Involvement of long noncoding RNAs in the pathogenesis of autoimmune diseases

Martin, 2012, Uncovering the role of genomic "dark matter" in human disease, J. Clin. Invest., 122, 1589, 10.1172/JCI60020 Maass, 2014, Long non-coding RNA in health and disease, J. Mol. Med. (Berl.), 92, 337, 10.1007/s00109-014-1131-8 Kazemzadeh, 2015, LncRNAs: emerging players in gene regulation and disease pathogenesis, J. Genet., 94, 771, 10.1007/s12041-015-0561-6 Djebali, 2012, Landscape of transcription in human cells, Nature, 489, 101, 10.1038/nature11233 Mt, 2012, Systematic localization of common disease-associated variation in regulatory DNA, Science (New York, N.Y.), 337, 1190, 10.1126/science.1222794 Okazaki, 2002, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563, 10.1038/nature01266 Struhl, 2007, Transcriptional noise and the fidelity of initiation by RNA polymerase II, Nat. Struct. Mol. Biol., 14, 103, 10.1038/nsmb0207-103 Bierhoff, 2010, Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes, Cold Spring Harbor Symp. Quant. Biol., 75, 357, 10.1101/sqb.2010.75.060 Zhao, 2016, NONCODE 2016: an informative and valuable data source of long non-coding RNAs, Nucleic Acids Res., 44, D203, 10.1093/nar/gkv1252 Quinn, 2016, Unique features of long non-coding RNA biogenesis and function, Nat. Rev. Genet., 17, 47, 10.1038/nrg.2015.10 Derrien, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res., 22, 1775, 10.1101/gr.132159.111 Nitsche, 2017, Evolutionary clues in lncRNAs, Wiley Interdiscip Rev RNA, 8, 10.1002/wrna.1376 Mercer, 2008, Specific expression of long noncoding RNAs in the mouse brain, Proc. Natl. Acad. Sci. U. S. A., 105, 716, 10.1073/pnas.0706729105 Dinger, 2008, Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation, Genome Res., 18, 1433, 10.1101/gr.078378.108 Shi, 2013 Marques-Rocha, 2015, Noncoding RNAs, cytokines, and inflammation-related diseases, Faseb. J., 29, 3595, 10.1096/fj.14-260323 Smith, 2017, Structural and functional annotation of long noncoding RNAs, Methods Mol. Biol., 1526, 65, 10.1007/978-1-4939-6613-4_4 Fitzgerald, 2014, Long noncoding RNAs in innate and adaptive immunity, Curr. Opin. Immunol., 26C, 140, 10.1016/j.coi.2013.12.001 Chen, 2016, Linking long noncoding RNA localization and function, Trends Biochem. Sci., 41, 761, 10.1016/j.tibs.2016.07.003 Engreitz, 2016, Local regulation of gene expression by lncRNA promoters, transcription and splicing, Nature, 539, 452, 10.1038/nature20149 Anderson, 2016, Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development, Nature, 539, 433, 10.1038/nature20128 Kopp, 2018, Functional classification and experimental dissection of long noncoding RNAs, Cell, 172, 393, 10.1016/j.cell.2018.01.011 Anderson, 2015, A micropeptide encoded by a putative long noncoding RNA regulates muscle performance, Cell, 160, 595, 10.1016/j.cell.2015.01.009 Matsumoto, 2017, mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide, Nature, 541, 228, 10.1038/nature21034 Wang, 2011, Molecular mechanisms of long noncoding RNAs, Mol. Cell, 43, 904, 10.1016/j.molcel.2011.08.018 Rinn, 2012, Genome regulation by long noncoding RNAs, Annu. Rev. Biochem., 81, 145, 10.1146/annurev-biochem-051410-092902 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 Yuan, 