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Article ; Online: Quantitative proteomics analysis of COVID-19 patients: Fetuin-A and tetranectin as potential modulators of innate immune responses

Alghanem, Bandar / Mansour, Fatmah A. / Shaibah, Hayat / Almuhalhil, Khawlah / Almourfi, Feras / Alamri, Hassan S. / Alajmi, Hala / Rashid, Mamoon / Alroqi, Fayhan / Jalouli, Maroua / Harrath, Abdel Halim / Boudjellal, Mohammad / Barhoumi, Tlili

Heliyon. 2023 Apr., v. 9, no. 4 p.e15224-

2023

Abstract: Treatment of severe cases of coronavirus disease 2019 (COVID-19) is extremely important to minimize death and end-organ damage. Here we performed a proteomic analysis of plasma samples from mild, moderate and severe COVID-19 patients. Analysis revealed ... ...

Abstract	Treatment of severe cases of coronavirus disease 2019 (COVID-19) is extremely important to minimize death and end-organ damage. Here we performed a proteomic analysis of plasma samples from mild, moderate and severe COVID-19 patients. Analysis revealed differentially expressed proteins and different therapeutic potential targets related to innate immune responses such as fetuin-A, tetranectin (TN) and paraoxonase-1 (PON1). Furthermore, protein changes in plasma showed dysregulation of complement and coagulation cascades in COVID-19 patients compared to healthy controls. In conclusion, our proteomics data suggested fetuin-A and TN as potential targets that might be used for diagnosis as well as signatures for a better understanding of the pathogenesis of COVID-19 disease.
Keywords	COVID-19 infection ; coagulation ; complement ; death ; gene expression regulation ; pathogenesis ; proteomics ; therapeutics ; Innate immunity ; Mass spectrometry ; Fetuin-A ; Tetranectin ; COVID-19
Language	English
Dates of publication	2023-04
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15224
Database	NAL-Catalogue (AGRICOLA)

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Article: Stimulatory effects of

Alghamdi, Khalid / Alehaideb, Zeyad / Kumar, Ashok / Al-Eidi, Hamad / Alghamdi, Sahar S / Suliman, Rasha / Ali, Rizwan / Almourfi, Feras / Alghamdi, Saleh M / Boudjelal, Mohamed / Matou-Nasri, Sabine

Frontiers in pharmacology

2023 Volume 14, Page(s) 1169812

Abstract: There is no first-line treatment for vitiligo, a skin disease characterized by a lack of melanin produced by the melanocytes, resulting in an urgent demand for new therapeutic drugs capable of stimulating melanocyte functions, including melanogenesis. In ...

Abstract	There is no first-line treatment for vitiligo, a skin disease characterized by a lack of melanin produced by the melanocytes, resulting in an urgent demand for new therapeutic drugs capable of stimulating melanocyte functions, including melanogenesis. In this study, traditional medicinal plant extracts were tested for cultured human melanocyte proliferation, migration, and melanogenesis using MTT, scratch wound-healing assays, transmission electron microscopy, immunofluorescence staining, and Western blot technology. Of the methanolic extracts,
Language	English
Publishing date	2023-04-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1169812
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Article: Quantitative proteomics analysis of COVID-19 patients: Fetuin-A and tetranectin as potential modulators of innate immune responses.

Alghanem, Bandar / Mansour, Fatmah A / Shaibah, Hayat / Almuhalhil, Khawlah / Almourfi, Feras / Alamri, Hassan S / Alajmi, Hala / Rashid, Mamoon / Alroqi, Fayhan / Jalouli, Maroua / Harrath, Abdel Halim / Boudjellal, Mohammad / Barhoumi, Tlili

Heliyon

2023 Volume 9, Issue 4, Page(s) e15224

Abstract	Treatment of severe cases of coronavirus disease 2019 (COVID-19) is extremely important to minimize death and end-organ damage. Here we performed a proteomic analysis of plasma samples from mild, moderate and severe COVID-19 patients. Analysis revealed differentially expressed proteins and different therapeutic potential targets related to innate immune responses such as fetuin-A, tetranectin (TN) and paraoxonase-1 (PON1). Furthermore, protein changes in plasma showed dysregulation of complement and coagulation cascades in COVID-19 patients compared to healthy controls. In conclusion, our proteomics data suggested fetuin-A and TN as potential targets that might be used for diagnosis as well as signatures for a better understanding of the pathogenesis of COVID-19 disease.
Language	English
Publishing date	2023-04-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15224
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Crystallization and preliminary crystallographic analysis of the putative sugar-binding protein Msmeg_0515 (AgaE) from Mycobacterium smegmatis.

