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Article: Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein

Matyushkina, Daria / Shokina, Varvara / Tikhonova, Polina / Manuvera, Valentin / Shirokov, Dmitry / Kharlampieva, Daria / Lazarev, Vasily / Varizhuk, Anna / Vedekhina, Tatiana / Pavlenko, Alexander / Penkin, Leonid / Arapidi, Georgij / Pavlov, Konstantin / Pushkar, Dmitry / Kolontarev, Konstantin / Rumyantsev, Alexander / Rumyantsev, Sergey / Rychkova, Lyubov / Govorun, Vadim

Viruses. 2022 May 25, v. 14, no. 6

2022

Abstract: COVID-19 caused by SARS-CoV-2 is continuing to spread around the world and drastically affect our daily life. New strains appear, and the severity of the course of the disease itself seems to be decreasing, but even people who have been ill on an ... ...

Abstract	COVID-19 caused by SARS-CoV-2 is continuing to spread around the world and drastically affect our daily life. New strains appear, and the severity of the course of the disease itself seems to be decreasing, but even people who have been ill on an outpatient basis suffer post-COVID consequences. Partly, it is associated with the autoimmune reactions, so debates about the development of new vaccines and the need for vaccination/revaccination continue. In this study we performed an analysis of the antibody response of patients with COVID-19 to linear and conformational epitopes of viral proteins using ELISA, chip array and western blot with analysis of correlations between antibody titer, disease severity, and complications. We have shown that the presence of IgG antibodies to the nucleoprotein can deteriorate the course of the disease, induce multiple direct COVID-19 symptoms, and contribute to long-term post-covid symptoms. We analyzed the cross reactivity of antibodies to SARS-CoV-2 with own human proteins and showed that antibodies to the nucleocapsid protein can bind to human proteins. In accordance with the possibility of HLA presentation, the main possible targets of the autoantibodies were identified. People with HLA alleles A01:01; A26:01; B39:01; B15:01 are most susceptible to the development of autoimmune processes after COVID-19.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; Western blotting ; antibody formation ; autoantibodies ; cross reaction ; disease severity ; epitopes ; humans ; nucleocapsid proteins ; nucleoproteins ; people ; vaccination
Language	English
Dates of publication	2022-0525
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14061141
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein.

Viruses

2022 Volume 14, Issue 6

Abstract	COVID-19 caused by SARS-CoV-2 is continuing to spread around the world and drastically affect our daily life. New strains appear, and the severity of the course of the disease itself seems to be decreasing, but even people who have been ill on an outpatient basis suffer post-COVID consequences. Partly, it is associated with the autoimmune reactions, so debates about the development of new vaccines and the need for vaccination/revaccination continue. In this study we performed an analysis of the antibody response of patients with COVID-19 to linear and conformational epitopes of viral proteins using ELISA, chip array and western blot with analysis of correlations between antibody titer, disease severity, and complications. We have shown that the presence of IgG antibodies to the nucleoprotein can deteriorate the course of the disease, induce multiple direct COVID-19 symptoms, and contribute to long-term post-covid symptoms. We analyzed the cross reactivity of antibodies to SARS-CoV-2 with own human proteins and showed that antibodies to the nucleocapsid protein can bind to human proteins. In accordance with the possibility of HLA presentation, the main possible targets of the autoantibodies were identified. People with HLA alleles A01:01; A26:01; B39:01; B15:01 are most susceptible to the development of autoimmune processes after COVID-19.
MeSH term(s)	Antibodies, Viral ; COVID-19/complications ; Humans ; Nucleoproteins ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	Antibodies, Viral ; Nucleoproteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14061141
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Article ; Online: Protein encoded in human telomerase RNA is involved in cell protective pathways.

Rubtsova, Maria / Naraykina, Yulia / Vasilkova, Daria / Meerson, Mark / Zvereva, Maria / Prassolov, Vladimir / Lazarev, Vasily / Manuvera, Valentin / Kovalchuk, Sergey / Anikanov, Nickolay / Butenko, Ivan / Pobeguts, Olga / Govorun, Vadim / Dontsova, Olga

Nucleic acids research

2018 Volume 46, Issue 17, Page(s) 8966–8977

Abstract: Several studies have described functional peptides encoded in RNA that are considered to be noncoding. Telomerase RNA together with telomerase reverse transcriptase and regulatory proteins make up the telomerase complex, the major component of the ... ...

