1
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Zhang Y, Zhai S, Huang H, Qin S, Sun M, Chen Y, Lan X, Li G, Huang Z, Wang D, Luo Y, Xiao W, Li H, He X, Chen M, Peng X, Song X. Efficient signal sequence of mRNA vaccines enhances the antigen expression to expand the immune protection against viral infection. J Nanobiotechnology 2024; 22:295. [PMID: 38807131 PMCID: PMC11134928 DOI: 10.1186/s12951-024-02488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
The signal sequence played a crucial role in the efficacy of mRNA vaccines against virus pandemic by influencing antigen translation. However, limited research had been conducted to compare and analyze the specific mechanisms involved. In this study, a novel approach was introduced by substituting the signal sequence of the mRNA antigen to enhance its immune response. Computational simulations demonstrated that various signal peptides differed in their binding capacities with the signal recognition particle (SRP) 54 M subunit, which positively correlated with antigen translation efficiency. Our data revealed that the signal sequences of tPA and IL-6-modified receptor binding domain (RBD) mRNA vaccines sequentially led to higher antigen expression and elicited more robust humoral and cellular immune protection against the SARS-CoV-2 compared to the original signal sequence. By highlighting the importance of the signal sequence, this research provided a foundational and safe approach for ongoing modifications in signal sequence-antigen design, aiming to optimize the efficacy of mRNA vaccines.
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Affiliation(s)
- Yupei Zhang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Songhui Zhai
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hai Huang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Min Sun
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuting Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xing Lan
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guohong Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiying Huang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Denggang Wang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaoyao Luo
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hao Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xi He
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
| | - Xingchen Peng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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2
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Mo C, Li X, Wu Q, Fan Y, Liu D, Zhu Y, Yang Y, Liao X, Zhou Z, Zhou L, Li Q, Zhang Q, Liu W, Zhou R, Tian X. SARS-CoV-2 mRNA vaccine requires signal peptide to induce antibody responses. Vaccine 2023; 41:6863-6869. [PMID: 37821314 DOI: 10.1016/j.vaccine.2023.09.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
New SARS-CoV-2 variants continue to prevail worldwide, and effective vaccines are needed to prevent an epidemic. mRNA vaccines are gradually being applied to the prevention and control of infectious diseases with significant safety and effectiveness. The spike (S) protein of SARS-CoV-2 is the main target of mRNA vaccine design, but the impact of the signal peptide (SP), transmembrane region (TM), and cytoplasmic tail (CT) on mRNA vaccine remains unclear. In this study, we constructed three forms of mRNA vaccines related to the S protein: full-length, deletion of the TM and CT, and simultaneous deletion of the SP, TM and CT, and compared their immunogenicity. Our experimental data show that full-length S protein and deletion of the TM and CT could effectively induce neutralizing antibody production in mice, while S protein without the SP and TM could not. This indicates that the S protein SP is necessary for the design of mRNA vaccine.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Mice
- COVID-19 Vaccines/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Protein Sorting Signals/genetics
- mRNA Vaccines/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- COVID-19/prevention & control
- COVID-19/immunology
- Mice, Inbred BALB C
- Female
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/administration & dosage
- Humans
- Immunogenicity, Vaccine
- Antibody Formation/immunology
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Affiliation(s)
- Chuncong Mo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Xiao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qianying Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ye Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yuhui Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yujie Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiaohong Liao
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Liling Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qiuru Li
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Qiong Zhang
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China.
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
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3
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Liu L, Bulla LA. Cell death signaling in Anopheles gambiae initiated by Bacillus thuringiensis Cry4B toxin involves Na +/K + ATPase. Exp Biol Med (Maywood) 2023; 248:1191-1205. [PMID: 37642306 PMCID: PMC10621475 DOI: 10.1177/15353702231188072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/10/2023] [Indexed: 08/31/2023] Open
Abstract
Identifying the mechanisms by which bacterial pathogens kill host cells is fundamental to understanding how to control and prevent human and animal disease. In the case of Bacillus thuringiensis (Bt), such knowledge is critical to using the bacterium to kill insect vectors that transmit human and animal disease. For the Cry4B toxin produced by Bt, its capacity to kill Anopheles gambiae, the primary mosquito vector of malaria, is the consequence of a variety of signaling activities. We show here that Cry4B, acting as first messenger, binds specifically to the bitopic cadherin BT-R3 G-protein-coupled receptor (GPCR) localized in the midgut of A. gambiae, activating the downstream second messenger cyclic adenosine monophosphate (cAMP). The direct result of the Cry4B-BT-R3 binding is the release of αs from the heterotrimeric αβγ-G-protein complex and its activation of adenylyl cyclase (AC). The upshot is an increased level of cAMP, which activates protein kinase A (PKA). The functional impact of cAMP-PKA signaling is the stimulation of Na+/K+-ATPase (NKA) which serves as an Na+/K+ pump to maintain proper gradients of extracellular Na+ and intracellular K+. Increased level of cAMP amplifies NKA and upsets normal ion concentration gradients. NKA, as a scaffolding protein, accelerates the first messenger signal to the nucleus, generating additional BT-R3 molecules and promoting their exocytotic trafficking to the cell membrane. Accumulation of BT-R3 on the cell surface facilitates recruitment of additional toxin molecules which, in turn, amplify the original signal in a cascade-like manner. This report provides the first evidence of a bacterial toxin using NKA via AC/PKA signaling to execute cell death.
