1
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Cho JY, Kim JW, Kim DG, Kim YS, Kim WJ, Kim YO, Kong HJ. The extracellular matrix protein EFEMP2 is involved in the response to VHSV infection in the olive flounder Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109681. [PMID: 38871142 DOI: 10.1016/j.fsi.2024.109681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
The EGF-containing fibulin-like extracellular matrix protein 2 (EFEMP2) is involved in connective tissue development, elastic fiber formation, and tumor growth. In this study, we characterized the cDNA of EFEMP2 (PoEFEMP2), a member of the fibulin family of ECM proteins, in the olive flounder Paralichthys olivaceus. The coding region of PoEFEMP2 encodes a protein that contains six calcium-binding EGF-like (EGF-CA) domains and four complement Clr-like EGF-like (cEGF) domains. PoEFEMP2 shows 67.51-96.77 % similarities to orthologs in a variety of fish species. PoEFEMP2 mRNA was detected in all tissues examined; the highest levels of PoEFEMP2 mRNA expression were observed in the heart, testis, ovary and muscle. The PoEFEMP2 mRNA level increases during early development. In addition, the PoEFEMP2 mRNA level increased at 3 h post-infection (hpi) and decreased from 6 to 48 hpi in flounder Hirame natural embryo (HINAE) cells infected with viral hemorrhagic septicemia virus (VHSV). Disruption of PoEFEMP2 using the clustered regularly interspaced short palindromic repeats/CRISPR-associated-9 (CRISPR/Cas9) system resulted in a significant upregulation of VHSV G mRNA levels and immune-related genes expression in knockout cells. These findings implicate PoEFEMP2 in antiviral responses in P. olivaceus.
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Affiliation(s)
- Ja Young Cho
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Young-Sam Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Woo-Jin Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea.
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2
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Stoup N, Liberelle M, Lebègue N, Van Seuningen I. Emerging paradigms and recent progress in targeting ErbB in cancers. Trends Pharmacol Sci 2024; 45:552-576. [PMID: 38797570 DOI: 10.1016/j.tips.2024.04.009] [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: 03/29/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024]
Abstract
The epidermal growth factor receptor (EGFR) family is a class of transmembrane proteins, highly regarded as anticancer targets due to their pivotal role in various malignancies. Standard cancer treatments targeting the ErbB receptors include tyrosine kinase inhibitors (TKIs) and monoclonal antibodies (mAbs). Despite their substantial survival benefits, the achievement of curative outcomes is hindered by acquired resistance. Recent advancements in anti-ErbB approaches, such as inhibitory peptides, nanobodies, targeted-protein degradation strategies, and bispecific antibodies (BsAbs), aim to overcome such resistance. More recently, emerging insights into the cell surface interactome of the ErbB family open new avenues for modulating ErbB signaling by targeting specific domains of ErbB partners. Here, we review recent progress in ErbB targeting and elucidate emerging paradigms that underscore the significance of EGF domain-containing proteins (EDCPs) as new ErbB-targeting pathways.
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Affiliation(s)
- Nicolas Stoup
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Maxime Liberelle
- University of Lille, Inserm, CHU Lille, UMR-S 1172 - LiNC -Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Nicolas Lebègue
- University of Lille, Inserm, CHU Lille, UMR-S 1172 - LiNC -Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Isabelle Van Seuningen
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.
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3
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McDonald B, Schmidt MHH. Structure, function, and recombinant production of EGFL7. Biol Chem 2024; 0:hsz-2023-0358. [PMID: 38805373 DOI: 10.1515/hsz-2023-0358] [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: 12/01/2023] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
The secreted factor Epidermal growth factor-like protein 7 (EGFL7) is involved in angiogenesis, vasculogenesis, as well as neurogenesis. Importantly, EGFL7 is also implicated in various pathological conditions, including tumor angiogenesis in human cancers. Thus, understanding the mechanisms through which EGFL7 regulates and promotes blood vessel formation is of clear practical importance. One principle means by which EGFL7's function is investigated is via the expression and purification of the recombinant protein. This mini-review describes three methods used to produce recombinant EGFL7 protein. First, a brief overview of EGFL7's genetics, structure, and function is provided. This is followed by an examination of the advantages and disadvantages of three common expression systems used in the production of recombinant EGFL7; (i) Escherichia coli (E. coli), (ii) human embryonic kidney (HEK) 293 cells or other mammalian cells, and (iii) a baculovirus-based Sf9 insect cell expression system. Based on the available evidence, we conclude that the baculovirus-based Sf9 insect cell expression currently has the advantages of producing active recombinant EGFL7 in the native conformation with the presence of acceptable posttranslational modifications, while providing sufficient yield and stability for experimental purposes.
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Affiliation(s)
- Brennan McDonald
- 9169 Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Mirko H H Schmidt
- 9169 Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Fetscherstr. 74, D-01307 Dresden, Germany
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4
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Park H, Youn B, Park DJ, Puthanveettil SV, Kang C. Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana. Sci Rep 2024; 14:9622. [PMID: 38671060 PMCID: PMC11052993 DOI: 10.1038/s41598-024-57975-2] [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: 01/13/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
The vacuolar sorting receptors (VSRs) are specific to plants and are responsible for sorting and transporting particular proteins from the trans-Golgi network to the vacuole. This process is critically important for various cellular functions, including storing nutrients during seed development. Despite many years of intense studies on VSRs, a complete relation between function and structure has not yet been revealed. Here, we present the crystal structure of the entire luminal region of glycosylated VSR1 from Arabidopsis thaliana (AtVSR1) for the first time. The structure provides insights into the tertiary and quaternary structures of VSR1, which are composed of an N-terminal protease-associated (PA) domain, a unique central region, and one epidermal growth factor (EGF)-like domain followed by two disordered EGF-like domains. The structure of VSR1 exhibits unique characteristics, the significance of which is yet to be fully understood.
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Affiliation(s)
- HaJeung Park
- X-Ray Core, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, 33458, USA
| | - BuHyun Youn
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Daniel J Park
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32827, USA
| | | | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
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5
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Elenbaas JS, Jung IH, Coler-Reilly A, Lee PC, Alisio A, Stitziel NO. The emerging Janus face of SVEP1 in development and disease. Trends Mol Med 2023; 29:939-950. [PMID: 37673700 PMCID: PMC10592172 DOI: 10.1016/j.molmed.2023.08.002] [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: 06/06/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Sushi, von Willebrand factor type A, EGF, and pentraxin domain containing 1 (SVEP1) is a large extracellular matrix protein that is also detected in circulation. Recent plasma proteomic and genomic studies have revealed a large number of associations between SVEP1 and human traits, particularly chronic disease. These include associations with cardiac death and disease, diabetes, platelet traits, glaucoma, dementia, and aging; many of these are causal. Animal models demonstrate that SVEP1 is critical in vascular development and disease, but its molecular and cellular mechanisms remain poorly defined. Future studies should aim to characterize these mechanisms and determine the diagnostic, prognostic, and therapeutic value of measuring or intervening on this enigmatic protein.
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Affiliation(s)
- Jared S Elenbaas
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Hyuk Jung
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ariella Coler-Reilly
- Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA; Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Paul C Lee
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Arturo Alisio
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nathan O Stitziel
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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6
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Waury K, de Wit R, Verberk IMW, Teunissen CE, Abeln S. Deciphering Protein Secretion from the Brain to Cerebrospinal Fluid for Biomarker Discovery. J Proteome Res 2023; 22:3068-3080. [PMID: 37606934 PMCID: PMC10476268 DOI: 10.1021/acs.jproteome.3c00366] [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: 06/19/2023] [Indexed: 08/23/2023]
Abstract
Cerebrospinal fluid (CSF) is an essential matrix for the discovery of neurological disease biomarkers. However, the high dynamic range of protein concentrations in CSF hinders the detection of the least abundant protein biomarkers by untargeted mass spectrometry. It is thus beneficial to gain a deeper understanding of the secretion processes within the brain. Here, we aim to explore if and how the secretion of brain proteins to the CSF can be predicted. By combining a curated CSF proteome and the brain elevated proteome of the Human Protein Atlas, brain proteins were classified as CSF or non-CSF secreted. A machine learning model was trained on a range of sequence-based features to differentiate between CSF and non-CSF groups and effectively predict the brain origin of proteins. The classification model achieves an area under the curve of 0.89 if using high confidence CSF proteins. The most important prediction features include the subcellular localization, signal peptides, and transmembrane regions. The classifier generalized well to the larger brain detected proteome and is able to correctly predict novel CSF proteins identified by affinity proteomics. In addition to elucidating the underlying mechanisms of protein secretion, the trained classification model can support biomarker candidate selection.
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Affiliation(s)
- Katharina Waury
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Renske de Wit
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Inge M. W. Verberk
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Sanne Abeln
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
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7
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Baker S, Miguel RN, Thomas D, Powell M, Furmaniak J, Smith BR. Cryo-electron microscopy structures of human thyroid peroxidase (TPO) in complex with TPO antibodies. J Mol Endocrinol 2023; 70:JME-22-0149. [PMID: 36537574 PMCID: PMC9986399 DOI: 10.1530/jme-22-0149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Determination of the structure of the extracellular domain of human thyroid peroxidase (hTPO) by cryo-electron microscopy (cryo-EM) is described. TPO, purified to homogeneity was complexed with the hTPO monoclonal autoantibody 2G4 Fab and also with a mouse monoclonal TPO antibody 4F5 Fab (which competes with autoantibody binding to TPO). Both complexes were analysed by cryo-EM. The two structures (global resolution 3.92 and 3.4 Å for the 2G4 complex and 4F5 complex, respectively) show TPO as a monomer with four domains; the N-terminal domain, the peroxidase domain (POD), the complement control protein (CCP)-like domain and the epidermal growth factor-like domain which are all visible in the structures. The relative positions of the domains are fixed with a disulphide bond between cysteine residues Cys146 in the POD and Cys756 in the CCP domain preventing significant flexibility of the molecule. The entrance to the enzyme active site, the haem group and the calcium binding site are clearly visible on the opposite side of the TPO molecule from the 2G4 and 4F5 binding sites. Extensive interactions are seen between TPO and the two antibodies which both bind to distinct epitopes on the POD domain, including some residues in the immunodominant region B mainly via different residues. However, the epitopes of the two antibodies contain three shared TPO residues. This is the first high-resolution structure of TPO to be reported and it should help guide the development of new inhibitors of TPO enzyme activity for therapeutic applications.
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Affiliation(s)
- Stuart Baker
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, UK
| | | | - Daniel Thomas
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, UK
| | - Michael Powell
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, UK
| | | | - Bernard Rees Smith
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, UK
- Correspondence should be addressed to B Rees Smith:
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8
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Adjou Moumouni PF, Naomasa S, Tuvshintulga B, Sato N, Okado K, Zheng W, Lee SH, Mosqueda J, Suzuki H, Xuan X, Umemiya-Shirafuji R. Identification and Characterization of Rhipicephalus microplus ATAQ Homolog from Haemaphysalis longicornis Ticks and Its Immunogenic Potential as an Anti-Tick Vaccine Candidate Molecule. Microorganisms 2023; 11:microorganisms11040822. [PMID: 37110244 PMCID: PMC10145298 DOI: 10.3390/microorganisms11040822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Although vaccines are one of the environmentally friendly means to prevent the spread of ticks, there is currently no commercial vaccine effective against Haemaphysalis longicornis ticks. In this study, we identified, characterized, localized, and evaluated the expression patterns, and tested the immunogenic potential of a homologue of Rhipicephalus microplus ATAQ in H. longicornis (HlATAQ). HlATAQ was identified as a 654 amino acid-long protein present throughout the midgut and in Malpighian tubule cells and containing six full and one partial EGF-like domains. HlATAQ was genetically distant (homology < 50%) from previously reported ATAQ proteins and was expressed throughout tick life stages. Its expression steadily increased (p < 0.001) during feeding, reached a peak, and then decreased slightly with engorgement. Silencing of HlATAQ did not result in a phenotype that was significantly different from the control ticks. However, H. longicornis female ticks fed on a rabbit immunized with recombinant HlATAQ showed significantly longer blood-feeding periods, higher body weight at engorgement, higher egg mass, and longer pre-oviposition and egg hatching periods than control ticks. These findings indicate that the ATAQ protein plays a role in the blood-feeding-related physiological processes in the midgut and Malpighian tubules and antibodies directed against it may affect these tissues and disrupt tick engorgement and oviposition.
