Research progress on long non-coding RNA’s anti infection function against Mycobacterium tuberculosis

doi:10.19982/j.issn.1000-6621.20220521

Abstract

Abstract:

The pathogenesis and immunological mechanism of Mycobacterium tuberculosis (MTB) infection and further development of active tuberculosis have not yet been fully elucidated. Recently, long non-coding RNA (lncRNA) has received more attention in MTB infection and active tuberculosis development study, for it is involved in a variety of biological processes, such as gene expression regulation, cell cycle regulation, cell differentiation, and so on. It is of great significance to illustrate the regulation mechanism of aberrant lncRNA in the developing and progression of tuberculosis, which could help us further understand the mechanism of host immunological response to MTB infection and progression. Therefore, we reviewed the research progress of impact and specific mechanisms of lncRNA affecting human immunological response to MTB infection, to facilitate future development of novel lncRNA-based immunotherapy of tuberculosis.

Key words: Mycobacterium tuberculosis, Infection, Immunity, RNA

CLC Number:

R52
R392

Dong Jing, Shi Yuting, Pan Liping, Zhang Zongde. Research progress on long non-coding RNA’s anti infection function against Mycobacterium tuberculosis[J]. Chinese Journal of Antituberculosis, 2023, 45(6): 613-619. doi: 10.19982/j.issn.1000-6621.20220521