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Affiliation(s)
- Li Liu
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080-3021 USA
| | - Lee A Bulla
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080-3021 USA
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4
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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5
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Zhang Z, Wan X, Li X, Wan C. Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196688. [PMID: 36235223 PMCID: PMC9570739 DOI: 10.3390/molecules27196688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2; the spike protein is a key structural protein that mediates infection of the host by SARS-CoV-2. In this study, we aimed to evaluate the effects of signal peptide on the secretion and release of SARS-CoV-2 spike protein. Therefore, we constructed a signal peptide deletion mutant and three signal peptide site-directed mutants. The (H) region and (C) region in the signal peptide of L5F-S13I mutant have changed significantly, compared with wild type, L5F and S13I. We demonstrated the effects of signal peptide on the secretion and synthesis of RBD protein, finding that mutation of S13 to I13 on the signal peptide is more conducive to the secretion of RBD protein, which was mainly due to the shift of the signal peptide cleavage site in the mutant S13I. Here, we not only investigated the structure of the N-terminal signal peptide of the SARS-CoV-2 spike protein but also considered possible secretory pathways. We suggest that the development of drugs that target the signal peptide of the SARS-CoV-2 spike protein may have potential to treat COVID-19 in the future.
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Affiliation(s)
- Zhikai Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xuan Wan
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xinyue Li
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chengsong Wan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Correspondence:
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6
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Complete Genome and Molecular Characterization of a New Cyprinid Herpesvirus 2 (CyHV-2) SH-01 Strain Isolated from Cultured Crucian Carp. Viruses 2022; 14:v14092068. [PMID: 36146873 PMCID: PMC9503944 DOI: 10.3390/v14092068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during outbreaks in crucian carp at a local fish farm near Shanghai, China. CyHV-2 SH-01 exhibited a high sensitivity to goldfish and crucian carp in our previous research. The complete genome of SH-01 is 290,428 bp with 154 potential open reading frames (ORFs) and terminal repeat (TR) regions at both ends. Compared to the sequenced genomes of other CyHVs, Carassius auratus herpesvirus (CaHV) and Anguillid herpesvirus 1 (AngHV-1), several variations were found in SH-01, including nucleotide mutations, deletions, and insertions, as well as gene duplications, rearrangements, and horizontal transfers. Overall, the genome of SH-01 shares 99.60% of its identity with that of ST-J1. Genomic collinearity analysis showed that SH-01 has a high degree of collinearity with another three CyHV-2 isolates, and it is generally closely related to CaHV, CyHV-1, and CyHV-3, although it contains many differences in locally collinear blocks (LCBs). The lowest degree of collinearity was found with AngHV-1, despite some homologous LCBs, indicating that they are evolutionarily the most distantly related. The results provide new clues to better understand the CyHV-2 genome through sequencing and sequence mining.
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7
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Hervouet K, Ferrié M, Ankavay M, Montpellier C, Camuzet C, Alexandre V, Dembélé A, Lecoeur C, Foe AT, Bouquet P, Hot D, Vausselin T, Saliou JM, Salomé-Desnoulez S, Vandeputte A, Marsollier L, Brodin P, Dreux M, Rouillé Y, Dubuisson J, Aliouat-Denis CM, Cocquerel L. An Arginine-Rich Motif in the ORF2 capsid protein regulates the hepatitis E virus lifecycle and interactions with the host cell. PLoS Pathog 2022; 18:e1010798. [PMID: 36007070 PMCID: PMC9451086 DOI: 10.1371/journal.ppat.1010798] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/07/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatitis E virus (HEV) infection is the most common cause of acute viral hepatitis worldwide. Hepatitis E is usually asymptomatic and self-limiting but it can become chronic in immunocompromised patients and is associated with increased fulminant hepatic failure and mortality rates in pregnant women. HEV genome encodes three proteins including the ORF2 protein that is the viral capsid protein. Interestingly, HEV produces 3 isoforms of the ORF2 capsid protein which are partitioned in different subcellular compartments and perform distinct functions in the HEV lifecycle. Notably, the infectious ORF2 (ORF2i) protein is the structural component of virions, whereas the genome-free secreted and glycosylated ORF2 proteins likely act as a humoral immune decoy. Here, by using a series of ORF2 capsid protein mutants expressed in the infectious genotype 3 p6 HEV strain as well as chimeras between ORF2 and the CD4 glycoprotein, we demonstrated how an Arginine-Rich Motif (ARM) located in the ORF2 N-terminal region controls the fate and functions of ORF2 isoforms. We showed that the ARM controls ORF2 nuclear translocation likely to promote regulation of host antiviral responses. This motif also regulates the dual topology and functionality of ORF2 signal peptide, leading to the production of either cytosolic infectious ORF2i or reticular non-infectious glycosylated ORF2 forms. It serves as maturation site of glycosylated ORF2 by furin, and promotes ORF2-host cell membrane interactions. The identification of ORF2 ARM as a unique central regulator of the HEV lifecycle uncovers how viruses settle strategies to condense their genetic information and hijack cellular processes.