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Affiliation(s)
- Paul Franck Adjou Moumouni
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Souichirou Naomasa
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Bumduuren Tuvshintulga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Nariko Sato
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Kiyoshi Okado
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Weiqing Zheng
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Seung-Hun Lee
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Juan Mosqueda
- Immunology and Vaccines Laboratory, C. A. Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Carretera a Chichimequillas, Queretaro 76140, Mexico
| | - Hiroshi Suzuki
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
| | - Rika Umemiya-Shirafuji
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Hokkaido, Japan
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9
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Möller-Kerutt A, Schönhoff B, Rellmann Y, George B, Braun DA, Pavenstädt H, Weide T. Loss of surface transport is a main cellular pathomechanism of CRB2 variants causing podocytopathies. Life Sci Alliance 2023; 6:6/3/e202201649. [PMID: 36549870 PMCID: PMC9780758 DOI: 10.26508/lsa.202201649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Crumbs2 (CRB2) is a central component of the renal filtration barrier and part of the slit diaphragm, a unique cell contact formed by glomerular podocytes. Some CRB2 variants cause recessive inherited forms of steroid-resistant nephrotic syndrome. However, the disease-causing potential of numerous CRB2 variants remains unknown. Here, we report the establishment of a live-cell imaging-based assay, allowing a quantitative evaluation of the pathogenic potential of so far non-categorized CRB2 variants. Based on in silico data analysis and protein prediction software, putative disease-associated CRB2 missense variants were selected, expressed as CRB2-GFP fusion proteins, and analyzed in reporter cell lines with BFP-labeled plasma membrane. We found that in comparison with PM-localized WT, disease-associated CRB2 variants remained predominantly at the ER. Accumulation at the ER was also present for several non-characterized CRB2 variants and variants in which putative disulfide bridge-forming cysteines were replaced. Strikingly, WT CRB2 retained inside the ER in cells lacking protein disulfide isomerase A3, indicating that posttranslational modification, especially the formation of disulfide bridges, is a crucial step for the CRB2 PM transport.
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Affiliation(s)
- Annika Möller-Kerutt
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
| | - Birgit Schönhoff
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
| | - Yvonne Rellmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany
| | - Britta George
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
| | - Daniela Anne Braun
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
| | - Hermann Pavenstädt
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
| | - Thomas Weide
- University Hospital of Muenster (UKM), Internal Medicine (MedD), Muenster, Germany
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10
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Hao P, Han L, Quan Z, Jin X, Li Y, Wu Y, Zhang X, Wang W, Gao C, Wang L, Wang H, Zhang W, Chang Y, Ding J. Integrative mRNA-miRNA interaction analysis associated with the immune response of Strongylocentrotus intermedius to Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108577. [PMID: 36773712 DOI: 10.1016/j.fsi.2023.108577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China and has experienced mass mortality owing to outbreaks of bacterial diseases such as black mouth disease. This has caused serious economic losses to the sea urchin farming industry. To investigate the immune response mechanism of S. intermedius with different tube feet colors in response to Vibrio harveyi infection, we examined the different tube feet-colored S. intermedius under V. harveyi challenge and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. We obtained 1813 differentially expressed genes (DEGs), 28 DE miRNAs, and 303 DE miRNA-DEG pairs in different tube feet-colored S. intermedius under V. harveyi challenge. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the most significant DEGs were associated with the Notch signaling and phagosome pathways. The target genes of immune-related miRNAs (miR-71, miR-184, miR-193) and genes (CALM1, SPSB4, DMBT, CSRP1) in S. intermedius were predicted and validated. This study provides insight into the molecular mechanisms that regulate genes involved in the immune response of S. intermedius infected with V. harveyi.
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Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China; Ningbo University, Ningbo, Zhejiang, 315832, PR China
| | - Zijiao Quan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Heng Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China.
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11
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Gomis-Rüth FX, Stöcker W. Structural and evolutionary insights into astacin metallopeptidases. Front Mol Biosci 2023; 9:1080836. [PMID: 36685277 PMCID: PMC9848320 DOI: 10.3389/fmolb.2022.1080836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.
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Affiliation(s)
- F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC), Barcelona, Catalonia, Spain,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
| | - Walter Stöcker
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz (JGU), Mainz, Germany,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
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12
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Cortés E, Pak JS, Özkan E. Structure and evolution of neuronal wiring receptors and ligands. Dev Dyn 2023; 252:27-60. [PMID: 35727136 PMCID: PMC10084454 DOI: 10.1002/dvdy.512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/04/2023] Open
Abstract
One of the fundamental properties of a neuronal circuit is the map of its connections. The cellular and developmental processes that allow for the growth of axons and dendrites, selection of synaptic targets, and formation of functional synapses use neuronal surface receptors and their interactions with other surface receptors, secreted ligands, and matrix molecules. Spatiotemporal regulation of the expression of these receptors and cues allows for specificity in the developmental pathways that wire stereotyped circuits. The families of molecules controlling axon guidance and synapse formation are generally conserved across animals, with some important exceptions, which have consequences for neuronal connectivity. Here, we summarize the distribution of such molecules across multiple taxa, with a focus on model organisms, evolutionary processes that led to the multitude of such molecules, and functional consequences for the diversification or loss of these receptors.
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Affiliation(s)
- Elena Cortés
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,The Neuroscience Institute, University of Chicago, Chicago, Illinois, USA
| | - Joseph S Pak
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,The Neuroscience Institute, University of Chicago, Chicago, Illinois, USA
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,The Neuroscience Institute, University of Chicago, Chicago, Illinois, USA
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13
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Stojanovski BM, Di Cera E. Comparative sequence analysis of vitamin K-dependent coagulation factors. J Thromb Haemost 2022; 20:2837-2849. [PMID: 36156849 PMCID: PMC9669250 DOI: 10.1111/jth.15897] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Prothrombin, protein C, and factors VII, IX, and X are vitamin K (VK)-dependent coagulation proteins that play an important role in the initiation, amplification, and subsequent attenuation of the coagulation response. Blood coagulation evolved in the common vertebrate ancestor as a specialization of the complement system and immune response, which in turn bear close evolutionary ties with developmental enzyme cascades. There is currently no comprehensive analysis of the evolutionary changes experienced by these coagulation proteins during the radiation of vertebrates and little is known about conservation of residues that are important for zymogen activation and catalysis. OBJECTIVES To characterize the conservation level of functionally important residues among VK-dependent coagulation proteins from different vertebrate lineages. METHODS The conservation level of residues important for zymogen activation and catalysis was analyzed in >1600 primary sequences of VK-dependent proteins. RESULTS Functionally important residues are most conserved in prothrombin and least conserved in protein C. Some of the most profound functional modifications in protein C occurred in the ancestor of bony fish when the basic residue in the activation site was replaced by an aromatic residue. Furthermore, during the radiation of placental mammals from marsupials, protein C acquired a cysteine-rich insert that introduced an additional disulfide in the EGF1 domain and evolved a proprotein convertase cleavage site in the activation peptide linker that also became significantly elongated. CONCLUSIONS Sequence variabilities at functionally important residues may lead to interspecies differences in the zymogen activation and catalytic properties of orthologous VK-dependent proteins.
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Affiliation(s)
- Bosko M. Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
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14
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Notch Missense Mutations in Drosophila Reveal Functions of Specific EGF-like Repeats in Notch Folding, Trafficking, and Signaling. Biomolecules 2022; 12:biom12121752. [PMID: 36551180 PMCID: PMC9775759 DOI: 10.3390/biom12121752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Notch signaling plays various roles in cell-fate specification through direct cell-cell interactions. Notch receptors are evolutionarily conserved transmembrane proteins with multiple epidermal growth factor (EGF)-like repeats. Drosophila Notch has 36 EGF-like repeats, and while some play a role in Notch signaling, the specific functions of most remain unclear. To investigate the role of each EGF-like repeat, we used 19 previously identified missense mutations of Notch with unique amino acid substitutions in various EGF-like repeats and a transmembrane domain; 17 of these were identified through a single genetic screen. We assessed these mutants' phenotypes in the nervous system and hindgut during embryogenesis, and found that 10 of the 19 Notch mutants had defects in both lateral inhibition and inductive Notch signaling, showing context dependency. Of these 10 mutants, six accumulated Notch in the endoplasmic reticulum (ER), and these six were located in EGF-like repeats 8-10 or 25. Mutations with cysteine substitutions were not always coupled with ER accumulation. This suggests that certain EGF-like repeats may be particularly susceptible to structural perturbation, resulting in a misfolded and inactive Notch product that accumulates in the ER. Thus, we propose that these EGF-like repeats may be integral to Notch folding.
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Pennarubia F, Ito A, Takeuchi M, Haltiwanger RS. Cancer-associated Notch receptor variants lead to O-fucosylation defects that deregulate Notch signaling. J Biol Chem 2022; 298:102616. [PMID: 36265581 PMCID: PMC9672452 DOI: 10.1016/j.jbc.2022.102616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
NOTCH1 is a transmembrane receptor that initiates a signaling pathway involved in embryonic development of adult tissue homeostasis. The extracellular domain of NOTCH1 is composed largely of epidermal growth factor-like repeats (EGFs), many of which can be O-fucosylated at a specific consensus sequence by protein O-fucosyltransferase 1 (POFUT1). O-fucosylation of NOTCH1 is necessary for its function. The Notch pathway is deregulated in many cancers, and alteration of POFUT1 has been reported in several cancers, but further investigation is needed to assess whether there is deregulation of the Notch pathway associated with mutations that affect O-fucosylation in cancers. Using Biomuta and COSMIC databases, we selected nine NOTCH1 variants that could cause a change in O-fucosylation of key EGFs. Mass spectral glycoproteomic site mapping was used to identify alterations in O-fucosylation of EGFs containing the mutations. Cell-based NOTCH-1 signaling assays, ligand-binding assays, and cellsurface analysis were used to determine the effect of each mutation on Notch activation. Two variants led to a gain of function (GOF), six to a loss of function (LOF), and one had minimal effects. Most GOF and LOF were associated with a change in O-fucosylation. Finally, by comparing our results with known NOTCH1 alterations in cancers from which our mutations originated, we were able to establish a correlation between our results and the known GOF or LOF of NOTCH1 in these cancers. This study shows that point mutations in N1 can lead to alterations in O-fucosylation that deregulate the Notch pathway and be associated with cancer processes.
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16
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Brewitz L, Onisko BC, Schofield CJ. Combined proteomic and biochemical analyses redefine the consensus sequence requirement for epidermal growth factor-like domain hydroxylation. J Biol Chem 2022; 298:102129. [PMID: 35700824 PMCID: PMC9293771 DOI: 10.1016/j.jbc.2022.102129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Epidermal growth factor-like domains (EGFDs) have important functions in cell-cell signaling. Both secreted and cell surface human EGFDs are subject to extensive modifications, including aspartate and asparagine residue C3-hydroxylations catalyzed by the 2-oxoglutarate oxygenase aspartate/asparagine-β-hydroxylase (AspH). Although genetic studies show AspH is important in human biology, studies on its physiological roles have been limited by incomplete knowledge of its substrates. Here, we redefine the consensus sequence requirements for AspH-catalyzed EGFD hydroxylation based on combined analysis of proteomic mass spectrometric data and mass spectrometry-based assays with isolated AspH and peptide substrates. We provide cellular and biochemical evidence that the preferred site of EGFD hydroxylation is embedded within a disulfide-bridged macrocycle formed of 10 amino acid residues. This definition enabled the identification of previously unassigned hydroxylation sites in three EGFDs of human fibulins as AspH substrates. A non-EGFD containing protein, lymphocyte antigen-6/plasminogen activator urokinase receptor domain containing protein 6B (LYPD6B) was shown to be a substrate for isolated AspH, but we did not observe evidence for LYPD6B hydroxylation in cells. AspH-catalyzed hydroxylation of fibulins is of particular interest given their important roles in extracellular matrix dynamics. In conclusion, these results lead to a revision of the consensus substrate requirements for AspH and expand the range of observed and potential AspH-catalyzed hydroxylation in cells, which will enable future study of the biological roles of AspH.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
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17
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Barbera S, Cucini C. A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates. BMC Genomics 2022; 23:420. [PMID: 35659564 PMCID: PMC9167495 DOI: 10.1186/s12864-022-08659-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Although these proteins belong to the same family, their phylogenetic relationship has never been dissected. To resolve their evolution and characterize their protein domain composition we investigated CTLDcp genes in gnathostomes and cyclostomes and, by means of phylogenetic approaches as well as synteny analyses, we inferred an evolutionary scheme that attempts to unravel their evolution in modern vertebrates.
