Autophagy, a housekeeping function, maintains intracellular quality control under stress. Both innate and adaptive immunity use autophagy. New vesicles, or phagophores, grow longer and larger during autophagy and develop into the two-membrane autophagosome. The autophagosome becomes a phagolysosome for recycling or degradation after merging with the lysosome (Shariq et al., 2021). In MTB infection, autophagy has evolved from a canonical degradation pathway to a complex host-pathogen interface. Canonical autophagy, mediated by autophagy related genes (ATG) proteins like ATG5, promotes phagosome-lysosome fusion and reduces neutrophil-driven inflammation early in infection, limiting MTB survival in alveolar macrophages. Latest research found that total loss of autophagy components like ATG7 and ATG16L1 made the host more susceptible to pathogen-induced phagosome damage and macrophage necrosis (Ren et al., 2025). The MTB genome encodes eleven eukaryotic-like serine-threonine protein kinases (STPKs) regulate virulence, growth, metabolism, and host-pathogen interactions. PknG is the only STPK released into host cells during infection. PknG also facilitates pathogen survival during MTB infection by inhibiting macrophage phagosome maturation, which is necessary for TB pathogenicity (Ge et al., 2022). The endoplasmic reticulum (ER) stress mechanisms of MTB cause apoptosis, while autophagy helps cells survive. In contrast, the autophagy inhibition increased MTB-induced apoptosis, suggesting moderate autophagy may protect cells. In this study, BAG2 (BCL2 associated athanogene 2) increased autophagy to reduce cell death during MTB infection, but autophagy inhibition eliminated its cytoprotective effects. BAG2’s role in MTB-induced ER stress and apoptosis-autophagy relationships was clarified (Liang et al., 2020). In addition, MTB infection diminished H3K9 and H3K27 acetylation, which is crucial for transcriptional activation, while augmenting H3K9 and H3K27 hypermethylation, important for transcriptional repression. These findings suggest that to enhance MTB survival, MTB PRT performs two histone modifications. Certain histone methyltransferases, such as G9a, Suv39h1/h2 (which facilitates H3K9 hypermethylation), and Ezh2 (which promotes H3K27 hypermethylation), induce histone hypermethylation (Sengupta et al., 2021). In this context, the association between PE_PGRS proteins and Rab1A enhances the GTP activity of Rab1A, hence boosting mTOR and preventing autophagy. Related to RablA-positive cells infected with the same mycobacteria, Rab1A knockdown cells (siRab1A) infected with either wild-type MTB or two complementing strains had reduced mTOR activation (measured by p-S6), suggesting that Rab1A regulates mTOR activity (Strong et al., 2021). Thus, the PE_PGRS protein of MTB suppresses the autophagy and capable of survive for g a long time in macrophages. Although, the roles of autophagy in the early detection of the transition from NIHS or LTBI to active TB illness remain largely unexplored. According to a recent study, anti-TB treatment reversed the up-regulation of LC3B and ATG5 in patients with active TB and those with high bacterial burden or advanced disease. These results imply that autophagy flux could be utilized to create tools for tracking the development of TB reactivation disease (Chen et al., 2025).

MicroRNAs (miRNAs) are small, non-coding RNA molecules. By binding to the 3′-UTR regions of target mRNAs, microRNAs meticulously regulate gene expression at the post-transcriptional level. Since miRNAs have an impact on a wide range of biological functions, including immune regulation, growth, development, homeostasis, and the progression of disease. In this case, miR-142-3p was markedly downregulated in macrophages after MTB infection. Specifically, miR-142-3p negatively regulated the production of pro-inflammatory mediators (NF-κB, TNF-α, and IL-6) via targeting interleukin receptor associated kinase (IRAK1). The precise target of miR-142-3p is still ambiguous. This work revealed that miR-142-3p markedly impeded phagosome development in macrophages, mitigated autophagy caused by MTB H37Ra, and enhanced intracellular bacterial survival in macrophages by inhibiting ATG16L1 and ATG4c (Figure 1). In contrast, miR-106a affects the autophagy process and mycobacterial removal in human macrophages by targeting ULK1, ATG7, and ATG16L1, which may help us better understand the host’s innate immune responses against MTB (Qu et al., 2021; Liu et al., 2021). Besides that, circRNA links to the autophagy in MTB infection, since monocytes from TB patients exhibited distinctly reduced levels of hsa_circ_0045474 compared to monocytes from healthy controls. Moreover, circRNAs have been found to participate in the autophagy of TB-associated macrophages. For instance, circRNA-0003528 facilitated MTB-associated macrophage polarization by up-regulating CTLA4 and down-regulating miR-224-5p, miR-324-5p, and miR-488-5p. Similarly, hsa_circ_0045474 or miR-582-5p partially mitigated the influence of TNKS2 or miR-582-5p on macrophage autophagy, suggesting that the miR-582-5p/TNKS2 axis played a role in the down-regulation of hsa_circ_0045474 to promote macrophage autophagy in TB (Table 1) (Wu et al., 2022; Huang et al., 2020).

