Transcriptional signatures of human peripheral blood mononuclear cells can identify the risk of tuberculosis progression from latent infection among individuals with silicosis

References

• Houben R, Dodd P. The global burden of latent tuberculosis infection: a re-estimation using mathematical modelling. PLoS Med. 2016;13(10):e1002152.
   PubMed Web of Science ®Google Scholar
• Leung CC, Yu IT, Chen W. Silicosis. Lancet. 2012;379(9830):2008–2018.
   PubMed Web of Science ®Google Scholar
• Targeted tuberculin testing and treatment of latent tuberculosis infection. American Thoracic Society. MMWR Recomm Rep. 2000;49(RR-6):1–51.
   Google Scholar
• Rangaka MX, Wilkinson KA, Glynn JR, et al. Predictive value of interferon-gamma release assays for incident active tuberculosis: a systematic review and meta-analysis. Lancet Infect Dis. 2012;12(1):45–55.
   PubMed Web of Science ®Google Scholar
• Diel R, Loddenkemper R, Niemann S, et al. Negative and positive predictive value of a whole-blood interferon-gamma release assay for developing active tuberculosis: an update. Am J Respir Crit Care Med. 2011;183(1):88–95.
   Web of Science ®Google Scholar
• Diel R, Loddenkemper R, Meywald-Walter K, et al. Predictive value of a whole blood IFN-gamma assay for the development of active tuberculosis disease after recent infection with Mycobacterium tuberculosis. Am J Respir Crit Care Med. 2008;177(10):1164–1170.
   PubMed Web of Science ®Google Scholar
• Getahun H, Matteelli A, Chaisson RE, et al. Latent Mycobacterium tuberculosis infection. N Engl J Med. 2015;372(22):2127–2135.
   PubMed Web of Science ®Google Scholar
• Zak DE, Penn-Nicholson A, Scriba TJ, et al. A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet. 2016;387(10035):2312–2322.
   PubMed Web of Science ®Google Scholar
• Suliman S, Thompson E, Sutherland J, et al. Four-gene Pan-African blood signature predicts progression to tuberculosis. Am J Respir Crit Care Med. 2018;197(9):1198–1208.
   PubMed Web of Science ®Google Scholar
• Ruan QL, Huang XT, Yang QL, et al. Efficacy and safety of weekly rifapentine and isoniazid for tuberculosis prevention in Chinese silicosis patients: a randomized controlled trial. Clin Microbiol Infect. 2021;27:576–582.
   Web of Science ®Google Scholar
• Andrews S. FastQC: a quality control tool for high throughput sequence data 2010. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Kim D, Pertea G, Trapnell C, et al. Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
   PubMed Web of Science ®Google Scholar
• Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–930.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550–570.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25(1):25–29.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, et al. Clusterprofiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613.
   PubMed Web of Science ®Google Scholar
• Gideon HP, Skinner JA, Baldwin N, et al. Early whole blood transcriptional signatures Are associated with severity of lung inflammation in cynomolgus macaques with Mycobacterium tuberculosis infection. J Immunol. 2016;197(12):4817–4828. Baltimore, 1950.
   Web of Science ®Google Scholar
• Lin PL, Rodgers M, Smith L, et al. Quantitative comparison of active and latent tuberculosis in the cynomolgus macaque model. Infect Immun. 2009;77(10):4631–4642.
   PubMed Web of Science ®Google Scholar
• Singhania A, Verma R, Graham CM, et al. A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection. Nat Commun. 2018;9(1):2308–2324.
   Web of Science ®Google Scholar
• Berry MP, Graham CM, McNab FW, et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature. 2010;466(7309):973–977.
   PubMed Web of Science ®Google Scholar
• Singhania A, Wilkinson RJ, Rodrigue M, et al. The value of transcriptomics in advancing knowledge of the immune response and diagnosis in tuberculosis. Nat Immunol. 2018;19(11):1159–1168.
   PubMed Web of Science ®Google Scholar
• Cooper AM. Cell-mediated immune responses in tuberculosis. Annu Rev Immunol. 2009;27:393–422.
   PubMed Web of Science ®Google Scholar
• Lee J, Kornfeld H. Interferon-gamma regulates the death of M. tuberculosis-infected macrophages. J Cell Death. 2010;3:1–11.
   Google Scholar
• Schoenborn JR, Wilson CB. Regulation of interferon-gamma during innate and adaptive immune responses. Adv Immunol. 2007;96:41–101.
   PubMed Web of Science ®Google Scholar
• Cooper AM, Dalton DK, Stewart TA, et al. Disseminated tuberculosis in interferon gamma gene-disrupted mice. J Exp Med. 1993;178(6):2243–2247.
   PubMed Web of Science ®Google Scholar
• Dupuis S, Doffinger R, Picard C, et al. Human interferon-gamma-mediated immunity is a genetically controlled continuous trait that determines the outcome of mycobacterial invasion. Immunol Rev. 2000;178:129–137.
   PubMed Web of Science ®Google Scholar
• Correa AF, Bailao AM, Bastos IM, et al. The endothelin system has a significant role in the pathogenesis and progression of Mycobacterium tuberculosis infection. Infect Immun. 2014;82(12):5154–5165.
   Web of Science ®Google Scholar
• Denisenko E, Guler R, Mhlanga M, et al. Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics. 2019;20(1):71–86.
   Web of Science ®Google Scholar
• Cai L, Li Z, Guan X, et al. The Research progress of host genes and tuberculosis susceptibility. Oxid Med Cell Longev. 2019;2019:9273056.
   Web of Science ®Google Scholar
• Alvarez IB, Pasquinelli V, Jurado JO, et al. Role played by the programmed death-1-programmed death ligand pathway during innate immunity against Mycobacterium tuberculosis. J Infect Dis. 2010;202(4):524–532.
   PubMed Web of Science ®Google Scholar
• Bhalla K, Chugh M, Mehrotra S, et al. Host ICAMs play a role in cell invasion by Mycobacterium tuberculosis and plasmodium falciparum. Nature Communication. 2015;6:6049–6061.
   Web of Science ®Google Scholar
• Verway M, Bouttier M, Wang TT, et al. Vitamin D induces interleukin-1beta expression: paracrine macrophage epithelial signaling controls M. tuberculosis infection. PLoS Pathog. 2013;9(6):e1003407.
   PubMed Web of Science ®Google Scholar