Extreme Polymorphism in a Vaccine Antigen and Risk of Clinical Malaria: Implications for Vaccine Development

Abstract

Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine. †To whom correspondence should be addressed. cplowe@medicine.umaryland.edu. * Present address: University of Maryland Dental School, Baltimore, MD 21201, USA. Author contributions: S.L.T. conceived the study concept, assisted with the sequencing, analyzed the data, and wrote the paper. D.C., M.A.T., K.T., A.N., and O.K.D. designed and conducted the malaria incidence study. A.H.B. determined the crystal structure of the AMA-1 protein and contributed to writing the paper. M.P.C. and A.A.E. assisted with the data analysis and contributed to writing the paper. A.O. assisted with the sequencing and contributed to writing the paper. A.A.D. contributed to writing the paper. C.V.P. designed the malaria incidence study, helped develop the study concept, assisted with the data analysis, contributed to writing the paper, and provided funding for study activities. SUPPLEMENTARY MATERIAL

Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1

“…Researchers have explored two approaches to tackle the issue of antigenic variation in AMA1: polyvalent formulations using multiple strains of AMA1 (47,48) and chimeric variants of AMA1 (51,68), which incorporate a subset of high-frequency polymorphisms into a small set of constructs. In both cases, allelic coverage is the guiding principle, meaning that the vaccine should incorporate as broad a range of polymorphic variation as is possible (43). The results of this theoretical study, along with the experimental results of Dutta et al (47), present an alternate approach: to directly enhance the cross-reactivity of the Ab response through the use of a polyvalent formulation that biases affinity maturation toward shared or cross-reactive epitopes.…”

“…A recent phase 2b AMA1 vaccine trial in 1-6-y-old children in Mali found 64% efficacy against malaria caused by vaccine-like strains, underscoring its potential as a malaria vaccine (41). Unfortunately, AMA1 displays immense antigenic variation: .10% of its residues are polymorphic, and .200 unique haplotypes have been identified (42,43). A crystal structure of AMA1 reveals that the protein consists of three domains that present two immunologically distinct regions: a conserved face, consisting of a cluster of largely conserved epitopes along domain I and III, and a polymorphic face, consisting of a cluster of highly polymorphic epitopes along domain II (44,45).…”

“…A crystal structure of AMA1 reveals that the protein consists of three domains that present two immunologically distinct regions: a conserved face, consisting of a cluster of largely conserved epitopes along domain I and III, and a polymorphic face, consisting of a cluster of highly polymorphic epitopes along domain II (44,45). Previous studies suggested that no fewer than 6-10 strains of AMA1, and possibly many more, must be included in a polyvalent vaccine to provide sufficient allelic coverage for broad protection (42,43,46). However, several studies developed polyvalent formulations of AMA1, using two to six strains, and demonstrated significant cross-reactivity and protection relative to the monovalent vaccine of any single strain (47)(48)(49)(50).…”

Far from the Madding Crowd: the Molecular Basis for Immunological Escape ofPlasmodium falciparum

“…T h e s e polymorphic residues surround a hydrophobic pocket suggested as being critical for AMA-1 function. Domain I has the major polymorphic sites, grouped into 3 clusters (C1, C2 and C3); regarding C1-L (loop containing residues 196, 197, 199, 200, 201, 204, 206 and 207), 1F9 mAb binds in loop Id and most human antibodies react against it (Bai et al, 2005;Dutta et al, 2007;Takala et al, 2009;Ouattara et al, 2013;Harris et al, 2014). However, once the epitope has been recognised it inhibits in vitro invasion in a strain-specific manner, as in the case of 1F9 mAb inhibiting in vitro growth of 3D7 and D10 parasite strains, but not HB3 or W2mef where a single aa substitution at the most highly polymorphic site (residue 197) in AMA-1 abolishes 1F9 mAb binding (Coley et al, 2006), thereby limiting the effectiveness of these antigens as vaccine components.…”

The Impact of Immune Responses on the Asexual Erythrocytic Stages of Plasmodium and the Implication for Vaccine Development

“…A clinical study in which volunteers were challenged by mosquito bite revealed that vaccination with AMA-1 was unable to provide sterile protection and only yielded a limited delay in the development of parasitemia in vaccinees compared to challenge control subjects (Spring et al, 2009). Characterization of the AMA-1 gene sequence revealed a fatal characteristic of this antigen which will likely preclude its use as a malaria vaccine in the field: well over 150 allelic variants of the antigen have been reported (Takala et al, 2009) and humoral responses against AMA-1 indicate that immunity is allele-specific and therefore, an AMA-based vaccine would primarily provide strain-specific protection at best. Efforts are underway to develop AMA-1 vaccines that induce allele-cross-reactive responses to overcome this limitation (Remarque et al, 2008;Dutta et al, 2010).…”