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. Author manuscript; available in PMC: 2019 Aug 1.
Published in final edited form as: Curr Opin Pharmacol. 2018 Jun 8;41:128–136. doi: 10.1016/j.coph.2018.05.012

Exploiting vita-PAMPs in vaccines

J Magarian Blander 1,2,3,4,5,*, Gaetan Barbet 1,2
PMCID: PMC6110613  NIHMSID: NIHMS974107  PMID: 29890457

Abstract

Live attenuated vaccines elicit stronger protective immunity than dead vaccines. Distinct PAMPs designated as vita-PAMPs signify microbial viability to innate immune cells. Two vita-PAMPs have been characterized: cyclic-di-adenosine-monophosphate (c-di-AMP) and prokaryotic mRNA. c-di-AMP produced by live Gram-positive bacteria elicits augmented production of STING-dependent type-I interferon, whereas prokaryotic mRNA from live bacteria is detected by TLR8 enabling discrimination of live from dead bacteria. Bacterial mRNA from live Gram-negative bacteria triggers a heightened type-I interferon and NLRP3 inflammasome response. By mobilizing unique viability-associated innate responses, vita-PAMPs mobilize adaptive immunity that best elicits protection, including follicular T helper cell and antibody responses. Here, we review the molecular mechanisms that confer the unique adjuvanticity of vita-PAMPs and discuss their applications in vaccine design.

Keywords: Vita-PAMP, TLR8, inflammasome, type I interferon, monocyte, phagocyte, vaccine, follicular T helper cell, germinal center, antibody response

Introduction

Vaccination is one of the most effective strategies to prevent infectious diseases and pandemics. It involves administration of a live attenuated or dead pathogen, or component thereof, to generate strong and specific immunity that protects against subsequent encounter with that pathogen. Historically, live attenuated pathogens have been used to successfully vaccinate populations, often with a single dose, leading to lasting protective immunity and disease control. The first vaccine involved inoculation with live cowpox to prevent smallpox infection [1]. Other live attenuated vaccines have followed suit including an oral typhoid vaccine consisting of a live attenuated strain of Salmonella typhi T21A, a polio virus vaccine (OPV), a rotavirus vaccine (RotaShield, ROTARIX, RIT4237 bovine), a Shigella flexneri 2a SC602 vaccine, a live attenuated intranasal influenza vaccine, a live attenuated yellow fever vaccine (YF-17D), as well as vaccines for chickenpox (Varicella), Rabies and tuberculosis (BCG) [2,3].

Despite efficacy, live vaccines face many challenges. In developed countries, fears of vaccination and vaccine refusal, particularly those vaccines based on live attenuated microorganisms, have resulted in poor vaccine coverage and gaps in protection of the general public [47]. The preservation and delivery of live vaccines require infrastructure often not available in developing countries. More recent vaccine strategies consist of dead pathogens, novel peptides, and recombinant proteins. While these are more stable and have fewer side effects, they are less effective and generally fail to convey long-lasting immunity requiring multiple boosters [8]. The exact nature of the cellular and molecular mechanisms by which broad-based immunity is elicited is elusive [9], and vaccine design has mostly followed Pasteur’s principles: “isolate, inactivate, and inject” [3,10].

Adjuvants increase the immunogenicity of vaccines. Despite the variety of compounds with adjuvant properties, only a handful of adjuvants have been licensed for human use including aluminum salts (used in DTaP vaccines, the pneumococcal conjugate vaccine and hepatitis B vaccines), MF59 (an oil-in-water emulsion of squalene oil used in the influenza vaccine Fluad for the elderly), CpG 1018 (used in the hepatitis B vaccine Heplisav-B), GlaxoSmithKline Biologicals AS03 (an oil-in-water emulsion of D,L-α-tocopherol and squalene with polysorbate 80 emulsifier used in an H5N1 influenza vaccine), AS04 (an aluminum hydroxide with monophosphoryl lipid A (MPL) combination used in the cervical cancer vaccine Cervarix), and AS01B (used in the shingles vaccine Shingrix, comprised of MPL, a purified fat-like substance, and QS-21 from the bark of the Quillaja Saponaria tree) [11]. There is a constant need for new adjuvants for safer protective vaccines. A comprehensive understanding of the molecular basis underlying the efficacy of live vaccines will guide the design of new adjuvants that specifically target the relevant immune pathways and induce optimal long-lived protective immunity.

