title: Inferring developmental stage composition from gene expression in human malaria.
abstract: In the current era of malaria eradication, reducing transmission is critical. Assessment of transmissibility requires tools that can accurately identify the various developmental stages of the malaria parasite, particularly those required for transmission (sexual stages). Here, we present a method for estimating relative amounts of Plasmodium falciparum asexual and sexual stages from gene expression measurements. These are modeled using constrained linear regression to characterize stage-specific expression profiles within mixed-stage populations. The resulting profiles were analyzed functionally by gene set enrichment analysis (GSEA), confirming differentially active pathways such as increased mitochondrial activity and lipid metabolism during sexual development. We validated model predictions both from microarrays and from quantitative RT-PCR (qRT-PCR) measurements, based on the expression of a small set of key transcriptional markers. This sufficient marker set was identified by backward selection from the whole genome as available from expression arrays, targeting one sentinel marker per stage. The model as learned can be applied to any new microarray or qRT-PCR transcriptional measurement. We illustrate its use in vitro in inferring changes in stage distribution following stress and drug treatment and in vivo in identifying immature and mature sexual stage carriers within patient cohorts. We believe this approach will be a valuable resource for staging lab and field samples alike and will have wide applicability in epidemiological studies of malaria transmission.
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Regina
authors.initials: R
authors.lastname: Joice
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Vagheesh
authors.initials: V
authors.lastname: Narasimhan
authors.affiliation: Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi ; Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
authors.forename: Jacqui
authors.initials: J
authors.lastname: Montgomery
authors.affiliation: The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
authors.forename: Amar Bir
authors.initials: AB
authors.lastname: Sidhu
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Keunyoung
authors.initials: K
authors.lastname: Oh
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Evan
authors.initials: E
authors.lastname: Meyer
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Willythssa
authors.initials: W
authors.lastname: Pierre-Louis
authors.affiliation: College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States of America ; Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi.
authors.forename: Karl
authors.initials: K
authors.lastname: Seydel
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Danny
authors.initials: D
authors.lastname: Milner
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America.
authors.forename: Kim
authors.initials: K
authors.lastname: Williamson
authors.affiliation: The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
authors.forename: Roger
authors.initials: R
authors.lastname: Wiegand
authors.affiliation: Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal.
authors.forename: Daouda
authors.initials: D
authors.lastname: Ndiaye
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America.
authors.forename: Johanna
authors.initials: J
authors.lastname: Daily
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America ; The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
authors.forename: Dyann
authors.initials: D
authors.lastname: Wirth
authors.affiliation: College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States of America ; Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi.
authors.forename: Terrie
authors.initials: T
authors.lastname: Taylor
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America ; The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Matthias
authors.initials: M
authors.lastname: Marti
mesh_terms: D000818:Animals; D015415:Biomarkers; D015870:Gene Expression; D006801:Humans; D016778:Malaria, Falciparum / Q000235:genetics*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D010963:Plasmodium falciparum / Q000235:genetics / Q000254:growth & development; D016133:Polymerase Chain Reaction; D060888:Real-Time Polymerase Chain Reaction; D012641:Selection, Genetic
chemical_list: D015415:Biomarkers