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Affiliation(s)
- Kévin Hervouet
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Martin Ferrié
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Maliki Ankavay
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- Division of Gastroenterology and Hepatology, Institute of Microbiology, Lausanne, Switzerland
| | - Claire Montpellier
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Charline Camuzet
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Virginie Alexandre
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Aïcha Dembélé
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Cécile Lecoeur
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Arnold Thomas Foe
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Peggy Bouquet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Thibaut Vausselin
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Michel Saliou
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Laurent Marsollier
- Université d’Angers, Nantes Université, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Angers, France
| | - Priscille Brodin
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, Lille, France
| | - Marlène Dreux
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm-U1111, CNRS-UMR5308, ENS-Lyon, Lyon, France
| | - Yves Rouillé
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Jean Dubuisson
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Cécile-Marie Aliouat-Denis
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Laurence Cocquerel
- University of Lille, CNRS, INSERM, CHU Lille, Pasteur Institute of Lille, U1019-UMR 9017-CIIL- Center for Infection and Immunity of Lille, Lille, France
- * E-mail:
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8
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Zhou W, Bias K, Lenczewski-Jowers D, Henderson J, Cupp V, Ananga A, Ochieng JW, Tsolova V. Analysis of Protein Sequence Identity, Binding Sites, and 3D Structures Identifies Eight Pollen Species and Ten Fruit Species with High Risk of Cross-Reactive Allergies. Genes (Basel) 2022; 13:genes13081464. [PMID: 36011375 PMCID: PMC9408803 DOI: 10.3390/genes13081464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/30/2022] Open
Abstract
Fruit allergens are proteins from fruits or pollen that cause allergy in humans, an increasing food safety concern worldwide. With the globalization of food trade and changing lifestyles and dietary habits, characterization and identification of these allergens are urgently needed to inform public awareness, diagnosis and treatment of allergies, drug design, as well as food standards and regulations. This study conducted a phylogenetic reconstruction and protein clustering among 60 fruit and pollen allergens from 19 species, and analyzed the clusters, in silico, for cross-reactivity (IgE), 3D protein structure prediction, transmembrane and signal peptides, and conserved domains and motifs. Herein, we wanted to predict the likelihood of their interaction with antibodies, as well as cross-reactivity between the many allergens derived from the same protein families, as the potential for cross-reactivity complicates the management of fruit allergies. Phylogenetic analysis classified the allergens into four clusters. The first cluster (n = 9) comprising pollen allergens showed a high risk of cross-reactivity between eight allergens, with Bet v1 conserved domain, but lacked a transmembrane helix and signal peptide. The second (n = 10) cluster similarly suggested a high risk of cross-reactivity among allergens, with Prolifin conserved domain. However, the group lacked a transmembrane helix and signal peptide. The third (n = 13) and fourth (n = 29) clusters comprised allergens with significant sequence diversity, predicted low risk of cross-reactivity, and showed both a transmembrane helix and signal peptide. These results are critical for treatment and drug design that mostly use transmembrane proteins as targets. The prediction of high risk of cross-reactivity indicates that it may be possible to design a generic drug that will be effective against the wide range of allergens. Therefore, in the past, we may have avoided the array of fruit species if one was allergic to any one member of the cluster.
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Affiliation(s)
- Wei Zhou
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
- Correspondence: (W.Z.); (A.A.); Tel.: +1-850-599-3249 (W.Z.)
| | - Kaylah Bias
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
| | - Dylan Lenczewski-Jowers
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
| | - Jiliah Henderson
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
| | - Victor Cupp
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
| | - Anthony Ananga
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
- Center for Viticulture and Small Fruits Research, College of Agriculture and Food Sciences, Florida A&M University, 6505 Mahan Drive, Tallahassee, FL 32317, USA
- Correspondence: (W.Z.); (A.A.); Tel.: +1-850-599-3249 (W.Z.)