Extracellular vesicles (EVs) and exosomes, which transport proteins, mRNAs, and non-coding RNAs (ncRNAs), are essential for facilitating intercellular communication among proximate and remote cells, thereby influencing numerous cellular and biological processes. Noticeably, the plasma exosomes from LTBI patients transmitted miR-7850-5p to THP1, inhibiting the expression of the critical iron death gene SLC11A1 and promoting MTB’s intracellular survival in THP1 (Cui et al., 2024; Shahzad et al., 2022). In addition, miR-144-3p has the potential to inhibit the activation of autophagy and enhance BCG infection through its targeting of ATG4a in RAW264.7 cells. In macrophage cells, miR-23a-5p may impact autophagy and mycobacterial viability by targeting TLR2 within the TLR2/MyD88/NF-κB signaling pathway during MTB infection (Lyu et al., 2019).

Single-cell lung events can cause or control TB. Single-cell technologies like RNA-sequencing (scRNA-seq) can objectively profile immune cell populations in healthy and diseased humans and animals. Although circulating NK cells are highly important in TB immunity, besides the study found CD27+ NK cells in macaque hosts’ lungs that regulate MTB infection. Memory-like responses and vaccine-induced MTB protection depend on CD27+ NK cell recognition, proliferation, and survival. The TNF receptor superfamily member CD27 may indicate mature or memory natural killer cells. In cytotoxicity, cytokine production, proliferation, and function, CD27+ NK cells outperform CD27-NK cells. Also, this study findings support NK cell TB protection. In LTBI patients, mycobacteria increase CD27+ NK cell growth. Human monocytes and AMs infected with MTB can be lysed by NK cells to boost immunity (Esaulova et al., 2021; Venkatasubramanian et al., 2017). Also, a similar study scRNA-seq analyzed distribution of γδT cell sub-clusters across the tested groups indicated that latent MTB infection induces a specific proliferation of CD81bright γδ T cells, skewing them towards AKT signaling, which is mediated by PI3K and involves cell activation through the second messenger PIP3. The PI3K/AKT pathway is a crucial signaling cascade that regulates metabolism, cellular growth, and survival (Shekarkar Azgomi et al., 2024). Furthermore, in CyTOF analysis reveals that non-progressing LTBI patients have fewer MAIT, NKT, and NK cells than those with PTB, suggesting lower microbial abundance. These cells are essential for mycobacteria regulation. PBMCs of LTBI patients who developed PTB had more CD16+CD56dimCD57+ early NK cells. Antigen-dependent cell cytotoxicity (ADCC) indicates microbicidal activity via CD16 (Fc gamma receptor III), while reduced CD56 and elevated CD57 indicate cellular senescence. Compared to active pulmonary TB (PTB), latent TB infection progression may have more CD16+CD56dimCD57+ early natural killer (NK) cells, suggesting the involvement of antibody-dependent cellular cytotoxicity (ADCC) cells that regulate organisms. In addition, the MAIT NKT cells contribute significantly to the initial response to mycobacteria and are effectively equipped with cytotoxic molecules through granzyme B activity (Kamolratanakul et al., 2024; Ruibal et al., 2021). In a recent study indicates that these distinct genes are essential for TB that gp91-phox subunit of the phagocytic oxidase complex, responsible for producing superoxide and other reactive oxygen species necessary for microbial destruction, is encoded by the CYBB gene. CYBB overexpression elevates reactive oxygen species (ROS), which can damage tissue and initiate clinical symptoms associated with LTBI. The ROS have historically been considered responsible for tissue damage in both acute and chronic inflammatory diseases. Notably, this study employed machine learning algorithms Lasso, random forest (RF), and SVM-RFE to identify specific genes associated with TB development and the inflammatory response (Ma et al., 2023; Frazão et al., 2015). In brief, to comprehend gp91phox, historically referred to as cytochrome b558, reveals that the NOX2 core complex comprises two transmembrane subunits: the auxiliary p22phox (p22) subunit and the catalytic NOX2 subunit, also known as gp91phox (Noreng et al., 2022). Recent findings from flow cytometry and single-cell RNA sequencing indicate an increase in the fraction of monocytes associated with active TB. However, the pathophysiology of TB, mortality was associated with monocyte dysfunction and the activation of the innate immune system (Janssen et al., 2017).