References 57

[1]	Fathizadeh H, Hayat S, Dao S, et al. Long non-coding RNA molecules in tuberculosis. Int J Biol Macromol, 2020, 156:340-346. doi:10.1016/j.ijbiomac.2020.04.030. doi: S0141-8130(20)32884-1 pmid: 32283111
[2]	Costa FF. Non-coding RNAs:new players in eukaryotic biology. Gene, 2005, 357(2): 83-94. doi:10.1016/j.gene.2005.06.019. doi: 10.1016/j.gene.2005.06.019 URL
[3]	Wei L, Liu K, Jia Q, et al. The Roles of Host Noncoding RNAs in Mycobacterium tuberculosis Infection. Front Immunol, 2021, 12:664787. doi:10.3389/fimmu.2021.664787. doi: 10.3389/fimmu.2021.664787
[4]	Guttman M, Russell P, Ingolia NT, et al. Ribosome profiling provides evidence that large noncoding RNAs do not encode roteins. Cell, 2013, 154(1):240-251. doi:10.1016/j.cell.2013.06.009. doi: 10.1016/j.cell.2013.06.009 URL
[5]	IIyer MK, Niknafs YS, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet, 2015, 47(3): 199-208. doi:10.1038/ng.3192. doi: 10.1038/ng.3192 pmid: 25599403
[6]	Lee JH, Wang R, Xiong F, et al. Enhancer RNA m6A methy-lation facilitates transcriptional condensate formation and gene activation. Mol Cell, 2021, 81(16):3368-3385. doi:10.1016/j.molcel.2021.07.024. doi: 10.1016/j.molcel.2021.07.024 URL
[7]	Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009, 458(7235): 223-227. doi:10.1038/nature07672. doi: 10.1038/nature07672
[8]	Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell, 2013, 154(1):26-46. doi:10.1016/j.cell.2013.06.020. doi: 10.1016/j.cell.2013.06.020 pmid: 23827673
[9]	Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteome. Cell, 2011, 147(4): 789-802. doi:10.1016/j.cell.2011.10.002. doi: 10.1016/j.cell.2011.10.002 URL
[10]	Ransohoff JD, Wei Y, Khavari PA. The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol, 2018, 19(3): 143-157. doi:10.1038/nrm.2017.104. doi: 10.1038/nrm.2017.104 URL
[11]	Taganov KD, Boldin MP, Chang KJ, et al. NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A, 2006, 103(33): 12481-12486. doi:10.1073/pnas.0605298103. doi: 10.1073/pnas.0605298103 URL
[12]	Yoon JH, Gorospe M. Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins. Methods Mol Biol, 2016, 1402:11-17. doi:10.1007/978-1-4939-3378-5_2. doi: 10.1007/978-1-4939-3378-5_2
[13]	Li JH, Liu S, Zheng LL, et al. Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol, 2015, 2: 88. doi:10.3389/fbioe.2014.00088. doi: 10.3389/fbioe.2014.00088
[14]	Salehi S, Taheri MN, Azarpira N, et al. State of the art technologies to explore long non-coding RNAs in cancer. J Cell Mol Med, 2017, 21(12):3120-3140. doi:10.1111/jcmm.13238. doi: 10.1111/jcmm.13238 pmid: 28631377
[15]	Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet, 2016, 17(1): 47-62. doi:10.1038/nrg.2015.10. doi: 10.1038/nrg.2015.10 pmid: 26666209
[16]	Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem, 2012, 81:145-166. doi:10.1146/annurev-biochem-051410-092902. doi: 10.1146/annurev-biochem-051410-092902 pmid: 22663078
[17]	Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci, 2021, 78(14): 5489-5504. doi:10.1007/s00018-021-03876-w. doi: 10.1007/s00018-021-03876-w
[18]	O’Leary VB, Ovsepian SV, Carrascosa LG, et al. PARTICLE, a Triplex-Forming Long ncRNA, Regulates Locus-Specific Methylation in Response to Low-Dose Irradiation. Cell Rep, 2015, 11(3): 474-485. doi:10.1016/j.celrep.2015.03.043. doi: 10.1016/j.celrep.2015.03.043 pmid: 25900080
[19]	Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet, 2018, 34(2): 142-157. doi:10.1016/j.tig.2017.11.005. doi: S0168-9525(17)30207-X pmid: 29249332
[20]	Wang SH, Zhang WJ, Wu XC, et al. The lncRNA MALAT 1 functions as a competing endogenous RNA to regulate MCL-1 expression by sponging miR-363-3p in gallbladder cancer. J Cell Mol Med, 2016, 20(12): 2299-2308. doi:10.1111/jcmm.12920. doi: 10.1111/jcmm.12920 URL
[21]	Xiao H, Tang K, Liu P, et al. LncRNA MALAT1 functions as a competing endogenous RNA to regulate ZEB2 expression by sponging miR-200s in clear cell kidney carcinoma. Oncotarget, 2015, 6(35): 38005-38015. doi:10.18632/oncotarget.5357. doi: 10.18632/oncotarget.5357 pmid: 26461224