Vita-PAMPs: Molecular signatures of microbial viability

The innate immune system can not only discriminate self from non-self via recognition of pathogen associated molecular patterns (PAMPs) [12,13], but it can also discriminate between live and dead microorganisms through a distinct set of PAMPs called vita-PAMPs associated uniquely with live microorganisms [14,15]. Vita-PAMPs are detected in combination with classic PAMPs such as lipopolysaccharide (LPS) and DNA, which are shared between live and dead microorganisms [14,15]. Detection of PAMPs in the absence of vita-PAMPs signifies a dead microbe, whereas detection of a vita-PAMP alongside a PAMP signifies live microbes and mediates a heightened immune response not warranted to dead microorganisms [15]. The activity of virulence factors associated with live pathogens elicits a vigorous immune response, but continued expression of virulence factors becomes unnecessary once a pathogen has gained access to sterile tissues. Targeting microbial viability per se independently of virulence factors is a far better strategy for the immune system to eliminate the infectious threat and protect tissue integrity. Two vita-PAMPs, bacterial mRNA in the context of a response to live Gram-negative bacteria [14,16,17], and c-di-AMP in the context of a response to live Gram-positive bacteria [18] have been identified so far. A broad array of vita-PAMPs likely exists, and much like PAMPs, vita-PAMPs may be unique to different classes of microorganisms according to the specific cellular processes conducted by each class.

Vita-PAMPs mobilize distinct cell-autonomous innate immune responses

Detection of live avirulent bacteria by antigen presenting cells (APC), macrophages or dendritic cells (DC), elicits augmented levels of type-I interferon (IFN) production compared to dead bacteria, and this is dependent on bacterial mRNA for Gram-negative bacteria and cyclic-di-adenosine monophosphate (c-di-AMP) for Gram-positive bacteria [14,18] (Figure 1). Murine APC also secrete IL-1β in response to avirulent live but not dead Gram-negative bacteria, but they do not do so to avirulent live Gram-positive bacteria [14,18] (Figure 1). Similarly, detection of live avirulent Gram-negative Escherichia coli by human CD14+CD16 monocytes elicits a distinct transcriptional response compared to killed E. coli, including IL12B and TNF [17]. An IFN-inducible gene, IFIT2 is differentially transcribed in response to live E. coli, and so are several genes positively regulated by IFN-γ [17]. IL-1β, IL-12 and TNFα are produced by human monocytes uniquely in response to live but not dead E. coli, Bacillus subtilis and Mycobacterium bovis BCG, as well as killed E. coli supplemented with bacterial RNA or CL075, an agonist for the single-stranded RNA receptors Toll-like receptor (TLR)7 and TLR8 [17].

Figure 1. The molecular and cellular events subsequent to vita-PAMP recognition.

Figure 1

In mice, mononuclear phagocytes respond to microbial viability. Live Gram-positive and Gram-negative bacteria contain vita-PAMPs, such as bacterial mRNA and c-di-AMP, respectively, which serve as the molecular signatures of bacterial viability. Both vita-PAMPs induce type-I interferon through the Toll-like receptor adaptor TRIF for Gram-negative bacteria and through the stimulator of interferon genes (STING) and the kinase TBK1 for Gram-positive bacteria. In the response to phagocytosed Gram-negative bacteria, bacterial mRNA which gains access to the cytosol activates the NLRP3 inflammasome (1a) and IFNAR activation by TRIF-dependent IFN-β (1b) licenses NLRP3 inflammasome activation by promoting Caspase-11 expression (2) and interaction with caspase-1 to mediate IL-1β cleavage and secretion (3). In the response to phagocytosed Gram-positive bacteria, c-di-AMP gains access to STING on endoplasmic reticulum(ER) membranes to induce ER stress and subsequent ER-stress induced autophagy to orchestrate translocation of STING to autophagosomal membranes, TBK1 activation, and induction of type-I IFN production.

