-017-1023-y RESEARCH ARTICLE Open Access Evolution of the p53-MDM2 pathway Emma Åberg1, Fulvio Saccoccia1, Manfred Grabherr1, Wai Ying Josefin Ore1, Per Jemth1* and Greta Hultqvist1,2* Abstract Background: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published. Results: Here, we have examined the evolution of the p53/p63/p73 protein family with particular focus on the p53/ p63/p73 transactivation domain (TAD) and its co-evolution with the p53/p63/p73-binding domain (p53/p63/p73BD) of MDM2. We found that the TAD and p53/p63/p73BD share a strong evolutionary connection. If one of the domains of the protein is lost in a phylum, then it seems very likely to be followed by loss of function by the other domain as well, and due to the loss of function it is likely to eventually disappear. By focusing our phylogenetic analysis to p53/p63/ p73 and MDM proteins from phyla that retain the interaction domains TAD and p53/p63/p73BD, we built phylogenetic trees of p53/p63/p73 and MDM based on both vertebrate and invertebrate species. -
Vracs Swallow Platinum Drugs
News & Views VRACs swallow platinum drugs Thomas Voets, Bernd Nilius & Rudi Vennekens Platinum-based drugs such as cisplatin react covalently with the N7 nitrogen in essential structural component of VRACs and carboplatin are on the WHO model list guanines (Galluzzi et al, 2012). This causes (Qiu et al, 2014; Voss et al, 2014). LRRC8 of essential medicines, as highly effective distortions in the DNA, which can provoke proteins form a small family of integral chemotherapeutic drugs for the treatment cell cycle arrest and ultimately programmed membrane proteins with four transmem- of various solid tumors. These drugs react cell death (Kelland, 2007; Galluzzi et al, brane helices and include five homologues with purine residues in DNA, thereby caus- 2012). However, before cisplatin and related (LRRC8A-E) in mammals and most other ing DNA damage, inhibition of cell division, drugs can exert their antiproliferative effects, chordates (Abascal & Zardoya, 2012). and eventually cell death. However, the they first need to be taken up by the targeted Current evidence indicates that functional mechanisms whereby platinum-based cells (Galluzzi et al, 2012). Cisplatin and VRAC channels are heteromultimers that drugs enter cancer cells remained poorly carboplatin are relatively polar, compared to contain the obligatory LRRC8A subunit understood. In this issue, Planells-Cases other classes of small-molecule (anticancer) supplemented with at least one of the other et al (2015) provide evidence that cells drugs. Consequently, their passive diffusion four isoforms (Voss et al, 2014). Based on take up cisplatin and carboplatin via through the plasma membrane is slow, and limited homology with pannexins, a hexam- volume-regulated anion channels (VRACs), other transport pathways, including trans- eric architecture has been proposed, but this more specifically VRACs composed of porters and channels, have been postulated. -
The LRRC8A:C Heteromeric Channel Is a Cgamp Transporter and the Dominant Cgamp Importer in Human Vasculature Cells
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted March 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells Lauren J. Lahey1,2, Xianlan Wen3, Rachel E. Mardjuki2,4, Volker Böhnert2,5, Gaelen T. Hess2,6, Christopher Ritchie2,5, Jacqueline A. Carozza2,4, Merritt Maduke3, Michael C. Bassik2,6, and Lingyin Li2,5,7,* 1Biophysics Program, 2Stanford ChEM-H, 3Department of Molecular and Cellular Physiology, 4Department of Chemistry, 5Department of Biochemistry, 6Department of Genetics, Stanford University, School of Medicine, Stanford, CA 94305 USA. 7Lead Contact *Correspondence: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.02.13.948273; this version posted March 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. SUMMARY Extracellular 2'3'-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import actiVity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient, and channel activation or inhibition modulates cGAMP transport. -
Searching the Evolutionary Origin of Epithelial Mucus Protein Components—Mucins and FCGBP Article Open Access
Searching the Evolutionary Origin of Epithelial Mucus Protein Components—Mucins and FCGBP Tiange Lang1,2, Sofia Klasson1, Erik Larsson1, Malin E. V. Johansson1, Gunnar C. Hansson1, and Tore Samuelsson*,1 1Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden 2Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China *Corresponding author: E-mail: [email protected] Associate editor: Katja Nowick Abstract The gel-forming mucins are large glycosylated proteins that are essential components of the mucus layers covering epithelial cells. Using novel methods of identifying mucins based on profile hidden Markov models, we have found a large number of such proteins in Metazoa, aiding in their classification and allowing evolutionary studies. Most vertebrates have 5–6 gel-forming mucin genes and the genomic arrangement of these genes is well conserved throughout verte- brates. An exception is the frog Xenopus tropicalis with an expanded repertoire of at least 26 mucins of this type. Furthermore, we found that the ovomucin protein, originally identified in chicken, is characteristic of reptiles, birds, and amphibians. Muc6 is absent in teleost fish, but we now show that it is present in animals such as ghost sharks, dem- onstrating an early origin in vertebrate evolution. Public RNA-Seq data were analyzed with respect to mucins in zebrafish, frog, and chicken, thus allowing comparison in regard of tissue and developmental specificity. Analyses of invertebrate proteins reveal that gel-forming-mucin type of proteins is widely distributed also in this group. Their presence in Cnidaria, Porifera, and in Ctenophora (comb jellies) shows that these proteins were present early in metazoan evolution. -