| | - Joel Winyo Ochieng
- Agricultural Biotechnology Programme, University of Nairobi, P.O. Box 29053, Nairobi 00625, Kenya
| | - Violeta Tsolova
- Food Science Program, College of Agriculture and Food Sciences, Florida A&M University, 1740 S. Martin Luther King Jr. Blvd. Room 305-A Perry Paige South, Tallahassee, FL 32307, USA
- Center for Viticulture and Small Fruits Research, College of Agriculture and Food Sciences, Florida A&M University, 6505 Mahan Drive, Tallahassee, FL 32317, USA
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9
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Zhang Y, Luo B, Liu MC, OuYang RH, Fan XM, Jiang N, Yang FJ, Wang LJ, Zhou BY. Analysis of immune response in BALB/c mice immunized with recombinant plasmids pMZ-X3-Ts14-3-3.3 and pMZ-X3-sp-Ts14-3-3.3 of Taenia solium. Acta Trop 2022; 232:106517. [PMID: 35595093 DOI: 10.1016/j.actatropica.2022.106517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/29/2022] [Accepted: 05/13/2022] [Indexed: 11/01/2022]
Abstract
There is a lack of vaccine against human cysticercosis, thus making a huge population at the risk of infection. In this study, we chose a novel potential antigen molecule Taenia solium 14-3-3.3 (Ts14-3-3.3) and optimized it as sp-Ts14-3-3.3 (sp is immunoglobulin H chain V-region precursor, partial) in order to construct recombinant plasmids pMZ-X3-Ts14-3-3.3 and pMZ-X3-sp-Ts14-3-3.3. BALB/c mice were divided into four groups for immunization: pMZ-X3-Ts14-3-3.3, pMZ-X3-sp-Ts14-3-3.3, pMZ-X3 plasmid control group and PBS control group. Compared with two control groups, the proliferation level of splenic lymphocytes increased significantly in pMZ-X3-Ts14-3-3.3 and pMZ-X3-sp-Ts14-3-3.3 groups and reached the maximum in week 6. And the same case arose as cytokines associated with Th1 response, IFN-γ, and IL-2 while those with Th2 response, IL-4, IL-10 went up and reached the maximum in week 4. The levels of serum specific IgG, IgG1 and IgG2a rose and reached the maximum in week 6, 4 and 6, respectively. Meanwhile, the proportion of CD4+/CD8+ splenic T lymphocytes increased and reached the peak in week 6. The results indicated that the recombinant plasmids pMZ-X3-Ts14-3-3.3 and pMZ-X3-sp-Ts14-3-3.3 can induce specific cellular and humoral immune responses in BALB/c mice with immunization. Notably, the recombinant plasmid pMZ-X3-sp-Ts14-3-3.3 has a better immune effect, which proves that Ts14-3-3.3 enjoys a higher possibility as a potential antigen molecule to T. solium vaccine.
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10
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Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022. [PMID: 34980915 DOI: 10.1038/s41587-41021-01156-41583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.
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Affiliation(s)
- Felix Teufel
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - José Juan Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Magnús Halldór Gíslason
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark
| | - Silas Irby Pihl
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark.,Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Henrik Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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11
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Ruan N, Yu X, Li H, Wang Y, Huang C. A HBDI-Based Fluorescent Probe for Labeling Endoplasmic Reticulum in Living Cells. Chem Asian J 2022; 17:e202200383. [PMID: 35674678 DOI: 10.1002/asia.202200383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/27/2022] [Indexed: 11/10/2022]
Abstract
The endoplasmic reticulum (ER) is an important organelle in eukaryotic cells and is closely involved in the synthesis and processing of proteins, as well as the storage, regulation, and release of calcium. A series of signaling pathways within the ER play a crucial part in the pathogenesis of various diseases, including cancer. Thus, it is necessary to design ER-targeting probes to monitor these signaling pathways. Additionally, precision medicine also requires new ER-targeting group to facilitate the delivery of drug cargoes to the ER. However, only a limited number of ER-targeting groups have been used for the design of fluorescent probes for ER imaging in living cells, as well as the development of ER-targeted drug delivery systems. Herein, a new ER-targeting fluorescent probe (BDI-ER) was designed and prepared. BDI-ER contains the hydrophilic fluorophore, derived from the core structure of GFP, and two hydrophobic octadecane chains. The amphipathic nature of BDI-ER facilitates localization in the ER. Live cell imaging demonstrated selective localization of BDI-ER towards ER compared to other organelles. Additionally, co-localization imaging in various cell lines indicate that BDI-ER is effective at targeting the ER.
