Abdirahman Abdi BSc, MSc, PhD

PERSONAL DETAILS

Name:         Abdirahman Abdi

Address:    KEMRI/Wellcome Trust Research Programme, PO Box 230, Kilifi, 80108, Kenya

Email:        This email address is being protected from spambots. You need JavaScript enabled to view it./ This email address is being protected from spambots. You need JavaScript enabled to view it.

Tel:            +254710987690

Current position: Principal investigator and a Wellcome Trust International Intermediate Fellow

QUALIFICATIONS

Ph. D. University of Heidelberg, Germany, Magna Cum Laude                  2010

MSc Biochemistry University of Nairobi                                                      2012

BSc Biochemistry/Chemistry, University of Nairobi, First Class Honours   2002

 

RECENT EMPLOYMENT & ACADEMIC POSITIONS

Wellcome Trust International Intermediate Fellow, Kemri-Wellcome Trust, CGMRC, Kilifi, Kenya                                                                                                                       2018-2023

Early Research Fellow, Kemri-Wellcome Trust, CGMRC, Kilifi, Kenya                   2016-2017

Wellcome Trust Training Fellow, Kemri-Wellcome Trust, CGMRC, Kilifi, Kenya     2014-2015

Postdoctoral Research Asssistant, Kemri-Wellcome Trust, CGMRC, Kilifi, Kenya 2010-2014

PhD student, University of Heidelberg, Germany                                                    2006-2010

Research Assistant,Kemri-Wellcome Trust, CGMRC, Kilifi, Kenya                         2005-2006

Research Assistant, National Museum of Kenya,                                                   2004–2005

Summary of Research interest

I am currently a Principal Investigator at KEMRI-WELLCOME TRUST, Centre for Geographic Medicine Research, coast

My current research work focuses on small vesicles released by all cells to their extracellular space which are generally referred to as extracellular vesicles (EVs). Their main function is for intercellular communication by serving as vehicles for transferring signalling competent proteins and functional RNA packaged within the vesicles to adjacent and/or distant recipient cells to control cellular response. I study these vesicles to understand the interaction between malaria parasites and the human host that lead to severe disease. I study both the content and the functional role of these vesicles to identify new interventions. This work was initially funded through a Wellcome Trust Training Fellowship (2014-2015) and was further consolidated by another fellowship from the Wellcome Trust (International Intermediate Fellowship 2018-2023). In my research, I apply multi-omics approach (genomic, transcriptomic, proteomic and metabolomic) coupled with cellular biology including cellular immunology.

In addition to malaria, I also study the “omics” of EVs circulating in human body fluids such as blood to understand the aetiology of common illness in children where the clinical syndrome strongly suggests infection, but current diagnostic methods have not identified a causative organism. I also study EVs circulating in blood to dissect the metabolic processes that mediate the interaction between infection and undernutrition in children.

Awards and Funding Obtained (Last 10 years)

Successful funding application

  • Pathogen Discovery in the context of unknown cause of death and encephalopathy amongst children BMGF Grand challenge 2019-2020, Co-PI (USD 100,000).
  • Plasmodium falciparum extracellular vesicles in malaria pathogenesis and immunity Wellcome Trust International Intermediate. Fellowship in Public Health and Tropical Medicine, (PI) 2018-2023, £739200.
  • Investigate the Aetiology and molecular biomarkers of non-traumatic coma of unknown cause in children using molecular approaches (Co-PI), Internal Kemri-grant, KES 3,985,000.
  • Dissecting the biochemical processes that underlie the human host response to malaria infection that would lead to protection in the context of controlled human malaria infection (PI). WIPO Re:Search. AUD 60,000.
  • KEMRI-Wellcome Trust programme Director’s bridge funding to generate preliminary data for a Wellcome Trust International.Intermediate Fellowship application, KES 11,853,355.
  • Identifying new intervention and diagnostic targets through characterization and functional analysis of the P. falciparum extracellular vesicles. Trust Training Fellowship in Public Health and Tropical Medicine (PI) 2014-2015, £100,000.
  • “Assessing whether an exported Plasmodium falciparum tyrosine kinase-like protein kinase (PfTKL2) is a target of natural immunity to malaria”
    National commission for Science, Technology & Innovation Postdoctorate Research grant, (PI), 2011-2012, KES 1000,000.
  • PhD Training Scholarship, AntiMAL International PhD programme, Full scholarship

