USF Genomics
John Adams
Functional Genomics of Malaria Parasites
Dr. Adams is a malaria researcher in USF’s College of public Health. Broadly, his research focuses on host-parasite interactions and improving the understanding of processes critical for infection and pathogenesis in Plasmodium falciparum and Plasmodium vivax. More specifically, his lab uses genomic studies to better understand key parasite processes and targets. A large scale transposon mutagenesis screen uses whole genome piggyBac insertional mutagenesis of P. falciparum to experimentally identify and validate critical processes and pathways that are novel anti-malarial drug targets. Chemogenetic profiling is used to define critical pathways linked to Artemisinin resistance, understand the mechanism of action of antimalarial drugs, and predict optimal drug combination therapies. Additionally, his lab uses functional genomic studies to identify essential genes of P. falciparum through whole genomic piggyBac mutagenesis and genotype-phenotype associations using forward genetic screens.
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Publications
- Zhang X, Wei H, Zhang Y, Zhao Y, Wang L, Hu Y, Nguitragool W, Sattabongkot J, Adams J, Cui L, Cao Y, Wang Q. Genetic diversity of Plasmodium vivax reticulocyte binding protein 2b in global parasite populations. Parasit Vectors. 2022 Jun 13;15(1):205. doi: 10.1186/s13071-022-05296-6. PMID: 35698238; PMCID: PMC9191549.
- Tipthara, P., Kobylinski, K. C., Godejohann, M., Hanboonkunupakarn, B., Roth, A., Adams, J. H., White, N. J., Jittamala, P., Day, N., & Tarning, J. (2021). Identification of the metabolites of ivermectin in humans. Pharmacology research & perspectives, 9(1), e00712. https://doi.org/10.1002/prp2.712
- De, S. L., May, S., Shah, K., Slawinski, M., Changrob, S., Xu, S., Barnes, S. J., Chootong, P., Ntumngia, F. B., & Adams, J. H. (2021). Variable immunogenicity of a vivax malaria blood-stage vaccine candidate. Vaccine, 39(19), 2668–2675. https://doi.org/10.1016/j.vaccine.2021.03.072
- De, S. L., Ntumngia, F. B., Nicholas, J., & Adams, J. H. (2021). Progress towards the development of a P. vivax vaccine. Expert review of vaccines, 20(2), 97–112. https://doi.org/10.1080/14760584.2021.1880898
- Zhang, M., Wang, C., Oberstaller, J., Thomas, P., Otto, T. D., Casandra, D., Boyapalle, S., Adapa, S. R., Xu, S., Button-Simons, K., Mayho, M., Rayner, J. C., Ferdig, M. T., Jiang, R., & Adams, J. H. (2021). The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite. Nature communications, 12(1), 4563. https://doi.org/10.1038/s41467-021-24814-1
- Oberstaller, J., Zoungrana, L., Bannerman, C. D., Jahangiri, S., Dwivedi, A., Silva, J. C., Adams, J. H., & Takala-Harrison, S. (2021). Integration of population and functional genomics to understand mechanisms of artemisinin resistance in Plasmodium falciparum. International journal for parasitology. Drugs and drug resistance, 16, 119–128. https://doi.org/10.1016/j.ijpddr.2021.05.006
- Chawla, J., Oberstaller, J., & Adams, J. H. (2021). Targeting Gametocytes of the Malaria Parasite Plasmodium falciparum in a Functional Genomics Era: Next Steps. Pathogens (Basel, Switzerland), 10(3), 346. https://doi.org/10.3390/pathogens10030346
- Oberstaller, J., Otto, T. D., Rayner, J. C., & Adams, J. H. (2021). Essential Genes of the Parasitic Apicomplexa. Trends in parasitology, 37(4), 304–316. https://doi.org/10.1016/j.pt.2020.11.007
- Medeiros, C., Moreira, E., Pires, C. V., Torres, L. M., Guimarães, L., Alves, J., Lima, B., Fontes, C., Costa, H. L., Brito, C., Sousa, T. N., Ntumngia, F. B., Adams, J. H., Kano, F. S., & Carvalho, L. H. (2020). Dynamics of IgM and IgG responses to the next generation of engineered Duffy binding protein II immunogen: Strain-specific and strain-transcending immune responses over a nine-year period. PloS one, 15(5), e0232786. https://doi.org/10.1371/journal.pone.0232786