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Affiliation(s)
- Nanan Ruan
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai, Frontiers Science Research Base of Biomimetic Catalysis, Shanghai Key Laboratory of Rare Earth Functional Materials, Department of Chemistry, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Xiang Yu
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai, Frontiers Science Research Base of Biomimetic Catalysis, Shanghai Key Laboratory of Rare Earth Functional Materials, Department of Chemistry, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Huan Li
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai, Frontiers Science Research Base of Biomimetic Catalysis, Shanghai Key Laboratory of Rare Earth Functional Materials, Department of Chemistry, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Yang Wang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai, Frontiers Science Research Base of Biomimetic Catalysis, Shanghai Key Laboratory of Rare Earth Functional Materials, Department of Chemistry, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Chusen Huang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai, Frontiers Science Research Base of Biomimetic Catalysis, Shanghai Key Laboratory of Rare Earth Functional Materials, Department of Chemistry, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
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12
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Chen D, Zhao YG, Zhang H. Endomembrane remodeling in SARS-CoV-2 infection. CELL INSIGHT 2022; 1:100031. [PMID: 37193051 PMCID: PMC9112566 DOI: 10.1016/j.cellin.2022.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/18/2022]
Abstract
During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.
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Affiliation(s)
- Di Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan G. Zhao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Goel P, Panchal T, Kaushik N, Chauhan R, Saini S, Ahuja V, Thakur CJ. In silico functional and structural characterization revealed virulent proteins of Francisella tularensis strain SCHU4. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2022; 11:73-84. [PMID: 36059929 PMCID: PMC9336787 DOI: 10.22099/mbrc.2022.43128.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Francisella tularensis is a pathogenic, aerobic gram-negative coccobacillus bacterium. It is the causative agent of tularemia, a rare infectious disease that can attack skin, lungs, eyes, and lymph nodes. The genome of F. tularensis has been sequenced, and ~16% of the proteome is still uncharacterized. Characterizations of these proteins are essential to find new drug targets for better therapeutics. In silico characterization of proteins has become an extremely important approach to determine the functionality of proteins as experimental functional elucidation is unable to keep pace with the current growth of the sequence database. Initially, we have annotated 577 Hypothetical Proteins (HPs) of F. tularensis strain SCHU4 with seven bioinformatics tools which characterized them based on the family, domain and motif. Out of 577 HPs, 119 HPs were annotated by five or more tools and are further screened to predict their virulence properties, subcellular localization, transmembrane helices as well as physicochemical parameters. VirulentPred predicted 66 HPs out of 119 as virulent. These virulent proteins were annotated to find the interacting partner using STRING, and proteins with high confidence interaction scores were used to predict their 3D structures using Phyre2. The three virulent proteins Q5NH99 (phosphoserine phosphatase), Q5NG42 (Cystathionine beta-synthase) and Q5NG83 (Rrf2-type helix turn helix domain) were predicted to involve in modulation of cytoskeletal and innate immunity of host, H2S (hydrogen sulfide) based antibiotic tolerance and nitrite and iron metabolism of bacteria. The above predicted virulent proteins can serve as novel drug targets in the era of antibiotic resistance.
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Affiliation(s)
- Prerna Goel
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India
| | - Tanya Panchal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India
| | - Nandini Kaushik
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India
| | - Ritika Chauhan
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India
| | - Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India,Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Vartika Ahuja
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 C, Chandigarh, India,Corresponding Author: Department of Bioinformatics,Goswami Ganesh Dutta Sanatan Dharma College Sector 32 C, Chandigarh, India, 160030. Tel: +91 8699776533; Fax: +91 1722661077, E. mail:
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14
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Madera S, Izzo F, Chervo MF, Dupont A, Chiauzzi VA, Bruni S, Petrillo E, Merin SS, De Martino M, Montero D, Levit C, Lebersztein G, Anfuso F, Roldán Deamicis A, Mercogliano MF, Proietti CJ, Schillaci R, Elizalde PV, Cordo Russo RI. Halting ErbB-2 isoforms retrograde transport to the nucleus as a new theragnostic approach for triple-negative breast cancer. Cell Death Dis 2022; 13:447. [PMID: 35534460 PMCID: PMC9084267 DOI: 10.1038/s41419-022-04855-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancer (TNBC) is clinically defined by the absence of estrogen and progesterone receptors and the lack of membrane overexpression or gene amplification of receptor tyrosine kinase ErbB-2/HER2. Due to TNBC heterogeneity, clinical biomarkers and targeted therapies for this disease remain elusive. We demonstrated that ErbB-2 is localized in the nucleus (NErbB-2) of TNBC cells and primary tumors, from where it drives growth. We also discovered that TNBC expresses both wild-type ErbB-2 (WTErbB-2) and alternative ErbB-2 isoform c (ErbB-2c). Here, we revealed that the inhibitors of the retrograde transport Retro-2 and its cyclic derivative Retro-2.1 evict both WTErbB-2 and ErbB-2c from the nucleus of BC cells and tumors. Using BC cells from several molecular subtypes, as well as normal breast cells, we demonstrated that Retro-2 specifically blocks proliferation of BC cells expressing NErbB-2. Importantly, Retro-2 eviction of both ErbB-2 isoforms from the nucleus resulted in a striking growth abrogation in multiple TNBC preclinical models, including tumor explants and xenografts. Our mechanistic studies in TNBC cells revealed that Retro-2 induces a differential accumulation of WTErbB-2 at the early endosomes and the plasma membrane, and of ErbB-2c at the Golgi, shedding new light both on Retro-2 action on endogenous protein cargoes undergoing retrograde transport, and on the biology of ErbB-2 splicing variants. In addition, we revealed that the presence of a functional signal peptide and a nuclear export signal (NES), both located at the N-terminus of WTErbB-2, and absent in ErbB-2c, accounts for the differential subcellular distribution of ErbB-2 isoforms upon Retro-2 treatment. Our present discoveries provide evidence for the rational repurposing of Retro-2 as a novel therapeutic agent for TNBC.