Results
Here, we evidenced the paralogy of the group XIV of CTLDcps in gnathostomes and discovered that a gene loss of CD248 and Clec14A occurred in different vertebrate groups, with CD248 being lost due to chromosome disruption in birds, while Clec14A loss in monotremes and marsupials did not involve chromosome rearrangements. Moreover, employing genome annotations of different lampreys as well as one hagfish species, we investigated the origin and evolution of modern group XIV of CTLDcps. Furthermore, we carefully retrieved and annotated gnathostome CTLDcp domains, pointed out important differences in domain composition between gnathostome classes, and assessed codon substitution rate of each domain by analyzing nonsynonymous (Ka) over synonymous (Ks) substitutions using one representative species per gnathostome order.
Conclusions
CTLDcps appeared with the advent of early vertebrates after a whole genome duplication followed by a sporadic tandem duplication. These duplication events gave rise to three CTLDcps in the ancestral vertebrate that underwent further duplications caused by the independent polyploidizations that characterized the evolution of cyclostomes and gnathostomes. Importantly, our analyses of CTLDcps in gnathostomes revealed critical inter-class differences in both extracellular and intracellular domains, which might help the interpretation of experimental results and the understanding of differences between animal models.
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Jayadev R, Morais MRPT, Ellingford JM, Srinivasan S, Naylor RW, Lawless C, Li AS, Ingham JF, Hastie E, Chi Q, Fresquet M, Koudis NM, Thomas HB, O’Keefe RT, Williams E, Adamson A, Stuart HM, Banka S, Smedley D, Sherwood DR, Lennon R. A basement membrane discovery pipeline uncovers network complexity, regulators, and human disease associations. SCIENCE ADVANCES 2022; 8:eabn2265. [PMID: 35584218 PMCID: PMC9116610 DOI: 10.1126/sciadv.abn2265] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/22/2022] [Indexed: 05/17/2023]
Abstract
Basement membranes (BMs) are ubiquitous extracellular matrices whose composition remains elusive, limiting our understanding of BM regulation and function. By developing a bioinformatic and in vivo discovery pipeline, we define a network of 222 human proteins and their animal orthologs localized to BMs. Network analysis and screening in C. elegans and zebrafish uncovered BM regulators, including ADAMTS, ROBO, and TGFβ. More than 100 BM network genes associate with human phenotypes, and by screening 63,039 genomes from families with rare disorders, we found loss-of-function variants in LAMA5, MPZL2, and MATN2 and show that they regulate BM composition and function. This cross-disciplinary study establishes the immense complexity of BMs and their impact on in human health.
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Affiliation(s)
- Ranjay Jayadev
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Mychel R. P. T. Morais
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Jamie M. Ellingford
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Sandhya Srinivasan
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Richard W. Naylor
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Anna S. Li
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Jack F. Ingham
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Eric Hastie
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Nikki-Maria Koudis
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Huw B. Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Raymond T. O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Emily Williams
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Antony Adamson
- Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Helen M. Stuart
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Genomics England Research Consortium
- William Harvey Research Institute, Charterhouse Square, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
- Genomics England, London, UK
| | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
- Department of Paediatric Nephrology, Royal Manchester Children’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
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Cartee NMP, Lee SJ, Young KZ, Zhang X, Wang MM. Trans-Reduction of Cerebral Small Vessel Disease Proteins by Notch-Derived EGF-like Sequences. Int J Mol Sci 2022; 23:ijms23073671. [PMID: 35409031 PMCID: PMC9115637 DOI: 10.3390/ijms23073671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 02/05/2023] Open
Abstract
Cysteine oxidation states of extracellular proteins participate in functional regulation and in disease pathophysiology. In the most common inherited dementia, cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), mutations in NOTCH3 that alter extracellular cysteine number have implicated NOTCH3 cysteine states as potential triggers of cerebral vascular smooth muscle cytopathology. In this report, we describe a novel property of the second EGF-like domain of NOTCH3: its capacity to alter the cysteine redox state of the NOTCH3 ectodomain. Synthetic peptides corresponding to this sequence (NOTCH3 N-terminal fragment 2, NTF2) readily reduce NOTCH3 N-terminal ectodomain polypeptides in a dose- and time-dependent fashion. Furthermore, NTF2 preferentially reduces regional domains of NOTCH3 with the highest intensity against EGF-like domains 12–15. This process requires cysteine residues of NTF2 and is also capable of targeting selected extracellular proteins that include TSP2 and CTSH. CADASIL mutations in NOTCH3 increase susceptibility to NTF2-facilitated reduction and to trans-reduction by NOTCH3 produced in cells. Moreover, NTF2 forms complexes with the NOTCH3 ectodomain, and cleaved NOTCH3 co-localizes with the NOTCH3 ectodomain in cerebral arteries of CADASIL patients. The potential for NTF2 to reduce vascular proteins and the enhanced preference for it to trans-reduce mutant NOTCH3 implicate a role for protein trans-reduction in cerebrovascular pathological states such as CADASIL.
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Affiliation(s)
- Naw May Pearl Cartee
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; (N.M.P.C.); (S.J.L.); (K.Z.Y.); (X.Z.)
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Soo Jung Lee
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; (N.M.P.C.); (S.J.L.); (K.Z.Y.); (X.Z.)
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Kelly Z. Young
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; (N.M.P.C.); (S.J.L.); (K.Z.Y.); (X.Z.)
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojie Zhang
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; (N.M.P.C.); (S.J.L.); (K.Z.Y.); (X.Z.)
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Michael M. Wang
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; (N.M.P.C.); (S.J.L.); (K.Z.Y.); (X.Z.)
- Neurology Service, VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: ; Tel.: +1-734-936-9075; Fax: +1-734-936-8813
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Hao P, Ding B, Han L, Xie J, Wu Y, Jin X, Zhang X, Wang W, Wang L, Zhang W, Chang Y, Ding J. Gene expression patterns of sea urchins (Strongylocentrotus intermedius) exposed to different combinations of temperature and hypoxia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100953. [PMID: 34942521 DOI: 10.1016/j.cbd.2021.100953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/13/2022]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China, and its growth and survival are severely constrained by ocean warming and the hypoxia that often accompanies high water temperatures. To elucidate the molecular mechanisms of S. intermedius that regulate gene expression in response to multi-causal environmental stresses. We performed a de novo transcriptome analysis of coelomocyte from S. intermedius to heat (25 °C), hypoxia (2 mg/L), and the combined stress. We identified 35,635, 29,107, and 29,440 differentially expressed genes (DEGs) in S. intermedius cultured under high temperature, low oxygen, and combined stress, respectively. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that these DEGs mainly enriched the functional categories of "Protein processing in endoplasmic reticulum," and "Glutathione metabolism" by heat stress, such as HSP70, GSTO1, PDIA4. After hypoxic stress, "Notch signaling pathway" and metabolism-related pathways such as "Glycerolipid metabolism", "Pyruvate metabolism" were significantly enriched. Exposure to combined stress resulted in a two-factor additive effect at the transcriptome level and have a more extensive impact on the immune correlated pathways in S. intermedius than single stress, the expression of related immune genes (C3, C5, and AIFM2) were up-regulated. Quantitative real-time PCR (qRT-PCR) analysis of the expression of 18 DEGs confirmed the RNA-Seq results. Observations in the present study will improve the understanding of the molecular mechanism of S. intermedius in response to multi-causal environmental stress.
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Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Beichen Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Ningbo University, Ningbo, Zhejiang 315832, PR China
| | - Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
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Ivanova ME, Lukoyanova N, Malhotra S, Topf M, Trapani JA, Voskoboinik I, Saibil HR. The pore conformation of lymphocyte perforin. SCIENCE ADVANCES 2022; 8:eabk3147. [PMID: 35148176 PMCID: PMC8836823 DOI: 10.1126/sciadv.abk3147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/17/2021] [Indexed: 05/05/2023]
Abstract
Perforin is a pore-forming protein that facilitates rapid killing of pathogen-infected or cancerous cells by the immune system. Perforin is released from cytotoxic lymphocytes, together with proapoptotic granzymes, to bind to a target cell membrane where it oligomerizes and forms pores. The pores allow granzyme entry, which rapidly triggers the apoptotic death of the target cell. Here, we present a 4-Å resolution cryo-electron microscopy structure of the perforin pore, revealing previously unidentified inter- and intramolecular interactions stabilizing the assembly. During pore formation, the helix-turn-helix motif moves away from the bend in the central β sheet to form an intermolecular contact. Cryo-electron tomography shows that prepores form on the membrane surface with minimal conformational changes. Our findings suggest the sequence of conformational changes underlying oligomerization and membrane insertion, and explain how several pathogenic mutations affect function.
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Affiliation(s)
- Marina E. Ivanova
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Natalya Lukoyanova
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Scientific Computing Department, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Fermi Ave, Harwell, Didcot OX11 0QX, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
- Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Joseph A. Trapani
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Ilia Voskoboinik
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London WC1E 7HX, UK
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22
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Turner N, Abeysinghe P, Peiris H, Vaswani K, Sadowski P, Cameron N, McGhee N, Logan J, Mitchell MD. Proteomic profiling of plasma-derived small extracellular vesicles: a novel tool for understanding the systemic effects of tick burden in cattle. J Anim Sci 2022; 100:6511758. [PMID: 35045163 PMCID: PMC8867580 DOI: 10.1093/jas/skac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022] Open
Abstract
Cattle ticks pose a significant threat to the health and profitability of cattle herds globally. The investigation of factors leading to natural tick resistance in cattle is directed toward targeted breeding strategies that may combat cattle tick infestation on the genetic level. Exosomes (EXs), small extracellular vesicles (EVs) of 50 to 150 nm diameter, are released from all cell types into biofluids such as blood plasma and milk, have been successfully used in diagnostic and prognostic studies in humans, and can provide essential information regarding the overall health state of animals. Mass spectrometry (MS) is a highly sensitive proteomics application that can be used to identify proteins in a complex mixture and is particularly useful for biomarker development. In this proof of principle study, EXs were isolated from the blood plasma of cattle (Bos taurus) with high (HTR) and low tick resistance (LTR) (n = 3/group). Cattle were classified as HTR or LTR using a tick scoring system, and EXs isolated from the cattle blood plasma using an established protocol. EXs were subjected to MS analysis in data-dependent acquisition mode and protein search performed using Protein Pilot against the B. taurus proteome. A total of 490 unique proteins were identified across all samples. Of these, proteins present in all replicates from each group were selected for further analysis (HTR = 121; LTR = 130). Gene ontology analysis was performed using PANTHER GO online software tool. Proteins unique to HTR and LTR cattle were divided by protein class, of which 50% were associated with immunity/defense in the HTR group, whereas this protein class was not detected in EXs from LTR cattle. Similarly, unique proteins in HTR cattle were associated with B-cell activation, immunoglobins, immune response, and cellular iron ion homeostasis. In LTR cattle, unique exosomal proteins were associated with actin filament binding, purine nucleotide binding, plasma membrane protein complex, and carbohydrate derivative binding. This is the first study to demonstrate that MS analysis of EXs derived from the blood plasma of HTR and LTR cattle can be successfully applied to profile the systemic effects of tick burden. Cattle ticks are a significant burden to cattle industries globally. Current methods to treat cattle ticks are costly and inefficient in the long term. It has been noted that while some cattle may exhibit a natural resistance to ticks, others carry a heavy tick burden. The study of small extracellular vesicles, or exosomes (EXs), isolated from cattle blood plasma provides a noninvasive way of analyzing changes at the cellular level and may be of use in understanding the systemic effects of tick burden or factors leading to natural resistance. The aim of this study was to assess high (HTR) and low tick resistance (LTR) cattle identified using a tick burden scoring system by analyzing the protein content of circulating EXs via qualitative proteomics analysis. We found that a class of proteins related to defense/immunity comprised 50% of proteins unique to HTR cattle, while this protein class was not detected in proteins unique to LTR cattle. Additionally, epidermal growth factor–calcium-binding protein domains were 2-fold increased in LTR cattle compared with HTR cattle, indicating a possible mechanism for widespread metabolic change. This is the first study to employ proteomic analysis of exosomal cargo as an approach to understanding the systemic effects of tick burden in cattle.