The Conserved DNMT1-Dependent Methylation Regions in Human Cells
Freeman et al. Epigenetics & Chromatin (2020) 13:17 https://doi.org/10.1186/s13072-020-00338-8 Epigenetics & Chromatin RESEARCH Open Access The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure Dana M. Freeman1 , Dan Lou1, Yanqiang Li1, Suzanne N. Martos1 and Zhibin Wang1,2,3* Abstract Background: Allele-specifc DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The signifcance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-tradi- tional ASMs are sensitive to exposures in association with human disease. Results: We frst explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal develop- ment and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24 h. Indeed,14 genes adjacent to our identifed regions were diferentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegenera- tion. -
Supporting Online Material
1 Conserved Transcriptomic Profiles Underpin Monogamy across 2 Vertebrates 3 4 Rebecca L. Younga,b,1, Michael H. Ferkinc, Nina F. Ockendon-Powelld, Veronica N. Orre, 5 Steven M. Phelpsa,f, Ákos Pogányg, Corinne L. Richards-Zawackih, Kyle Summersi, 6 Tamás Székelyd,j,k, Brian C. Trainore, Araxi O. Urrutiaj,l, Gergely Zacharm, Lauren A. 7 O’Connelln, and Hans A. Hofmanna,b,f,1 8 9 1correspondence to: [email protected]; [email protected] 10 1 www .pnas.org/cgi/doi/10.1073/pnas.1813775115 11 Materials and Methods 12 Sample collection and RNA extraction 13 Reproductive males of each focal species were sacrificed and brains were rapidly 14 dissected and stored to preserve RNA (species-specific details provided below). All animal 15 care and use practices were approved by the respective institutions. For each species, 16 RNA from three individuals was pooled to create an aggregate sample for transcriptome 17 comparison. The focus of this study is to characterize similarity among species with 18 independent species-level transitions to a monogamous mating system rather than to 19 characterize individual-level variation in gene expression. Pooled samples are reflective 20 of species-level gene expression variation of each species and limit potentially 21 confounding individual variation for species-level comparisons (1, 2). While exploration of 22 individual variation is critical to identify mechanisms underlying differences in behavioral 23 expression, high levels of variation between two pooled samples of conspecifics could 24 obscure more general species-specific gene expression patterns. Note that two pooled 25 replicates per species would not be sufficiently large for estimating within species 26 variance, and the effect of an outlier within a pool of two individuals would be considerable. -
A FRET Sensor of C-Terminal Movement Reveals VRAC Activation
RESEARCH ARTICLE A FRET sensor of C-terminal movement reveals VRAC activation by plasma membrane DAG signaling rather than ionic strength Benjamin Ko¨ nig1, Yuchen Hao2,3,4, Sophia Schwartz1, Andrew JR Plested2,3,4, Tobias Stauber1* 1Institute of Chemistry and Biochemistry, Freie Universita¨ t Berlin, Berlin, Germany; 2Institute of Biology, Humboldt Universita¨ t zu Berlin, Berlin, Germany; 3Leibniz Forschungsinstitut fu¨ r Molekulare Pharmakologie (FMP), Berlin, Germany; 4NeuroCure, Charite´ Universita¨ tsmedizin, Berlin, Germany Abstract Volume-regulated anion channels (VRACs) are central to cell volume regulation. Recently identified as hetero-hexamers formed by LRRC8 proteins, their activation mechanism remains elusive. Here, we measured Fo¨ rster resonance energy transfer (FRET) between fluorescent proteins fused to the C-termini of LRRC8 subunits. Inter-subunit FRET from LRRC8 complexes tracked VRAC activation. With patch-clamp fluorometry, we confirmed that the cytoplasmic domains rearrange during VRAC opening. With these FRET reporters, we determined VRAC activation, non-invasively, in live cells and their subcompartments. Reduced intracellular ionic strength did not directly activate VRACs, and VRACs were not activated on endomembranes. Instead, pharmacological manipulation of diacylglycerol (DAG), and protein kinase D (PKD) activity, activated or inhibited plasma membrane-localized VRACs. Finally, we resolved previous contradictory reports concerning VRAC activation, using FRET to detect robust activation by PMA that was absent during whole-cell patch clamp. Overall, non-invasive VRAC measurement by FRET *For correspondence: is an essential tool for unraveling its activation mechanism. [email protected] DOI: https://doi.org/10.7554/eLife.45421.001 Competing interests: The authors declare that no competing interests exist.