title: Predicting functional and regulatory divergence of a drug resistance transporter gene in the human malaria parasite.
abstract: BACKGROUND
  The paradigm of resistance evolution to chemotherapeutic agents is that a key coding mutation in a specific gene drives resistance to a particular drug. In the case of resistance to the anti-malarial drug chloroquine (CQ), a specific mutation in the transporter pfcrt is associated with resistance. Here, we apply a series of analytical steps to gene expression data from our lab and leverage 3 independent datasets to identify pfcrt-interacting genes. Resulting networks provide insights into pfcrt's biological functions and regulation, as well as the divergent phenotypic effects of its allelic variants in different genetic backgrounds.
  
  
  RESULTS
  To identify pfcrt-interacting genes, we analyze pfcrt co-expression networks in 2 phenotypic states - CQ-resistant (CQR) and CQ-sensitive (CQS) recombinant progeny clones - using a computational approach that prioritizes gene interactions into functional and regulatory relationships. For both phenotypic states, pfcrt co-expressed gene sets are associated with hemoglobin metabolism, consistent with CQ's expected mode of action. To predict the drivers of co-expression divergence, we integrate topological relationships in the co-expression networks with available high confidence protein-protein interaction data. This analysis identifies 3 transcriptional regulators from the ApiAP2 family and histone acetylation as potential mediators of these divergences. We validate the predicted divergences in DNA mismatch repair and histone acetylation by measuring the effects of small molecule inhibitors in recombinant progeny clones combined with quantitative trait locus (QTL) mapping.
  
  
  CONCLUSIONS
  This work demonstrates the utility of differential co-expression viewed in a network framework to uncover functional and regulatory divergence in phenotypically distinct parasites. pfcrt-associated co-expression in the CQ resistant progeny highlights CQR-specific gene relationships and possible targeted intervention strategies. The approaches outlined here can be readily generalized to other parasite populations and drug resistances.
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. siwomolbio@gmail.com.|Geisel School of Medicine, Dartmouth College, Hanover, NH, USA. siwomolbio@gmail.com.
authors.forename: Geoffrey H
authors.initials: GH
authors.lastname: Siwo
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. asako926@gmail.com.|Epicentre, Madison, WI, USA. asako926@gmail.com.
authors.forename: Asako
authors.initials: A
authors.lastname: Tan
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. Katrina.A.Button-Simons.1@nd.edu.
authors.forename: Katrina A
authors.initials: KA
authors.lastname: Button-Simons
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. upeka.samarakoon@gmail.com.|Harvard Medical School, Boston, MA, USA. upeka.samarakoon@gmail.com.
authors.forename: Upeka
authors.initials: U
authors.lastname: Samarakoon
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. Lisa.Checkley.2@nd.edu.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Checkley
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. rpinapat@nd.edu.
authors.forename: Richard S
authors.initials: RS
authors.lastname: Pinapati
authors.affiliation: Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA. ferdig.1@nd.edu.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Ferdig
mesh_terms: D000818:Animals; D002738:Chloroquine / Q000627:therapeutic use; D004351:Drug Resistance / Q000235:genetics*; D005786:Gene Expression Regulation; D014644:Genetic Variation; D006801:Humans; D016778:Malaria, Falciparum / Q000188:drug therapy / Q000235:genetics* / Q000469:parasitology; D026901:Membrane Transport Proteins / Q000096:biosynthesis / Q000235:genetics*; D009154:Mutation; D010963:Plasmodium falciparum / Q000187:drug effects / Q000235:genetics*; D060066:Protein Interaction Maps / Q000235:genetics; D015800:Protozoan Proteins / Q000096:biosynthesis / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics
chemical_list: D026901:Membrane Transport Proteins; C416369:PfCRT protein, Plasmodium falciparum; D015800:Protozoan Proteins; D002738:Chloroquine