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Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
| | - Hassendrini Peiris
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
| | - Kanchan Vaswani
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT Gardens Point, Brisbane City, QLD, Australia
| | | | | | - Jayden Logan
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), South Brisbane, QLD, Australia
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23
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OUP accepted manuscript. Glycobiology 2022; 32:616-628. [DOI: 10.1093/glycob/cwac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 11/14/2022] Open
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24
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Pennarubia F, Nairn AV, Takeuchi M, Moremen KW, Haltiwanger RS. Modulation of the NOTCH1 Pathway by LUNATIC FRINGE Is Dominant over That of MANIC or RADICAL FRINGE. Molecules 2021; 26:molecules26195942. [PMID: 34641486 PMCID: PMC8512825 DOI: 10.3390/molecules26195942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Fringes are glycosyltransferases that transfer a GlcNAc to O-fucose residues on Epidermal Growth Factor-like (EGF) repeats. Three Fringes exist in mammals: LUNATIC FRINGE (LFNG), MANIC FRINGE (MFNG), and RADICAL FRINGE (RFNG). Fringe modification of O-fucose on EGF repeats in the NOTCH1 (N1) extracellular domain modulates the activation of N1 signaling. Not all O-fucose residues of N1 are modified by all Fringes; some are modified by one or two Fringes and others not modified at all. The distinct effects on N1 activity depend on which Fringe is expressed in a cell. However, little data is available on the effect that more than one Fringe has on the modification of O-fucose residues and the resulting downstream consequence on Notch activation. Using mass spectral glycoproteomic site mapping and cell-based N1 signaling assays, we compared the effect of co-expression of N1 with one or more Fringes on modification of O-fucose and activation of N1 in three cell lines. Individual expression of each Fringe with N1 in the three cell lines revealed differences in modulation of the Notch pathway dependent on the presence of endogenous Fringes. Despite these cell-based differences, co-expression of several Fringes with N1 demonstrated a dominant effect of LFNG over MFNG or RFNG. MFNG and RFNG appeared to be co-dominant but strongly dependent on the ligands used to activate N1 and on the endogenous expression of Fringes. These results show a hierarchy of Fringe activity and indicate that the effect of MFNG and/or RFNG could be small in the presence of LFNG.
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25
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Schellens R, de Vrieze E, Graave P, Broekman S, Nagel-Wolfrum K, Peters T, Kremer H, Collin RWJ, van Wijk E. Zebrafish as a Model to Evaluate a CRISPR/Cas9-Based Exon Excision Approach as a Future Treatment Option for EYS-Associated Retinitis Pigmentosa. Int J Mol Sci 2021; 22:ijms22179154. [PMID: 34502064 PMCID: PMC8431288 DOI: 10.3390/ijms22179154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinal disease (IRD) with an overall prevalence of 1 in 4000 individuals. Mutations in EYS (Eyes shut homolog) are among the most frequent causes of non-syndromic autosomal recessively inherited RP and act via a loss-of-function mechanism. In light of the recent successes for other IRDs, we investigated the therapeutic potential of exon skipping for EYS-associated RP. CRISPR/Cas9 was employed to generate zebrafish from which the region encompassing the orthologous exons 37-41 of human EYS (eys exons 40-44) was excised from the genome. The excision of these exons was predicted to maintain the open reading frame and to result in the removal of exactly one Laminin G and two EGF domains. Although the eysΔexon40-44 transcript was found at levels comparable to wild-type eys, and no unwanted off-target modifications were identified within the eys coding sequence after single-molecule sequencing, EysΔexon40-44 protein expression could not be detected. Visual motor response experiments revealed that eysΔexon40-44 larvae were visually impaired and histological analysis revealed a progressive degeneration of the retinal outer nuclear layer in these zebrafish. Altogether, the data obtained in our zebrafish model currently provide no indications for the skipping of EYS exons 37-41 as an effective future treatment strategy for EYS-associated RP.
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Affiliation(s)
- Renske Schellens
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
- Donders Institute for Brain Cognition and Behaviour, 6500 GL Nijmegen, The Netherlands;
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
- Donders Institute for Brain Cognition and Behaviour, 6500 GL Nijmegen, The Netherlands;
| | - Pam Graave
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Sanne Broekman
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
| | - Kerstin Nagel-Wolfrum
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany;
- Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Theo Peters
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
- Donders Institute for Brain Cognition and Behaviour, 6500 GL Nijmegen, The Netherlands;
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Rob W. J. Collin
- Donders Institute for Brain Cognition and Behaviour, 6500 GL Nijmegen, The Netherlands;
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.S.); (E.d.V.); (S.B.); (T.P.); (H.K.)
- Donders Institute for Brain Cognition and Behaviour, 6500 GL Nijmegen, The Netherlands;
- Correspondence:
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26
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Emery MA, Dimos BA, Mydlarz LD. Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits. Front Immunol 2021; 12:689463. [PMID: 34248980 PMCID: PMC8260672 DOI: 10.3389/fimmu.2021.689463] [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: 03/31/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pattern recognition receptors (PRRs) are evolutionarily ancient and crucial components of innate immunity, recognizing danger-associated molecular patterns (DAMPs) and activating host defenses. Basal non-bilaterian animals such as cnidarians must rely solely on innate immunity to defend themselves from pathogens. By investigating cnidarian PRR repertoires we can gain insight into the evolution of innate immunity in these basal animals. Here we utilize the increasing amount of available genomic resources within Cnidaria to survey the PRR repertoires and downstream immune pathway completeness within 15 cnidarian species spanning two major cnidarian clades, Anthozoa and Medusozoa. Overall, we find that anthozoans possess prototypical PRRs, while medusozoans appear to lack these immune proteins. Additionally, anthozoans consistently had higher numbers of PRRs across all four classes relative to medusozoans, a trend largely driven by expansions in NOD-like receptors and C-type lectins. Symbiotic, sessile, and colonial cnidarians also have expanded PRR repertoires relative to their non-symbiotic, mobile, and solitary counterparts. Interestingly, cnidarians seem to lack key components of mammalian innate immune pathways, though similar to PRR numbers, anthozoans possess more complete immune pathways than medusozoans. Together, our data indicate that anthozoans have greater immune specificity than medusozoans, which we hypothesize to be due to life history traits common within Anthozoa. Overall, this investigation reveals important insights into the evolution of innate immune proteins within these basal animals.
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Affiliation(s)
- Madison A Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
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27
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Dulla K, Slijkerman R, van Diepen HC, Albert S, Dona M, Beumer W, Turunen JJ, Chan HL, Schulkens IA, Vorthoren L, den Besten C, Buil L, Schmidt I, Miao J, Venselaar H, Zang J, Neuhauss SCF, Peters T, Broekman S, Pennings R, Kremer H, Platenburg G, Adamson P, de Vrieze E, van Wijk E. Antisense oligonucleotide-based treatment of retinitis pigmentosa caused by USH2A exon 13 mutations. Mol Ther 2021; 29:2441-2455. [PMID: 33895329 PMCID: PMC8353187 DOI: 10.1016/j.ymthe.2021.04.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Mutations in USH2A are among the most common causes of syndromic and non-syndromic retinitis pigmentosa (RP). The two most recurrent mutations in USH2A, c.2299delG and c.2276G > T, both reside in exon 13. Skipping exon 13 from the USH2A transcript presents a potential treatment modality in which the resulting transcript is predicted to encode a slightly shortened usherin protein. Morpholino-induced skipping of ush2a exon 13 in zebrafish ush2armc1 mutants resulted in the production of usherinΔexon 13 protein and a completely restored retinal function. Antisense oligonucleotides were investigated for their potential to selectively induce human USH2A exon 13 skipping. Lead candidate QR-421a induced a concentration-dependent exon 13 skipping in induced pluripotent stem cell (iPSC)-derived photoreceptor precursors from an Usher syndrome patient homozygous for the c.2299delG mutation. Mouse surrogate mQR-421a reached the retinal outer nuclear layer after a single intravitreal injection and induced a detectable level of exon skipping until at least 6 months post-injection. In conclusion, QR-421a-induced exon skipping proves to be a highly promising treatment option for RP caused by mutations in USH2A exon 13.
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Affiliation(s)
- Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Ralph Slijkerman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Silvia Albert
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Margo Dona
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Janne J Turunen
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Hee Lam Chan
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Iris A Schulkens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Lars Vorthoren
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Levi Buil
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Iris Schmidt
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Jiayi Miao
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jingjing Zang
- University of Zürich, Institute of Molecular Life Sciences, 8057 Zürich, Switzerland
| | - Stephan C F Neuhauss
- University of Zürich, Institute of Molecular Life Sciences, 8057 Zürich, Switzerland
| | - Theo Peters
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Peter Adamson
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands; UCL, Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
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28
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Westin IM, Jonsson F, Österman L, Holmberg M, Burstedt M, Golovleva I. EYS mutations and implementation of minigene assay for variant classification in EYS-associated retinitis pigmentosa in northern Sweden. Sci Rep 2021; 11:7696. [PMID: 33833316 PMCID: PMC8032658 DOI: 10.1038/s41598-021-87224-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/25/2021] [Indexed: 11/24/2022] Open
Abstract
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of inherited retinal degenerations. The ortholog of Drosophila eyes shut/spacemaker, EYS on chromosome 6q12 is a major genetic cause of recessive RP worldwide, with prevalence of 5 to 30%. In this study, by using targeted NGS, MLPA and Sanger sequencing we uncovered the EYS gene as one of the most common genetic cause of autosomal recessive RP in northern Sweden accounting for at least 16%. The most frequent pathogenic variant was c.8648_8655del that in some patients was identified in cis with c.1155T>A, indicating Finnish ancestry. We also showed that two novel EYS variants, c.2992_2992+6delinsTG and c.3877+1G>A caused exon skipping in human embryonic kidney cells, HEK293T and in retinal pigment epithelium cells, ARPE-19 demonstrating that in vitro minigene assay is a straightforward tool for the analysis of intronic variants. We conclude, that whenever it is possible, functional testing is of great value for classification of intronic EYS variants and the following molecular testing of family members, their genetic counselling, and inclusion of RP patients to future treatment studies.
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Affiliation(s)
- Ida Maria Westin
- Medical Biosciences/Medical and Clinical Genetics, University of Umeå, 901 87, Umeå, Sweden
| | - Frida Jonsson
- Medical Biosciences/Medical and Clinical Genetics, University of Umeå, 901 87, Umeå, Sweden
| | - Lennart Österman
- Medical Biosciences/Medical and Clinical Genetics, University of Umeå, 901 87, Umeå, Sweden
| | - Monica Holmberg
- Medical Biosciences/Medical and Clinical Genetics, University of Umeå, 901 87, Umeå, Sweden
| | - Marie Burstedt
- Clinical Science/Ophthalmology, University of Umeå, 901 85, Umeå, Sweden
| | - Irina Golovleva
- Medical Biosciences/Medical and Clinical Genetics, University of Umeå, 901 87, Umeå, Sweden.