Dissection of the innate signaling pathways mobilized in APC upon detection of vita-PAMPs during phagocytosis of bacteria has provided a mechanistic basis for the differential production of inflammatory cytokines to live versus dead bacteria. During the innate response of murine APC to Gram-positive bacteria, direct detection of c-di-AMP by the receptor stimulator of interferon genes (STING) culminates in a TBK1 and IRF3 dependent type-I IFN response [18]. STING detection of c-di-AMP triggers an elaborate cell-autonomous stress response that begins with rapid phosphorylation of effectors of the endoplasmic reticulum (ER) stress response, PERK and IRE-1α, and subsequent inactivation of the mechanistic target of rapamycin mTORC1 [18]. These events in turn precipitate autophagy of the ER (reticulophagy or ER-phagy), which translocates STING from the ER to autophagosomes as a prerequisite to its ability to initiate type-I IFN signaling [18] (Figure 1). On the other hand, murine APC detection of bacterial mRNA released during phagosomal degradation of internalized live Gram-negative bacteria elicits an augmented IRF3-mediated IFN-β response dependent on the TLR adaptor TIR-domain-containing adapter-inducing interferon-β (TRIF) [14] (Figure 1). Despite the differences in the innate signaling pathways mobilized downstream of live Gram-positive versus Gram-negative bacteria, detection of vita-PAMPs optimizes protection against infection in mice [14,16,18].

Innate recognition of bacterial RNA varies according to the species and cells studied [19]. Human monocytes sense bacterial RNA through endosomal TLR8 while both human and murine plasmacytoid DC do so through TLR7 [1923]. TLR8 is recruited to bacteria-carrying phagosomes [20,22], and senses bacterial RNA during infection with Group B Streptococci or Borellia burgdorferi to induce IL-6, IL-12 and IFN-β [20,21]. Human monocytes uniquely respond to live E. coli and bacterial RNA through TLR8 and MyD88 with higher levels of IL-12 and TNF-α production than to killed E. coli (Figure 1) [17]. This pathway is conserved in porcine cells [17], but not functional in murine cells where TLR8 is suggested to be non-responsive [24]. MyD88 is also involved in sensing bacterial RNA by murine bone marrow-derived macrophages and DC, but in this case, Unc93B1, which delivers nucleic acid sensing TLRs from the ER to endolysosomes, and TLR13 have been implicated [19]. Both mouse TLR13 and human TLR8 are sensors for bacterial 23S ribosomal RNA [19,22]. Whether Unc93B1 and TLR13 can specifically sense microbial viability has not been tested.

In mice and humans, detection of live but not dead Gram-negative bacteria also elicits IL-1β secretion [14,17,18] (Figure 1). In murine macrophages and DC, this is dependent on detection of bacterial mRNA and activation of the NLRP3 inflammasome irrespective of virulence factor expression [14]. This feature is unique to Gram-negative and not Gram-positive bacteria [18], and is likely dependent on concomitant cytosolic detection of the Gram-negative PAMP LPS [25], rather than inherent differences between RNA from Gram-positive versus Gram-negative bacteria [18,19]. While MyD88 is important for the transcriptional induction of Il1b and Nlrp3, murine NLRP3 inflammasome activation and IL-1β secretion by live Gram-negative bacteria and bacterial mRNA is dependent on TRIF [14]. TRIF-dependent IFN-β licenses NLRP3 inflammasome activation through transcriptional induction of pro-caspase-11 [25]. The human NLRP3 inflammasome has also been reported to sense bacterial RNA including ribosomal, messenger, transfer, and small RNA [26], but its involvement in the ability of human APC to sense microbial viability has not been tested.

It is worthwhile noting here the pre-clinical success of mRNA vaccines for cancer and infectious disease [27]. Although mRNA vaccines were initially designed to induce expression and presentation of antigens in APC, they often contain double-stranded RNA contaminants, formed during in vitro transcription, that contribute to their adjuvanticity by eliciting type-I IFN production [28]. Recent vaccine formulations have enhanced the adjuvanticity of these mRNA vaccines to induce robust antigen specific protective antibody and cytotoxic T cell responses [29]. A number of ongoing clinical trials for Rabies, influenza virus, and Zika virus use lipid nanoparticles as a delivery tool, and notably interim findings from the mRNA vaccine against H10N8 and H7N9 influenza viruses report antibody titers above the expected protective threshold [29].