2020, Emerging roles of HOTAIR in human cancer, J. Cell. Biochem., 10.1002/jcb.29591 Wang, 2011, A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression, Nature, 472, 120, 10.1038/nature09819 Engreitz, 2016, Local regulation of gene expression by lncRNA promoters, transcription and splicing, Nature, 539, 452, 10.1038/nature20149 Paralkar, 2016, Unlinking an lncRNA from its associated cis element, Mol. Cell., 62, 104, 10.1016/j.molcel.2016.02.029 Rapicavoli, 2013, A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics, Elife, 2, 10.7554/eLife.00762 Li, 2014, The long noncoding RNA THRIL regulates TNF expression through its interaction with hnRNPL, Proc. Natl. Acad. Sci. Unit. States Am., 111, 1002, 10.1073/pnas.1313768111 Thomson, 2016, Endogenous microRNA sponges: evidence and controversy, Nat. Rev. Genet., 17, 272, 10.1038/nrg.2016.20 Cesana, 2011, A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA, Cell, 147, 358, 10.1016/j.cell.2011.09.028 Faghihi, 2008, Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase, Nat. Med., 14, 723, 10.1038/nm1784 Wang, 2014, The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation, Science, 344, 310, 10.1126/science.1251456 Liu, 2015, A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis, Canc. Cell, 27, 370, 10.1016/j.ccell.2015.02.004 Taniue, 2016, Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1, Proc. Natl. Acad. Sci. U. S. A., 113, 1273, 10.1073/pnas.1500992113 Sharma, 2011, Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex, Proc. Natl. Acad. Sci. U. S. A., 108, 11381, 10.1073/pnas.1019711108 Zou, 2018, Long noncoding RNA LERFS negatively regulates rheumatoid synovial aggression and proliferation, J. Clin. Invest., 128, 4510, 10.1172/JCI97965 Silva, 2015, The clinical relevance of long non-coding RNAs in cancer, Cancers, 7, 2169, 10.3390/cancers7040884 Yang, 2014, LncRNA: a link between RNA and cancer, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1839, 1097, 10.1016/j.bbagrm.2014.08.012 Chew, 2018, Noncoding RNAs: master regulators of inflammatory signaling, Trends Mol. Med., 24, 66, 10.1016/j.molmed.2017.11.003 Cooles, 2011, Pathophysiology of rheumatoid arthritis, Curr. Opin. Rheumatol., 23, 233, 10.1097/BOR.0b013e32834518a3 McInnes, 2011, The pathogenesis of rheumatoid arthritis, N. Engl. J. Med., 365, 2205, 10.1056/NEJMra1004965 McGonagle, 2018, Mechanistic immunological based classification of rheumatoid arthritis, Autoimmun. Rev., 17, 1115, 10.1016/j.autrev.2018.06.001 Brzustewicz, 2015, The role of cytokines in the pathogenesis of rheumatoid arthritis – practical and potential application of cytokines as biomarkers and targets of personalized therapy, Cytokine, 76, 527, 10.1016/j.cyto.2015.08.260 Lefevre, 2015, Role of synovial fibroblasts in rheumatoid arthritis, Curr. Pharmaceut. Des., 21, 130, 10.2174/1381612820666140825122036 Yuan, 2017, Long noncoding RNA profiling revealed differentially expressed lncRNAs associated with disease activity in PBMCs from patients with rheumatoid arthritis, PloS One, 12, 10.1371/journal.pone.0186795 Song, 2015, PBMC and exosome-derived Hotair is a critical regulator and potent marker for rheumatoid arthritis, Clin. Exp. Med., 15, 121, 10.1007/s10238-013-0271-4 Luo, 2017, Comprehensive