Abstract	Several studies have described functional peptides encoded in RNA that are considered to be noncoding. Telomerase RNA together with telomerase reverse transcriptase and regulatory proteins make up the telomerase complex, the major component of the telomere length-maintaining machinery. In contrast to protein subunits, telomerase RNA is expressed constitutively in most somatic cells where telomerase reverse transcriptase is absent. We show here that the transcript of human telomerase RNA codes a 121 amino acid protein (hTERP). The existence of hTERP was shown by immunoblotting, immunofluorescence microscopy and mass spectroscopy. Gain-of-function and loss-of-function experiments showed that hTERP protects cells from drug-induced apoptosis and participates in the processing of autophagosome. We suggest that hTERP regulates crosstalk between autophagy and apoptosis and is involved in cellular adaptation under stress conditions.
MeSH term(s)	Adaptation, Physiological/genetics ; Amino Acid Sequence ; Animals ; Antibiotics, Antineoplastic/pharmacology ; Apoptosis/drug effects ; Apoptosis/genetics ; Autophagosomes/drug effects ; Autophagosomes/metabolism ; Autophagy/drug effects ; Autophagy/genetics ; Cats ; Cell Line, Tumor ; Cloning, Molecular ; Doxorubicin/pharmacology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression Regulation ; HEK293 Cells ; Horses ; Humans ; Jurkat Cells ; Mice ; RNA/genetics ; RNA/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction ; Stress, Physiological ; Telomerase/genetics ; Telomerase/metabolism ; Telomere/chemistry ; Telomere/metabolism ; Telomere Homeostasis
Chemical Substances	Antibiotics, Antineoplastic ; RNA, Messenger ; Recombinant Proteins ; telomerase RNA ; RNA (63231-63-0) ; Doxorubicin (80168379AG) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2018-08-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky705
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Article: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients

Galeeva, Julia / Babenko, Vladislav / Bakhtyev, Ramiz / Baklaushev, Vladimir / Balykova, Larisa / Bashkirov, Pavel / Bespyatykh, Julia / Blagonravova, Anna / Boldyreva, Daria / Fedorov, Dmitry / Gafurov, Ilshat / Gaifullina, Raushaniya / Galova, Elena / Gospodaryk, Alina / Ilina, Elena / Ivanov, Konstantin / Kharlampieva, Daria / Khromova, Polina / Klimina, Ksenia /

Kolontarev, Konstantin / Kolyshkina, Nadezhda / Koritsky, Andrey / Kuropatkin, Vyacheslav / Lazarev, Vasily / Manolov, Alexander / Manuvera, Valentin / Matyushkina, Daria / Morozov, Maxim / Moskaleva, Ekaterina / Musarova, Varvara / Ogarkov, Oleg / Orlova, Elizaveta / Pavlenko, Alexander / Petrova, Alla / Pozhenko, Natalia / Pushkar, Dmitry / Rumyantsev, Alexander / Rumyantsev, Sergey / Rumyantsev, Vladimir / Rychkova, Lyubov / Samoilov, Alexander / Shirokova, Irina / Sinkov, Vyacheslav / Solovieva, Svetlana / Starikova, Elizaveta / Tikhonova, Polina / Trifonova, Galina / Troitsky, Alexander / Tulichev, Alexander / Udalov, Yuri / Varizhuk, Anna / Vasiliev, Alexander / Veselovsky, Vladimir / Vereshchagin, Rinat / Volnukhin, Alexey / Yusubalieva, Gaukhar / Govorun, Vadim

Data in Brief. 2022 Feb., v. 40

2022

Abstract: The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the ... ...

Abstract	The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism. This data article describes the microbiome dataset from the upper respiratory tract of SARS-CoV-2 positive patients from Russia. This dataset reports the microbial community profile of 335 human nasopharyngeal swabs collected between 2020-05 and 2021-03 during the first and the second epidemic waves. Samples were collected from both inpatients and outpatients in 4 cities of the Russian Federation (Moscow, Kazan, Irkutsk, Nizhny Novgorod) and sequenced using the 16S rRNA gene amplicon sequencing of V3-V4 region. Data contains information about the patient such as age, sex, hospitalization status, percent of damaged lung tissue, oxygen saturation (SpO2), respiratory rate, need for supplemental oxygen, chest computer tomography severity score, SARS-CoV-2 lineage, and also information about smoking and comorbidities. The amplicon sequencing data were deposited at NCBI SRA as BioProject PRJNA751478.
Keywords	COVID-19 infection ; Russia ; Severe acute respiratory syndrome coronavirus 2 ; chest ; computed tomography ; data collection ; disease severity ; genes ; humans ; immune system ; lungs ; microbial communities ; microbiome ; microorganisms ; oxygen ; pandemic ; patients ; respiratory rate
Language	English
Dates of publication	2022-02
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.107770
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients.