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Affiliation(s)
- Santiago Madera
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Franco Izzo
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - María F Chervo
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Agustina Dupont
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Violeta A Chiauzzi
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Sofia Bruni
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - Sharon S Merin
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Mara De Martino
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Diego Montero
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Claudio Levit
- Servicio de Ginecología, Sanatorio Sagrado Corazón, Buenos Aires, Argentina
| | | | - Fabiana Anfuso
- Servicio de Ginecología, Sanatorio Sagrado Corazón, Buenos Aires, Argentina
| | - Agustina Roldán Deamicis
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - María F Mercogliano
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Cecilia J Proietti
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Roxana Schillaci
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina
| | - Patricia V Elizalde
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina.
| | - Rosalía I Cordo Russo
- Laboratory of Molecular Mechanisms of Carcinogenesis and Molecular Endocrinology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina.
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15
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Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022; 40:1023-1025. [PMID: 34980915 PMCID: PMC9287161 DOI: 10.1038/s41587-021-01156-3] [Citation(s) in RCA: 698] [Impact Index Per Article: 349.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022]
Abstract
Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data. A new version of SignalP predicts all types of signal peptides.
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Affiliation(s)
- Felix Teufel
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - José Juan Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Magnús Halldór Gíslason
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark
| | - Silas Irby Pihl
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark.,Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Henrik Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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16
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The Signal Peptide and Chaperone UNC93B1 Both Influence TLR8 Ectodomain Intracellular Endosomal Localization. Vaccines (Basel) 2021; 10:vaccines10010014. [PMID: 35062674 PMCID: PMC8778924 DOI: 10.3390/vaccines10010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Toll-like receptor 8 (TLR8) is a single-stranded RNA sensing receptor and is localized in the cellular compartments, where it encounters foreign or self-nucleic acids and activates innate and adaptive immune responses. However, the mechanism controlling intracellular localization TLR8 is not completely resolved. We previously revealed the intracellular localization of TLR8 ectodomain (ECD), and in this study, we investigated the mechanism of the intracellular localization. Here we found that TLR8 ECDs from different species as well as ECDs from different TLRs are all intracellularly localized, similarly to the full-length porcine TLR8. Furthermore, porcine, bovine, and human TLR8 ECDs are all localized in cell endosomes, reflecting the cellular localization of TLR8. Intriguingly, none of post-translational modifications at single sites, including glycosylation, phosphorylation, ubiquitination, acetylation, and palmitoylation alter porcine TLR8-ECD endosomal localization. Nevertheless, the signal peptide of porcine TLR8-ECD determines its endosomal localization. On the other hand, signaling regulator UNC93B1 also decides the endosomal localization of porcine, bovine, and human TLR8 ECDs. The results from this study shed light on the mechanisms of not only TLR8 intracellular localization but also the TLR immune signaling.
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17
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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18
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Berger K, Pauwels E, Parkinson G, Landberg G, Le T, Demillo VG, Lumangtad LA, Jones DE, Islam MA, Olsen R, Kapri T, Intasiri A, Vermeire K, Rhost S, Bell TW. Reduction of Progranulin-Induced Breast Cancer Stem Cell Propagation by Sortilin-Targeting Cyclotriazadisulfonamide (CADA) Compounds. J Med Chem 2021; 64:12865-12876. [PMID: 34428050 PMCID: PMC10501753 DOI: 10.1021/acs.jmedchem.1c00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclotriazadisulfonamide (CADA) compounds selectively down-modulate two human proteins of potential therapeutic interest, cluster of differentiation 4 (CD4) and sortilin. Progranulin is secreted from some breast cancer cells, causing dedifferentiation of receiving cancer cells and cancer stem cell proliferation. Inhibition of progranulin binding to sortilin, its main receptor, can block progranulin-induced metastatic breast cancer using a triple-negative in vivo xenograft model. In the current study, seven CADA compounds (CADA, VGD020, VGD071, TL020, TL023, LAL014, and DJ010) were examined for reduction of cellular sortilin expression and progranulin-induced breast cancer stem cell propagation. In addition, inhibition of progranulin-induced mammosphere formation was examined and found to be most significant for TL020, TL023, VGD071, and LAL014. Full experimental details are given for the synthesis and characterization of the four new compounds (TL020, TL023, VGD071, and DJ010). Comparison of solubilities, potencies, and cytotoxicities identified VGD071 as a promising candidate for future studies using mouse breast cancer models.
