In silico analysis of miRNA target genes possibly induced by tuberculosis infection

Authors

  • Elba Rodríguez-Hernández Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias. Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal https://orcid.org/0000-0002-9551-7111
  • Laura Itzel Quintas-Granados Universidad Autónoma de la Ciudad de México. Colegio de Ciencias y Humanidades, Plantel Cuautepec. Ciudad de México, México. https://orcid.org/0000-0002-8622-2004
  • Feliciano Milian Suazo Universidad Autónoma de Querétaro https://orcid.org/0000-0003-4893-4868
  • Ana María Anaya Escalera Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias. Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal

DOI:

https://doi.org/10.22319/rmcp.v15i1.6463

Keywords:

Mycobacterium, miR-146a, miR-146b, miR-155, predicción, diagnóstico

Abstract

The objective was to identify, through in silico analysis, the genes to which miR-146a, miR-146b, and miR-155 bind and to analyze the metabolic pathways in which they participate during tuberculosis infection. For the analysis, it was used: miRBase, UniProtKB, TargetScan Human, miRDB, and miRTarBase. miR-146a interacts with or binds to genes important in cell adhesion and  the process of  phagocytosis  (CLDN16  and ATP6V1C2,  respectively) (P< 0.05); this interaction could have important implications in the pathogenesis of tuberculosis or related diseases. The results of this work suggest that the activation of specific molecular mechanisms in response to tuberculosis is regulated by miR-146a, miR-146b, and miR-155. The genes with which miR-146a and miR-155 interact or bind are involved in the immune response and cellular processes essential during tuberculosis infection.

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References

Cohen A, Mathiasen VD, Schön T, Wejse C. The global prevalence of latent tuberculosis: a systematic review and meta-analysis. Eur Respir J 2019;54(3).

Organization WH. Tuberculosis. Accessed Ago 15, 2023.

Bagcchi S. WHO's Global Tuberculosis Report 2022. Lancet Microbe 2023;4(1):e20.

Bostanghadiri N, Jazi FM, Razavi S, Fattorini L, Darban-Sarokhalil D. Mycobacterium tuberculosis and SARS-CoV-2 Coinfections: A Review. Front Microbiol 2022;12:4039.

Gao Y, Liu M, Chen Y, Shi S, Geng J, Tian J. Association between tuberculosis and COVID‐19 severity and mortality: A rapid systematic review and meta‐analysis. J Med Virol 2021;93(1):194-196.

Proaño R, Morales N, Cajiao D. Vista de tuberculosis miliar en paciente con infección por COVID-19 (Doble Problema). Prac Fam Rur Hosp Ecu 2021;6(1).

Afsar I, Gunes M, Er H, Sener AG. Comparison of culture, microscopic smear and molecular methods in diagnosis of tuberculosis. Rev Española Quimioter 2018;31(5):435.

Ryu YJ. Diagnosis of pulmonary tuberculosis: recent advances and diagnostic algorithms. Tuberculosis and Respiratory Dis 2015;78(2):64-71.

Sinigaglia A, Peta E, Riccetti S, Venkateswaran S, Manganelli R, Barzon L. Tuberculosis-associated microRNAs: from pathogenesis to disease biomarkers. Cells 2020;9(10):2160.

Iwakawa H-o, Tomari Y. The functions of microRNAs: mRNA decay and translational repression. Trends Cell Biol 2015;25(11):651-665.

Daniel EA, Sathiyamani B, Thiruvengadam K, Vivekanandan S, Vembuli H, Hanna LE. MicroRNAs as diagnostic biomarkers for Tuberculosis: A systematic review and meta-analysis. Front immunol 2022;13:954396.

Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, et al. Circulating microRNAs as potential biomarkers of infectious disease. Front Immunol 2017;8:118.

Sharbati J, Lewin A, Kutz-Lohroff B, Kamal E, Einspanier R, Sharbati S. Integrated microRNA-mRNA-analysis of human monocyte derived macrophages upon Mycobacterium avium subsp. hominissuis infection. PloS one 2011;6(5):e20258.

Yi Z, Fu Y, Ji R, Li R, Guan Z. Altered microRNA signatures in sputum of patients with active pulmonary tuberculosis. PloS One 2012;7(8):e43184.

Chauhan D, Davuluri KS. microRNAs associated with the pathogenesis and their role in regulating various signaling pathways during Mycobacterium tuberculosis infection. Front Cell Infect Microbiol 2022:1577.

Fu Y, Yi Z, Wu X, Li J, Xu F. Circulating microRNAs in patients with active pulmonary tuberculosis. J Clin Microbiol 2011;49(12):4246-4251.

Rothchild AC, Sissons JR, Shafiani S, Plaisier C, Min D, Mai D, et al. MiR-155–regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis. PNAS 2016;113(41):E6172-E81.

Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2022;50(D1):D20.

Griffiths-Jones S. miRBase: the microRNA sequence database: MicroRNA Protocols; 2006 [129-38]. https://www.mirbase.org/.

Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife. 2015;4:e05005.http://www.targetscan.org.

Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008;14(6):101-117. http://mirdb.org.

Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic acids research 2020;48(D1):D127-D31. http://mirdb.org.

Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res 2019;47(D1):D155-D62. https://mirdb.org/ontology.html.

Huang HY, Lin YCD, Cui S, Huang Y, Tang Y, Xu J, et al. miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions. Nucleic Acids Res 2022;50(D1):D222-D30. https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php.