Bacterial viability and bacterial RNA elicit TFH responses in mice and humans

Characterization of the innate response to vita-PAMPs has set the stage for investigating their use as unique adjuvants that could augment the performance of dead vaccines to the levels achieved by equivalent live vaccines. As proof of principle, addition of bacterial RNA to a dead vaccine comprised of killed E. coli elevated serum titers of class-switched antibodies to those induced by a counterpart live vaccine [14]. Identification of the vita-PAMP as well as the viability-associated innate pathways and effector cytokines involved enabled a targeted and systematic evaluation of the impact on the ensuing adaptive immune response [16,17]. This led to the discovery that innate detection of bacterial RNA as the vita-PAMP signifying microbial viability is a particularly robust signal for differentiation of both murine and human follicular T helper (TFH) cells [16,17]. A comparison of three E. coli vaccines in mice – live, dead and a vita-PAMP-supplemented dead vaccine (vita-vaccine) – showed that only the live and vita vaccines induced a TFH response [16]. These vaccines also activated most subsets of B cells including B1, marginal zone and the predominant follicular B2 cells. Vaccination of domestic pigs with the live but not dead form of an attenuated Salmonella vaccine increased the frequency of TFH cells. Human monocytes also promoted TFH cell differentiation in culture after stimulation with live but not dead E. coli as well as the TLR8 agonists CL075 and R848 [17]. The TFH response in mice and pigs correlated with augmented germinal center formation, IgG class-switching, and frequencies of plasma cells in response to the live vaccine [16,17], and in mice to the vita-vaccine as well [16]. Similarly, human TFH cells induced by E. coli-stimulated monocytes promoted plasma cell differentiation of co-cultured B cells and production of IgG [17]. These studies collectively show that prokaryotic RNA as a proxy of bacterial viability comprises a physiological innate trigger for TFH differentiation in both mice and humans (Figure 2). They provide a mechanistic basis for the characteristic ability of live vaccines to elicit higher serum levels of class-switched antibodies [16,17]. They also identify a much-needed pathway for the rational design of vaccines that succeed in eliciting robust TFH responses, which in turn directly promote development of the antibody response.

Figure 2. Cellular activation after sensing the vita-PAMP bacterial mRNA.

Figure 2

Bacterial mRNA recognition by monocytes increases follicular T helper cell differentiation, enhances IgG antibody response through higher follicular T helper cells and higher germinal center formation for mouse, human, and porcine (not shown) models. In mice, TFH cell differentiation by a live vaccine comprised of Gram-negative bacteria or a dead counterpart vaccine supplemented with bacterial mRNA is dependent on TRIF signaling and downstream cytokines IFN-β and IL-1β. Both cytokines act directly on mouse T cells to promote full TFH differentiation. In the human model, activation of the MyD88-dependent TLR8 receptor on monocytes induces the expression of IL-12, the main cytokine promoting human TFH cell differentiation, and induces TFH differentiation of co-cultured activated CD4 T cells. Human IL-1β is also produced in response to live bacteria by a yet to be explored inflammasome pathway and has additive effects on TFH differentiation. Despite the different cytokine requirements for TFH cell differentiation, detection of bacterial viability by either mouse or human monocytes serves as the physiological trigger for TFH cell differentiation and subsequent B cell class-switching and IgG production.

Whether the vita-PAMP c-di-AMP similarly augments TFH cell differentiation remains to be assessed. Nonetheless, cyclic-di-nucleotides (CDNs) such as c-di-AMP, c-di-GMP, and c-GAMP all serve as STING agonists and have been highly successful in inducing potent antibody and T cell responses in experimental models of vaccination [30]. Their potent adjuvanticity may stem from their ability to relay microbial viability to the innate immune system. Research and development surrounding STING agonists is presently a top priority for pharmaceutical companies, many of which have several cancer immunotherapy clinical trials already underway using synthetic CDN STING agonists alone or in combination with the checkpoint blockade inhibitor anti-PD1.