analysis of long non-coding RNA and mRNA expression profiles in rheumatoid arthritis, Exp Ther Med, 14, 5965 Zhang, 2016, Long noncoding RNA expression profile in fibroblast-like synoviocytes from patients with rheumatoid arthritis, Arthritis Res. Ther., 18, 227, 10.1186/s13075-016-1129-4 Sun, 2019 Qin, 2019, Plasma long non-coding RNA expression profiles in patients with rheumatoid arthritis, Clin. Lab., 65 Gong, 2017, Circulating lnc-ITSN1-2 expression presents a high value in diagnosis of rheumatoid arthritis and correlates with disease activity, Int. J. Clin. Exp. Pathol., 10, 10451 Jiang, 2016, LncRNAs expression in adjuvant-induced arthritis rats reveals the potential role of LncRNAs contributing to rheumatoid arthritis pathogenesis, Gene, 593, 131, 10.1016/j.gene.2016.08.012 Mueller, 2014, Interleukin-6 and Tumour Necrosis Factor-alpha differentially regulate lincRNA transcripts in cells of the innate immune system in vivo in human subjects with rheumatoid arthritis, Cytokine, 68, 65, 10.1016/j.cyto.2014.03.004 Jiang, 2016, LncRNAs expression in adjuvant-induced arthritis rats reveals the potential role of LncRNAs contributing to rheumatoid arthritis pathogenesis, Gene, 593, 131, 10.1016/j.gene.2016.08.012 H, 2019, Effect of astragalosides on long non-coding RNA expression profiles in rats with adjuvant-induced arthritis, Int. J. Mol. Med., 44, 1344 Bhan, 2015, LncRNA HOTAIR: A master regulator of chromatin dynamics and cancer, Biochim. Biophys. Acta Rev. Canc, 1856, 151, 10.1016/j.bbcan.2015.07.001 Rajagopal, 2020, HOTAIR LncRNA: a novel oncogenic propellant in human cancer, Clin. Chim. Acta, 503, 1, 10.1016/j.cca.2019.12.028 Hj, 2017, LncRNA HOTAIR alleviates rheumatoid arthritis by targeting miR-138 and inactivating NF-κB pathway, Int. Immunopharm., 50, 283, 10.1016/j.intimp.2017.06.021 Yan, 2019, Long non-coding RNA HIX003209 promotes inflammation by sponging miR-6089 via TLR4/NF-kappaB signaling pathway in rheumatoid arthritis, Front. Immunol., 10, 2218, 10.3389/fimmu.2019.02218 Yang, 2018, lncRNA NTT/PBOV1 Axis promotes monocyte differentiation and is elevated in rheumatoid arthritis, Int. J. Mol. Sci., 19, 10.3390/ijms19092806 Chen, 2017, LincRNa-p21: function and mechanism in cancer, Med. Oncol., 34 Spurlock, 2014, Methotrexate inhibits NF-κB activity via long intergenic (noncoding) RNA-p21 induction, Arthritis & Rheumatology, 66, 2947, 10.1002/art.38805 Lu, 2016, Increased expression of long noncoding RNAs LOC100652951 and LOC100506036 in T cells from patients with rheumatoid arthritis facilitates the inflammatory responses, Immunol. Res., 64, 576, 10.1007/s12026-015-8756-8 Moharamoghli, 2019, The expression of GAS5, THRIL, and RMRP lncRNAs is increased in T cells of patients with rheumatoid arthritis, Clin. Rheumatol., 38, 3073, 10.1007/s10067-019-04694-z Kurreeman, 2007, A candidate gene approach identifies the TRAF1/C5 region as a risk factor for rheumatoid arthritis, PLoS Med., 4, 1515 Messemaker, 2016, A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels, Gene Immun., 17, 85, 10.1038/gene.2015.54 Ayesh, 2002, Possible physiological role of H19 RNA, Mol. Carcinog., 35, 63, 10.1002/mc.10075 Matouk, 2010, The oncofetal H19 RNA connection: hypoxia, p53 and