[22]	Zhu S, Wang JZ, Chen D, et al. An oncopeptide regulates m(6)A recognition by the m(6)A reader IGF2BP1 and tumorigenesis. Nat Commun, 2020, 11(1):1685. doi:10.1038/s41467-020-15403-9. doi: 10.1038/s41467-020-15403-9
[23]	Huang JZ, Chen M, Chen D, et al. A Peptide Encoded by a Putative lncRNA HOXB-AS 3 Suppresses Colon Cancer Growth. Mol Cell, 2017, 68(1):171-184.e6. doi:10.1016/j.molcel.2017.09.015. doi: 10.1016/j.molcel.2017.09.015 URL
[24]	Wang Y, Wu S, Zhu X, et al. LncRNA-encoded polypeptide ASRPS inhibits triple-negative breast cancer angiogenesis. J Exp Med, 2020, 217(3): jem.20190950. doi:10.1084/jem.20190950. doi: 10.1084/jem.20190950
[25]	Rohrig H, Schmidt J, Miklashevichs E, et al. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc Natl Acad Sci U S A, 2002, 99(4):1915-1920. doi:10.1073/pnas.02266479. doi: 10.1073/pnas.02266479 URL
[26]	Levine MT, Jones CD, Kern AD, et al. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A, 2006, 103(26): 9935-9939. doi:10.1073/pnas.0509809103. doi: 10.1073/pnas.0509809103 URL
[27]	Fesenko I, Kirov I, Kniazev A, et al. Distinct types of short open reading frames are translated in plant cells. Genome Res, 2019, 29(9):1464-1477. doi:10.1101/gr.253302.119. doi: 10.1101/gr.253302.119 pmid: 31387879
[28]	Huang S, Huang Z, Luo Q, et al. The Expression of lncRNA NEAT 1 in Human Tuberculosis and Its Antituberculosis Effect. Biomed Res Int, 2018, 2018:9529072. doi:10.1155/2018/9529072. doi: 10.1155/2018/9529072
[29]	Li Y, Sun L, Liu J, et al. Down-regulation of GAS5 has diagnostic value for tuberculosis and regulates the inflammatory response in mycobacterium tuberculosis infected THP-1 cells. Tuberculosis(Edinb), 2022, 132:102141. doi:10.1016/j.tube.2021.102141. doi: 10.1016/j.tube.2021.102141
[30]	Sun W, He X, Zhang X, et al. Diagnostic value of lncRNA NORAD in pulmonary tuberculosis and its regulatory role in Mycobacterium tuberculosis infection of macrophages. Microbiol Immunol, 2022, 66(9):433-441. doi:10.1111/1348-0421.12986. doi: 10.1111/1348-0421.12986 URL
[31]	Sun W, Zhang X, He X, et al. Long non-coding RNA SNHG 16 silencing inhibits proliferation and inflammation in Mycobacterium tuberculosis-infected macrophages by targeting miR-140-5p expression. Infect Genet Evol, 2022, 103:105325. doi:10.1016/j.meegid.2022.105325. doi: 10.1016/j.meegid.2022.105325
[32]	Sampath P, Periyasamy KM, Ranganathan UD, et al. Monocyte and Macrophage miRNA: Potent Biomarker and Target for Host-Directed Therapy for Tuberculosis. Front Immunol, 2021, 12:667206. doi:10.3389/fimmu.2021.667206. doi: 10.3389/fimmu.2021.667206
[33]	Li M, Cui J, Niu W, et al. Long non-coding PCED1B-AS 1 regulates macrophage apoptosis and autophagy by sponging miR-155 in active tuberculosis. Biochem Biophys Res Commun, 2019, 509(3):803-809. doi:10.1016/j.bbrc.2019.01.005. doi: 10.1016/j.bbrc.2019.01.005 URL
[34]	Jiang F, Lou J, Zheng XM, et al. LncRNA MIAT regulates autophagy and apoptosis of macrophage infected by Mycobacterium tuberculosis through the miR-665/ULK1 signaling axis. Mol Immunol, 2021, 139: 42-49. doi:10.1016/j.molimm.2021.07.023. doi: 10.1016/j.molimm.2021.07.023 pmid: 34454184
[35]	Luo XB, Li LT, Xi JC, et al. Negative pressure promotes macrophage M1 polarization after Mycobacterium tuberculosis infection via the lncRNA XIST/microRNA-125b-5p/A20/NF-kappaB axis. Ann N Y Acad Sci, 2022, 1514(1): 116-131. doi:10.1111/nyas.14781. doi: 10.1111/nyas.14781 URL
[36]	付育, 何天柳, 李霓. RNA结合蛋白与巨噬细胞炎症因子表达. 中国生物化学与分子生物学报, 2022, 38(12):1612-1620. doi:10.13865/j.cnki.cjbmb.2022.04.1653. doi: 10.13865/j.cnki.cjbmb.2022.04.1653
[37]	Yao Q, Xie Y, Xu D, et al. Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3. Cell Mol Immunol, 2022, 19(8):883-897. doi:10.1038/s41423-022-00878-x. doi: 10.1038/s41423-022-00878-x
[38]	Gcanga L, Tamgue O, Ozturk M, et al. Host-Directed Targeting of LincRNA-MIR99AHG Suppresses Intracellular Growth of Mycobacterium tuberculosis. Nucleic Acid Ther, 2022, 32(5): 421-437. doi:10.1089/nat.2022.0009. doi: 10.1089/nat.2022.0009 pmid: 35895506