- Wang, C., Gibbons, J., Adapa, S. R., Oberstaller, J., Liao, X., Zhang, M., Adams, J. H., & Jiang, R. (2020). The human malaria parasite genome is configured into thousands of coexpressed linear regulatory units. Journal of genetics and genomics = Yi chuan xue bao, 47(9), 513–521. https://doi.org/10.1016/j.jgg.2020.08.005
- Urusova, D., Carias, L., Huang, Y., Nicolete, V. C., Popovici, J., Roesch, C., Salinas, N. D., Dechavanne, S., Witkowski, B., Ferreira, M. U., Adams, J. H., Gross, M. L., King, C. L., & Tolia, N. H. (2019). Structural basis for neutralization of Plasmodium vivax by naturally acquired human antibodies that target DBP. Nature microbiology, 4(9), 1486–1496. https://doi.org/10.1038/s41564-019-0461-2
- George, M. T., Schloegel, J. L., Ntumngia, F. B., Barnes, S. J., King, C. L., Casey, J. L., Foley, M., & Adams, J. H. (2019). Identification of an Immunogenic Broadly Inhibitory Surface Epitope of the Plasmodium vivax Duffy Binding Protein Ligand Domain. mSphere, 4(3), e00194-19. https://doi.org/10.1128/mSphere.00194-19
- Carias, L. L., Dechavanne, S., Nicolete, V. C., Sreng, S., Suon, S., Amaratunga, C., Fairhurst, R. M., Dechavanne, C., Barnes, S., Witkowski, B., Popovici, J., Roesch, C., Chen, E., Ferreira, M. U., Tolia, N. H., Adams, J. H., & King, C. L. (2019). Identification and Characterization of Functional Human Monoclonal Antibodies to Plasmodium vivax Duffy-Binding Protein. Journal of immunology (Baltimore, Md. : 1950), 202(9), 2648–2660. https://doi.org/10.4049/jimmunol.1801631
- Gnidehou, S., Mitran, C. J., Arango, E., Banman, S., Mena, A., Medawar, E., Lima, B., Doritchamou, J., Rajwani, J., Jin, A., Gavina, K., Ntumngia, F., Duffy, P., Narum, D., Ndam, N. T., Nielsen, M. A., Salanti, A., Kano, F. S., Carvalho, L. H., Adams, J. H., … Yanow, S. K. (2019). Cross-Species Immune Recognition Between Plasmodium vivax Duffy Binding Protein Antibodies and the Plasmodium falciparum Surface Antigen VAR2CSA. The Journal of infectious diseases, 219(1), 110–120. https://doi.org/10.1093/infdis/jiy467
- Pires, C. V.,
Alves, J., Lima, B., Paula, R. B., Costa, H. L., Torres, L. M., Sousa, T. N.,
Soares, I. S., Sanchez, B., Fontes, C., Ntumngia, F. B., Adams, J. H., Kano, F.
S., & Carvalho, L. H. (2018). Blood-stage Plasmodium vivax antibody
dynamics in a low transmission setting: A nine year follow-up study in the
Amazon region. PloS one, 13(11), e0207244.
https://doi.org/10.1371/journal.pone.0207244
Armistead JS, Moraes Barrosa RR, Gibson TJ, Kite WA, Mershon JP, Lambert L, Orr-Gonzalez S, Sá JM, Adams JH, Wellems TE. (2018) Infection of mosquitoes from in vitro cultivated Plasmodium knowlesi H strain. International Journal for Parasitology, 8: 601–610. oi.org/10.1016/j.ijpara.2018.02.004.
- Zhang M, Wang CCQ, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Li S, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, JiangRHY, Adams JH. (2018) Uncovering the essential genome of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science, 360, eaap7847. DOI: 10.1126/science.aap7847.
- Ntumngia FB, Thomson-Luque R, Galusic S, Frato G, Frischmann S, Peabody DS, Chackerian B, Ferreira MU, King CL, Adams JH. (2018) Identification and immunological characterization of the ligand domain of Plasmodium vivax reticulocyte binding protein 1a. Journal of Infectious Diseases. 2018 May 7. doi: 10.1093/infdis/jiy273.
- Roth A, Maher SP, Conway A, Ubalee R, Chaumeau V, Andolina C, Kaba SA, Vantaux A, Bakowski MA, Thomson Luque R, Adapa SR, Singh N, Barnes SJ, Cooper C, Rouillier M, McNamara CW, Mikolajczak SA, Sather N, Witkowski B, Campo B, Kappe SHI, Lanar DE, Nosten F, Davidson S, Jiang RHY, Kyle DE,Adams JH. (2018) A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum. Nature Communications, 9:1837. DOI: 10.1038/s41467-018-04221-9.
- Prinz H, Sattler JM, Roth A, Ripp J, Adams JH, Frischknecht F. (2018) Immunization efficacy of cryopreserved genetically attenuated Plasmodium bergheisporozoites. Parasitology Research 2018 May 24. doi: 10.1007/s00436-018-5937-0.
