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  1. Article: The Hidden Enemy Within: Non-canonical Peptides in Virus-Induced Autoimmunity.

    Lodha, Manivel / Erhard, Florian / Dölken, Lars / Prusty, Bhupesh K

    Frontiers in microbiology

    2022  Volume 13, Page(s) 840911

    Abstract: Viruses play a key role in explaining the pathogenesis of various autoimmune disorders, whose underlying principle is defined by the activation of autoreactive T-cells. In many cases, T-cells escape self-tolerance due to the failure in encountering ... ...

    Abstract Viruses play a key role in explaining the pathogenesis of various autoimmune disorders, whose underlying principle is defined by the activation of autoreactive T-cells. In many cases, T-cells escape self-tolerance due to the failure in encountering certain MHC-I self-peptide complexes at substantial levels, whose peptides remain invisible from the immune system. Over the years, contribution of unstable defective ribosomal products (DRiPs) in immunosurveillance has gained prominence. A class of unstable products emerge from non-canonical translation and processing of unannotated mammalian and viral ORFs and their peptides are cryptic in nature. Indeed, high throughput sequencing and proteomics have revealed that a substantial portion of our genomes comprise of non-canonical ORFs, whose generation is significantly modulated during disease. Many of these ORFs comprise short ORFs (sORFs) and upstream ORFs (uORFs) that resemble DRiPs and may hence be preferentially presented. Here, we discuss how such products, normally "hidden" from the immune system, become abundant in viral infections activating autoimmune T-cells, by discussing their emerging role in infection and disease. Finally, we provide a perspective on how these mechanisms can explain several autoimmune disorders in the wake of the COVID-19 pandemic.
    Language English
    Publishing date 2022-02-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.840911
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data.

    Berg, Kevin / Lodha, Manivel / Delazer, Isabel / Bartosik, Karolina / Garcia, Yilliam Cruz / Hennig, Thomas / Wolf, Elmar / Dölken, Lars / Lusser, Alexandra / Prusty, Bhupesh K / Erhard, Florian

    Nucleic acids research

    2024  Volume 52, Issue 7, Page(s) e35

    Abstract: Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA ... ...

    Abstract Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA expression profiles from a single sequencing library. Cytotoxicity due to extended periods of labelling or high 4sU concentrations has been described, but the effects of extensive 4sU labelling on expression estimates from nucleotide conversion RNA-seq have not been studied. Here, we performed nucleotide conversion RNA-seq with escalating doses of 4sU with short-term labelling (1h) and over a progressive time course (up to 2h) in different cell lines. With high concentrations or at later time points, expression estimates were biased in an RNA half-life dependent manner. We show that bias arose by a combination of reduced mappability of reads carrying multiple conversions, and a global, unspecific underrepresentation of labelled RNA emerging during library preparation and potentially global reduction of RNA synthesis. We developed a computational tool to rescue unmappable reads, which performed favourably compared to previous read mappers, and a statistical method, which could fully remove remaining bias. All methods developed here are freely available as part of our GRAND-SLAM pipeline and grandR package.
    MeSH term(s) Thiouridine/metabolism ; Thiouridine/chemistry ; RNA-Seq/methods ; Humans ; RNA/genetics ; Sequence Analysis, RNA/methods ; Nucleotides/genetics
    Chemical Substances Thiouridine (13957-31-8) ; RNA (63231-63-0) ; Nucleotides
    Language English
    Publishing date 2024-02-21
    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/gkae120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Decoding murine cytomegalovirus.

    Lodha, Manivel / Muchsin, Ihsan / Jürges, Christopher / Juranic Lisnic, Vanda / L'Hernault, Anne / Rutkowski, Andrzej J / Prusty, Bhupesh K / Grothey, Arnhild / Milic, Andrea / Hennig, Thomas / Jonjic, Stipan / Friedel, Caroline C / Erhard, Florian / Dölken, Lars

    PLoS pathogens

    2023  Volume 19, Issue 5, Page(s) e1010992

    Abstract: The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor ≈170 open reading frames (ORFs). More recently, omics ... ...