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29
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Russell JJ, Grisanti LA, Brown SM, Bailey CA, Bender SB, Chandrasekar B. Reversion inducing cysteine rich protein with Kazal motifs and cardiovascular diseases: The RECKlessness of adverse remodeling. Cell Signal 2021; 83:109993. [PMID: 33781845 DOI: 10.1016/j.cellsig.2021.109993] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
The Reversion Inducing Cysteine Rich Protein With Kazal Motifs (RECK) is a glycosylphosphatidylinositol (GPI) anchored membrane-bound regulator of matrix metalloproteinases (MMPs). It is expressed throughout the body and plays a role in extracellular matrix (ECM) homeostasis and inflammation. In initial studies, RECK expression was found to be downregulated in various invasive cancers and associated with poor prognostic outcome. Restoring RECK, however, has been shown to reverse the metastatic phenotype. Downregulation of RECK expression is also reported in non-malignant diseases, such as periodontal disease, renal fibrosis, and myocardial fibrosis. As such, RECK induction has therapeutic potential in several chronic diseases. Mechanistically, RECK negatively regulates various matrixins involved in cell migration, proliferation, and adverse remodeling by targeting the expression and/or activation of multiple MMPs, A Disintegrin And Metalloproteinase Domain-Containing Proteins (ADAMs), and A Disintegrin And Metalloproteinase With Thrombospondin Motifs (ADAMTS). Outside of its role in remodeling, RECK has also been reported to exert anti-inflammatory effects. In cardiac diseases, for example, it has been shown to counteract several downstream effectors of Angiotensin II (Ang-II) that play a role in adverse cardiac and vascular remodeling, such as Interleukin-6 (IL-6)/IL-6 receptor (IL-6R)/glycoprotein 130 (IL-6 signal transducer) signaling and Epidermal Growth Factor Receptor (EGFR) transactivation. This review article focuses on the current understanding of the multifunctional effects of RECK and how its downregulation may contribute to adverse cardiovascular remodeling.
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Affiliation(s)
- Jacob J Russell
- Biomedical Sciences, University of Missouri, Columbia, MO, United States of America; Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States of America.
| | - Laurel A Grisanti
- Biomedical Sciences, University of Missouri, Columbia, MO, United States of America.
| | - Scott M Brown
- Biomedical Sciences, University of Missouri, Columbia, MO, United States of America; Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States of America.
| | - Chastidy A Bailey
- Biomedical Sciences, University of Missouri, Columbia, MO, United States of America; Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States of America.
| | - Shawn B Bender
- Biomedical Sciences, University of Missouri, Columbia, MO, United States of America; Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States of America; Dalton Cardiovascular Center, University of Missouri, Columbia, MO, United States of America.
| | - B Chandrasekar
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States of America; Medicine, University of Missouri School of Medicine, Columbia, MO, United States of America; Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, United States of America; Dalton Cardiovascular Center, University of Missouri, Columbia, MO, United States of America.
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30
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Koči J, Bista S, Chirania P, Yang X, Kitsou C, Rana VS, Yas OB, Sonenshine DE, Pal U. Antibodies against EGF-like domains in Ixodes scapularis BM86 orthologs impact tick feeding and survival of Borrelia burgdorferi. Sci Rep 2021; 11:6095. [PMID: 33731754 PMCID: PMC7971074 DOI: 10.1038/s41598-021-85624-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/01/2021] [Indexed: 11/15/2022] Open
Abstract
Ixodes scapularis ticks transmit multiple pathogens, including Borrelia burgdorferi sensu stricto, and encode many proteins harboring epidermal growth factor (EGF)-like domains. We show that I. scapularis produces multiple orthologs for Bm86, a widely studied tick gut protein considered as a target of an anti-tick vaccine, herein termed as Is86. We show that Is86 antigens feature at least three identifiable regions harboring EGF-like domains (termed as EGF-1, EGF-2, and EGF-3) and are differentially upregulated during B. burgdorferi infection. Although the RNA interference-mediated knockdown of Is86 genes did not show any influences on tick engorgement or B. burgdorferi sensu stricto persistence, the immunization of murine hosts with specific recombinant EGF antigens marginally reduced spirochete loads in the skin, in addition to affecting tick blood meal engorgement and molting. However, given the borderline impact of EGF immunization on tick engorgement and pathogen survival in the vector, it is unlikely that these antigens, at least in their current forms, could be developed as potential vaccines. Further investigations of the biological significance of Is86 (and other tick antigens) would enrich our knowledge of the intricate biology of ticks, including their interactions with resident pathogens, and contribute to the development of anti-tick measures to combat tick-borne illnesses.
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Affiliation(s)
- Juraj Koči
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA. .,Institute of Zoology, Slovak Academy of Sciences, Dúbravská cesta 9, 84506, Bratislava, Slovakia. .,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia.
| | - Sandhya Bista
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Payal Chirania
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Xiuli Yang
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Chrysoula Kitsou
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Vipin Singh Rana
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Ozlem Buyuktanir Yas
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Istinye University, Zeytinburnu, İstanbul, 34010, Turkey
| | - Daniel E Sonenshine
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA. .,Virginia-Maryland Regional College of Veterinary Medicine, College Park, MD, USA.
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31
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Stubbs MJ, Coppo P, Cheshire C, Veyradier A, Dufek S, Levine AP, Thomas M, Patel V, Connolly JO, Hubank M, Benhamou Y, Galicier L, Poullin P, Kleta R, Gale DP, Stanescu H, Scully MA. Identification of a novel genetic locus associated with immune mediated thrombotic thrombocytopenic purpura. Haematologica 2021; 107:574-582. [PMID: 33596643 PMCID: PMC8883548 DOI: 10.3324/haematol.2020.274639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/05/2022] Open
Abstract
Immune thrombotic thrombocytopenic purpura (iTTP) is an ultra-rare, life-threatening disorder, mediated through severe ADAMTS13 deficiency causing multi-system micro-thrombi formation, and has specific human leukocyte antigen associations. We undertook a large genome-wide association study to investigate additional genetically distinct associations in iTTP. We compared two iTTP patient cohorts with controls, following standardized genome-wide quality control procedures for single-nucleotide polymorphisms and imputed HLA types. Associations were functionally investigated using expression quantitative trait loci (eQTL), and motif binding prediction software. Independent associations consistent with previous findings in iTTP were detected at the HLA locus and in addition a novel association was detected on chromosome 3 (rs9884090, P=5.22x10-10, odds ratio 0.40) in the UK discovery cohort. Meta-analysis, including the French replication cohort, strengthened the associations. The haploblock containing rs9884090 is associated with reduced protein O-glycosyltransferase 1 (POGLUT1) expression (eQTL P<0.05), and functional annotation suggested a potential causative variant (rs71767581). This work implicates POGLUT1 in iTTP pathophysiology and suggests altered post-translational modification of its targets may influence disease susceptibility.
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Affiliation(s)
- Matthew J Stubbs
- Haemostasis Research Unit, UCL (London, UK); Department of Renal Medicine.
| | - Paul Coppo
- Centre de Référence des Microangiopathies Thrombotiques, Hôpital Saint-Antoine (Paris, France)
| | | | - Agnès Veyradier
- Department d'Hematologie, Centre de Référence des Microangiopathies Thrombotiques, Hôpital Lariboisière (Paris, France)
| | | | | | - Mari Thomas
- Haemostasis Research Unit, UCL (London, UK); National Institute for Health Research Cardiometabolic Programme, UCLH/UCL Cardiovascular BRC (London, UK)
| | | | | | | | - Ygal Benhamou
- Centre de Référence des Microangiopathies Thrombotiques, Hôpital Saint-Antoine (Paris, France)
| | - Lionel Galicier
- Centre de Référence des Microangiopathies Thrombotiques, Hôpital Saint-Antoine (Paris, France)
| | - Pascale Poullin
- Centre de Référence des Microangiopathies Thrombotiques, Hôpital Saint-Antoine (Paris, France)
| | | | | | | | - Marie A Scully
- Haemostasis Research Unit, UCL (London, UK); National Institute for Health Research Cardiometabolic Programme, UCLH/UCL Cardiovascular BRC (London, UK)
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32
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Chen W, Yang F, Wang C, Narula J, Pascua E, Ni I, Ding S, Deng X, Chu MLH, Pham A, Jiang X, Lindquist KC, Doonan PJ, Van Blarcom T, Yeung YA, Chaparro-Riggers J. One size does not fit all: navigating the multi-dimensional space to optimize T-cell engaging protein therapeutics. MAbs 2021; 13:1871171. [PMID: 33557687 PMCID: PMC7889206 DOI: 10.1080/19420862.2020.1871171] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
T-cell engaging biologics is a class of novel and promising immune-oncology compounds that leverage the immune system to eradicate cancer. Here, we compared and contrasted a bispecific diabody-Fc format, which displays a relatively short antigen-binding arm distance, with our bispecific IgG platform. By generating diverse panels of antigen-expressing cells where B cell maturation antigen is either tethered to the cell membrane or located to the juxtamembrane region and masked by elongated structural spacer units, we presented a systematic approach to investigate the role of antigen epitope location and molecular formats in immunological synapse formation and cytotoxicity. We demonstrated that diabody-Fc is more potent for antigen epitopes located in the membrane distal region, while bispecific IgG is more efficient for membrane-proximal epitopes. Additionally, we explored other parameters, including receptor density, antigen-binding affinity, and kinetics. Our results show that molecular format and antigen epitope location, which jointly determine the intermembrane distance between target cells and T cells, allow decoupling of cytotoxicity and cytokine release, while antigen-binding affinities appear to be positively correlated with both readouts. Our work offers new insight that could potentially lead to a wider therapeutic window for T-cell engaging biologics in general.
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Affiliation(s)
- Wei Chen
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Asher Bio, Protein Sciences , San Carlos, CA, USA
| | - Fan Yang
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA
| | - Carole Wang
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA
| | - Jatin Narula
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA
| | | | - Irene Ni
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Asher Bio, Protein Sciences , San Carlos, CA, USA
| | - Sheng Ding
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Gilead Sciences, Biology Department , Foster City, CA, USA
| | - Xiaodi Deng
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Dren Bio, Biologics Department , San Carlos, CA, USA
| | - Matthew Ling-Hon Chu
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Tizona Therapeutics, Protein Sciences , Antibody Development & Technical Operations, South San Francisco, CA, USA
| | - Amber Pham
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Arcus Biosciences, Protein Sciences , Hayward, CA, USA
| | - Xiaoyue Jiang
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Nektar Therapeutics, Biologics Analytical Development , San Francisco, CA, USA
| | | | - Patrick J Doonan
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Janssen BioTherapeutics, Janssen Research & Development, LLC , Spring House, PA, USA
| | - Tom Van Blarcom
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Allogene Therapeutics, Protein Engineering , South San Francisco, CA, USA
| | - Yik Andy Yeung
- Pfizer Worldwide R&D , BioMedicine Design, CA, USA.,Asher Bio, Protein Sciences , San Carlos, CA, USA
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33
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Ricaurte-Contreras LA, Lovera A, Moreno-Pérez DA, Bohórquez MD, Suárez CF, Gutiérrez-Vásquez E, Cuy-Chaparro L, Garzón-Ospina D, Patarroyo MA. Two 20-Residue-Long Peptides Derived from Plasmodium vivax Merozoite Surface Protein 10 EGF-Like Domains Are Involved in Binding to Human Reticulocytes. Int J Mol Sci 2021; 22:ijms22041609. [PMID: 33562650 PMCID: PMC7915351 DOI: 10.3390/ijms22041609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Plasmodium parasites’ invasion of their target cells is a complex, multi-step process involving many protein-protein interactions. Little is known about how complex the interaction with target cells is in Plasmodium vivax and few surface molecules related to reticulocytes’ adhesion have been described to date. Natural selection, functional and structural analysis were carried out on the previously described vaccine candidate P. vivax merozoite surface protein 10 (PvMSP10) for evaluating its role during initial contact with target cells. It has been shown here that the recombinant carboxyl terminal region (rPvMSP10-C) bound to adult human reticulocytes but not to normocytes, as validated by two different protein-cell interaction assays. Particularly interesting was the fact that two 20-residue-long regions (388DKEECRCRANYMPDDSVDYF407 and 415KDCSKENGNCDVNAECSIDK434) were able to inhibit rPvMSP10-C binding to reticulocytes and rosette formation using enriched target cells. These peptides were derived from PvMSP10 epidermal growth factor (EGF)-like domains (precisely, from a well-defined electrostatic zone) and consisted of regions having the potential of being B- or T-cell epitopes. These findings provide evidence, for the first time, about the fragments governing PvMSP10 binding to its target cells, thus highlighting the importance of studying them for inclusion in a P. vivax antimalarial vaccine.
