Targeting tuberculosis with LNP-mRNA vaccines: opportunities, challenges and future directions

The need for novel tuberculosis vaccines

Five years after the start of the COVID-19 pandemic, one of humanities oldest pathogens, Mycobacterium tuberculosis, is once again the leading cause of death globally from a single infectious agent. In 2023 alone, there were an estimated 10.8 million new cases of tuberculosis (TB) and 1.25 million deaths worldwide.¹ A major challenge for TB control is the absence of an effective vaccine. Bacillus Calmette–Guérin (BCG) is the only licensed vaccine against TB and, although it is protective in young children, efficacy against pulmonary infection in adults is inconsistent, ranging between 0 and 80%.² A more reliable and effective vaccine would offer significant benefits to global public health and the economy.^3,4 However, the TB vaccine development pipeline remains limited, with only a few candidates progressing to late-stage clinical trials despite more than a century of research (Table 1). Notably, all advanced candidates rely on traditional vaccine platforms, such as protein subunits, live attenuated strains or inactivated bacteria.

Potential of the LNP-mRNA vaccine platform against tuberculosis

The mRNA vaccine platform is attractive for use against TB for several reasons. Firstly, although still a highly technological process, the cell free method of production allows for rapid, scalable and cost-effective development.⁵ This not only facilitates increased speed of screening target antigens, which has been a major historical bottleneck in TB vaccine development,³ but makes mass distribution of these vaccines in low-income countries, who have the greatest burden of TB, economically viable.⁴ Efforts are also being made with the support of the World Health Organization (WHO) to establish facilities in these countries to enable local production of mRNA vaccines.⁶ Furthermore, mRNA vaccines are non-infectious, meaning they are safe for use in immunocompromised individuals, such as those infected with the human immunodeficiency virus (HIV), for whom TB is the leading cause of death.¹

To date, all mRNA vaccines licenced for use in humans target viral infections, including Pfizer’s COMIRNATY (BNT162b) and Moderna’s SPIKEVAX (mRNA-1273) against SARS-CoV-2, and Moderna’s mRESVIA (mRNA-1345) for respiratory syncytial virus (RSV).⁷ For these infections, protection is primarily associated with the generation of high-titre, vaccine-specific neutralising antibodies that prevent entry of the virus into host cells.⁸ In addition to this humoral immunity, mRNA vaccines also elicit strong Th1 CD4⁺ T cell responses, producing IFN-γ, IL-2 and TNF cytokines that mediate further innate and adaptive immune responses targeted against intracellular pathogens.⁹ This is particularly relevant for TB, where Th1 immunity is considered essential for host protection.^10,11

Encouragingly, recent preclinical studies – including our own – have demonstrated the potential of mRNA vaccines to induce protective immune responses against M. tuberculosis.^12–16 Our group developed an mRNA vaccine encoding for CysVac2, a fusion protein of M. tuberculosis antigens Ag85B and CysD, and demonstrated robust generation of vaccine-specific CD4⁺ T cells producing multiple cytokines (e.g. IFN-γ, IL-2 and TNF).¹² This was associated with significant protection against M. tuberculosis in mice. Similar protective outcomes have been reported by others using different mRNA constructs.^13,15

However, these findings come with caveats. In our extended infection model, the CysVac2 mRNA vaccine failed to provide sustained protection beyond the acute phase of infection.¹² This suggests that current mRNA formulations may be suboptimal for long-term control of TB. Moreover, the field still lacks a validated correlate of protection (CoP) for TB,³ complicating the interpretation of immune readouts in animal models and limiting predictive value for human efficacy. Although mRNA platforms show promise, significant gaps remain in translating preclinical findings into durable, clinically relevant protection against TB.

mRNA vaccines for tuberculosis: additional challenges

Ongoing efforts to define CoPs against TB has garnered interest in lung mucosal immunity, particularly the role of resident memory T (T_RM) cells. T_RM cells are antigen-experienced memory T cells located in peripheral tissues, and are therefore well posed to rapidly respond to pathogens at their site of infection.¹⁷ The induction of vaccine-specific CD4⁺ T_RM cells in the lung has correlated with protection against M. tuberculosis challenge across diverse vaccine platforms. For example, Flórido et al.¹⁸ used an intranasal influenza vector vaccine to induce polyfunctional, Th1-skewed (IFN-γ⁺, TNF⁺, IL-2⁺) CD4⁺ T_RM cells in the lung parenchyma and demonstrated that protection was independent of circulating T cell populations. Intranasal administration of BCG also induced protective lung T_RM cells expressing markers of Th-17 polarisation.¹⁹ Similarly, intratracheal delivery of the CysVac2 protein with adjuvant led to the formation of functionally analogous T_RM cells in the lung.²⁰ Therefore, the induction of lung T_RM cells is thought to be essential for robust protection against TB.

