Departments & Divisions
Currently seeking M.S. & Ph.D. students.
Department of Microbiology, Immunology & Molecular Genetics
The overall research goal of the Bunnik laboratory is to understand the development and maintenance of protective antibody responses in malaria-experienced individuals and to use this knowledge towards 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 B cells responses to Plasmodium falciparum infection. Using high-parameter flow cytometry and single-cell sequencing, we aim to better understand how B cells respond to different antigens and which B cell responses underlie long-lived immunological memory. Using B cell receptor (BCR) sequencing to track clonally related cells, we investigate the development and differentiation pathways of B cells in Plasmodium-exposed individuals.
An additional focus of the lab is the regulation of gene expression in the malaria parasite, Plasmodium falciparum, by epigenetic, transcriptional, and post-transcriptional mechanisms
Research in the Bunnik Lab is aimed at understanding the nature and the development of protective immune responses to malaria, with the overall goal to design an effective malaria vaccine. In endemic regions, malaria exposure results in an immune response that protects against clinical disease. However, this protective immunity takes years to develop, leaving children highly susceptible to severe disease and death. A better understanding of this immunological protection will facilitate malaria vaccine development. Our approach to increasing our knowledge about protective immune responses is to learn from nature, i.e. to study immune responses elicited as a result of natural infection.
NIH/NIAID: R01 AI153425 - Defining conserved epitopes on polymorphic malaria antigens (02/19/21 - 01/31/26)
Gonzales SJ, Clarke K, Batugedara G, Garza R, Braddom AE, Reyes RA, Ssewanyana I, Garrison KC, Ippolito G, Greenhouse B, Bol S, Bunnik EM. A molecular analysis of memory B cell and antibody responses against Plasmodium falciparum merozoite surface protein 1 in children and adults from Uganda. Frontiers in Immunology (2022) 2;13:809264
Reyes RA, Clarke K, Gonzales SJ, Cantwell AM, Garza R, Catano G, Tragus R, Patterson T, Bol S, Bunnik EM. SARS-CoV-2 spike-specific memory B cells express higher levels of T-bet and FcRL5 after non-severe COVID-19 as compared to severe disease. PLOS ONE (2021) 16(12): e0261656
Gonzales SJ, Bol S, Braddom AE, Sullivan RT, Reyes RA, Ssewanyana I, Eggers E, Greenhouse B, Bunnik EM. Longitudinal analysis of FcRL5 expression and clonal relationships in classical and atypical memory B cells following malaria. Malaria Journal (2021) 20(1): 435
Braddom AE, Bol S, Gonzales SJ, Reyes RA, Musinguzi K, Nankya F, Ssewanyana I, Greenhouse B, Bunnik EM. B cell receptor repertoire analysis in malaria-naive and malaria-experienced individuals reveals unique characteristics of atypical memory B cells. mSphere (2021) 6(5):e00726-21
Gonzales SJ, Reyes RA, Braddom AE, Batugedara G, Bol S, Bunnik EM. Naturally acquired humoral immunity against Plasmodium falciparum malaria. Frontiers in Immunology (2020) 11:594653
Braddom AE, Batugedara G, Bol S, Bunnik EM. Potential functions of atypical memory B cells in Plasmodium-exposed individuals. International Journal for Parasitology (2020) 50(13):1033-1042
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.