cancer, Biochim. Biophys. Acta, 1803, 443, 10.1016/j.bbamcr.2010.01.010 Stuhlmuller, 2003, Detection of oncofetal h19 RNA in rheumatoid arthritis synovial tissue, Am. J. Pathol., 163, 901, 10.1016/S0002-9440(10)63450-5 Af, 2017, No association of single nucleotide polymorphisms within H19 and HOX transcript antisense RNA (HOTAIR) with genetic susceptibility to systemic lupus erythematosus, rheumatoid arthritis, and primary Sjögren’s syndrome in a Chinese Han population, Clin. Rheumatol., 36, 2447, 10.1007/s10067-017-3833-0 Ye, 2018, LncRNA ZFAS1 promotes cell migration and invasion of fibroblast-like synoviocytes by suppression of miR-27a in rheumatoid arthritis, Hum. Cell, 31, 14, 10.1007/s13577-017-0179-5 Mo, 2018, Long non-coding RNA GAPLINC promotes tumor-like biologic behaviors of fibroblast-like synoviocytes as MicroRNA sponging in rheumatoid arthritis patients, Front. Immunol., 9, 702, 10.3389/fimmu.2018.00702 Bi, 2019, LncRNA PICSAR promotes cell proliferation, migration and invasion of fibroblast-like synoviocytes by sponging miRNA-4701-5p in rheumatoid arthritis, EBioMedicine, 50, 408, 10.1016/j.ebiom.2019.11.024 H, 2019 Pan, 2016, Quercetin promotes the apoptosis of fibroblast-like synoviocytes in rheumatoid arthritis by upregulating lncRNA MALAT1, Int. J. Mol. Med., 38, 1507, 10.3892/ijmm.2016.2755 Yan, 2018, UCA1 impacts progress of rheumatoid arthritis by inducing the apoptosis of fibroblast-like synoviocyte, Eur. Rev. Med. Pharmacol. Sci., 22, 914 Wang, 2019, LncRNA DILC participates in rheumatoid arthritis by inducing apoptosis of fibroblast-like synoviocytes and down-regulating IL-6, Biosci. Rep., 39, 10.1042/BSR20182374 Z, 2017, Lnc-IL7R promotes the growth of fibroblast-like synoviocytes through interaction with enhancer of zeste homolog 2 in rheumatoid arthritis, Mol. Med. Rep., 15, 1412, 10.3892/mmr.2017.6150 Wang, 2020, FOXM1/LINC00152 feedback loop regulates proliferation and apoptosis in rheumatoid arthritis fibroblast-like synoviocytes via Wnt/beta-catenin signaling pathway, Biosci. Rep., 40, 10.1042/BSR20191900 Li, 2018, Tanshinone IIA promotes the apoptosis of fibroblast-like synoviocytes in rheumatoid arthritis by up-regulating lncRNA GAS5, Biosci. Rep., 38, 10.1042/BSR20180626 Ma, 2019, LncRNA GAS5 overexpression downregulates IL-18 and induces the apoptosis of fibroblast-like synoviocytes, Clin. Rheumatol., 38, 3275, 10.1007/s10067-019-04691-2 Yue, 2019, Downregulation of lncRNA ITSN1-2 correlates with decreased disease risk and activity of rheumatoid arthritis (RA), and reduces RA fibroblast-like synoviocytes proliferation and inflammation via inhibiting NOD2/RIP2 signaling pathway, Am J Transl Res, 11, 4650 Yr, 2019, Long noncoding RNA MEG3 regulates rheumatoid arthritis by targeting NLRC5, J. Cell. Physiol., 234, 14270, 10.1002/jcp.28126 Li, 2019, LncRNA MEG3 inhibits rheumatoid arthritis through miR-141 and inactivation of AKT/mTOR signalling pathway, J. Cell Mol. Med., 23, 7116, 10.1111/jcmm.14591 Zhang, 2019, Long non-coding RNA PVT1 knockdown suppresses fibroblast-like synoviocyte inflammation and induces apoptosis in rheumatoid arthritis through demethylation of sirt6, J. Biol. Eng., 13, 60, 10.1186/s13036-019-0184-1 Yang, 2015, Shikonin inhibits inflammatory response in