Almourfi, Feras M / Rodgers, H Fiona / Sedelnikova, Svetlana E / Baker, Patrick J

Acta crystallographica. Section F, Structural biology communications

2015 Volume 71, Issue Pt 2, Page(s) 189–193

Abstract: Msmeg_0515, a gene from Mycobacterium smegmatis strain 155 encoding the ligand-binding domain, AgaE, of a putative ABC sugar transporter system, has been cloned into a pET-28a vector system, overexpressed in Escherichia coli and purified. The truncated ... ...

Abstract	Msmeg_0515, a gene from Mycobacterium smegmatis strain 155 encoding the ligand-binding domain, AgaE, of a putative ABC sugar transporter system, has been cloned into a pET-28a vector system, overexpressed in Escherichia coli and purified. The truncated protein lacking the first 27 residues, which correspond to a N-terminal signal sequence, was crystallized using the sitting-drop vapour-diffusion technique. The crystals of this protein diffracted to 1.48 Å resolution and belonged to space group P212121, with unit-cell parameters a = 64.06, b = 69.26, c = 100.74 Å, α = β = γ = 90° and with one molecule in the asymmetric unit.
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/chemistry ; Crystallization ; Crystallography, X-Ray ; Electrophoresis, Polyacrylamide Gel ; Ligands ; Molecular Sequence Data ; Mycobacterium smegmatis/chemistry ; Receptors, Cell Surface/chemistry
Chemical Substances	Bacterial Proteins ; Ligands ; Receptors, Cell Surface ; saccharide-binding proteins
Language	English
Publishing date	2015-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2053-230X
ISSN (online)	2053-230X
DOI	10.1107/S2053230X15000035
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comprehensive multi-omics analysis of G6PC3 deficiency-related congenital neutropenia with inflammatory bowel disease.

Dasouki, Majed / Alaiya, Ayodeele / ElAmin, Tanziel / Shinwari, Zakia / Monies, Dorota / Abouelhoda, Mohamed / Jabaan, Amjad / Almourfi, Feras / Rahbeeni, Zuhair / Alsohaibani, Fahad / Almohareb, Fahad / Al-Zahrani, Hazzaa / Guzmán Vega, Francisco J / Arold, Stefan T / Aljurf, Mahmoud / Ahmed, Syed Osman

iScience

2021 Volume 24, Issue 3, Page(s) 102214

Abstract: Autosomal recessive mutations ... ...

Abstract	Autosomal recessive mutations in
Language	English
Publishing date	2021-02-25
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102214
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic

Subramanian, Kalyanasundaram / Mitusińska, Karolina / Raedts, John / Almourfi, Feras / Joosten, Henk-Jan / Hendriks, Sjon / Sedelnikova, Svetlana E / Kengen, Servé W M / Hagen, Wilfred R / Góra, Artur / Martins Dos Santos, Vitor A P / Baker, Patrick J / van der Oost, John / Schaap, Peter J

Biomolecules

2019 Volume 9, Issue 6

Abstract: The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic ... ...

Abstract	The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon
MeSH term(s)	Enzyme Inhibitors/pharmacology ; Glucose-6-Phosphate Isomerase/antagonists & inhibitors ; Glucose-6-Phosphate Isomerase/chemistry ; Glucose-6-Phosphate Isomerase/genetics ; Glucose-6-Phosphate Isomerase/metabolism ; Manganese/metabolism ; Molecular Dynamics Simulation ; Mutant Proteins/antagonists & inhibitors ; Mutant Proteins/chemistry ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Mutation ; Protein Conformation ; Protein Engineering ; Pyrococcus furiosus/enzymology ; Temperature ; Water/metabolism
Chemical Substances	Enzyme Inhibitors ; Mutant Proteins ; Water (059QF0KO0R) ; Manganese (42Z2K6ZL8P) ; Glucose-6-Phosphate Isomerase (EC 5.3.1.9)
Language	English
Publishing date	2019-05-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom9060212
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Article ; Online: Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase

Subramanian, Kalyanasundaram / Mitusińska, Karolina / Raedts, John / Almourfi, Feras / Joosten, Henk Jan / Hendriks, Sjon / Sedelnikova, Svetlana E. / Kengen, Servé W.M. / Hagen, Wilfred R. / Góra, Artur / Martins Dos Santos, Vitor A.P. / Baker, Patrick J. / van der Oost, John / Schaap, Peter J.

Biomolecules

2019 Volume 9, Issue 6

Abstract: The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics ... ...