Data in brief

2021 Volume 40, Page(s) 107770

Abstract	The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism. This data article describes the microbiome dataset from the upper respiratory tract of SARS-CoV-2 positive patients from Russia. This dataset reports the microbial community profile of 335 human nasopharyngeal swabs collected between 2020-05 and 2021-03 during the first and the second epidemic waves. Samples were collected from both inpatients and outpatients in 4 cities of the Russian Federation (Moscow, Kazan, Irkutsk, Nizhny Novgorod) and sequenced using the 16S rRNA gene amplicon sequencing of V3-V4 region. Data contains information about the patient such as age, sex, hospitalization status, percent of damaged lung tissue, oxygen saturation (SpO2), respiratory rate, need for supplemental oxygen, chest computer tomography severity score, SARS-CoV-2 lineage, and also information about smoking and comorbidities. The amplicon sequencing data were deposited at NCBI SRA as BioProject PRJNA751478.
Language	English
Publishing date	2021-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.107770
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Article: Application of Spiroplasma melliferum Proteogenomic Profiling for the Discovery of Virulence Factors and Pathogenicity Mechanisms in Host-associated Spiroplasmas

Alexeev, Dmitry / Kostrjukova Elena / Aliper Alexander / Popenko Anna / Bazaleev Nikolay / Tyakht Alexander / Selezneva Oksana / Akopian Tatyana / Prichodko Elena / Kondratov Ilya / Chukin Mikhail / Demina Irina / Galyamina Maria / Kamashev Dmitri / Vanyushkina Anna / Ladygina Valentina / Levitskii Sergei / Lazarev Vasily / Govorun Vadim

Journal of Proteome Research. 2012 Jan. 01, v. 11, no. 1

2012

Abstract: To date, no genome of any of the species from the genus Spiroplasma has been completely sequenced. Long repetitive sequences similar to mobile units present a major obstacle for current genome sequencing technologies. Here, we report the assembly of the ... ...

Abstract	To date, no genome of any of the species from the genus Spiroplasma has been completely sequenced. Long repetitive sequences similar to mobile units present a major obstacle for current genome sequencing technologies. Here, we report the assembly of the Spiroplasma melliferum KC3 genome into 4 contigs, followed by proteogenomic annotation and metabolic reconstruction based on the discovery of 521 expressed proteins and comprehensive metabolomic profiling. A systems approach allowed us to elucidate putative pathogenicity mechanisms and to discover major virulence factors, such as Chitinase utilization enzymes and toxins never before reported for insect pathogenic spiroplasmas.
Keywords	Spiroplasma melliferum ; chitinase ; genome ; insects ; metabolomics ; protein synthesis ; proteome ; repetitive sequences ; toxins ; virulence
Language	English
Dates of publication	2012-0101
Size	p. 224-236.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Fpr2008626
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Application of Spiroplasma melliferum proteogenomic profiling for the discovery of virulence factors and pathogenicity mechanisms in host-associated spiroplasmas.

Alexeev, Dmitry / Kostrjukova, Elena / Aliper, Alexander / Popenko, Anna / Bazaleev, Nikolay / Tyakht, Alexander / Selezneva, Oksana / Akopian, Tatyana / Prichodko, Elena / Kondratov, Ilya / Chukin, Mikhail / Demina, Irina / Galyamina, Maria / Kamashev, Dmitri / Vanyushkina, Anna / Ladygina, Valentina / Levitskii, Sergei / Lazarev, Vasily / Govorun, Vadim

Journal of proteome research

2012 Volume 11, Issue 1, Page(s) 224–236

Abstract	To date, no genome of any of the species from the genus Spiroplasma has been completely sequenced. Long repetitive sequences similar to mobile units present a major obstacle for current genome sequencing technologies. Here, we report the assembly of the Spiroplasma melliferum KC3 genome into 4 contigs, followed by proteogenomic annotation and metabolic reconstruction based on the discovery of 521 expressed proteins and comprehensive metabolomic profiling. A systems approach allowed us to elucidate putative pathogenicity mechanisms and to discover major virulence factors, such as Chitinase utilization enzymes and toxins never before reported for insect pathogenic spiroplasmas.
MeSH term(s)	Animals ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Chromosome Mapping ; Codon ; Genome, Bacterial ; Host-Pathogen Interactions ; Insecta/microbiology ; Molecular Sequence Annotation ; Multigene Family ; Peptide Mapping ; Proteome/genetics ; Proteome/metabolism ; Proteomics ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Spiroplasma/genetics ; Spiroplasma/metabolism ; Spiroplasma/physiology ; Virulence Factors/genetics ; Virulence Factors/metabolism
Chemical Substances	Bacterial Proteins ; Codon ; Proteome ; Virulence Factors
Language	English
Publishing date	2012-01-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/pr2008626
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Article ; Online: Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients

