The overall research goal of the Bunnik laboratory is to understand the development and maintenance of protective immunity in malaria-exposed individuals and to use this knowledge for the design of a novel, effective malaria vaccine. To identify targets of protective anti-malaria humoral immunity, we screen and clone antibodies from protected individuals living in malaria-endemic regions, followed by further characterization of antibodies reactive against the malaria parasite.
In addition, we study the development of this humoral immune response over time, in particular with respect to affinity maturation and the development of subsets of non-responsive (or atypical) malaria-specific memory B cells. An additional focus of the lab is the role of chromatin structure and genome organization on gene expression during normal B cell development and in dysfunctional B cells in malaria-exposed individuals.
Bunnik EM, Batugedara G, Saraf A, Prudhomme J, Florens A, Le Roch KG. The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. Genome Biology (2016) 17:147.
Ay F*, Bunnik EM*, Varoquaux N*, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Three-dimensional modelling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Research (2014), 24:974-988. (*contributed equally)
Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG. DNA-encoded nucleosome occupancy is associated with transcriptional levels in the human malaria parasite Plasmodium falciparum. BMC Genomics (2014), 15:347.
Bunnik EM, Chung DWD, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG. Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biology (2013), 14(11):R128.
Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, Frantzell A, Petropoulos CJ, Coakley E, Schuitemaker H, Harrigan PR, van 't Wout AB. Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing. PLoS Pathogens (2011), 7(6):e1002106.
Bunnik EM, Euler Z, Welkers MRA, Boeser-Nunnink BDM, Grijsen ML, Prins JM, Schuitemaker H. Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level. Nature Medicine (2010), 16(9):995-997.