    Abstract The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor ≈170 open reading frames (ORFs). More recently, omics approaches revealed HCMV gene expression to be substantially more complex comprising several hundred viral ORFs. Here, we provide a state-of-the art reannotation of lytic MCMV gene expression based on integrative analysis of a large set of omics data. Our data reveal 365 viral transcription start sites (TiSS) that give rise to 380 and 454 viral transcripts and ORFs, respectively. The latter include >200 small ORFs, some of which represented the most highly expressed viral gene products. By combining TiSS profiling with metabolic RNA labelling and chemical nucleotide conversion sequencing (dSLAM-seq), we provide a detailed picture of the expression kinetics of viral transcription. This not only resulted in the identification of a novel MCMV immediate early transcript encoding the m166.5 ORF, which we termed ie4, but also revealed a group of well-expressed viral transcripts that are induced later than canonical true late genes and contain an initiator element (Inr) but no TATA- or TATT-box in their core promoters. We show that viral upstream ORFs (uORFs) tune gene expression of longer viral ORFs expressed in cis at translational level. Finally, we identify a truncated isoform of the viral NK-cell immune evasin m145 arising from a viral TiSS downstream of the canonical m145 mRNA. Despite being ≈5-fold more abundantly expressed than the canonical m145 protein it was not required for downregulating the NK cell ligand, MULT-I. In summary, our work will pave the way for future mechanistic studies on previously unknown cytomegalovirus gene products in an important virus animal model.
    MeSH term(s) Animals ; Mice ; Humans ; Muromegalovirus ; Cytomegalovirus/genetics ; Cytomegalovirus/metabolism ; Base Sequence ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Open Reading Frames
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2023-05-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1010992
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Two murine cytomegalovirus microRNAs target the major viral immediate early 3 gene.

    Herb, Stefanie / Zeleznjak, Jelena / Hennig, Thomas / L'Hernault, Anne / Lodha, Manivel / Jürges, Christopher / Trsan, Tihana / Juranic Lisnic, Vanda / Jonjic, Stipan / Erhard, Florian / Krmpotic, Astrid / Dölken, Lars

    The Journal of general virology

    2022  Volume 103, Issue 11

    Abstract: Human cytomegalovirus is responsible for morbidity and mortality in immune compromised patients and is the leading viral cause of congenital infection. Virus-encoded microRNAs (miRNAs) represent interesting targets for novel antiviral agents. While many ... ...

    Abstract Human cytomegalovirus is responsible for morbidity and mortality in immune compromised patients and is the leading viral cause of congenital infection. Virus-encoded microRNAs (miRNAs) represent interesting targets for novel antiviral agents. While many cellular targets that augment productive infection have been identified in recent years, regulation of viral genes such as the major viral immediate early protein 72 (IE72) by hcmv-miR-UL112-1 may contribute to both the establishment and the maintenance of latent infection. We employed photoactivated ribonucleotide-enhanced individual nucleotide resolution crosslinking (PAR-iCLIP) to identify murine cytomegalovirus (MCMV) miRNA targets during lytic infection. While the PAR-iCLIP data were of insufficient quality to obtain a comprehensive list of cellular and viral miRNA targets, the most prominent PAR-iCLIP peak in the MCMV genome mapped to the 3' untranslated region of the major viral immediate early 3 (
    MeSH term(s) Humans ; Mice ; Animals ; Muromegalovirus/genetics ; Genes, Immediate-Early ; CD8-Positive T-Lymphocytes/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Cytomegalovirus/genetics ; 3' Untranslated Regions
    Chemical Substances MicroRNAs ; 3' Untranslated Regions ; microRNA-UL112, human cytomegalovirus
    Language English
    Publishing date 2022-11-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001804
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Selective inhibition of miRNA processing by a herpesvirus-encoded miRNA.

    Hennig, Thomas / Prusty, Archana B / Kaufer, Benedikt B / Whisnant, Adam W / Lodha, Manivel / Enders, Antje / Thomas, Julius / Kasimir, Francesca / Grothey, Arnhild / Klein, Teresa / Herb, Stefanie / Jürges, Christopher / Sauer, Markus / Fischer, Utz / Rudel, Thomas / Meister, Gunter / Erhard, Florian / Dölken, Lars / Prusty, Bhupesh K

    Nature

    2022  Volume 605, Issue 7910, Page(s) 539–544

    Abstract: Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and ... ...