- Changrob S, McHenry AM, Nyunt MH, Sattabongkot J, Han ET, Adams JH, Chootong P. (2018) Persistence of Long-lived Memory B Cells specific to Duffy Binding Protein in individuals exposed to Plasmodium vivax. Scientific Reports. 2018 May 29;8(1):8347. doi: 10.1038/s41598-018-26677-x.
- Liu C, Mhashilkar AS, Xu S, Chabanon J, Lustigman S, Adams JH, Unnasch TR. (2018) Development of a toolkit for piggyBac-mediated stable integrative transfection of the human filarial parasite Brugia malayi. PLos Neglected Tropical Diseases, 12(5): e0006509. https://doi.org/10.1371/journal.pntd.0006509.
- Thomson-Luque R*, Wang C, Xu S, Ntumngia FB, Xu S, Szerkes K, Conway A, Adapa SR, Barnes SJ, Adams JH, Jiang RHY. (2018) In depth phenotypic characterization of reticulocyte maturation using mass cytometry. Blood Cells, Molecules and Diseases. In press.
- Armistead JS, Adams JH. (2017). Advancing research models and technologies to overcome biological barriers to Plasmodium vivax control. Trends in Parasitology, in press. doi: 10.1016/j.pt.2017.10.009.
- Brancucci, N. M. B., Gerdt, J. P., Wang, C., De Niz, M., Philip, N., Adapa, S. R., … Marti, M. (2017). Lysophosphatidylcholine Regulates Sexual Stage Differentiation in the Human Malaria Parasite Plasmodium falciparum. Cell, 171(7), 1532–1544.e15. https://doi.org/10.1016/j.cell.2017.10.020
- Ntumngia, F. B., Pires, C. V, Barnes, S. J., George, M. T., Thomson-Luque, R., Kano, F. S., … Adams, J. H. (2017). An engineered vaccine of the Plasmodium vivax Duffy binding protein enhances induction of broadly neutralizing antibodies. Scientific Reports, 7(1), 13779. https://doi.org/10.1038/s41598-017-13891-2
- Singh, N., Barnes, S. J., Kennedy, S., & Adams, J. H. (2017). Experimental evaluation of cryopreservative solutions to maintain in vitro and in vivo infectivity of P. berghei sporozoites. PloS One, 12(5), e0177304. https://doi.org/10.1371/journal.pone.0177304
- Adams, J. H., & Mueller, I. (2017). The Biology of Plasmodium vivax. Cold Spring Harbor Perspectives in Medicine, 7(9). https://doi.org/10.1101/cshperspect.a025585
- Demanga, C. G., Eng, J. W. L., Gardiner, D. L., Roth, A., Butterworth, A., Adams, J. H., … Dalton, J. P. (2017). The development of sexual stage malaria gametocytes in a Wave Bioreactor. Parasites & Vectors, 10(1), 216. https://doi.org/10.1186/s13071-017-2155-z
- Kano, F. S., Souza-Silva, F. A., Torres, L. M., Lima, B. A. S., Sousa, T. N., Alves, J. R. S., … Carvalho, L. H. (2016). The Presence, Persistence and Functional Properties of Plasmodium vivax Duffy Binding Protein II Antibodies Are Influenced by HLA Class II Allelic Variants. PLoS Neglected Tropical Diseases, 10(12), e0005177. https://doi.org/10.1371/journal.pntd.0005177
- Thomas, P., Sedillo, J., Oberstaller, J., Li, S., Zhang, M., Singh, N., … Adams, J. H. (2016). Phenotypic Screens Identify Parasite Genetic Factors Associated with Malarial Fever Response in Plasmodium falciparum piggyBac Mutants. MSphere, 1(5). https://doi.org/10.1128/mSphere.00273-16
- Ntumngia, F. B., Thomson-Luque, R., Torres, L. de M., Gunalan, K., Carvalho, L. H., & Adams, J. H. (2016). A Novel Erythrocyte Binding Protein of Plasmodium vivax Suggests an Alternate Invasion Pathway into Duffy-Positive Reticulocytes. MBio, 7(4). https://doi.org/10.1128/mBio.01261-16
- Van Voorhis, W. C., Adams, J. H., Adelfio, R., Ahyong, V., Akabas, M. H., Alano, P., … Willis, P. A. (2016). Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathogens, 12(7), e1005763. https://doi.org/10.1371/journal.ppat.1005763
- Shaw-Saliba, K., Thomson-Luque, R., Obaldia, N. 3rd, Nunez, M., Dutary, S., Lim, C., … Pasini, E. M. (2016). Insights into an Optimization of Plasmodium vivax Sal-1 In Vitro Culture: The Aotus Primate Model. PLoS Neglected Tropical Diseases, 10(7), e0004870. https://doi.org/10.1371/journal.pntd.0004870
- Bronner IF, Otto TD, Zhang M, Udenze K, Wang C, Quail MA, Jiang RHY, Adams JH, Rayner JC. 2016. Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Res 26:980–9.