How vita-PAMPs elicit TFH cell differentiation in mice and humans

TFH cells have common and divergent requirements for differentiation in mice versus humans [31]. Detection of the vita-PAMP bacterial mRNA by either human or murine APC fulfills the criteria for instructing TFH differentiation in both species [16,17]. In both mouse and human APC, PAMPs shared by live and dead bacteria elicit similar levels of certain cytokines such as IL-6. However, live and not dead bacteria uniquely induce IL-1β production by human monocytes [17], and while dead bacteria can elicit IL-12 production [17,32], the levels produced in response to live bacteria are significantly higher than those to dead bacteria [17]. IL-12, and to a lesser extent IL-23, is the best inducer of ICOS, CXCR5, Bcl-6 and IL-21 expression by activated human CD4 T cells [3234]. TGF-β promotes human TFH differentiation by either IL-12 or IL-23, and the additional presence of IL-1β, secreted uniquely in response to live bacteria [17], further drives commitment towards the TFH fate [35]. TLR8-MyD88 signaling augments IL-12 production in response to live bacteria [17]. For both human and porcine APC, the TLR8 agonists bacterial RNA, CL075 and R848 trigger the highest levels of IL-12 and TFH differentiation, while silencing monocyte TLR8 and MyD88 expression has the opposite effect [17]. TFH differentiation was unaffected by the presence or absence of IL-6, IL-27, or IFN-β in human monocyte-CD4 T cell co-cultures, and neutralization of IL-1β partially inhibited TFH cell differentiation [17], consistent with its promoter role in human TFH differentiation [35]. Notably, hypermorphic TLR8 polymorphism in humans is associated with improved BCG vaccine-mediated protection [17], and IL-12 receptor β1 deficiency is associated with a lower number of circulating TFH cells and lymph node germinal centers, as well as lower avidity, albeit normal levels, of circulating antibodies [34]. Collectively, these results point to TLR8 agonists as potential TFH cell skewing adjuvants.

In mice, IL-12 induces both Il21 and Bcl6 via the transcription factor STAT4 prior to CD4 T cell commitment to either TH1 or TFH cell fates [36]. The cytokines which play dominant roles in skewing towards mouse TFH cell differentiation are the STAT3 activating cytokines, IL-6, IL-21 and IL-27 [37,38], although TFH differentiation was reduced but not abrogated in the combined absence of IL-6 and IL-21 during an acute infection with lymphocytic choriomeningitis virus (LCMV) [39]. Additional cytokines such as IL-1β may be important. LCMV and other viruses such as influenza A virus, elicit inflammasome activation and IL-1β production in mice [4042]. IL-1β and IL-1R1 are also essential in the early immune response to Mycobacterium tuberculosis and Candida albicans [43]. IL-1β is secreted in response to bacterial viability [14,17], which also triggers TFH cell differentiation in both mice and humans [16,17]. Linking the highly inflammatory and tightly regulated production of IL-1β to an adaptive TFH response that best drives neutralizing antibody production would be beneficial to the host. Indeed, dissection of the mechanisms behind the higher antibody titers elicited by live vaccines has supported a role for IL-1β as a critical mediator of TFH differentiation.

Because of the central role of TRIF in orchestrating the innate response to live Gram-negative bacteria and bacterial mRNA in mice, vaccine-induced TFH responses are critically dependent on TRIF and also rely on IRF3-mediated IFN-β and caspases 1 and 11 dependent IL-1β production. Patrolling CX3CR1+CCR2 monocytes isolated from the spleen produce IL-1β within a few hours of injecting live E. coli, and these monocytes instruct the TFH response [16]. IFN-β and IL-1β elicited by live bacteria and bacterial RNA play non-redundant roles in promoting TFH cell differentiation [16]. In mice, IL-1β induces expression of the TFH-specific transcription factor Bcl6 and TFH-specific marker CXCR5 through IL-1R1 on T cells [16], and its injection during immunization significantly increases TFH cell generation [16,44]. On the other hand, TRIF-dependent IFN-β plays two distinct roles in TFH differentiation; to mediate inflammasome activation and innate IL-1β secretion through type I interferon receptor (IFNAR) engagement on APC [25,45], and to promote TFH production of IL-21 through IFNAR engagement on T cells [16] (Figure 2). Notably, type IIFN induces STAT1 binding to the Bcl6 locus in activated CD4 T cell cultures to sustain its expression but fails to induce IL-21 production on its own unless combined with IL-6 [46]. In the murine response to vaccination when cytokines such as IL-12 and IL-6 are also present, the specific and hierarchical induction of IFN-β and IL-1β in response to a live or vita vaccine sets the stage for optimal TFH differentiation. TRIF-dependent IFN-β licenses NLRP3 inflammasome and caspase-1 activation by upregulating and activating caspase-11 through IFN-β/IFNAR signaling [25]. As such, IL-1β cleavage is downstream of and dependent on IFN-β production and availability. Addition of IL-1β, whose secretion by human monocytes is also significantly higher in response to live bacteria [17], to the combination of IL-12, TGF-β, and IL-6 in activated human CD4 T cell cultures, yields the highest expression of the master TFH transcription factor BCL-6 [35].

