World Health Organization. Global tuberculosis report 2021. https://www.who.int/publications/digital/global-tuberculosis-report-2021.
Carabalí-Isajar ML, Rodríguez-Bejarano OH, Amado T, Patarroyo MA, Izquierdo MA, Lutz JR, Ocampo M. Clinical manifestations and immune response to tuberculosis. World J Microbiol Biotechnol. 2023;39(8):206.
Aravindan PP. Host genetics and berculosis: theory of genetic polymorphism and tuberculosis. Lung India. 2019;36(3):244–52.
Akkerman OW, Ter Beek L, Centis R, Maeurer M, Visca D, Muñoz-Torrico M, Tiberi S, Migliori GB. Rehabilitation, optimized nutritional care, and boosting host internal milieu to improve long-term treatment outcomes in tuberculosis patients. Int J Infect Dis. 2020;92S:S10–4.
Zhang TP, Chen SS, Zhang GY, Shi SJ, Wei L, Li HM. Association of vitamin D pathway genes polymorphisms with pulmonary tuberculosis susceptibility in a Chinese population. Genes Nutr. 2021;16(1):6. https://doi.org/10.1186/s12263-021-00687-3.
Zheng R, Li Z, He F, Liu H, Chen J, Chen J, et al. Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese. Nat Commun. 2018;9(1):4072.
Zhang K, Sowers ML, Cherryhomes EI, Singh VK, Mishra A, Restrepo BI, Khan A, Jagannath C. Sirtuin-dependent metabolic and epigenetic regulation of macrophages during tuberculosis. Front Immunol. 2023;14:1121495.
Salie M, van der Merwe L, Möller M, et al. Associations between human leukocyte antigen class I variants and the Mycobacterium tuberculosis subtypes causing disease. J Infect Dis. 2014;209(2):216–23.
Yuliwulandari R, Sachrowardi Q, Nakajima H, et al. Association of HLA-A, -B, and -DRB1 with pulmonary tuberculosis in Western Javanese Indonesia. Hum Immunol. 2010;71(7):697–701.
Guastafierro T, Bacalini MG, Marcoccia A, Gentilini D, Pisoni S, Di Blasio AM, et al. Genome-wide DNA methylation analysis in blood cells from patients with Werner syndrome. Clin Epigenetics. 2017;9:92.
Wang M, Kong W, He B, Li Z, Song H, Shi P, Wang J. Vitamin D and the promoter methylation of its metabolic pathway genes in association with the risk and prognosis of tuberculosis. Clin Epigenetics. 2018;10(1):118.
Ni Cheallaigh C, Keane J, Lavelle EC, Hope JC, Harris J. Autophagy in the immune response to tuberculosis: clinical perspectives. Clin Exp Immunol. 2011;164:291e300.
Vergne I, Chua J, Singh SB, Deretic V. Cell biology of mycobacterium tuberculosis phagosome. Annu Rev Cell Dev Biol. 2004;20:367–94.
Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, Rao KV. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell. 2010;140(5):731–43.
Zhang RR, Liang L, Chen WW, Wen C, Wan BS, Luo LL, Zhao YL, Chen J, Yue J. ULK1 polymorphisms confer susceptibility to pulmonary tuberculosis in a Chinese population. Int J Tuberc Lung Dis. 2019;23(2):265–71.
Yuan L, Ke Z, Ma J, Guo Y, Li Y. IRGM gene polymorphisms and haplotypes associate with susceptibility of pulmonary tuberculosis in Chinese Hubei Han population. Tuberculosis (Edinb). 2016;96:58–64.
Xiao S, Zhou T, Pan J, Ma X, Shi G, Jiang B, Xiang YG. Identifying autophagy-related genes as potential targets for immunotherapy in tuberculosis. Int Immunopharmacol. 2023;118:109956.
Peng W, Chen H, Zhao Z, et al. TLR1 polymorphisms are significantly associated with the occurrence, presentation and drug-adverse reactions of tuberculosis in Western Chinese adults. Oncotarget. 2017;9(2):1691–704.
Zhang TP, Li R, Wang LJ, et al. Impact of m6A demethylase (ALKBH5, FTO) genetic polymorphism and expression levels on the development of pulmonary tuberculosis. Front Cell Infect Microbiol. 2022;12:1074380.
Li Z, Zhang Z, He Z, Tang W, Li T, Zeng Z, et al. A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the shesis. Cell Res. 2009;19:519–23. http://analysis.bio-x.cn.
Cai XQ, Huang Q, Zhang TP. The Methylation in B7-H4 and BTLA Genes are Associated with the Risk of Pulmonary Tuberculosis. Immunotargets Ther. 2023;12:149–63.
Zhang TP, Li R, Wang LJ, et al. Roles of the m6A methyltransferases METTL3, METTL14, and WTAP in pulmonary tuberculosis. Front Immunol. 2022;13:992628.
Arnett E, Schlesinger LS. Live and let die: TB control by enhancing apoptosis. Immunity. 2021;54(8):1625–7.
Münz C. Enhancing immunity through autophagy. Annu Rev Immunol. 2009;27:423–49.
Jagannath C, Lindsey DR, Dhandayuthapani S, Xu Y, Hunter RL Jr, Eissa NT. Autophagy enhances the efficacy of BCG vaccine by increasing peptide presentation in mouse dendritic cells. Nat Med. 2009;15:267–76.