rheumatoid arthritis synovial fibroblasts via lncRNA-NR024118, Evid Based Complement Alternat Med, 2015, 10.1155/2015/631737 Rahman, 2008, Systemic lupus erythematosus, N. Engl. J. Med., 358, 929, 10.1056/NEJMra071297 Zhang, 2019, Integrated analysis of lncRNA, miRNA and mRNA expression profiling in patients with systemic lupus erythematosus, Arch. Med. Sci., 15, 872, 10.5114/aoms.2018.79145 Ye, 2019, Full high-throughput sequencing analysis of differences in expression profiles of long noncoding RNAs and their mechanisms of action in systemic lupus erythematosus, Arthritis Res. Ther., 21, 70, 10.1186/s13075-019-1853-7 Lj, 2017, Comprehensive long non-coding RNA expression profiling reveals their potential roles in systemic lupus erythematosus, Cell. Immunol., 319, 17, 10.1016/j.cellimm.2017.06.004 Wang, 2018, Long noncoding RNA expression profile and association with SLEDAI score in monocyte-derived dendritic cells from patients with systematic lupus erythematosus, Arthritis Res. Ther., 20, 138, 10.1186/s13075-018-1640-x Wu, 2019, Differential plasma expression profiles of long non-coding RNAs reveal potential biomarkers for systemic lupus erythematosus, Biomolecules, 9, 10.3390/biom9060206 Zhang, 2016, Identification of the long noncoding RNA NEAT1 as a novel inflammatory regulator acting through MAPK pathway in human lupus, J. Autoimmun., 75, 96, 10.1016/j.jaut.2016.07.012 Dong, 2020, Granulocytic myeloid-derived suppressor cells contribute to IFN-I signaling activation of B cells and disease progression through the lncRNA NEAT1-BAFF axis in systemic lupus erythematosus, Biochim. Biophys. Acta (BBA) - Mol. Basis Dis., 1866, 10.1016/j.bbadis.2019.165554 Suarez-Gestal, 2009, Replication of recently identified systemic lupus erythematosus genetic associations: a case-control study, Arthritis Res. Ther., 11, R69, 10.1186/ar2698 Ghaforui-Fard, 2019, Growth arrest specific transcript 5 in tumorigenesis process: an update on the expression pattern and genomic variants, Biomed. Pharmacother., 112, 10.1016/j.biopha.2019.108723 Kino, 2010, Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor, Sci. Signal., 3, ra8, 10.1126/scisignal.2000568 Williams, 2011, A critical role for non-coding RNA GAS5 in growth arrest and rapamycin inhibition in human T-lymphocytes, Biochem. Soc. Trans., 39, 482, 10.1042/BST0390482 Haywood, 2006, Overlapping BXSB congenic intervals, in combination with microarray gene expression, reveal novel lupus candidate genes, Gene Immun., 7, 250, 10.1038/sj.gene.6364294 Mayama, 2016, Differential expression of glucocorticoid receptor noncoding RNA repressor Gas5 in autoimmune and inflammatory diseases, Horm. Metab. Res., 48, 550, 10.1055/s-0042-106898 Wu, 2017, Identification of long non-coding RNAs GAS5, linc0597 and lnc-DC in plasma as novel biomarkers for systemic lupus erythematosus, Oncotarget, 8, 23650, 10.18632/oncotarget.15569 Wu, 2015, Association of large intergenic noncoding RNA expression with disease activity and organ damage in systemic lupus erythematosus, Arthritis Res. Ther., 17, 131, 10.1186/s13075-015-0632-3 Wang, 2019, Expression of several long noncoding RNAs in peripheral blood mononuclear cells of patients with systemic lupus erythematosus, Adv. Med. Sci., 64, 