Abstract	The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of PfPGI was found to be the dominant co-evolving mutation. The position of these selected residues was found to be non-obvious to conventional protein engineering methods. We designed a small smart library of variants by substituting the co-evolved pair and screened their biochemical activity, which revealed their functional relevance. Four mutants were further selected from the library for purification, measurement of their specific activity, crystal structure determination, and metal cofactor coordination analysis. Though the mutant structures and metal cofactor coordination were strikingly similar, variations in their activity correlated with their fine-tuned dynamics and solvent access regulation. Alternative, small smart libraries for enzyme optimization are suggested by our approach, which is able to identify non-obvious yet beneficial mutations.
Keywords	Comulator ; Protein engineering ; Pyrococcus furiosus ; cupin phosphoglucose isomerase ; solvent access
Subject code	572
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	2701262-1
ISSN	2218-273X
ISSN	2218-273X
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

Zhang, Qian / Bastard, Paul / Liu, Zhiyong / Le Pen, Jérémie / Moncada-Velez, Marcela / Chen, Jie / Ogishi, Masato / Sabli, Ira K D / Hodeib, Stephanie / Korol, Cecilia / Rosain, Jérémie / Bilguvar, Kaya / Ye, Junqiang / Bolze, Alexandre / Bigio, Benedetta / Yang, Rui / Arias, Andrés Augusto / Zhou, Qinhua / Zhang, Yu /

Onodi, Fanny / Korniotis, Sarantis / Karpf, Léa / Philippot, Quentin / Chbihi, Marwa / Bonnet-Madin, Lucie / Dorgham, Karim / Smith, Nikaïa / Schneider, William M / Razooky, Brandon S / Hoffmann, Hans-Heinrich / Michailidis, Eleftherios / Moens, Leen / Han, Ji Eun / Lorenzo, Lazaro / Bizien, Lucy / Meade, Philip / Neehus, Anna-Lena / Ugurbil, Aileen Camille / Corneau, Aurélien / Kerner, Gaspard / Zhang, Peng / Rapaport, Franck / Seeleuthner, Yoann / Manry, Jeremy / Masson, Cecile / Schmitt, Yohann / Schlüter, Agatha / Le Voyer, Tom / Khan, Taushif / Li, Juan / Fellay, Jacques / Roussel, Lucie / Shahrooei, Mohammad / Alosaimi, Mohammed F / Mansouri, Davood / Al-Saud, Haya / Al-Mulla, Fahd / Almourfi, Feras / Al-Muhsen, Saleh Zaid / Alsohime, Fahad / Al Turki, Saeed / Hasanato, Rana / van de Beek, Diederik / Biondi, Andrea / Bettini, Laura Rachele / D'Angio', Mariella / Bonfanti, Paolo / Imberti, Luisa / Sottini, Alessandra / Paghera, Simone / Quiros-Roldan, Eugenia / Rossi, Camillo / Oler, Andrew J / Tompkins, Miranda F / Alba, Camille / Vandernoot, Isabelle / Goffard, Jean-Christophe / Smits, Guillaume / Migeotte, Isabelle / Haerynck, Filomeen / Soler-Palacin, Pere / Martin-Nalda, Andrea / Colobran, Roger / Morange, Pierre-Emmanuel / Keles, Sevgi / Çölkesen, Fatma / Ozcelik, Tayfun / Yasar, Kadriye Kart / Senoglu, Sevtap / Karabela, Şemsi Nur / Rodríguez-Gallego, Carlos / Novelli, Giuseppe / Hraiech, Sami / Tandjaoui-Lambiotte, Yacine / Duval, Xavier / Laouénan, Cédric / Snow, Andrew L / Dalgard, Clifton L / Milner, Joshua D / Vinh, Donald C / Mogensen, Trine H / Marr, Nico / Spaan, András N / Boisson, Bertrand / Boisson-Dupuis, Stéphanie / Bustamante, Jacinta / Puel, Anne / Ciancanelli, Michael J / Meyts, Isabelle / Maniatis, Tom / Soumelis, Vassili / Amara, Ali / Nussenzweig, Michel / García-Sastre, Adolfo / Krammer, Florian / Pujol, Aurora / Duffy, Darragh / Lifton, Richard P / Zhang, Shen-Ying / Gorochov, Guy / Béziat, Vivien / Jouanguy, Emmanuelle / Sancho-Shimizu, Vanessa / Rice, Charles M / Abel, Laurent / Notarangelo, Luigi D / Cobat, Aurélie / Su, Helen C / Casanova, Jean-Laurent

Science (New York, N.Y.)

2020 Volume 370, Issue 6515

Abstract: Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function ( ... ...