Unsuccessful grant applications

  • 2019: Pathogen discovery in the context of TB-like syndrome associated with high mortality in rural Kenya. BMGF 2019 grand challenges annual meeting-call to action (PI): USD 100,000.
  • 2018: Controlled Human Malaria Infection in Kenya: Accelerating Vaccine Development, MRC, UK (Co-PI). £3,999,389
  • 2018: Decording signals of wasting to design nutraceuticals, BMGF 2018 grand challenges annual meeting-call to action (PI): USD 200,000
  • Drug resistance and malaria surveillance in East Africa, BMGF 2018 grand challenges annual meeting-call to action (Co-PI): USD 200,000
  • 2016: Identifying correlates of naturally acquired immunity to malaria through analysis of gene expression in parasites placed under immune selection, Isaac Newton Trust / Wellcome Trust ISSF / University of Cambridge Joint Research Grants Scheme (Co-PI). £83400
  • 2016: Monitoring and mapping antimalarial resistance in East Africa, MRC, GCRF (Co-PI)

Capacity Building and postgraduate Supervision

I have successfully supervised five intern postgraduate students, two postgraduate diploma students, and three MSc students. I am currently supervising two MSc, two PhD students and one Postdoc. I also teach Biochemistry at Pwani University and acted as an external examiner for University of Nairobi.

Training workshops

  • July 25-30, 2011, Introduction to statistic course, Kemri/welcome trust, kilifi, Kenya.
  • Nov 24–26, 2008, MalPar/AntiMal Training Course ‘Project Management Workshop with Bowman Group business consultants. Montpellier, France
  • Nov 19 – 27, 2007: MalPar/AntiMal Training Course ‘Scientific Writing and presenting in English’, London, UK
  • March 18 – 26 2007: Functional genomics of malaria parasite; Biomalpar/HHMI/WHO special programme for research and training in tropical diseases (TDR) practical course. Biotec, Thailand Science Park, Pathumthani, Thailand.
  • Oct 9-20, 2006: MalPar/AntiMal core Course “The challenge of malaria in the post genomic era” Montpellier, France.

Publications:
I have authored and co-authored 25 publications in peer-reviewed journals including Nature. First authorship=8, last authorship=2