By contrast, mRNA vaccines appear to have limited capacity to induce lung-resident T_RM cells (Fig. 1). This has been observed consistently across both human and animal studies. For instance, following vaccination with the widely used BNT162b COVID-19 mRNA vaccine, T_RM cells were either absent, or present at very low frequencies in the lungs of vaccinated individuals and mice.^9,21 Furthermore, in one study where lung T_RM cells were detected post-mRNA vaccination, their frequencies were significantly lower than in individuals who had recovered from infection, and polyfunctional CD4⁺ and CD8⁺ T cells were virtually absent.²² These findings suggest that in their current form, mRNA vaccines display a limited capacity to establish lung-localised T cell populations considered critical for effective TB protection, and may explain the lack of sustained protection against the bacterium.

Fig. 1.

The ability of mRNA vaccines to induce protective immune responses against TB. mRNA vaccines can induce robust systemic responses including polyfunctional Th1 (IL-2⁺, TNF⁺, IFN-γ⁺) and Th17 (IL-17⁺) effector memory T (T_EM) cells. These circulating T cells can traffic through the lung and contribute to anti-TB immunity. Lung-resident T (T_RM) cells, positioned at the site of infection, are also thought to play a critical role in protection against TB. It remains unclear, however, whether current mRNA vaccine platforms are capable of inducing T_RM cells with a phenotype associated with durable TB immunity.

Prospects for mRNA-based tuberculosis vaccines

mRNA vaccines are well established to induce robust systemic immune responses when delivered intramuscularly. However, their inability to induce T_RM cells in the lung restricts immunity against TB, where localised mucosal immunity is considered essential. Thus, new strategies are needed to improve the ability of mRNA vaccines to establish protective lung immunity.

Preclinical vaccines have shown that vaccines capable of inducing lung T_RM cells typically use intrapulmonary delivery routes, such as intranasal and intratracheal administration. Attempts to apply these methods to mRNA vaccines have been made; however, lipid nanoparticle (LNP) formulations are highly inflammatory when delivered into the lung, leading to significant morbidity and mortality in animal models.²³ Thus, there is interest in the development of new LNP formulations that are safe for mucosal delivery.^24,25 Although a subset of LNP formulations have successfully elicited mucosal antibody responses,^26,27 reports of robust T_RM cells induction have been limited. Additionally, intrapulmonary vaccination alone often results in limited systemic immunity, which may be insufficient for protection against extrapulmonary or disseminated TB.

An alternative approach involves alerting the physicochemical properties (i.e. size or surface charge) of mRNA vaccine formulations to achieve tissue-specific targeting following intramuscular vaccination. Cationic LNPs, for example, have been shown to promote concentrated mRNA expression in the lung following systemic administration.^28,29 However, it is unclear if this strategy enhances vaccine-specific immune responses and protective lung-resident memory. Additionally, there are concerns regarding the toxicity and reactogenicity of some cationic LNPs, including associations with clotting and other adverse event.³⁰ Therefore, safety profiling of mRNA vaccines must be a priority in the development of next-generation LNP formulations.

Künzli and colleagues have shown that these challenges can, at least in part, be addressed.³¹ Using a self-amplifying mRNA platform and a novel, low reactogenicity dendron based nanoparticle, they were able to induce lung T_RM cells in mice by intramuscular and intranasal vaccination. In addition, they demonstrated the potential for combined vaccine strategies, using an initial intramuscular dose followed by an intranasal boost to first induce systemic memory then draw cells into the lung. This study provides proof-of-concept that rational design of both the mRNA platform and delivery system can support mucosal T cell immunity, while avoiding the toxicity seen with earlier formulations.

Conclusion

Although mRNA vaccines offer speed, scalability and strong systemic immunity, their current formulations fall short in eliciting the lung-resident T cell responses considered essential for durable TB protection. Overcoming this will require innovation in both delivery routes and lipid formulations, efforts that are already showing promise and will be critical to realising the potential of mRNA vaccines in TB control.