title: Plasmodium falciparum gene expression measured directly from tissue during human infection.
abstract: BACKGROUND
  During the latter half of the natural 48-h intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium of tissues, away from the spleen and inaccessible to peripheral blood. These late-stage parasites may cause tissue damage and likely contribute to clinical disease, and a more complete understanding of their biology is needed. Because these life cycle stages are not easily sampled due to deep tissue sequestration, measuring in vivo gene expression of parasites in the trophozoite and schizont stages has been a challenge.
  
  
  METHODS
  We developed a custom nCounter® gene expression platform and used this platform to measure malaria parasite gene expression profiles in vitro and in vivo. We also used imputation to generate global transcriptional profiles and assessed differential gene expression between parasites growing in vitro and those recovered from malaria-infected patient tissues collected at autopsy.
  
  
  RESULTS
  We demonstrate, for the first time, global transcriptional expression profiles from in vivo malaria parasites sequestered in human tissues. We found that parasite physiology can be correlated with in vitro data from an existing life cycle data set, and that parasites in sequestered tissues show an expected schizont-like transcriptional profile, which is conserved across tissues from the same patient. Imputation based on 60 landmark genes generated global transcriptional profiles that were highly correlated with genome-wide expression patterns from the same samples measured by microarray. Finally, differential expression revealed a limited set of in vivo upregulated transcripts, which may indicate unique parasite genes involved in human clinical infections.
  
  
  CONCLUSIONS
  Our study highlights the utility of a custom nCounter® P. falciparum probe set, validation of imputation within Plasmodium species, and documentation of in vivo schizont-stage expression patterns from human tissues.
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA USA.
authors.forename: Daria
authors.initials: D
authors.lastname: Van Tyne
authors.affiliation: Broad Institute, Cambridge, MA USA ; Graduate Program in Bioinformatics, Boston University, Boston, MA USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Tan
authors.affiliation: Albert Einstein College of Medicine, Bronx, NY USA.
authors.forename: Johanna P
authors.initials: JP
authors.lastname: Daily
authors.affiliation: University of Malawi College of Medicine, Blantyre, Malawi.
authors.forename: Steve
authors.initials: S
authors.lastname: Kamiza
authors.affiliation: Michigan State University, College of Osteopathic Medicine, East Lansing, MI USA ; The Blantyre Malaria Project, Blantyre, Malawi.
authors.forename: Karl
authors.initials: K
authors.lastname: Seydel
authors.affiliation: Michigan State University, College of Osteopathic Medicine, East Lansing, MI USA ; The Blantyre Malaria Project, Blantyre, Malawi.
authors.forename: Terrie
authors.initials: T
authors.lastname: Taylor
authors.affiliation: Broad Institute, Cambridge, MA USA.
authors.forename: Jill P
authors.initials: JP
authors.lastname: Mesirov
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA USA ; Broad Institute, Cambridge, MA USA.
authors.forename: Dyann F
authors.initials: DF
authors.lastname: Wirth
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA USA ; Broad Institute, Cambridge, MA USA ; University of Malawi College of Medicine, Blantyre, Malawi ; The Blantyre Malaria Project, Blantyre, Malawi ; Brigham and Women's Hospital, Boston, MA USA.
authors.forename: Danny A
authors.initials: DA
authors.lastname: Milner