430, 10.1016/j.advms.2019.08.002 Yang, 2017, Long noncoding RNA MALAT-1 is a novel inflammatory regulator in human systemic lupus erythematosus, Oncotarget, 8, 77400, 10.18632/oncotarget.20490 Suravajhala, 2015, Potential role of lncRNA cyp2c91-protein interactions on diseases of the immune system, Front. Genet., 6, 255, 10.3389/fgene.2015.00255 Cao, 2020, Clinical significance of reduced expression of lncRNA TUG1 in the peripheral blood of systemic lupus erythematosus patients, Int. J. Rheum. Dis., 23, 428, 10.1111/1756-185X.13786 Cao, 2020, The protection of NF-kappaB inhibition on kidney injury of systemic lupus erythematosus mice may be correlated with lncRNA TUG1, Kaohsiung J. Med. Sci., 10.1002/kjm2.12183 Liao, 2019, Identification of renal long non-coding RNA RP11-2B6.2 as a positive regulator of type I interferon signaling pathway in lupus nephritis, Front. Immunol., 10, 975, 10.3389/fimmu.2019.00975 Lundberg, 2018, Classification of myositis, Nat. Rev. Rheumatol., 14, 269, 10.1038/nrrheum.2018.41 Satoh, 2005, Novel autoantibodies against 7SL RNA in patients with polymyositis/dermatomyositis, J. Rheumatol., 32, 1727 Peng, 2016, Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis, Sci. Rep., 6 Pd, 2017, Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis, Sci. Rep., 7, 8024, 10.1038/s41598-017-08603-9 Denton, 2017, Systemic sclerosis, Lancet, 390, 1685, 10.1016/S0140-6736(17)30933-9 Wang, 2016, Long non-coding RNA TSIX is upregulated in scleroderma dermal fibroblasts and controls collagen mRNA stabilization, Exp. Dermatol., 25, 131, 10.1111/exd.12900 Messemaker, 2018, Antisense long non-coding RNAs are deregulated in skin tissue of patients with systemic sclerosis, J. Invest. Dermatol., 138, 826, 10.1016/j.jid.2017.09.053 Dolcino, 2019, In systemic sclerosis, a unique long non coding RNA regulates genes and pathways involved in the three main features of the disease (vasculopathy, fibrosis and autoimmunity) and in carcinogenesis, J. Clin. Med., 8 Mariotti, 2019, The long non-coding RNA NRIR drives IFN-response in monocytes: implication for systemic sclerosis, Front. Immunol., 10, 100, 10.3389/fimmu.2019.00100 Brito-Zeron, 2016, Sjogren syndrome, Nat Rev Dis Primers, 2, 16047, 10.1038/nrdp.2016.47 Wang, 2016, Upregulation of long noncoding RNA TMEVPG1 enhances T helper type 1 cell response in patients with Sjogren syndrome, Immunol. Res., 64, 489, 10.1007/s12026-015-8715-4 Shi, 2016, Long non-coding RNA expression profile in minor salivary gland of primary Sjogren’s syndrome, Arthritis Res. Ther., 18, 109, 10.1186/s13075-016-1005-2 Dolcino, 2019, Long non-coding RNAs modulate sjogren’s syndrome associated gene expression and are involved in the pathogenesis of the disease, J. Clin. Med., 8 J, 2019, LncRNA PVT1 links Myc to glycolytic metabolism upon CD4 T cell activation and Sjögren’s syndrome-like autoimmune response, J. Autoimmun. Zhang, 2017, Differentially expressed mRNAs, lncRNAs, and miRNAs with associated co-expression and ceRNA networks in ankylosing spondylitis, Oncotarget, 8, 113543, 10.18632/oncotarget.22708 Z, 2019, H19 increases IL-17a/IL-23 releases via regulating VDR by interacting with miR675-5p/miR22-5p in ankylosing spondylitis. Molecular therapy, Nucleic acids, 19, 393