Tuberculosis is one of the most deadly infectious diseases in the world, and about one-quarter of the world’s population has been infected with Mycobacterium tuberculosis (Wilkins et al., 2022). According to the latest World Health Organization (WHO) report, there were approximately 10.6 million new cases and 1.3 million deaths worldwide in 2022 (Mi et al., 2024). The incidence and mortality of tuberculosis are still high worldwide, although its prevention and treatment have cost a lot (Drain et al., 2018; Huang et al., 2019). The main reason is the long-term incubation of tuberculosis and the delay in the emergence of new and effective anti-tuberculosis drugs (Venketaraman et al., 2015; Cole, 2016). Therefore, the research on new drug targets for tuberculosis is the focus of developing anti-tuberculosis drugs (Gashaw et al., 2011).

Drug targets refer to the binding sites of drugs in vivo, including biological macromolecules such as gene sites, receptors, enzymes, ion channels and nucleic acids. The key to modern new drug research and development is first to find, determine and prepare drug screening targets (Eder and Herrling, 2016). Transcription factors are important molecules that control gene expression and the convergence point of multiple signal pathways in eukaryotic cells, and play an important role in the function of cells and the healthy development of the body (Vaquerizas et al., 2009; Papavassiliou and Papavassiliou, 2016). Transcription factors and their corresponding target genes construct a corresponding regulatory network, and the key factors in this regulatory network are the targets of drug action or clinical diagnosis. Therefore, new potential drug targets for tuberculosis can be explored by constructing a transcription factor regulatory network for tuberculosis.

In this study, differentially expressed genes were screened in tuberculosis patients and healthy people by using mRNA sequencing technology. The transcription factors of the differentially expressed genes were screened in the AnimalTFDB 3.0 database (Hu W. et al., 2019) to construct a regulatory network, then the key targets and their related pathways were further screened by MCODE cluster analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (Kanehisa et al., 2017) and the pathogenesis of tuberculosis and its potential new drug targets were analyzed.

In recent years, tuberculosis has made a comeback, with a significant rise in its incidence and mortality, and the resistance of M. tuberculosis to anti-tuberculosis drugs commonly used at present has become increasingly serious, which has become a thorny problem in the clinical treatment of tuberculosis (Suárez et al., 2019; Olivença et al., 2022). In the past 30 years, no new and efficient anti-tuberculosis drugs have been developed. Therefore, it is urgent to find potential targets of new anti-tuberculosis drugs for studying and developing new anti-tuberculosis drugs to achieve effective control of tuberculosis (Rode et al., 2019). In this study, 556 differentially expressed genes were screened out by mRNA sequencing, and 430 important differentially expressed genes were identified by constructing a PPI regulatory network and removing free genes. Twenty-six transcription factors and 66 target genes regulated by them were identified from 430 important differentially expressed genes through the AnimalTFDB 3.0 database.

A transcription factor regulatory network of 26 transcription factors and 66 target genes regulated by them was constructed. It was found by the analysis of the transcription factor regulatory network that the target genes corresponding to TP53 were the most common (59), and its Degree value ranked second in the PPI regulatory network. TP53 is the coding gene of the tumor suppressor gene p53 protein, located on human chromosome 17 (Hu H. et al., 2019). TP53 wild-type mutation will lead to apoptosis of cancer cells, while TP53 mutant will increase the risk of cancer, so that the mutation status of TP53 may be a biomarker to predict the response of different cancer types to cancer immunotherapy (Li et al., 2020). In addition, some studies have pointed out that TP53 can regulate human immune function and affect the host immune system (Yuan et al., 2018). GATA2 is the second most common transcription factor (9), corresponding to the target gene. GATA2 is a zinc-finger transcription factor expressed in human hematopoietic stem cells and various hematopoietic progenitor cells (Oleaga-Quintas et al., 2021). There are also many target genes corresponding to the transcription factor GATA2 (9), and the GATA2 gene is believed to regulate the ontogeny and function of monocytes, macrophages, dendritic cells, B cells and NK cells (Yuag et al., 2017; Monif et al., 2018). Therefore, we find that both TP53 and GATA2 are closely related to the body’s immune system.

