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  1. AU="Messemaker, Tobias C"
  2. AU="Daniel, Maria Urszula"
  3. AU=Edwards Robert J AU=Edwards Robert J
  4. AU="Shriver, Craig D"
  5. AU="Huang, Xiang-Zhong"
  6. AU=Cabanne Eglantine
  7. AU="Bernal, A"
  8. AU="Malorie Perry"
  9. AU="Oppenheim, Alan"
  10. AU="Ozcan, Muhit"
  11. AU="Zhang, Cissy"
  12. AU="Blaize, Justin L"
  13. AU="R, Ram Babu"
  14. AU="Khalili Arash"
  15. AU="Bhatia, Sandeep"
  16. AU="Ticha, Johnson M"
  17. AU="Aranzabal Barrio, N"

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  1. Artikel ; Online: Immunogenetics of rheumatoid arthritis: Understanding functional implications.

    Messemaker, Tobias C / Huizinga, Tom W / Kurreeman, Fina

    Journal of autoimmunity

    2015  Band 64, Seite(n) 74–81

    Abstract: The last decade has seen a dramatic technological revolution. The characterisation of the majority of the common variations in our genetic code in 2003 precipitated the discovery of the genetic risk factors predisposing to Rheumatoid Arthritis ... ...

    Abstract The last decade has seen a dramatic technological revolution. The characterisation of the majority of the common variations in our genetic code in 2003 precipitated the discovery of the genetic risk factors predisposing to Rheumatoid Arthritis development and progression. Prior to 2007, only a handful of genetic risk factors had been identified, HLA, PTPN22 and CTLA4. Since then, over 100 genetic risk loci have been described, with the prediction that an ever-increasing number of risk alleles with consistently decreasing effect sizes will be discovered in the years to come. Each risk locus harbours multiple candidate genes and the proof of causality of each of these candidates is as yet unknown. An enrichment of these RA-associated genes is found in three pathways: T-cell receptor signalling, JAK-STAT signalling and the NF-κB signalling cascade, and currently drugs targeting these pathways are available for the treatment of RA. However, the role that RA-associated genes have in these pathways and how they contribute to disease is not always clear. Major efforts in understanding the contribution of genetic risk factors are currently under way with studies querying the role of genetic variation in gene expression of coding and non-coding genes, epigenetic marks and other regulatory mechanisms yielding ever more valuable insights into mechanisms of disease. Recent work has suggested a possible enrichment of non-coding RNAs as well as super-enhancers in RA genetic loci indicating possible new insights into disease mechanism. This review brings together these emerging genetic data with an emphasis on the immunogenetic links these findings have provided and what we expect the future will bring.
    Mesh-Begriff(e) Animals ; Arthritis, Rheumatoid/genetics ; Arthritis, Rheumatoid/immunology ; Arthritis, Rheumatoid/metabolism ; Autoimmunity ; Gene Expression Regulation ; Gene Regulatory Networks ; Genetic Loci ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; HLA Antigens/genetics ; HLA Antigens/immunology ; Humans ; Immunogenetics ; RNA, Untranslated/genetics ; Regulatory Sequences, Nucleic Acid ; Signal Transduction
    Chemische Substanzen HLA Antigens ; RNA, Untranslated
    Sprache Englisch
    Erscheinungsdatum 2015-11
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 639452-8
    ISSN 1095-9157 ; 0896-8411
    ISSN (online) 1095-9157
    ISSN 0896-8411
    DOI 10.1016/j.jaut.2015.07.007
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot.

    Messemaker, Tobias C / van Leeuwen, Selina M / van den Berg, Patrick R / 't Jong, Anke E J / Palstra, Robert-Jan / Hoeben, Rob C / Semrau, Stefan / Mikkers, Harald M M

    Scientific reports

    2018  Band 8, Heft 1, Seite(n) 386

    Abstract: The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. This gatekeeper function requires well-regulated Sox2 levels. We postulated that Sox2 regulation is partially controlled by the Sox2 overlapping long non- ... ...

    Abstract The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. This gatekeeper function requires well-regulated Sox2 levels. We postulated that Sox2 regulation is partially controlled by the Sox2 overlapping long non-coding RNA (lncRNA) gene Sox2ot. Here we show that the RNA levels of Sox2ot and Sox2 are inversely correlated during neural differentiation of mouse embryonic stem cells (ESCs). Through allele-specific enhanced transcription of Sox2ot in mouse Sox2eGFP knockin ESCs we demonstrate that increased Sox2ot transcriptional activity reduces Sox2 RNA levels in an allele-specific manner. Enhanced Sox2ot transcription, yielding lower Sox2 RNA levels, correlates with a decreased chromatin interaction of the upstream regulatory sequence of Sox2 and the ESC-specific Sox2 super enhancer. Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development.
    Mesh-Begriff(e) Alleles ; Animals ; Cell Differentiation ; Gene Expression Regulation, Developmental ; Gene Knock-In Techniques ; Mice ; Mouse Embryonic Stem Cells/cytology ; Neurogenesis ; RNA, Long Noncoding/genetics ; SOXB1 Transcription Factors/genetics ; Transcription, Genetic
    Chemische Substanzen RNA, Long Noncoding ; SOXB1 Transcription Factors ; Sox2 protein, mouse ; long noncoding RNA Sox2OT, mouse
    Sprache Englisch
    Erscheinungsdatum 2018-01-10
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-017-18649-4
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis.

    Messemaker, Tobias C / Chadli, Loubna / Cai, Guoshuai / Goelela, Varshna S / Boonstra, Maaike / Dorjée, Annemarie L / Andersen, Stefan N / Mikkers, Harald M M / van 't Hof, Peter / Mei, Hailiang / Distler, Oliver / Draisma, Harmen H M / Johnson, Michael E / Orzechowski, Nicole M / Simms, Robert W / Toes, Rene E M / Aarbiou, Jamil / Huizinga, Tom W / Whitfield, Michael L /
    DeGroot, Jeroen / de Vries-Bouwstra, Jeska / Kurreeman, Fina

    The Journal of investigative dermatology

    2017  Band 138, Heft 4, Seite(n) 826–835

    Abstract: Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis ... ...

    Abstract Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a false discovery rate <5% were detected in patients versus controls. Upregulated genes clustered in immunologic, cell adhesion, and keratin-related processes. Interestingly, 676 deregulated non-coding genes were detected, 257 of which were classified as antisense genes. Sense genes expressed opposite of these antisense genes were also deregulated in 42% of the observed sense-antisense gene pairs. The majority of the antisense genes had a similar effect sizes in an independent North American dataset with three genes (CTBP1-AS2, OTUD6B-AS1, and AGAP2-AS1) exceeding the study-wide Bonferroni-corrected P-value (P
    Mesh-Begriff(e) Cells, Cultured ; Humans ; RNA, Long Noncoding/biosynthesis ; RNA, Long Noncoding/genetics ; Scleroderma, Systemic/genetics ; Scleroderma, Systemic/metabolism ; Scleroderma, Systemic/pathology ; Skin/metabolism ; Skin/pathology ; Transcription Factors ; Transcriptional Activation ; Up-Regulation
    Chemische Substanzen RNA, Long Noncoding ; Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2017-11-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80136-7
    ISSN 1523-1747 ; 0022-202X
    ISSN (online) 1523-1747
    ISSN 0022-202X
    DOI 10.1016/j.jid.2017.09.053
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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