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Affiliation(s)
- Laura Alejandra Ricaurte-Contreras
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
- MSc Programme in Microbiology, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Andrea Lovera
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Darwin Andrés Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Michel David Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Carlos Fernando Suárez
- Biomathematics Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia;
| | - Elizabeth Gutiérrez-Vásquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Laura Cuy-Chaparro
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Diego Garzón-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Carrera 9#51-11, Bogotá 110231, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
- Correspondence:
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34
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Lin YC, Niceta M, Muto V, Vona B, Pagnamenta AT, Maroofian R, Beetz C, van Duyvenvoorde H, Dentici ML, Lauffer P, Vallian S, Ciolfi A, Pizzi S, Bauer P, Grüning NM, Bellacchio E, Del Fattore A, Petrini S, Shaheen R, Tiosano D, Halloun R, Pode-Shakked B, Albayrak HM, Işık E, Wit JM, Dittrich M, Freire BL, Bertola DR, Jorge AAL, Barel O, Sabir AH, Al Tenaiji AMJ, Taji SM, Al-Sannaa N, Al-Abdulwahed H, Digilio MC, Irving M, Anikster Y, Bhavani GSL, Girisha KM, Haaf T, Taylor JC, Dallapiccola B, Alkuraya FS, Yang RB, Tartaglia M. SCUBE3 loss-of-function causes a recognizable recessive developmental disorder due to defective bone morphogenetic protein signaling. Am J Hum Genet 2021; 108:115-133. [PMID: 33308444 PMCID: PMC7820739 DOI: 10.1016/j.ajhg.2020.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is a member of a small family of multifunctional cell surface-anchored glycoproteins functioning as co-receptors for a variety of growth factors. Here we report that bi-allelic inactivating variants in SCUBE3 have pleiotropic consequences on development and cause a previously unrecognized syndromic disorder. Eighteen affected individuals from nine unrelated families showed a consistent phenotype characterized by reduced growth, skeletal features, distinctive craniofacial appearance, and dental anomalies. In vitro functional validation studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, and their dysregulating effect on bone morphogenetic protein (BMP) signaling. We show that SCUBE3 acts as a BMP2/BMP4 co-receptor, recruits the BMP receptor complexes into raft microdomains, and positively modulates signaling possibly by augmenting the specific interactions between BMPs and BMP type I receptors. Scube3-/- mice showed craniofacial and dental defects, reduced body size, and defective endochondral bone growth due to impaired BMP-mediated chondrogenesis and osteogenesis, recapitulating the human disorder. Our findings identify a human disease caused by defective function of a member of the SCUBE family, and link SCUBE3 to processes controlling growth, morphogenesis, and bone and teeth development through modulation of BMP signaling.
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Affiliation(s)
- Yuh-Charn Lin
- Department of Physiology, School of Medicine, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Otolaryngology - Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
| | - Alistair T Pagnamenta
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer Terrace, SW17 0RE London, UK
| | | | - Hermine van Duyvenvoorde
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Peter Lauffer
- Department of Paediatric Endocrinology, Emma Children's Hospital, Amsterdam University Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Sadeq Vallian
- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, 8174673441 Isfahan, Iran
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Del Fattore
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia; Qatar Biomedical Research Institute, Hamad Bin Khalifa University, 34110 Doha, Qatar
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, 352540 Haifa, Israel
| | - Rana Halloun
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Hatice Mutlu Albayrak
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Emregül Işık
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Institute of Bioinformatics, Julius Maximilians University, 97070 Würzburg, Germany
| | - Bruna L Freire
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Debora R Bertola
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 05403000 Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, 52621 Tel-Hashomer, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Ataf H Sabir
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK; Birmingham Women's and Children's NHS Foundation Trust, University of Birmingham, B4 6NH Birmingham, UK
| | - Amal M J Al Tenaiji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | - Sulaima M Taji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | | | | | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Gandham S L Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Jenny C Taylor
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Pharmacology, School of Medicine, National Yang-Ming University, 112304, Taipei, Taiwan.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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35
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Rouka E, Gourgoulianni N, Lüpold S, Hatzoglou C, Gourgoulianis K, Blanckenhorn WU, Zarogiannis SG. The Drosophila septate junctions beyond barrier function: Review of the literature, prediction of human orthologs of the SJ-related proteins and identification of protein domain families. Acta Physiol (Oxf) 2021; 231:e13527. [PMID: 32603029 DOI: 10.1111/apha.13527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
The involvement of Septate Junctions (SJs) in critical cellular functions that extend beyond their role as diffusion barriers in the epithelia and the nervous system has made the fruit fly an ideal model for the study of human diseases associated with impaired Tight Junction (TJ) function. In this study, we summarized current knowledge of the Drosophila melanogaster SJ-related proteins, focusing on their unconventional functions. Additionally, we sought to identify human orthologs of the corresponding genes as well as protein domain families. The systematic literature search was performed in PubMed and Scopus databases using relevant key terms. Orthologs were predicted using the DIOPT tool and aligned protein regions were determined from the Pfam database. 3-D models of the smooth SJ proteins were built on the Phyre2 and DMPFold protein structure prediction servers. A total of 30 proteins were identified as relatives to the SJ cellular structure. Key roles of these proteins, mainly in the regulation of morphogenetic events and cellular signalling, were highlighted. The investigation of protein domain families revealed that the SJ-related proteins contain conserved domains that are required not only for cell-cell interactions and cell polarity but also for cellular signalling and immunity. DIOPT analysis of orthologs identified novel human genes as putative functional homologs of the fruit fly SJ genes. A gap in our knowledge was identified regarding the domains that occur in the proteins encoded by eight SJ-associated genes. Future investigation of these domains is needed to provide functional information.
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Affiliation(s)
- Erasmia Rouka
- Department of Physiology Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
| | - Natalia Gourgoulianni
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Stefan Lüpold
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Chrissi Hatzoglou
- Department of Physiology Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
- Department of Respiratory Medicine Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
| | - Konstantinos Gourgoulianis
- Department of Respiratory Medicine Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Sotirios G. Zarogiannis
- Department of Physiology Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
- Department of Respiratory Medicine Faculty of Medicine School of Health Sciences University of ThessalyBIOPOLIS Larissa Greece
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36
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Pawolski V, Schmidt MHH. Neuron-Glia Interaction in the Developing and Adult Enteric Nervous System. Cells 2020; 10:E47. [PMID: 33396231 PMCID: PMC7823798 DOI: 10.3390/cells10010047] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/17/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022] Open
Abstract
The enteric nervous system (ENS) constitutes the largest part of the peripheral nervous system. In recent years, ENS development and its neurogenetic capacity in homeostasis and allostasishave gained increasing attention. Developmentally, the neural precursors of the ENS are mainly derived from vagal and sacral neural crest cell portions. Furthermore, Schwann cell precursors, as well as endodermal pancreatic progenitors, participate in ENS formation. Neural precursorsenherite three subpopulations: a bipotent neuron-glia, a neuronal-fated and a glial-fated subpopulation. Typically, enteric neural precursors migrate along the entire bowel to the anal end, chemoattracted by glial cell-derived neurotrophic factor (GDNF) and endothelin 3 (EDN3) molecules. During migration, a fraction undergoes differentiation into neurons and glial cells. Differentiation is regulated by bone morphogenetic proteins (BMP), Hedgehog and Notch signalling. The fully formed adult ENS may react to injury and damage with neurogenesis and gliogenesis. Nevertheless, the origin of differentiating cells is currently under debate. Putative candidates are an embryonic-like enteric neural progenitor population, Schwann cell precursors and transdifferentiating glial cells. These cells can be isolated and propagated in culture as adult ENS progenitors and may be used for cell transplantation therapies for treating enteric aganglionosis in Chagas and Hirschsprung's diseases.
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Affiliation(s)
| | - Mirko H. H. Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01307 Dresden, Germany;
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37
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Stsiapanava A, Xu C, Brunati M, Zamora‐Caballero S, Schaeffer C, Bokhove M, Han L, Hebert H, Carroni M, Yasumasu S, Rampoldi L, Wu B, Jovine L. Cryo-EM structure of native human uromodulin, a zona pellucida module polymer. EMBO J 2020; 39:e106807. [PMID: 33196145 PMCID: PMC7737619 DOI: 10.15252/embj.2020106807] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/19/2022] Open
Abstract
Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous polymerization module known as zona pellucida (ZP) "domain". Despite the conservation of this element from hydra to humans, no detailed information is available on the filamentous conformation of any ZP module protein. Here, we report a cryo-electron microscopy study of uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant protein in human urine and an archetypal ZP module-containing molecule, in its mature homopolymeric state. UMOD forms a one-start helix with an unprecedented 180-degree twist between subunits enfolded by interdomain linkers that have completely reorganized as a result of propeptide dissociation. Lateral interaction between filaments in the urine generates sheets exposing a checkerboard of binding sites to capture uropathogenic bacteria, and UMOD-based models of heteromeric vertebrate egg coat filaments identify a common sperm-binding region at the interface between subunits.
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Affiliation(s)
- Alena Stsiapanava
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Chenrui Xu
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- NTU Institute of Structural BiologyNanyang Technological UniversitySingaporeSingapore
| | - Martina Brunati
- Molecular Genetics of Renal DisordersDivision of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | | | - Céline Schaeffer
- Molecular Genetics of Renal DisordersDivision of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marcel Bokhove
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Ling Han
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Hans Hebert
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Biomedical Engineering and Health SystemsKTH Royal Institute of TechnologyHuddingeSweden
| | - Marta Carroni
- Department of Biochemistry and BiophysicsScience for Life LaboratoryStockholm UniversityStockholmSweden
| | - Shigeki Yasumasu
- Department of Materials and Life SciencesFaculty of Science and TechnologySophia UniversityTokyoJapan
| | - Luca Rampoldi
- Molecular Genetics of Renal DisordersDivision of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Bin Wu
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- NTU Institute of Structural BiologyNanyang Technological UniversitySingaporeSingapore
| | - Luca Jovine
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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38
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Wu X, Bacic A, Johnson KL, Humphries J. The Role of Brachypodium distachyon Wall-Associated Kinases (WAKs) in Cell Expansion and Stress Responses. Cells 2020; 9:E2478. [PMID: 33202612 PMCID: PMC7698158 DOI: 10.3390/cells9112478] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
The plant cell wall plays a critical role in signaling responses to environmental and developmental cues, acting as both the sensing interface and regulator of plant cell integrity. Wall-associated kinases (WAKs) are plant receptor-like kinases located at the wall-plasma membrane-cytoplasmic interface and implicated in cell wall integrity sensing. WAKs in Arabidopsis thaliana have been shown to bind pectins in different forms under various conditions, such as oligogalacturonides (OG)s in stress response, and native pectin during cell expansion. The mechanism(s) WAKs use for sensing in grasses, which contain relatively low amounts of pectin, remains unclear. WAK genes from the model monocot plant, Brachypodium distachyon were identified. Expression profiling during early seedling development and in response to sodium salicylate and salt treatment was undertaken to identify WAKs involved in cell expansion and response to external stimuli. The BdWAK2 gene displayed increased expression during cell expansion and stress response, in addition to playing a potential role in the hypersensitive response. In vitro binding assays with various forms of commercial polysaccharides (pectins, xylans, and mixed-linkage glucans) and wall-extracted fractions (pectic/hemicellulosic/cellulosic) from both Arabidopsis and Brachypodium leaf tissues provided new insights into the binding properties of BdWAK2 and other candidate BdWAKs in grasses. The BdWAKs displayed a specificity for the acidic pectins with similar binding characteristics to the AtWAKs.