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Affiliation(s)
- Karoline Berger
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Eva Pauwels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Gabrielle Parkinson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Göran Landberg
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Truc Le
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Violeta G Demillo
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Liezel A Lumangtad
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
- Nanosyn, 3100 Central Expressway, Santa Clara, California 95051, United States
| | - Dylan E Jones
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Md Azizul Islam
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Ryan Olsen
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Topprasad Kapri
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Amarawan Intasiri
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
| | - Kurt Vermeire
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Sara Rhost
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, Nevada 89557-0216, United States
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19
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Pauwels E, Rutz C, Provinciael B, Stroobants J, Schols D, Hartmann E, Krause E, Stephanowitz H, Schülein R, Vermeire K. A Proteomic Study on the Membrane Protein Fraction of T Cells Confirms High Substrate Selectivity for the ER Translocation Inhibitor Cyclotriazadisulfonamide. Mol Cell Proteomics 2021; 20:100144. [PMID: 34481949 PMCID: PMC8477212 DOI: 10.1016/j.mcpro.2021.100144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/09/2021] [Accepted: 08/30/2021] [Indexed: 11/15/2022] Open
Abstract
Cyclotriazadisulfonamide (CADA) inhibits the cotranslational translocation of type I integral membrane protein human CD4 (huCD4) across the endoplasmic reticulum in a signal peptide (SP)–dependent way. Previously, sortilin was identified as a secondary substrate for CADA but showed reduced CADA sensitivity as compared with huCD4. Here, we performed a quantitative proteomic study on the crude membrane fraction of human T-cells to analyze how many proteins are sensitive to CADA. To screen for these proteins, we employed stable isotope labeling by amino acids in cell culture technique in combination with quantitative MS on CADA-treated human T-lymphoid SUP-T1 cells expressing high levels of huCD4. In line with our previous reports, our current proteomic analysis (data available via ProteomeXchange with identifier PXD027712) demonstrated that only a very small subset of proteins is depleted by CADA. Our data also confirmed that cellular expression of both huCD4 and sortilin are affected by CADA treatment of SUP-T1 cells. Furthermore, three additional targets for CADA are identified, namely, endoplasmic reticulum lectin 1 (ERLEC1), inactive tyrosine-protein kinase 7 (PTK7), and DnaJ homolog subfamily C member 3 (DNAJC3). Western blot and flow cytometry analysis of ERLEC1, PTK7, and DNAJC3 protein expression validated susceptibility of these substrates to CADA, although with varying degrees of sensitivity. Additional cell-free in vitro translation/translocation data demonstrated that the new substrates for CADA carry cleavable SPs that are targets for the cotranslational translocation inhibition exerted by CADA. Thus, our quantitative proteomic analysis demonstrates that ERLEC1, PTK7, and DNAJC3 are validated additional substrates of CADA; however, huCD4 remains the most sensitive integral membrane protein for the endoplasmic reticulum translocation inhibitor CADA. Furthermore, to our knowledge, CADA is the first compound that specifically interferes with only a very small subset of SPs and does not affect signal anchor sequences. About 3007 proteins quantified in SILAC/MS study on CD4+ T-cells treated with CADA. Three new targets for CADA were identified: ERLEC1, PTK7, and DNAJC3. All CADA substrates carry cleavable signal peptides for translocation into ER. huCD4 remains the most sensitive substrate for the ER translocation inhibitor CADA.
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Affiliation(s)
- Eva Pauwels
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Claudia Rutz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Becky Provinciael
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Joren Stroobants
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Stephanowitz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Ralf Schülein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium.
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20
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Lomize AL, Schnitzer KA, Todd SC, Pogozheva ID. Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles. J Chem Inf Model 2021; 61:2884-2896. [PMID: 34029472 DOI: 10.1021/acs.jcim.1c00161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP 2.0 identifies locations of α-helices in the amino acid sequence, generates their three-dimensional models in planar bilayers or spherical micelles, and estimates their thermodynamic stabilities and tilt angles, depending on temperature and pH. The method was tested for 723 peptides (926 data points) experimentally studied in different environments and for 170 single-pass transmembrane (TM) proteins with available crystal structures. FMAP 2.0 detected more than 95% of experimentally observed α-helices with an average error in helix end determination of around 2, 3, 4, and 5 residues per helix for peptides in water, micelles, bilayers, and TM proteins, respectively. Helical and nonhelical residue states were predicted with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient was from 0.64 to 0.88 depending on the environment. Experimental micelle- and membrane-binding energies and tilt angles of peptides were reproduced with a root-mean-square deviation of around 2 kcal/mol and 7°, respectively. The TM and non-TM states of hydrophobic and pH-triggered α-helical peptides in various lipid bilayers were reproduced in more than 95% of cases. The FMAP 2.0 web server (https://membranome.org/fmap) is publicly available to explore the structural polymorphism of antimicrobial, cell-penetrating, fusion, and other membrane-binding peptides, which is important for understanding the mechanisms of their biological activities.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kevin A Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Spencer C Todd
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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21
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Li P, Li Y, Ma L. Potential role of chimeric genes in pathway-related gene co-expression modules. World J Surg Oncol 2021; 19:149. [PMID: 33980272 PMCID: PMC8117532 DOI: 10.1186/s12957-021-02248-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. Methods Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. Results Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-β superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. Conclusions Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02248-9.