    Abstract Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and reactivation
    MeSH term(s) Herpesviridae/genetics ; Herpesviridae/metabolism ; Humans ; Immune Evasion ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA Interference ; RNA Processing, Post-Transcriptional ; Virus Latency/genetics
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2022-05-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-04667-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Decoding murine cytomegalovirus.

    Manivel Lodha / Ihsan Muchsin / Christopher Jürges / Vanda Juranic Lisnic / Anne L'Hernault / Andrzej J Rutkowski / Bhupesh K Prusty / Arnhild Grothey / Andrea Milic / Thomas Hennig / Stipan Jonjic / Caroline C Friedel / Florian Erhard / Lars Dölken

    PLoS Pathogens, Vol 19, Iss 5, p e

    2023  Volume 1010992

    Abstract: The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor ≈170 open reading frames (ORFs). More recently, omics ... ...

    Abstract The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor ≈170 open reading frames (ORFs). More recently, omics approaches revealed HCMV gene expression to be substantially more complex comprising several hundred viral ORFs. Here, we provide a state-of-the art reannotation of lytic MCMV gene expression based on integrative analysis of a large set of omics data. Our data reveal 365 viral transcription start sites (TiSS) that give rise to 380 and 454 viral transcripts and ORFs, respectively. The latter include >200 small ORFs, some of which represented the most highly expressed viral gene products. By combining TiSS profiling with metabolic RNA labelling and chemical nucleotide conversion sequencing (dSLAM-seq), we provide a detailed picture of the expression kinetics of viral transcription. This not only resulted in the identification of a novel MCMV immediate early transcript encoding the m166.5 ORF, which we termed ie4, but also revealed a group of well-expressed viral transcripts that are induced later than canonical true late genes and contain an initiator element (Inr) but no TATA- or TATT-box in their core promoters. We show that viral upstream ORFs (uORFs) tune gene expression of longer viral ORFs expressed in cis at translational level. Finally, we identify a truncated isoform of the viral NK-cell immune evasin m145 arising from a viral TiSS downstream of the canonical m145 mRNA. Despite being ≈5-fold more abundantly expressed than the canonical m145 protein it was not required for downregulating the NK cell ligand, MULT-I. In summary, our work will pave the way for future mechanistic studies on previously unknown cytomegalovirus gene products in an important virus animal model.
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Th17 cell master transcription factor RORC2 regulates HIV-1 gene expression and viral outgrowth.

    Wiche Salinas, Tomas Raul / Zhang, Yuwei / Sarnello, Daniele / Zhyvoloup, Alexander / Marchand, Laurence Raymond / Fert, Augustine / Planas, Delphine / Lodha, Manivel / Chatterjee, Debashree / Karwacz, Katarzyna / Oxenford, Sally / Routy, Jean-Pierre / Irlbeck, David / Amrine-Madsen, Heather / Ancuta, Petronela / Fassati, Ariberto

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 118, Issue 48

    Abstract: ... Among ... ...

    Abstract Among CD4
    MeSH term(s) Adult ; CD4-Positive T-Lymphocytes/immunology ; Cell Differentiation/immunology ; Cytokines/metabolism ; Female ; Gene Expression/genetics ; Gene Expression Regulation, Viral/genetics ; HIV Infections/immunology ; HIV-1/genetics ; HIV-1/growth & development ; Humans ; Lymphocyte Activation ; Male ; Middle Aged ; Nuclear Receptor Subfamily 1, Group F, Member 3/genetics ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Primary Cell Culture ; T-Lymphocyte Subsets/immunology ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/metabolism ; Th17 Cells/physiology ; Transcription Factors/metabolism ; Viremia/immunology ; Viremia/virology ; Virus Replication/physiology
    Chemical Substances Cytokines ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; RORC protein, human ; Transcription Factors
    Language English
    Publishing date 2022-01-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2105927118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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