Bock G, Goode JA, editors. The KEGG database. ‘In silico’simulation of biological processes: Novartis Foundation Symposium. Wiley Online Library. 2002:247. https://doi.org/10.1002/0470857897.ch8.

Ghoumid J, Drevillon L, Alavi-Naini SM, Bondurand N, Rio M, Briand-Suleau A, et al. ZEB2 zinc-finger missense mutations lead to hypomorphic alleles and a mild Mowat–Wilson syndrome. Hum Mol Genet 2013;22(13):2652-2661.

Hou J, Goodenough DA. Claudin-16 and claudin-19 function in the thick ascending limb. Curr Opin Nephrol Hypertens 2010;19(5):483.

Das P, Goswami P, Das TK, Nag T, Sreenivas V, Ahuja V, et al. Comparative tight junction protein expressions in colonic Crohn’s disease, ulcerative colitis, and tuberculosis: a new perspective. Virchows Archiv 2012;460(3):261-270.

Sánchez-Garibay C, Salinas-Lara C, Gómez-López MA, Soto-Rojas LO, Castillón-Benavides NK, Castillón-Benavides OJ, et al. Mycobacterium tuberculosis infection induces BCSFB disruption but No BBB disruption in vivo: Implications in the pathophysiology of tuberculous meningitis. Int J Mol Sci 2022;23(12):6436.

López M, Quitian LV, Calderón MN, Soto CY. The P-type ATPase CtpG preferentially transports Cd2+ across the Mycobacterium tuberculosis plasma membrane. Arch Microbiol 2018;200(3):483-492.

Smith AN, Borthwick KJ, Karet FE. Molecular cloning and characterization of novel tissue-specific isoforms of the human vacuolar H+-ATPase C, G and d subunits, and their evaluation in autosomal recessive distal renal tubular acidosis. Gene 2002;297(1-2):169-77.

Chaudhary D, Marzuki M, Lee A, Bouzeyen R, Singh A, Gosain TP, et al. Disulfiram inhibits M. tuberculosis growth by altering methionine pool, redox status and host-immune response. bioRxiv 2020; http://dx.doi.org/10.2139/ssrn.3696891.

Quist J, Hill AR. Serum lactate dehydrogenase (LDH) in Pneumocystis carinii pneumonia, tuberculosis, and bacterial pneumonia. Chest 1995;108(2):415-418.

Hover BM, Tonthat NK, Schumacher MA, Yokoyama K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. PNAS 2015;112(20):6347-6352.

Williams MJ, Kana BD, Mizrahi V. Functional analysis of molybdopterin biosynthesis in mycobacteria identifies a fused molybdopterin synthase in Mycobacterium tuberculosis. J Bacteriol 2011;193(1):98-106.

Zhong Q, Kobe B, Kappler U. Molybdenum enzymes and how they support virulence in pathogenic bacteria. Front Microbiol 2020;11:615860.

Shi T, Xie J. Molybdenum enzymes and molybdenum cofactor in mycobacteria. J Cell Biochem 2011;112(10):2721-2728.

Levillain F, Poquet Y, Mallet L, Mazères S, Marceau M, Brosch R, et al. Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation. PLoS Pathog 2017;13(11):e1006752.

Suchard MS, Adu‐Gyamfi CG, Cumming BM, Savulescu DM. Evolutionary views of tuberculosis: indoleamine 2, 3‐dioxygenase catalyzed nicotinamide synthesis reflects shifts in macrophage metabolism: indoleamine 2, 3‐dioxygenase reflects altered macrophage metabolism during tuberculosis pathogenesis. BioEssays 2020;42(5):1900220.

Blumenthal A, Nagalingam G, Huch JH, Walker L, Guillemin GJ, Smythe GA, et al. M. tuberculosis induces potent activation of IDO-1, but this is not essential for the immunological control of infection. PloS one 2012;7(5):e37314.

Gautam US, Foreman TW, Bucsan AN, Veatch AV, Alvarez X, Adekambi T, et al. In vivo inhibition of tryptophan catabolism reorganizes the tuberculoma and augments immune-mediated control of Mycobacterium tuberculosis. PNAS 2018;115(1):E62-E71.

Katz JB, Muller AJ, Prendergast GC. Indoleamine 2, 3‐dioxygenase in T‐cell tolerance and tumoral immune escape. Immunol Rev 2008;222(1):206-21.

Davies NW, Guillemin G, Brew BJ. Tryptophan, neurodegeneration and HIV-associated neurocognitive disorder. Int J Tryp Res 2010;3. doi:10.4137/IJTR.S4321

Guta S, Casal J, Napp S, Saez JL, Garcia-Saenz A, Perez de Val B, et al. Epidemiological investigation of bovine tuberculosis herd breakdowns in Spain 2009/2011. PLoS One 2014;9(8):e104383.

Golby P, Nunez J, Witney A, Hinds J, Quail MA, Bentley S, et al. Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression. BMC Genom 2013;14(1):1-18.

Diamond J. Evolution, consequences and future of plant and animal domestication. Nature 2002;418(6898):700-707.

Mostowy S, Cousins D, Brinkman J, Aranaz A, Behr MA. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis 2002;186(1):74-80.

Published

2024-01-19

How to Cite

Rodríguez-Hernández , E., Quintas-Granados , L. I., Milian Suazo, F., & Anaya Escalera, A. M. (2024). In silico analysis of miRNA target genes possibly induced by tuberculosis infection. Revista Mexicana De Ciencias Pecuarias, 15(1), 192–207. https://doi.org/10.22319/rmcp.v15i1.6463
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