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Affiliation(s)
- Xingwen Wu
- School of BioSciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora 3086, Victoria, Australia; (A.B.); (K.L.J.)
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora 3086, Victoria, Australia; (A.B.); (K.L.J.)
- Sino-Australia Plant Cell Wall Research Centre, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville 3010, Victoria, Australia
- La Trobe Institute for Agriculture and Food, La Trobe University, Bundoora 3086, Victoria, Australia; (A.B.); (K.L.J.)
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39
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Iwamoto S, Shimizu K, Negishi L, Suzuki N, Nagata K, Suzuki M. Characterization of the chalky layer-derived EGF-like domain-containing protein (CgELC) in the pacific oyster, Crassostrea gigas. J Struct Biol 2020; 212:107594. [PMID: 32736075 DOI: 10.1016/j.jsb.2020.107594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022]
Abstract
The shells of the Pacific oyster Crassostrea gigas contain calcite crystals with three types of microstructures: prismatic, chalky, and foliated layers. Many shell matrix proteins were annotated from the shells of C. gigas; however, it is unclear which SMPs play important roles in their shell mineralization. The matrix proteins have never been reported from the chalky layer. In this study, we identified a chalky layer-derived EGF-like domain-containing protein (CgELC) from the chalky layer of C. gigas shells. The gene sequence of the CgELC was encoded under CGI_ 10,017,544 of the C. gigas genome database. Only peptide fragments in the N-terminal region of CGI_ 10,017,544 were detected by LC-MS/MS analyses, suggesting that CGI_ 10,017,544 was digested at the predicted protease digestion dibasic site by post-translational modification to become a mature CgELC protein. We produced three types of CgELC recombinant proteins, namely, the full length CgELC, as well as the N-terminal and C-terminal parts of CgELC (CgELC-N or -C, respectively), for in vitro crystallization experiments. In the presence of these recombinant proteins, the aggregation of polycrystalline calcite was observed. Some fibrous organic components seemed to be incorporated into the calcite crystals in the presence of the r-CgELC protein. We also noted different features in the crystallization between CgELC-N and CgELC-C; some crystals were inhibited crystal plane formation and contained many columnar prisms inside the crystals (CgELC-N) and formed numerous holes on their surfaces (CgELC-C). These results suggest that CgELC is involved in crystal aggregation and incorporated into calcite crystals.
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Affiliation(s)
- Shihori Iwamoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Nobuo Suzuki
- Institute of Nature and Environmental Technology, Kanazawa University, 4-1 Ogimu, Notocho, Hosu-gun, Ishikawa 927-0553, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
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40
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Manshaei R, Merico D, Reuter MS, Engchuan W, Mojarad BA, Chaturvedi R, Heung T, Pellecchia G, Zarrei M, Nalpathamkalam T, Khan R, Okello JBA, Liston E, Curtis M, Yuen RKC, Marshall CR, Jobling RK, Oechslin E, Wald RM, Silversides CK, Scherer SW, Kim RH, Bassett AS. Genes and Pathways Implicated in Tetralogy of Fallot Revealed by Ultra-Rare Variant Burden Analysis in 231 Genome Sequences. Front Genet 2020; 11:957. [PMID: 33110418 PMCID: PMC7522597 DOI: 10.3389/fgene.2020.00957] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF (n = 175) or related CHD. We adapted a burden test originally developed for de novo variants to assess ultra-rare variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets and for multiple testing. For truncating variants, the gene burden test confirmed significant burden in FLT4 (Bonferroni corrected p-value < 0.01). For missense variants, burden in NOTCH1 achieved genome-wide significance only when restricted to constrained genes (i.e., under negative selection, Bonferroni corrected p-value = 0.004), and showed enrichment for variants affecting the extracellular domain, especially those disrupting cysteine residues forming disulfide bonds (OR = 39.8 vs. gnomAD). Individuals with NOTCH1 ultra-rare missense variants, all with TOF, were enriched for positive family history of CHD. Other genes not previously implicated in CHD had more modest statistical support in gene burden tests. Gene-set burden tests for truncating variants identified a cluster of pathways corresponding to VEGF signaling (FDR = 0%), and of mouse phenotypes corresponding to abnormal vasculature (FDR = 0.8%); these suggested additional candidate genes not previously identified (e.g., WNT5A and ZFAND5). Results for the most promising genes were driven by the TOF subset of the cohort. The findings support the importance of ultra-rare variants disrupting genes involved in VEGF and NOTCH signaling in the genetic architecture of TOF, accounting for 11–14% of individuals in the TOF cohort. These proof-of-principle data indicate that this statistical methodology could assist in analyzing case-only sequencing data in which ultra-rare variants, whether de novo or inherited, contribute to the genetic etiopathogenesis of a complex disorder.
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Affiliation(s)
- Roozbeh Manshaei
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniele Merico
- Deep Genomics Inc., Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bahareh A Mojarad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rajiv Chaturvedi
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.,The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Reem Khan
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - John B A Okello
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eriskay Liston
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Meredith Curtis
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rebekah K Jobling
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Erwin Oechslin
- Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Rachel M Wald
- Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Candice K Silversides
- Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Raymond H Kim
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.,The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada.,Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Mental Health, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
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41
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Hoogmartens J, Hens E, Engelborghs S, Vandenberghe R, De Deyn PP, Cacace R, Van Broeckhoven C. Contribution of homozygous and compound heterozygous missense mutations in VWA2 to Alzheimer's disease. Neurobiol Aging 2020; 99:100.e17-100.e23. [PMID: 33023779 DOI: 10.1016/j.neurobiolaging.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease is the most frequent diagnosis of neurodegenerative dementia with early (≤65 years) and late (>65 years) onset ages in familial and sporadic patients. Causal mutations in 3 autosomal dominant Alzheimer genes, i.e. amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2), explain only 5%-10% of early-onset patients leaving the majority of patients genetically unresolved. To discover potential missing genetics, we used whole genome sequencing data of 17 early-onset patients with well-documented clinical diagnosis of Alzheimer's disease. In the discovery group, the mean onset age was 55.71 ± 6.83 years (range 37-65). Six patients had a brain autopsy and neuropathology confirmed Alzheimer's disease. Analysis of the genetic data identified in one patient a homozygous p.V366M missense mutation in the Von Willebrand factor A domain containing 2 gene (VWA2). Resequencing of the VWA2 coding region in an Alzheimer's disease patient cohort from Flanders-Belgium (n = 1148), including 152 early and 996 late onset patients, identified additional homozygous and compound heterozygous missense mutations in 1 early and 3 late-onset patients. Allele-sharing analysis identified common haplotypes among the compound heterozygous VWA2 mutation carriers, suggesting shared ancestors. Overall, we identified 5 patient carriers of homozygous or compound heterozygous missense mutations (5/1165; 0.43 %), 2 in early (2/169; 1.18 %) and 3 in late-onset (3/996; 0.30 %) patients. The frequencies of the homozygous and compound heterozygous missense mutations in patients are higher than expected from the frequencies calculated based on their combined single alleles. None of the homozygous/compound heterozygous missense mutation carriers had a family history of autosomal dominant Alzheimer's disease. Our findings suggest that homozygous and compound heterozygous missense mutations in VWA2 might contribute to the risk of Alzheimer's disease in sporadic patients.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elisabeth Hens
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Edegem, Belgium; Department of Neurology, University Hospital Brussel and Center for Neurosciences, Free University Brussels, Brussels, Belgium
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology, University Hospital Brussel and Center for Neurosciences, Free University Brussels, Brussels, Belgium
| | - Rik Vandenberghe
- Department of Neurology, University Hospitals Leuven and Department of Neurosciences, KU Leuven, Belgium
| | - Peter-P De Deyn
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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42
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Farhat S, Tanguy A, Pales Espinosa E, Guo X, Boutet I, Smolowitz R, Murphy D, Rivara GJ, Allam B. Identification of variants associated with hard clam, Mercenaria mercenaria, resistance to Quahog Parasite Unknown disease. Genomics 2020; 112:4887-4896. [PMID: 32890702 DOI: 10.1016/j.ygeno.2020.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
Severe losses in aquacultured and wild hard clam (Mercenaria mercenaria) stocks have been previously reported in the northeastern United States due to a protistan parasite called QPX (Quahog Parasite Unknown). Previous work demonstrated that clam resistance to QPX is under genetic control. This study identifies single nucleotide polymorphism (SNP) associated with clam survivorship from two geographically segregated populations, both deployed in an enzootic site. The analysis contrasted samples collected before and after undergoing QPX-related mortalities and relied on a robust draft clam genome assembly. ~200 genes displayed significant variant enrichment at each sampling point in both populations, including 18 genes shared between both populations. Markers from both populations were identified in genes related to apoptosis pathways, protein-protein interaction, receptors, and signaling. This research begins to identify genetic markers associated with clam resistance to QPX disease, leading the way for the development of resistant clam stocks through marker-assisted selection.
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Affiliation(s)
- Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-5000, USA
| | - Arnaud Tanguy
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, Place Georges Teissier, 29680 Roscoff, France
| | - Emmanuelle Pales Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-5000, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Isabelle Boutet
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, Place Georges Teissier, 29680 Roscoff, France
| | - Roxanna Smolowitz
- Roger Williams University, Department of Biology, Marine Biology, and Environmental Science, 1 Old Ferry Rd, Bristol, RI 02809, USA
| | - Diane Murphy
- Cape Cod Cooperative Extension, 3195 Main St, Barnstable, MA 02630, NY 1197, USA
| | - Gregg J Rivara
- Cornell University Cooperative Extension of Suffolk County, 3690 Cedar Beach Rd, Southold, NY 11971, USA
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-5000, USA.
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43
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Mouse WIF1 Is Only Modified with O-Fucose in Its EGF-like Domain III Despite Two Evolutionarily Conserved Consensus Sites. Biomolecules 2020; 10:biom10091250. [PMID: 32872229 PMCID: PMC7565927 DOI: 10.3390/biom10091250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/12/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
The Wnt Inhibitory Factor 1 (Wif1), known to inhibit Wnt signaling pathways, is composed of a WIF domain and five EGF-like domains (EGF-LDs) involved in protein interactions. Despite the presence of a potential O-fucosylation site in its EGF-LDs III and V, the O-fucose sites occupancy has never been demonstrated for WIF1. In this study, a phylogenetic analysis on the distribution, conservation and evolution of Wif1 proteins was performed, as well as biochemical approaches focusing on O-fucosylation sites occupancy of recombinant mouse WIF1. In the monophyletic group of gnathostomes, we showed that the consensus sequence for O-fucose modification by Pofut1 is highly conserved in Wif1 EGF-LD III while it was more divergent in EGF-LD V. Using click chemistry and mass spectrometry, we demonstrated that mouse WIF1 was only modified with a non-extended O-fucose on its EGF-LD III. In addition, a decreased amount of mouse WIF1 in the secretome of CHO cells was observed when the O-fucosylation site in EGF-LD III was mutated. Based on sequence comparison and automated protein modeling, we suggest that the absence of O-fucose on EGF-LD V of WIF1 in mouse and probably in most gnathostomes, could be related to EGF-LD V inability to interact with POFUT1.