[39]	Zhou L, Ma J. MIR99AHG/miR-204-5p/TXNIP/Nrf2/ARE Signaling Pathway Decreases Glioblastoma Temozolomide Sensitivity. Neurotox Res, 2022, 40(5): 1152-1162. doi:10.1007/s12640-022-00536-0. doi: 10.1007/s12640-022-00536-0
[40]	Li D, Gao C, Zhao L, et al. Inflammatory response is modulated by lincRNACox 2 via the NF-kB pathway in macrophages infected by Mycobacterium tuberculosis. Mol Med Rep, 2020, 21(6): 2513-2521. doi:10.3892/mmr.2020.11053. doi: 10.3892/mmr.2020.11053
[41]	Ke Z, Lu J, Zhu J, et al. Down-regulation of lincRNA-EPS regulates apoptosis and autophagy in BCG-infected RAW264.7 macrophages via JNK/MAPK signaling pathway. Infect Genet Evol, 2020, 77: 104077. doi:10.1016/j.meegid.2019.104077. doi: 10.1016/j.meegid.2019.104077
[42]	Sui X, Kong N, Ye L, et al. p38 and JNK MAPK pathways control the balance of apoptosis and autophagy in response to chemotherapeutic agents. Cancer Lett, 2014, 344(2): 174-179. doi:10.1016/j.canlet.2013.11.019. doi: 10.1016/j.canlet.2013.11.019 pmid: 24333738
[43]	柯昌浩, 王正龙, 石蓓. lncRNA在树突状细胞中的研究进展. 中国免疫学杂志, 2021, 37(21): 2580-2583. doi:10.3969/j.issn.1000-484X.2021.21.004. doi: 10.3969/j.issn.1000-484X.2021.21.004
[44]	Wang P, Xue Y, Han Y, et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science, 2014, 344(6181): 310-313. doi:10.1126/science.1251456. doi: 10.1126/science.1251456 pmid: 24744378
[45]	Del Vecchio F, Martinez-Rodriguez V, Schukking M, et al. Professional killers: The role of extracellular vesicles in the reciprocal interactions between natural killer, CD8⁺ cytotoxic T-cells and tumour cells. J Extracell Vesicles, 2021, 10(6): e12075. doi:10.1002/jev2.12075. doi: 10.1002/jev2.12075
[46]	胡诗芸, 奕天飞, 王家立, 等. 长链非编码RNA在肿瘤免疫微环境中的作用. 生命科学, 2022, 34(2): 212-219. doi:10.13376/j.cbls/2022025. doi: 10.13376/j.cbls/2022025
[47]	侯媛媛. CD49a参与人蜕膜NK细胞的功能调控. 合肥:安徽医科大学, 2018.
[48]	江南. 构建中性粒细胞自发凋亡过程lncRNA-miRNA-mRNA内源竞争性RNA网络筛选中性粒细胞自发凋亡过程中关键的lncRNA. 泸州:西南医科大学, 2019.
[49]	O’Garra A, Redford PS, McNab FW, et al. The immune response in tuberculosis. Annu Rev Immunol, 2013, 31: 475-527. doi:10.1146/annurev-immunol-032712-095939. doi: 10.1146/annurev-immunol-032712-095939 pmid: 23516984
[50]	Agresta L, Hoebe KHN, Janssen EM. The Emerging Role of CD244 Signaling in Immune Cells of the Tumor Microenvironment. Front Immunol, 2018, 9: 2809. doi:10.3389/fimmu.2018.02809. doi: 10.3389/fimmu.2018.02809 pmid: 30546369
[51]	Turner M, Galloway A, Vigorito E. Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol, 2014, 15(6): 484-491. doi:10.1038/ni.2887. doi: 10.1038/ni.2887 pmid: 24840979
[52]	Hu G, Tang Q, Sharma S, et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat Immunol, 2013, 14(11): 1190-1198. doi:10.1038/ni.2712. doi: 10.1038/ni.2712 pmid: 24056746
[53]	Fu Y, Gao K, Tao E, et al. Aberrantly Expressed Long Non-Coding RNAs In CD8⁺ T Cells Response to Active Tuberculosis. J Cell Biochem, 2017, 118(12): 4275-4284. doi:10.1002/jcb.26078. doi: 10.1002/jcb.26078 URL
[54]	Hong GH, Guan Q, Peng H, et al. Identification and validation of a T-cell-related MIR600HG/hsa-mir-21-5p competing endogenous RNA network in tuberculosis activation based on integrated bioinformatics approaches. Front Genet, 2022, 13: 979213. doi:10.3389/fgene.2022.979213. doi: 10.3389/fgene.2022.979213
[55]	Yang F, Yang Y, Chen L, et al. The gut microbiota mediates protective immunity against tuberculosis via modulation of lncRNA. Gut Microbes, 2022, 14(1):2029997. doi:10.1080/19490976.2022.2029997. doi: 10.1080/19490976.2022.2029997
[56]	Wang JF, Wang H, Kang L. LINC00870 regulates Th1/Th2 via the JAK/STAT pathway in peripheral blood mononuclear cells infected with Mycobacterium tuberculosis. Int Immunopharmacol, 2022, 102: 107188. doi:10.1016/j.intimp.2020.107188. doi: 10.1016/j.intimp.2020.107188
[57]	Fu Y, Xu X, Xue J, et al. Deregulated lncRNAs in B Cells from Patients with Active Tuberculosis. PLoS One, 2017, 12(1): e170712. doi:10.1371/journal.pone.0170712. doi: 10.1371/journal.pone.0170712