  1. Kivisi CA, Muthui M, Hunt M, Fegan G, Otto TD, Githinji G, Warimwe GM, Rance R, Marsh K, Bull PC, Abdi AI (2019): Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy. Front Immunol. 2019 Oct 9;10:2328. doi: 10.3389/fimmu.2019.02328. eCollection 2019.
  1. Wamae K, Okanda D, Ndwiga L, Osoti V, Kimenyi KM, Abdi AI, Bejon P, Sutherland C, Ochola-Oyier LI (2019).No evidence of P. falciparum K13 artemisinin conferring mutations over a 24-year analysis in Coastal Kenya, but a near complete reversion to chloroquine wild type parasites: Antimicrob Agents Chemother. 2019 Oct 7. pii: AAC.01067-19. doi: 10.1128/AAC.01067-19
  2. Tuju J, Mackinnon MJ, Abdi AI, Karanja H, Musyoki JN, Warimwe GM, Gitau EN, Marsh K, Bull PC, Urban BC (2019). Antigenic cartography of immune responses to Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1): PLoS Pathog. 2019 Jul 1;15(7):e1007870. doi: 10.1371/journal.ppat.1007870. eCollection 2019 Jul.
  3. Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S, Stewart LB, Campino S, Kekre M, Hamilton WL, Claessens A, Volkman SK, Ndiaye D, AmambuaNgwa A, Diakite M, Fairhurst RM, Conway DJ, Franck M, Newbold CI, Berriman M (2018). Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Res. doi:10.12688/wellcomeopenres.14571.1. eCollection 2018.
  4. Abdirahman I. Abdi, Lu Yu, Martin Rono, David Coulding, Philip Bejon, Jyoti Choudhary and Julian C. Rayner (2017): Proteomic analysis of extracellular vesicles from a Plasmodium falciparum clinical isolate from Kenya defines a core parasite secretome. Wellcome Open Res. 2017 Nov 22;2:50. doi: 10.12688/wellcomeopenres.11910.2. eCollection 2017
  5. Kathrin Pieper, Joshua Tan, Luca Piccoli, Mathilde Foglierini, Sonia Barbieri, Yiwei Chen, Chiara Silacci-Fregni, Tobias Wolf, David Jarrossay, Marica Anderle, Abdirahman Abdi, Tuan Tran, Said Jongo, Isabelle Zenklusen, Peter Crompton, Claudia Daubenberger, Peter Bull, Federica Sallusto & Antonio Lanzavecchia: Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature. 2017 Aug 31;548(7669):597-601. doi: 10.1038/nature23670. Epub 2017 Aug PMCID:PMC5635981[Available on 2018-02-23]
  6. Abdirahman I. Abdi, Susanne H. Hodgson, Michelle K. Muthui, Cheryl A. Kivisi, Gathoni Kamuyu, Domtila Kimani, Stephen L. Hoffman, Elizabeth Juma, Bernhards Ogutu, Simon J. Draper, Faith Osier, Philip Bejon, Kevin Marsh, Peter C. Bull: Plasmodium falciparum malaria parasite var gene expression is modified by host antibodies: longitudinal evidence from controlled infections of Kenyan adults with varying natural exposure BMC Infect Dis. 2017 Aug 23;17(1):585. doi: 10.1186/s12879-017-2686-0. PMCID:PMC5569527
  7. George M. Warimwe, Abdirahman I. Abdi, Michelle Muthui, Greg Fegan, Jennifer N. Musyoki, Kevin Marsh, and Peter C. Bull. Antigenic PfEMP1 variants associated with life-threatening malaria exhibit limited serological diversity. Infection and Immunity, 2016 Apr 22;84(5):1331-5. doi: 10.1128/IAI.00772-15.
  8. Peter C. Bull Abdirahman I. Abdi (2015) The role of PfEMP1 as targets of naturally acquired immunity to childhood malaria: review, Parasitology. 2016 Feb;143(2):171-86. doi: 10.1017
  9. Abdirahman I. Abdi George M. Warimwe, Michelle K. Muthui, Cheryl A. Kivisi, Gregory W. Fegan, Esther W. Kiragu, Peter C. Bull (2016) Global selection of Plasmodium falciparum virulence antigen expression by host antibodies. Scientific Report. 2016 Jan 25;6:19882. doi: 10.1038/srep19882.
  10. Joshua Tan, Kathrin Pieper, Luca Piccoli Abdirahman Abdi, Claire Maria Tully, Mathilde Foglierini Perez, Roger Geiger, David Jarrossay, Francis Maina Ndungu, Juliana Wambua, Philip Bejon2, Chiara Silacci Fregni, Blanca Fernandez-Rodriguez, Sonia Barbieri, Siro Bianchi, Kevin Marsh, Vandana Thathy, Davide Corti, Federica Sallusto, Peter Bull, and Antonio Lanzavecchia (2016). A LAIR-1 insertion creates broadly reactive antibodies against malaria variant antigens. Nature. 2016 Jan 7;529(7584):105-9. doi: 10.1038/nature16450.
  11. Abdirahman I. Abdi, Symon M Kariuki, Michelle Muthui, Cheryl Andisi, Gregory Fegan, Evelyn Gitau, Charles R Newton and Peter C. Bull (2015). Malarial Retinopathy is associated with low Plasmodium falciparum var gene expression in Kenyan children with cerebral malaria. Scientific Reports, 2015 Dec 14;5:18034. doi: 10.1038/srep18034.
