1. M ALARIA RESEARCH IN THE POST - GENOMIC ERA Presenter: Reihaneh Rabbany Presented in Bioinformatics Course (CMPUT 606), Instructed by Prof. Guohui Lin, Computing Science Department, University of Alberta, Winter 2009 Elizabeth Ann Winzeler, (2008) Nature, 455 (7214), pp. 751-756

2. W HAT IS IN THIS REVIEW? In 2002 the genome sequence of Plasmodium falciparum was completed The parasite causing the most severe type of human malaria Genome-dependent research have provided new discoveries which would lead to new therapies This review is on these discoveries

3. M ALARIA - H OW SIGNIFICANT ? Shaped the human genome Evolutionary response providing protection Negatively effect on human society Decreasing productivity Increasing poverty 515 million cases each year

4. M ALARIA – C AUSE AND E FFECTS Caused by Plasmodium, four species: P. falciparum, P. vivax, P. ovale and P. malariae Transmitted by the bites of anopheline mosquitoes P. falciparum Has the greatest toll Fever, anaemia, coma, death Impaired ability to learn in survived children

5. M ALARIA PARASITE ’ S LIFE CYCLE

6. M ALARIA CONTROL - D RUGS Some cheap and safe drugs that are still used But their continued use poses widespread parasite resistance At present, World Health Organization is recommending the use of a herbal drug Parasite resistance in the rodent models A few cases of treatment failure in human patients The need for continued drug discovery research 6

7. M ALARIA CONTROL - V ACCINE Subunit vaccines RTS,S Based on P. falciparum protein Is targeted for licensing in 2011 Reduced the number of severe cases Children still developed malaria Decrease malaria severity and morbidity There are still more than 40 subunit vaccines in development and 16 in clinical trials Attenuated vaccines Sporozoite are attenuated less practical than single-subunit vaccines efforts are being made to overcome its obstacles 7

8. M ALARIA CONTROL – V ACCINE Still don’t have a fully protective and licensed malaria vaccine despite decades of effort These are initiated decades ago When researchers were limited by their ability to work with malaria parasites in the laboratory Thus vaccine research efforts were mostly focused on a relatively small number of very abundant proteins that could be easily studied Now we are in genomic era 8

9. M ALARIA GENOMES - S EQUENCING 2002: Complete genome sequence of P. falciparum A partial sequence of rodent parasite, 2005: sequences of several other rodent parasites P. vivax (a human malaria parasite) P. knowlesi (primarily a monkey parasite) + sequence of: Human genome Anopheles mosquito New Candidates for drug and vaccine pipeline 9

10. P LASMODIUM GENOMES 23–27 million bases 14 chromosomes ~5,500 genes Rich in low-complexity regions High A+T content P. falciparum: 79.6% P. vivax: 67.7% Extreme A+T content has probably not too much to do with the disease 10

11. P LASMODIUM GENOMES (C ONT.) Differences between the species P. falciparum: many of the multigene families involved in immune evasion are located near the ends of chromosomes P. knowlesi: members of multigene families are scattered across the chromosomes 77% of the proteins are conserved 11

12. P LASMODIUM GENOMES – WE KNOW AS LITTLE AS WE DO Many of the identified genes do not have homologues in commonly studied model organisms and often lack a clear cellular function We don’t know The basis for sex determination and How parasites become committed to sexual development The liver stages and How the parasites home to the liver but then pass through transverse some cells while forming parasitophorous vacuoles in others Parasite metabolism inside a human may differ from parasite metabolism in laboratory culture 12

13. F UNCTIONAL STUDIES OF MALARIA GENOMES Functional genomics: What different genes do for the organism? Using microarrays or mass spectrometers Analyzing expression pattern in different life cycle stages to predict possible functions if a gene shows a large induction during early liver stage development, there is a good chance that this is the time when its protein product will be required Analysis of the parasite proteome from male and female gametocytes has revealed genes contributing to the differences of different sexes PlasmoDB New genetic tools for testing these predictions 13

14. F UNCTIONAL STUDIES OF MALARIA GENOMES Good correlation between transcript and protein abundance but In a number of cases genes are transcribed but then not translated until the organism has made the rapid transition between warm- and cold-blooded hosts transcripts needed for gamete formation in the mosquito are produced in the mammalian host Groups of genes with a probable involvement in the parasite’s interaction with the mosquito Could be candidates for transmission-blocking vaccines Prevent an infected individual from passing the disease on to the next person 14

15. G ENOME - WIDE ANALYSIS OF ANTIGENIC VARIATION Genome-wide transcription studies how parasites evade the host immune system Expression analysis and genome sequence has permitted the transcription of the 60 var genes How antigenic variation in parasites may be regulated One exceptionally abundant sporozoite protein in P. berghei which was more immunogenic than some of the historical antigens Antigens derived from this protein are found in an experimental vaccine Identification of parasite genes that are specifically transcribed while the parasite resides in the mosquito salivary gland Disruption of these genes has led to attenuated parasites which are unable to colonize but induce a protective immune response. 15

16. G ENETIC DIVERSITY IN MALARIA PARASITES Change how genes involved in drug resistance are discovered Previously Identified through mapping studies or Candidate gene approaches Genome-dependent methods have revealed new candidate genes that may be involved in drug resistance Studies of genetic variation revealed that a universally effective single-subunit malaria vaccine may be difficult to develop vastly different rates of variability in different parasite gene classes 16

17. F ROM THE GENOME TO CELL BIOLOGY 17 Import of nutrients and export of motif proteins involved in immune evasion occurring Also found in exported proteins from the plant pathogen the motif is attached to small proteins introduced into the plant cytoplasm where they interfere with the plant defense systems A few seem to be transcribed in the early liver stage like CSP downregulating many genes involved in immune signalling and upregulating other genes involved in cell adhesion and possibly apoptosis

18. F ROM THE GENOME TO CELL BIOLOGY 18

19. T HE GENOME AND DRUG DISCOVERY Recent drug discovery campaigns may be shifting from the single-enzyme screening approaches to cell-based methods where one can test for inhibition of all essential proteins simultaneously Still much work ahead: RTS,S and irradiated sporozoite vaccines are both imperfect Drug development: laboratory setting If basic research continues to be a priority and if support is sustained, new drugs and effective vaccines are likely to be developed, and this could make the goal of global malaria eradication achievable 19

20. Q UESTIONS 20