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Affiliation(s)
- Piaopiao Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Yingxia Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Lei Ma
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China.
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22
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Badawi S, Ali BR. ACE2 Nascence, trafficking, and SARS-CoV-2 pathogenesis: the saga continues. Hum Genomics 2021; 15:8. [PMID: 33514423 PMCID: PMC7844112 DOI: 10.1186/s40246-021-00304-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
With the emergence of the novel coronavirus SARS-CoV-2 since December 2019, more than 65 million cases have been reported worldwide. This virus has shown high infectivity and severe symptoms in some cases, leading to over 1.5 million deaths globally. Despite the collaborative and concerted research efforts that have been made, no effective medication for COVID-19 (coronavirus disease-2019) is currently available. SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) as an initial mediator for viral attachment and host cell invasion. ACE2 is widely distributed in the human tissues including the cell surface of lung cells which represent the primary site of the infection. Inhibiting or reducing cell surface availability of ACE2 represents a promising therapy for tackling COVID-19. In this context, most ACE2-based therapeutic strategies have aimed to tackle the virus through the use of angiotensin-converting enzyme (ACE) inhibitors or neutralizing the virus by exogenous administration of ACE2, which does not directly aim to reduce its membrane availability. However, through this review, we present a different perspective focusing on the subcellular localization and trafficking of ACE2. Membrane targeting of ACE2, and shedding and cellular trafficking pathways including the internalization are not well elucidated in literature. Therefore, we hereby present an overview of the fate of newly synthesized ACE2, its post translational modifications, and what is known of its trafficking pathways. In addition, we highlight the possibility that some of the identified ACE2 missense variants might affect its trafficking efficiency and localization and hence may explain some of the observed variable severity of SARS-CoV-2 infections. Moreover, an extensive understanding of these processes is necessarily required to evaluate the potential use of ACE2 as a credible therapeutic target.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Zayed Centre for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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23
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Syntheses and anti-HIV and human cluster of differentiation 4 (CD4) down-modulating potencies of pyridine-fused cyclotriazadisulfonamide (CADA) compounds. Bioorg Med Chem 2020; 28:115816. [PMID: 33181479 DOI: 10.1016/j.bmc.2020.115816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 01/10/2023]
Abstract
CADA compounds selectively down-modulate human cell-surface CD4 protein and are of interest as HIV entry inhibitors and as drugs for asthma, rheumatoid arthritis, diabetes and some cancers. Postulating that fusing a pyridine ring bearing hydrophobic substituents into the macrocyclic scaffold of CADA compounds may lead to potent compounds with improved properties, 17 macrocycles were synthesized, 14 with 12-membered rings having an isobutylene head group, two arenesulfonyl side arms, and fused pyridine rings bearing a para substituent. The analogs display a wide range of CD4 down-modulating and anti-HIV potencies, including some with greater potency than CADA, proving that a highly basic nitrogen atom in the 12-membered ring is not required for potency and that hydrophobic substituents enhance potency of pyridine-fused CADA compounds. Cytotoxicities of the new compounds compared favorably with those of CADA, showing that incorporation of a pyridine ring into the macrocyclic scaffold can produce selective compounds for potently down-modulating proteins of medicinal interest.
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24
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O'Keefe S, High S. Membrane translocation at the ER: with a little help from my friends. FEBS J 2020; 287:4607-4611. [PMID: 32301242 DOI: 10.1111/febs.15309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022]
Abstract
The Sec61 complex is the proteinaceous pore through which one-third of mammalian polypeptides access the lumen of the endoplasmic reticulum (ER) during their translocation across, or insertion into, the ER membrane. N-terminal ER signal peptides mediate polypeptide targeting to, and opening of, the Sec61 channel in a substrate-specific manner. Here, we discuss the recently defined features of ER signal peptides which necessitate the use of the accessory components Sec62 and Sec63 during the Sec61-mediated cotranslational translocation of newly synthesized secretory proteins.
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Affiliation(s)
- Sarah O'Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, UK
| | - Stephen High
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, UK
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