- Chen E, Salinas ND, Huang Y, Ntumngia F, Plasencia MD, Gross ML, Adams JH, Tolia NH. 2016. Broadly neutralizing epitopes in the Plasmodium vivax vaccine candidate Duffy Binding Protein. Proc Natl Acad Sci U S A 113:6277–82.
- Pradhan A, Siwo GH, Singh N, Martens B, Balu B, Button-Simons KA, Tan A, Zhang M, Udenze KO, Jiang RHY, Ferdig MT, Adams JH, Kyle DE. 2015. Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery. Sci Rep 5:15930.
- Mikolajczak SA, Vaughan AM, Kangwanrangsan N, Roobsoong W, Fishbaugher M, Yimamnuaychok N, Rezakhani N, Lakshmanan V, Singh N, Kaushansky A, Camargo N, Baldwin M, Lindner SE, Adams JH, Sattabongkot J, Prachumsri J, Kappe SHI. 2015. Plasmodium vivax liver stage development and hypnozoite persistence in human liver-chimeric mice. Cell Host Microbe 17:526–35.
- Lupton EJ, Roth A, Patrapuvich R, Maher SP, Singh N, Sattabongkot J, Adams JH. 2015. Enhancing longevity of Plasmodium vivax and P. falciparum sporozoites after dissection from mosquito salivary glands. Parasitol Int 64:211–218.
- Chootong P, McHenry AM, Ntumngia FB, Sattabongkot J, Adams JH. 2014. The association of Duffy binding protein region II polymorphisms and its antigenicity in Plasmodium vivax isolates from Thailand. Parasitol Int 63:858–64.
- Souza-Silva FA, Torres LM, Santos-Alves JR, Tang ML, Sanchez BAM, Sousa TN, Fontes CJF, Nogueira PA, Rocha RS, Brito CFA, Adams JH, Kano FS, Carvalho LH. 2014. Duffy antigen receptor for chemokine (DARC) polymorphisms and its involvement in acquisition of inhibitory anti-duffy binding protein II (DBPII) immunity. PLoS One 9:e93782.
- Campbell CO, Santiago DN, Guida WC, Manetsch R, Adams JH. 2014. In silico characterization of an atypical MAPK phosphatase of Plasmodium falciparum as a suitable target for drug discovery. Chem Biol Drug Des 84:158–68.
- Ntumngia FB, Schloegel J, McHenry AM, Barnes SJ, George MT, Kennedy S, Adams JH. 2013. Immunogenicity of single versus mixed allele vaccines of Plasmodium vivax Duffy binding protein region II. Vaccine 31:4382–8.
- Handa S, Ramamoorthy D, Spradling TJ, Guida WC, Adams JH, Bendinskas KG, Merkler DJ. 2013. Production of recombinant 1-deoxy-d-xylulose-5-phosphate synthase from Plasmodium vivax in Escherichia coli. FEBS Open Bio 3:124–9.
- Auliff AM, Balu B, Chen N, O’Neil MT, Cheng Q, Adams JH. 2012. Functional analysis of Plasmodium vivax dihydrofolate reductase-thymidylate synthase genes through stable transformation of Plasmodium falciparum. PLoS One 7:e40416.
- Ntumngia FB, Schloegel J, Barnes SJ, McHenry AM, Singh S, King CL, Adams JH. 2012. Conserved and variant epitopes of Plasmodium vivax Duffy binding protein as targets of inhibitory monoclonal antibodies. Infect Immun 80:1203–8.
- King CL, Adams JH, Xianli J, Grimberg BT, McHenry AM, Greenberg LJ, Siddiqui A, Howes RE, da Silva-Nunes M, Ferreira MU, Zimmerman PA. 2011. Fy(a)/Fy(b) antigen polymorphism in human erythrocyte Duffy antigen affects susceptibility to Plasmodium vivax malaria. Proc Natl Acad Sci U S A 108:20113–8.
- Balu B, Maher SP, Pance A, Chauhan C, Naumov A V, Andrews RM, Ellis PD, Khan SM, Lin J-W, Janse CJ, Rayner JC, Adams JH. 2011. CCR4-associated factor 1 coordinates the expression of Plasmodium falciparum egress and invasion proteins. Eukaryot Cell 10:1257–63.
- Fonager J, Franke-Fayard BMD, Adams JH, Ramesar J, Klop O, Khan SM, Janse CJ, Waters AP. 2011. Development of the piggyBac transposable system for Plasmodium berghei and its application for random mutagenesis in malaria parasites. BMC Genomics 12:155.
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