RIG-I-dependent type-I IFN produced by dermal human CD14+ DC in response to Dengue virus, which initiates infection through a mosquito bite, induces IL-27 expression through IFNAR signaling, and as such enables the CD14+ DC to instruct TFH differentiation [47]. Interestingly, Dengue virus RNA replication, a proxy for viral viability, is necessary for production of both type-I IFN and IL-27 and is a critical determinant of the formation of IL-21-producing CXCR5+PD1+BCL6+ human TFH cells [47]. Through IFNAR signaling on both mouse and human APC, type-I IFNs thus play an important role in instructing TFH differentiation by controlling the secretion of additional key cytokines such as IL-1β and IL-27 that act directly on CD4 T cells to drive their differentiation into TFH cells [16,47,48]. By specifically promoting TFH differentiation at different steps during the response to microbial viability, both the IRF3/IFN-β and inflammasome/IL-1β pathways impact long-term protection, germinal center formation and IgG class-switched antibody responses in vaccinated mice [16], consistent with observations in other models [45,49]. The inflammasomes and IL-1R1 signals are also necessary for eliciting mucosal IgA and systemic IgG responses during respiratory infection with influenza A virus [50].

The unique adjuvant properties of the vita-PAMP bacterial mRNA stem from its ability to induce both type-I IFN and inflammasome pathways. The contribution of inflammasome activation and IL-1β secretion to the TFH cell response is in line with previous observations in mice including dependence of the potent humoral response elicited by aluminum-containing (alum) adjuvants on NLRP3 inflammasome activation [51,52], the enhancement of antibody production through IL-1 administration during immunization [5355], and the significant impairment of antibody production noted in IL-1α/β-deficient mice [56,57]. The attribution of alum adjuvanticity to the NLRP3 inflammasome has been contested, and the oil-in-water emulsion MF59 also works independently of NLRP3 [5860]. Nonetheless, many particulate adjuvants that induce potent humoral responses are IL-1β inducers by both mouse and human APC [43]. The collective experimental evidence, at least so far in mice, supports the use of inflammasome activating adjuvants in vaccine design [43]. Whether NLRP3 inflammasome activation also promotes TFH responses in humans remains to be formally tested.

CONCLUDING REMARKS

Continued research is necessary to characterize more molecules with vita-PAMP properties as well as to better understand the mechanisms through which microbial viability signals are communicated to different cells of the immune system. For example, different APC have been reported to elicit TFH and antibody responses [16,61,62]. Thus, depending on the route of infection and the immunological context of the tissue, different requirements might be necessary to elicit a potent immune response. Elucidating the cellular and molecular events which lead to the robust immunity and long-lived memory that a live vaccine affords will guide the design of new adjuvants. Vita-PAMPs hold the promise of such adjuvants. Their incorporation into already existing killed and subunit vaccines would recapitulate the efficacy of live attenuated vaccines. The unparalleled performance expected of vita-vaccines would lay in their ability to effectively trigger the same immune pathways that live vaccines would mobilize but without their associated safety risks.

HIGHLIGHTS.

  • vita-PAMPs are specific PAMPs expressed only by live microbes

  • vita-PAMPs induce type I IFNs and/or inflammasome activation

  • Bacterial viability and bacterial RNA elicit follicular T helper cell and antibody responses

  • vita-PAMP supplemented (dead) vaccines induce better protection

Acknowledgments

Our work on vita-PAMPs has been supported by the US National Institutes of Health (NIH) grants AI095245, AI127658 and AI080959, the Searle Scholars Award, and the Burroughs Wellcome Fund to J.M.B. G.B. was supported by the Crohn’s and Colitis Foundation. J.M.B. and her laboratory were supported by NIH grants AI123284, AI073899, DK072201, and DK111862.

Footnotes

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Conflict of interest statement

J.M.B has a patent related to bacterial RNA: PCT/US2012/047087 “Use of Bacterial RNA or Structural Motifs thereof as adjuvants for vaccines”.

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