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44
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Peirasmaki D, Ma'ayeh SY, Xu F, Ferella M, Campos S, Liu J, Svärd SG. High Cysteine Membrane Proteins (HCMPs) Are Up-Regulated During Giardia-Host Cell Interactions. Front Genet 2020; 11:913. [PMID: 33014015 PMCID: PMC7461913 DOI: 10.3389/fgene.2020.00913] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Giardia intestinalis colonizes the upper small intestine of humans and animals, causing the diarrheal disease giardiasis. This unicellular eukaryotic parasite is not invasive but it attaches to the surface of small intestinal epithelial cells (IECs), disrupting the epithelial barrier. Here, we used an in vitro model of the parasite’s interaction with host IECs (differentiated Caco-2 cells) and RNA sequencing (RNAseq) to identify differentially expressed genes (DEGs) in Giardia, which might relate to the establishment of infection and disease induction. Giardia trophozoites interacted with differentiated Caco-2 cells for 1.5, 3, and 4.5 h and at each time point, 61, 89, and 148 parasite genes were up-regulated more than twofold, whereas 209, 265, and 313 parasite genes were down-regulated more than twofold. The most abundant DEGs encode hypothetical proteins and members of the High Cysteine Membrane Protein (HCMP) family. Among the up-regulated genes we also observed proteins associated with proteolysis, cellular redox balance, as well as lipid and nucleic acid metabolic pathways. In contrast, genes encoding kinases, regulators of the cell cycle and arginine metabolism and cytoskeletal proteins were down-regulated. Immunofluorescence imaging of selected, up-regulated HCMPs, using C-terminal HA-tagging, showed localization to the plasma membrane and peripheral vesicles (PVs). The expression of the HCMPs was affected by histone acetylation and free iron-levels. In fact, the latter was shown to regulate the expression of many putative giardial virulence factors in subsequent RNAseq experiments. We suggest that the plasma membrane localized and differentially expressed HCMPs play important roles during Giardia-host cell interactions.
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Affiliation(s)
- Dimitra Peirasmaki
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Showgy Y Ma'ayeh
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Feifei Xu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marcela Ferella
- Eukaryotic Single Cell Genomics Platform, Karolinska Institute, Science for Life Laboratory (SciLifeLab), Solna, Sweden
| | - Sara Campos
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jingyi Liu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
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45
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Karimi M, Crossett B, Cordwell SJ, Pattison DI, Davies MJ. Characterization of disulfide (cystine) oxidation by HOCl in a model peptide: Evidence for oxygen addition, disulfide bond cleavage and adduct formation with thiols. Free Radic Biol Med 2020; 154:62-74. [PMID: 32370994 DOI: 10.1016/j.freeradbiomed.2020.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/19/2023]
Abstract
Disulfide bonds play a key role in stabilizing proteins by cross-linking secondary structures. Whilst many disulfides are effectively unreactive, it is increasingly clear that some disulfides are redox active, participate in enzymatic reactions and/or regulate protein function by allosteric mechanisms. Previously (Karimi et al., Sci. Rep. 2016, 6, 38752) we have shown that some disulfides react rapidly with biological oxidants due to favourable interactions with available lone-pairs of electrons. Here we present data from kinetic, mechanistic and product studies for HOCl-mediated oxidation of a protected nine-amino acid model peptide containing a N- to C-terminal disulfide bond. This peptide reacts with HOCl with k2 1.8 × 106 M-1 s-1, similar to other highly-reactive disulfide-containing compounds. With low oxidant excesses, oxidation yields multiple oxidation products from the disulfide, with reaction predominating at the N-terminal Cys to give sulfenic, sulfinic and sulfonic acids, and disulfide bond cleavage. Limited oxidation occurs, with higher oxidant excesses, at Trp and His residues to give mono- and di- (for Trp) oxygenated products. Site-specific backbone cleavage also occurs between Arg and Trp, probably via initial side-chain modification. Treatment of the previously-oxidised peptide with thiols (GSH, N-Ac-Cys), results in adduction of the thiol to the oxidised peptide, with this occurring at the original disulfide bond. This gives an open-chain peptide, and a new mixed disulfide containing GSH or N-Ac-Cys as determined by mass spectrometry. Disulfide bond oxidation may therefore markedly alter the structure, activity and function of disulfide-containing proteins, and provides a potential mechanism for protein glutathionylation.
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Affiliation(s)
- Maryam Karimi
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia
| | - Ben Crossett
- Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart J Cordwell
- Faculty of Medicine, The University of Sydney, NSW, 2006, Australia; Charles Perkins Centre, School of Life and Environmental Sciences, Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - David I Pattison
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia
| | - Michael J Davies
- The Heart Research Institute, 7 Eliza St, Newtown, NSW, 2042, Australia; Faculty of Medicine, The University of Sydney, NSW, 2006, Australia; Department of Biomedical Science, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
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46
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Pennarubia F, Germot A, Pinault E, Maftah A, Legardinier S. The single EGF-like domain of mouse PAMR1 is modified by O-Glucose, O-Fucose and O-GlcNAc. Glycobiology 2020; 31:55-68. [PMID: 32518939 DOI: 10.1093/glycob/cwaa051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
Epidermal growth factor-like domains (EGF-LDs) of membrane and secreted proteins can be modified by N-glycans and/or potentially elongated O-linked monosaccharides such as O-glucose (O-Glc) found at two positions (O-Glc 1 and O-Glc2), O-fucose (O-Fuc) and O-N-acetylglucosamine (O-GlcNAc). The presence of three O-linked sugars within the same EGF-LD, such as in EGF-LD 20 of NOTCH1, has rarely been evidenced. We searched in KEGG GENES database to list mouse and human proteins with an EGF-LD sequence including one, two, three or four potential O-glycosylation consensus sites. Among the 129 murine retrieved proteins, most had predicted O-fucosylation and/or O-GlcNAcylation sites. Around 68% of EGF-LDs were subjected to only one O-linked sugar modification and near 5% to three modifications. Among these latter, we focused on the peptidase domain-containing protein associated with muscle regeneration 1 (PAMR1), having only one EGF-LD. To test the ability of this domain to be glycosylated, a correctly folded EGF-LD was produced in Escherichia coli periplasm, purified and subjected to in vitro incubations with the recombinant O-glycosyltransferases POGLUT1, POFUT1 and EOGT, adding O-Glc1, O-Fuc and O-GlcNAc, respectively. Using click chemistry and mass spectrometry, isolated PAMR1 EGF-LD was demonstrated to be modified by the three O-linked sugars. Their presence was individually confirmed on EGF-LD of full-length mouse recombinant PAMR1, with at least some molecules modified by both O-Glc1 and O-Fuc. Overall, these results are consistent with the presence of a triple O-glycosylated EGF-LD in mouse PAMR1.
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Affiliation(s)
- Florian Pennarubia
- University of Limoges, PEIRENE, EA 7500, Glycosylation and Cell Differentiation, F-87060 Limoges, France
| | - Agnès Germot
- University of Limoges, PEIRENE, EA 7500, Glycosylation and Cell Differentiation, F-87060 Limoges, France
| | - Emilie Pinault
- University of Limoges, PEIRENE, EA 7500, Glycosylation and Cell Differentiation, F-87060 Limoges, France.,University of Limoges, BISCEm, US 42 INSERM - UMS 2015 CNRS, Mass Spectrometry Platform, F-87025 Limoges, France
| | - Abderrahman Maftah
- University of Limoges, PEIRENE, EA 7500, Glycosylation and Cell Differentiation, F-87060 Limoges, France
| | - Sébastien Legardinier
- University of Limoges, PEIRENE, EA 7500, Glycosylation and Cell Differentiation, F-87060 Limoges, France
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Gaber A, Lenarčič B, Pavšič M. Current View on EpCAM Structural Biology. Cells 2020; 9:cells9061361. [PMID: 32486423 PMCID: PMC7349879 DOI: 10.3390/cells9061361] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
EpCAM, a carcinoma cell-surface marker protein and a therapeutic target, has been primarily addressed as a cell adhesion molecule. With regard to recent discoveries of its role in signaling with implications in cell proliferation and differentiation, and findings contradicting a direct role in mediating adhesion contacts, we provide a comprehensive and updated overview on the available structural data on EpCAM and interpret it in the light of recent reports on its function. First, we describe the structure of extracellular part of EpCAM, both as a subunit and part of a cis-dimer which, according to several experimental observations, represents a biologically relevant oligomeric state. Next, we provide a thorough evaluation of reports on EpCAM as a homophilic cell adhesion molecule with a structure-based explanation why direct EpCAM participation in cell–cell contacts is highly unlikely. Finally, we review the signaling aspect of EpCAM with focus on accessibility of signaling-associated cleavage sites.
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Affiliation(s)
- Aljaž Gaber
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.G.); (B.L.)
| | - Brigita Lenarčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.G.); (B.L.)
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Miha Pavšič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.G.); (B.L.)
- Correspondence: ; Tel.: +386-1-479-8550
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48
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Gorelik A, Illes K, Nagar B. Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme. Structure 2020; 28:426-436.e3. [DOI: 10.1016/j.str.2020.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/02/2020] [Accepted: 02/11/2020] [Indexed: 11/30/2022]
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49
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Liberelle M, Jonckheere N, Melnyk P, Van Seuningen I, Lebègue N. EGF-Containing Membrane-Bound Mucins: A Hidden ErbB2 Targeting Pathway? J Med Chem 2020; 63:5074-5088. [PMID: 32027502 DOI: 10.1021/acs.jmedchem.9b02001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane-bound mucins belong to a heterogeneous family of large O-glycoproteins involved in numerous cancers and inflammatory diseases of the epithelium. Some of them are also involved in protein-protein interactions, with receptor tyrosine kinase ErbB2, and fundamental and clinical data showed that these complexes have a detrimental impact on cancer outcome, thus raising interest in therapeutic targeting. This paper aims to demonstrate that MUC3, MUC4, MUC12, MUC13, and MUC17 have a common evolutionary origin and share a common structural organization with EGF-like and SEA domains. Theoretical structure-function relationship analysis of the conserved domains indicated that the studied membrane-bound mucins share common biological properties along with potential specific functions. Finally, the potential druggability of these complexes is discussed, revealing ErbB2-related pathways of cell signaling to be targeted.
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Affiliation(s)
- Maxime Liberelle
- Univ. Lille, Inserm CHU Lille, UMR-S1172-JPArc-Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000 Lille, France.,Univ. Lille, Inserm, CHU Lille, UMR-S 1172-LiNC-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Nicolas Jonckheere
- Univ. Lille, Inserm CHU Lille, UMR-S1172-JPArc-Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Patricia Melnyk
- Univ. Lille, Inserm CHU Lille, UMR-S1172-JPArc-Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000 Lille, France.,Univ. Lille, Inserm, CHU Lille, UMR-S 1172-LiNC-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Isabelle Van Seuningen
- Univ. Lille, Inserm CHU Lille, UMR-S1172-JPArc-Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Nicolas Lebègue
- Univ. Lille, Inserm CHU Lille, UMR-S1172-JPArc-Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000 Lille, France.,Univ. Lille, Inserm, CHU Lille, UMR-S 1172-LiNC-Lille Neuroscience & Cognition, F-59000 Lille, France
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50
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Khan KA, McMurray JL, Mohammed F, Bicknell R. C-type lectin domain group 14 proteins in vascular biology, cancer and inflammation. FEBS J 2019; 286:3299-3332. [PMID: 31287944 PMCID: PMC6852297 DOI: 10.1111/febs.14985] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/21/2019] [Accepted: 07/05/2019] [Indexed: 02/06/2023]
Abstract
The C‐type lectin domain (CTLD) group 14 family of transmembrane glycoproteins consist of thrombomodulin, CD93, CLEC14A and CD248 (endosialin or tumour endothelial marker‐1). These cell surface proteins exhibit similar ectodomain architecture and yet mediate a diverse range of cellular functions, including but not restricted to angiogenesis, inflammation and cell adhesion. Thrombomodulin, CD93 and CLEC14A can be expressed by endothelial cells, whereas CD248 is expressed by vasculature associated pericytes, activated fibroblasts and tumour cells among other cell types. In this article, we review the current literature of these family members including their expression profiles, interacting partners, as well as established and speculated functions. We focus primarily on their roles in the vasculature and inflammation as well as their contributions to tumour immunology. The CTLD group 14 family shares several characteristic features including their ability to be proteolytically cleaved and engagement of some shared extracellular matrix ligands. Each family member has strong links to tumour development and in particular CD93, CLEC14A and CD248 have been proposed as attractive candidate targets for cancer therapy.
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Affiliation(s)
- Kabir A Khan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Canada
| | - Jack L McMurray
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Fiyaz Mohammed
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Roy Bicknell
- Institutes of Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, UK
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