Schmid D, Pypaert M, Munz C. Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity. 2007;26:79–92.
Luo HL, Pi J, Zhang JA, Yang EZ, Xu H, Luo H, Shen L, Peng Y, Liu GB, Song CM, Li KY, Wu XJ, Zheng BY, Shen HB, Chen ZW, Xu JF. Circular RNA TRAPPC6B inhibits intracellular Mycobacterium tuberculosis growth while inducing autophagy in macrophages by targeting microRNA-874-3p. Clin Transl Immunol. 2021;10(2):e1254.
Grosjean I, Roméo B, Domdom MA, Belaid A, D’Andréa G, Guillot N, et al. Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases. Autophagy. 2022;18(11):2519–36.
Fujioka Y, Noda NN, Nakatogawa H, Ohsumi Y, Inagaki F. Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy. J Biol Chem. 2010;285(2):1508–15.
Moazeni-Roodi A, Tabasi F, Ghavami S, Hashemi M. Investigation of ATG16L1 rs2241880 polymorphism with Cancer risk: A Meta-Analysis. Med (Kaunas). 2019;55(8):425. https://doi.org/10.3390/medicina55080425. PMID: 31370304; PMCID: PMC6722794.
Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet. 2007;39(2):207–11.
Zhang BB, Liang Y, Yang B, Tan YJ. Association between ATG16L1 gene polymorphism and the risk of crohn’s disease. J Int Med Res. 2017;45(6):1636–50.
Kee BP, Ng JG, Ng CC, Hilmi I, Goh KL, Chua KH. Genetic polymorphisms of ATG16L1 and IRGM genes in Malaysian patients with crohn’s disease. J Dig Dis. 2020;21(1):29–37.
Songane M, Kleinnijenhuis J, Alisjahbana B, Sahiratmadja E, Parwati I, Oosting M, Plantinga TS, Joosten LA, Netea MG, Ottenhoff TH, van de Vosse E, van Crevel R. Polymorphisms in autophagy genes and susceptibility to tuberculosis. PLoS ONE. 2012;7(8):e41618.
Jounai N, Takeshita F, Kobiyama K, Sawano A, Miyawaki A, Xin KQ, et al. The Atg5 Atg12 conjugate associates with innate antiviral immune responses. Proc Natl Acad Sci USA. 2007;104:14050–5.
Zhang YX, Qiao S, Cai MT, Lai QL, Shen CH, Ding MP. Association between autophagy-related protein 5 gene polymorphisms and epilepsy in Chinese patients. Neurosci Lett. 2021;753:135870.
Nikseresht M, Shahverdi M, Dehghani M, Abidi H, Mahmoudi R, Ghalamfarsa G, Manzouri L, Ghavami S. Association of single nucleotide autophagy-related protein 5 gene polymorphism rs2245214 with susceptibility to non-small cell lung cancer. J Cell Biochem. 2019;120(2):1924–31.
Ahmad ES, Diab SM, Behiry EG, Bassyoni SEBESE, Ishak SR, Ramadan A. Autophagy-related 5 gene mRNA expression and ATG5 rs510432 polymorphism in children with bronchial asthma. Pediatr Pulmonol. 2022;57(11):2659–64.
Li N, Fan X, Wang X, Deng H, Zhang K, Zhang X, Han Q, Lv Y, Liu Z. Autophagy-Related 5 gene rs510432 polymorphism is associated with hepatocellular carcinoma in patients with chronic hepatitis B virus infection. Immunol Invest. 2019;48(4):378–91.
Li HM, Wang LJ, Tang F, Pan HF, Zhang TP. Association of leptin and leptin receptor genes variants and pulmonary tuberculosis susceptibility, clinical manifestations in a Chinese population. Microb Pathog. 2022;165:105499.
Xie H, Li C, Zhang M, Zhong N, Chen L. Association between IRGM polymorphisms and tuberculosis risk: A meta-analysis. Med (Baltim). 2017;96(43):e8189.
Deretic V. Autophagy in infection. Curr Opin Cell Biol. 2010;22:252e62.
Singh SB, Davis AS, Taylor GA, Deretic V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science. 2006;313:1438e41.
Che N, Li S, Gao T, Zhang Z, Han Y, Zhang X, Sun Y, Liu Y, Sun Z, Zhang J, Ren W, Tian M, Li Y, Li W, Cheng J, Li C. Identification of a novel IRGM promoter single nucleotide polymorphism associated with tuberculosis. Clin Chim Acta. 2010;411(21–22):1645–9.
Bahari G, Hashemi M, Taheri M, Naderi M, Eskandari-Nasab E, Atabaki M. Association of IRGM polymorphisms and susceptibility to pulmonary tuberculosis in zahedan, Southeast Iran. ScientificWorldJournal. 2012;2012:950801.
Horne DJ, Graustein AD, Shah JA, Peterson G, Savlov M, Steele S, Narita M, Hawn TR. Human ULK1 variation and susceptibility to Mycobacterium tuberculosis infection. J Infect Dis. 2016;214(8):1260–7.
Li L, Hu L, Qiao X, Mo R, Liu G, Hu L. Integrative Analysis of DNA methylation and gene expression data identifies potential biomarkers and functional epigenetic modules for SARS-CoV-2. Biochem Genet. 2023;5:1–12.
Ren LL, Fang JY. Progress of epigenetic study on autophagy in tumor. China Oncol. 2011;21(6):484–8.
Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015;523:212–6.