The fatal illness TB is associated with monocytes. Though, numerous studies have demonstrated that autoimmunity has a role in TB. The innate and adaptive immune systems are essential for combating MTB. Cells of the innate and adaptive immune responses are involved in TB granuloma, with a particular emphasis on monocytes. In a recent study, the PPI network contained three essential monocyte-related genes SERPINA1, FUCA2, and HP. Haptoglobin (HP) is the only gene directly connected to TB development and activity. In an acute-phase response, the haptoglobin protein aids tissue repair, infection prevention, and internal environment stability. In TB pleurisy, HP expression is high (Li et al., 2021; Gao et al., 2019). The study’s clinical sample verification found that active TB patients’ PBMCs had higher HP levels than latent TB and healthy controls. This study suggested that tissue hypoxia raises HP levels in active TB. Under hypoxia, many red blood cells lysed, raising tissue hemoglobin levels. As hemoglobin is absorbed, haptoglobin expression rises. Patients with active TB were sensitive. Serine protease inhibitor A1 (SERPINA1) inhibits over 90% of plasma proteases due to its highly conserved protein structure. Arya et al. found that active TB had high SERPINA1 expression using the iTRAQ-I experiment and Western blotting. Acute-phase reactive protein is mostly produced by liver cells, however epithelial, monocyte, and macrophages can also manufacture it. Active TB also causes lung inflammation (Li et al., 2021; Arya et al., 2020; Zoller et al., 2018). Notably, the PTB patients displayed a diminished proportion of CD14+CD16− monocytes and an increased prevalence of CD14+CD16+ and CD14−CD16+ monocytes in comparison to healthy controls. Monocytes contain CD163, a scavenger receptor that endocytoses haptoglobin-hemoglobin complexes and is indicative of M2 macrophages (Canton et al., 2013). The proliferation of CD16+CD163+MerTK+ monocytes in TB diminishes the host’s defense against MTB due to their reduced pro-/anti-inflammatory cytokine production ratio and restricted T cell activation. CD163 and MerTK signify M2-like macrophage activation, characterized by immunomodulatory and pathogen-permissive properties (Liu et al., 2019; Lastrucci et al., 2015). To comprehend the DosR (dormancy of survival) regulon in the LTBI state, a segment of the MTB genome activated during dormancy comprises 50 genes. Patients with LTBI exhibit more pronounced immune responses to these antigens compared to those with active TB, hence facilitating the differentiation between infection and disease (Meier et al., 2018). These antigens may help assess ATB treatment success as well as distinguish LTBI from ATB. The most promising M. tuberculosis DosR regulon encoded antigens were Rv0081, Rv1733c, Rv1737c, Rv2029c, and Rv2628, which showed immunogenic potential across studies and regions. The DosR regulon’s transcriptional regulator Rv0081 may be important in hypoxia. Long-term incubation studies in Ethiopia and South Africa showed this antigen’s immunogenicity (Mensah et al., 2014; Araujo et al., 2015; Bai et al., 2016). The median monocyte-to-lymphocyte ratio (MLR) in IGRA+ subgroup B was 0.52, greater than subgroup A (0.35, p = 0.04). This ratio is linked to blood transcriptomes and TB risk. However, the IGRA+ B subgroup, MLR level increased marginally (Broderick et al., 2021; Naranbhai et al., 2015).

Multiple factors contribute to the progression of TB, particularly as MTB employs various genes for intracellular survival. Analyses of the transcriptome and proteome facilitate the development of diagnostic markers and antimycobacterial agents. Small RNAs, including miRNA, lncRNA, circRNA, and the ceRNA network, will have important roles in gene regulation and translational research. In this context, numerous miRNAs are essential in the regulation of autophagy; specifically, miR-155 inhibits autophagy in human dendritic cells by targeting ATG3. In macrophages infected with MTB, miR-17-5p regulates autophagy by targeting Mcl-1 and STAT3. MiR-27a facilitates the survival of MTB within cells by modulating Ca2+-associated autophagy. In human monocytes and macrophages, miR-144-5p suppresses antibacterial autophagy and the innate immune response to MTB by targeting DRAM2. MTB inhibits integrated autophagic pathways that promote bacterial intracellular survival and persistence through the production of miR-33 and miR-33*. Research indicates that miR-20a targets ATG7 and ATG16L1, resulting in reduced autophagy and increased BCG survival in murine macrophages (Etna et al., 2018; Liu et al., 2018; Kim et al., 2017; Liu et al., 2021). Thus, analyses of small RNAs and their interaction with autophagy in clinical strains will identify potential diagnostic markers. Pathogenic mycobacteria expressing PE and PPE families inhibit autophagy, thereby enhancing bacterial survival within macrophages during host-microbe interactions. The expression of PE or PPE proteins markedly enhanced mTOR signaling in Mycobacterium smegmatis, indicating a potential mechanism for the inhibition of autophagy induced by mycobacteria (Strong et al., 2020). This analysis of mycobacterial self-defense mechanisms against autophagosome-lysosome fusion presents a promising tool for the development of antimycobacterial agents.