Abstract	Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Alleles ; Asymptomatic Infections ; Betacoronavirus ; COVID-19 ; Child ; Child, Preschool ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; Female ; Genetic Loci ; Genetic Predisposition to Disease ; Humans ; Infant ; Interferon Regulatory Factor-7/deficiency ; Interferon Regulatory Factor-7/genetics ; Interferon Type I/immunology ; Loss of Function Mutation ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral/genetics ; Pneumonia, Viral/immunology ; Receptor, Interferon alpha-beta/deficiency ; Receptor, Interferon alpha-beta/genetics ; SARS-CoV-2 ; Toll-Like Receptor 3/deficiency ; Toll-Like Receptor 3/genetics ; Young Adult
Chemical Substances	IFNAR1 protein, human ; IRF7 protein, human ; Interferon Regulatory Factor-7 ; Interferon Type I ; TLR3 protein, human ; Toll-Like Receptor 3 ; Receptor, Interferon alpha-beta (156986-95-7)
Keywords	covid19
Language	English
Publishing date	2020-09-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abd4570
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Article ; Online: Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

Zhang, Qian / Bastard, Paul / Liu, Zhiyong / Le Pen, Jérémie / Moncada-Velez, Marcela / Chen, Jie / Ogishi, Masato / Sabli, Ira / Hodeib, Stephanie / Korol, Cecilia / Rosain, Jérémie / Bilguvar, Kaya / Ye, Junqiang / Bolze, Alexandre / Bigio, Benedetta / Yang, Rui / Arias, Andrés Augusto / Zhou, Qinhua / Zhang, Yu /

Onodi, Fanny / Korniotis, Sarantis / Karpf, Léa / Philippot, Quentin / Chbihi, Marwa / Bonnet-Madin, Lucie / Dorgham, Karim / Smith, Nikaïa / Schneider, William / Razooky, Brandon / Hoffmann, Hans-Heinrich / Michailidis, Eleftherios / Moens, Leen / Han, Ji Eun / Lorenzo, Lazaro / Bizien, Lucy / Meade, Philip / Neehus, Anna-Lena / Ugurbil, Aileen Camille / Corneau, Aurélien / Kerner, Gaspard / Zhang, Peng / Rapaport, Franck / Seeleuthner, Yoann / Manry, Jeremy / Masson, Cecile / Schmitt, Yohann / Schlüter, Agatha / Le Voyer, Tom / Khan, Taushif / Li, Juan / Fellay, Jacques / Roussel, Lucie / Shahrooei, Mohammad / Alosaimi, Mohammed / Mansouri, Davood / Al-Saud, Haya / Al-Mulla, Fahd / Almourfi, Feras / Al-Muhsen, Saleh Zaid / Alsohime, Fahad / Al Turki, Saeed / Hasanato, Rana / Van De Beek, Diederik / Biondi, Andrea / Bettini, Laura Rachele / D’Angio, Mariella / Bonfanti, Paolo / Imberti, Luisa / Sottini, Alessandra / Paghera, Simone / Quiros-Roldan, Eugenia / Rossi, Camillo / Oler, Andrew / Tompkins, Miranda / Alba, Camille / Vandernoot, Isabelle / Goffard, Jean-Christophe / Smits, Guillaume / Migeotte, Isabelle / Haerynck, Filomeen / Soler-Palacin, Pere / Martin-Nalda, Andrea / Colobran, Roger / Morange, Pierre-Emmanuel / Keles, Sevgi / Çölkesen, Fatma / Ozcelik, Tayfun / Yasar, Kadriye Kart / Senoglu, Sevtap / Karabela, Şemsi Nur / Gallego, Carlos Rodríguez / Novelli, Giuseppe / Hraiech, Sami / Tandjaoui-Lambiotte, Yacine / Duval, Xavier / Laouénan, Cédric / Snow, Andrew / Dalgard, Clifton / Milner, Joshua / Vinh, Donald / Mogensen, Trine / Marr, Nico / Spaan, András / Boisson, Bertrand / Boisson-Dupuis, Stéphanie / Bustamante, Jacinta / Puel, Anne / Ciancanelli, Michael / Meyts, Isabelle / Maniatis, Tom / Soumelis, Vassili / Amara, Ali / Nussenzweig, Michel / García-Sastre, Adolfo / Krammer, Florian / Pujol, Aurora / Duffy, Darragh / Lifton, Richard / Zhang, Shen-Ying / Gorochov, Guy / Béziat, Vivien / Jouanguy, Emmanuelle / Sancho-Shimizu, Vanessa / Rice, Charles / Abel, Laurent / Notarangelo, Luigi / Cobat, Aurélie / Su, Helen / Casanova, Jean-Laurent

ISSN: 0036-8075 ; EISSN: 1095-9203 ; Science ; https://hal.archives-ouvertes.fr/hal-02950982 ; Science, American Association for the Advancement of Science, 2020, pp.eabd4570. ⟨10.1126/science.abd4570⟩

2020

Abstract: International ... ...

Abstract	International audience
Keywords	[SDV]Life Sciences [q-bio] ; covid19
Language	English
Publishing date	2020-09-24
Publisher	HAL CCSD
Publishing country	fr
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

2020

Abstract: International ... ...

Abstract	International audience
Keywords	[SDV]Life Sciences [q-bio] ; covid19
Language	English
Publishing date	2020-09-24
Publisher	HAL CCSD
Publishing country	fr
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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