The analysis of target genes regulated by transcription factors showed that TP53, AKT1, GATA2 and PBX1 were the four target genes most regulated by transcription factors, regulating 11, 9, 7 and 6 target genes, respectively. Our previous study has shown that genes TP53 and GATA2 are very important transcription factors and are closely related to immune function. AKT1 is a serine/threonine protein kinase, also known as Akt kinase. Akt can regulate the development and function of innate immune cells such as neutrophils, macrophages and dendritic cells, which play an important role in the regulation of immune cells (Xia et al., 2020). AKT1 plays a key role in the process of controlling the growth of M. tuberculosis cells and is a key kinase involved in controlling the growth of M. tuberculosis cells. AKT1 inhibitors have the potential to be used as antibiotics to treat tuberculosis (Wang et al., 2010). The PBX1 gene promotes the early development of NK cells by directly up-regulating the expression of Nfil3 (Xu et al., 2020). PBX1 is required to maintain the self-renewal of hematopoietic stem cells during the development of the immune system. PBX1 deficient embryonic stem cells cannot produce lymphoid progenitor cells, leading to the loss of B and NK cells as well as the impaired development of T cells (Niu et al., 2017; Gu et al., 2023). Therefore, these four target genes that are most regulated by transcription factors are also closely related to the immune function of the body.

Through MCODE cluster analysis, a core sub-network of the transcription factor regulatory network was constructed, and four important nodes, AKT1, TP53, KLF5, and GATA2 were screened out. As described above, AKT1 is an important gene regulated by transcription factors, TP53 and GATA2 are important transcription factors, and AKT1, TP53, and GATA2 are all related to the immune function of the body. The MCODE cluster analysis showed that transcription factor KLF5 was closely related to other key genes (Figure 5B) although it only regulated three target genes (Table 3). Some studies have shown that KLF5 plays an important role in the differential regulation of angiogenesis progress induced by M. tuberculosis, closely related to the pathogenesis of pulmonary tuberculosis, and the expression of the KLF5 gene has also been verified by immunofluorescence imaging in these studies (Mukherjee et al., 2022). It can be inferred that tuberculosis may activate the expression of the AKT1 gene by regulating the transcription factors TP53, KLF5, and GATA2, thus leading to the infection and invasion of M. tuberculosis.

The GO analysis and KEGG analysis of 430 important differentially expressed genes screened were also performed in this study. The GO analysis showed that the enrichment of the mitotic cell cycle was the most significant in the biological processes (BP), and it is well known that mitosis is an important process to maintain the normal growth and development of individuals. It has been indicated in some studies that the mitotic index of tuberculosis patients who have received treatment with anti-tuberculosis drugs will improve (Jaju et al., 1983). In the cell components (CC), the enrichment of cytoplasm was the most significant. The cytoplasm is the main place for metabolism and plays a regulatory role in the nucleus. In the molecular functions (MF), the enrichment of protein binding was the most significant. The GO enrichment analysis results suggest that M. tuberculosis may play a regulatory role in the nucleus by changing the function of the main metabolic sites, thus affecting the protein binding function.

In the KEGG pathway analysis of differential genes, we screened out 16 pathways, of which central carbon metabolism in cancer was the most significant. Tuberculosis and cancer are two diseases that tend to produce resistance to the host immune system, with certain similarities in the regulation of immune response (Bickett and Karam, 2020). B cell receiver signaling pathway is one of the most significant signal pathways, mainly related to immunity (Sun et al., 2020; Tanaka and Baba, 2020). The key gene AKT1 can regulate this pathway, and the gene AKT1 is one of the four key nodes we screened out. Therefore, the gene AKT1 is likely to be the key gene to activate the B cell receiver signaling pathway.

Four key genes and a pathway closely related to tuberculosis were screened out by constructing the tuberculosis transcription factor network, of which TP53, KLF5, and GATA2 are transcription factors and AKT1 is the target gene. Mycobacterium tuberculosis may activate the expression of the AKT1 gene by regulating the transcription factors TP53, KLF5 and GATA2, thus leading to the infection and invasion of M. tuberculosis through the B cell receptor signaling pathway.