Babenko, Vladislav Viktorovich / Bakhtyev, Ramiz Romanovich / Baklaushev, Vladimir Pavlovich / Balykova, Larisa Alexandrovna / Bashkirov, Pavel Viktorovich / Bespyatykh, Julia Andreevna / Blagonravova, Anna Sergeevna / Boldyreva, Daria Igorevna / Fedorov, Dmitry Evgenievich / Gafurov, Ilshat Rafkatovich / Gaifullina, Raushaniya Faritovna / Galeeva, Julia Sergeevna / Galova, Elena Anatolyevna / Gospodaryk, Alina Vladimirovna / Ilina, Elena Nikolaevna / Ivanov, Konstantin Pavlovich / Kharlampieva, Daria Dmitrievna / Khromova, Polina Andreevna / Klimina, Ksenia Mikhailovna /

Kolontarev, Konstantin Borisovich / Kolyshkina, Nadezhda Aleksandrovna / Koritsky, Andrey Vladimirovich / Kuropatkin, Vyacheslav Alexandrovich / Lazarev, Vasily Nikolaevich / Manolov, Alexander Ivanovich / Manuvera, Valentin Alexandrovich / Matyushkina, Daria Sergeevna / Morozov, Maxim Denisovich / Moskaleva, Ekaterina Vladimirovna / Musarova, Varvara Alexandrovna / Ogarkov, Oleg Borisovich / Orlova, Elizaveta Andreevna / Pavlenko, Alexander Vladimirovich / Petrova, Alla Germanovna / Pozhenko, Natalia Sergeevna / Pushkar, Dmitry Yurievich / Rumyantsev, Alexander Grigorievich / Rumyantsev, Sergey Aleksandrovich / Rumyantsev, Vladimir Alexandrovich / Rychkova, Lyubov Vladimirovna / Samoilov, Alexander Sergeevich / Shirokova, Irina Yurievna / Sinkov, Vyacheslav Vladimirovich / Solovieva, Svetlana Vladimirovna / Starikova, Elizaveta Valentinovna / Tikhonova, Polina Olegovna / Trifonova, Galina Sergeevna / Troitsky, Alexander Vitalievich / Tulichev, Alexander Alekseevich / Udalov, Yuri Dmitrievich / Varizhuk, Anna Mikhailovna / Vasiliev, Alexander Olegovich / Veselovsky, Vladimir Alexandrovich / Volnukhin, Alexey Igorevich / Yusubalieva, Gaukhar Maratovna / Govorun, Vadim Markovich

bioRxiv

Abstract: The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, like the intestinal microbiota, it is involved in modulating the immune response to infectious agents in the host organism. A causal relationship ... ...

Abstract	The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, like the intestinal microbiota, it is involved in modulating the immune response to infectious agents in the host organism. A causal relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be hypothesized. We analyze biomaterial from nasopharyngeal smears from 336 patients with a confirmed diagnosis of COVID-19, selected during the first and second waves of the epidemic in Russia. Sequences from a similar study conducted in Spain were also included in the analysis. We investigated associations between disease severity and microbiota at the level of microbial community (community types) and individual microbes (differentially represented species). To search for associations, we performed multivariate analysis, taking into account comorbidities, type of community and lineage of the virus. We found that two out of six community types are associated with a more severe course of the disease, and one of the community types is characterized by high stability (very similar microbiota profiles in different patients) and low level of lung damage. Differential abundance analysis with respect to comorbidities and community type suggested association of Rothia and Streptococcus genera representatives with more severe lung damage, and Leptotrichia, unclassified Lachnospiraceae and Prevotella with milder forms of the disease.
Keywords	covid19
Language	English
Publishing date	2021-09-20
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.09.20.461025
Database	COVID19

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Article: Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein

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Article ; Online: Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein.

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Article ; Online: Protein encoded in human telomerase RNA is involved in cell protective pathways.

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Article: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients

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Article ; Online: 16S rRNA gene sequencing data of the upper respiratory tract microbiome in the SARS-CoV-2 infected patients.

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Article: Application of Spiroplasma melliferum Proteogenomic Profiling for the Discovery of Virulence Factors and Pathogenicity Mechanisms in Host-associated Spiroplasmas

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Article ; Online: Application of Spiroplasma melliferum proteogenomic profiling for the discovery of virulence factors and pathogenicity mechanisms in host-associated spiroplasmas.

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Article ; Online: Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients

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