  12. Abdirahman I. Abdi Michelle Muthui Esther Kiragu and Peter C. Bull (2014): measuring soluble ICAM-1 in African populations. PLoS One. 2014 Oct 7;9(10):e108956. doi: 10.1371/journal.pone.0108956. eCollection 2014.
  13. Abdirahman I. Abdi, Gregory Fegan, Michelle Muthui, Esther Kiragu, Jennifer N. Musyoki, Michael Opiyo, Kevin Marsh, George Warimwe, and Peter C. Bull (2014) Plasmodium falciparum antigenic variation: relationships between widespread endothelial activation, PfEMP1 expression and severe malaria. BMC Infect Dis. 2014 Mar 28;14(1):170. doi: 0.1186/1471-2334-14-170.
  14. Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B, et al (2013). Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. Sci Rep 3,Article number: 3318 doi: 10.1038/srep03318
  15. Abdirahman I. Abdi, Teresa G. Carvalho, Jonathan M. Wilkes, Christian Doerig (2013). A secreted Plasmodium falciparum kinase reveals a signature motif for classification of tyrosine kinase-like kinases. Microbiology doi: 10.1099/mic.0.070409-0
  16. John Okombo, Abdirahman Abdi, Steven Kiara, Leah Mwai, Lewa Pole, Colin Sutherland, Alexis Nzila, and Lynette Ochola-Oyier (2013). Repeat Polymorphisms in the Low Complexity Regions of Plasmodium falciparum ABC Transporters and Associations with In Vitro Antimalarial Responses.
    Antimicrobial Agents and Chemotherapy vol. 57 no. 12 pages 6196-6204 PMID: 24080667
  17. Okombo J, Kiara SM, Abdirahman A, Mwai L, Ohuma E, Borrmann S, Nzila A, Ward S (2013) Antimalarial activity of isoquine against Kenyan Plasmodium falciparum clinical isolates and association with polymorphisms in pfcrt and pfmdr1 genes. J Antimicrob Chemother: 68 (4): pages 786-788
  18. Lev Solyakov, Jean Halbert, Mahmood M. Alam, Jean-Philippe Semblat, Dominique DorinSemblat, Luc Reininger, Andrew Bottrill4
    , Sharad Mistry, Abdirhaman Abdi, et al (2011). Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. Nature Communications.2: 565 |DoI: 10.1038/ncomms1558
  19. Abdirahman Abdi, Sylvain Eschenlauer, Christian Doerig (2010). SAM domain-dependent activity
    of PfTKL3, an essential tyrosine kinase-like kinase of the human malaria parasite Plasmodium
    falciparum. Cellular and Molecular Life Sciences. Vol: 67, Issue 19, Pages 3355-3369
  20. Githui EK, Peterson DS, Aman RA, Abdi AI (2010). Prevalence of 5′ insertion mutants and analysis of single nucleotide polymorphism in the erythrocyte binding-like 1 (ebl-1) gene in Kenyan Plasmodium falciparum field isolates. Infect Genet Evol. Vol 10, Issue 6, Pages 833-838
  21. Doerig C, Abdi A, Bland N, Eschenlauer S, Dorin-Semblat D, Fennell C, Halbert J, Holland Z, Nivez MP, Semblat JP, Sicard A, Reininger L (2010).Malaria: Targeting parasite and host cell kinomes. Biochim Biophys Acta. Volume 1804, Issue 3, Pages 604-612
  22. Mwai L, Kiara SM, Abdirahman A, Pole L, Rippert A, Diriye A, Bull P, Marsh K, Borrmann S, Nzila A (2009). In vitro activity of piperaquine, lumefantrine and dihydroartemisinin in Kenyan Plasmodium falciparum isolates and polymorphisms in Pfcrt and Pfmdr1. Antimicrob Agents Chemotherapy. vol. 53 no. 12 pages 5069-5073; PMID:19770282
  23. Sasi P, Abdulrahaman A, Mwai L, Muriithi S, Straimer J, Schieck E, Rippert A, Bashraheil M, Salim A, Peshu J, Awuondo K, Lowe B, Pirmohamed M, Winstanley P, Ward S, Nzila A, Borrmann S (2009). In vivo and in vitro efficacy of amodiaquine against Plasmodium falciparum in an area of
    continued use of 4-aminoquinolines in East Africa. J Infect Dis. Volume 199, Issue 11 Pages 1575- 1582
  24. Mwai L, Ochong E, Abdirahman A, Kiara SM, Ward S, Kokwaro G, Sasi P, Marsh K, Borrmann S, Mackinnon M, Nzila A (2009). Chloroquine resistance before and after its withdrawal in Kenya. Malar J: 8:106 doi:10.1186/1475-2875-8-106: PMID:19450282

Referees

Professor Philip Bejon
KEMRI/Wellcome Trust Research Programme,
(Centre for Geographic Medicine Research-Coast)
P.O.Box 230, 80108, Kilifi, Kenya
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Professor Julian Rayner, PhD

Director, Cambridge Institute for Medical Research
Director, Wellcome Genome Campus Connecting Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

 
Dr Benjamin Tsofa

Director, KEMRI- Centre for Geographic Medicine Research-Coast
P.O.Box 230, 80108, Kilifi, Kenya
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.