Approches génomiques du paludisme chronique asymptomatique (A. Claessens)

Approches génomiques du paludisme chronique asymptomatique

Comment le parasite du paludisme Plasmodium falciparum arrive-t-il à établir une infection chronique et asymptomatique chez un hôte humain ? L'équipe GATAC-Malaria aborde cette question en utilisant des isolats sanguins collectés sur le terrain et la technologie de séquençage à haut-débit.

 

Notre équipe ATIP-Avenir fait partie de ParaFrap, un consortium de parasitologues, et de MalariaGEN, un consortium de génomique du paludisme. Nous sommes actuellement financés par un «ANR-JCJC» attribué à Antoine Claessens.

 

Les infections asymptomatiques à Plasmodium falciparum constituent un défi majeur pour toute campagne d'élimination du paludisme. Néanmoins, ces infections peuvent fournir des informations utiles sur les interactions hôte-pathogène sur une longue période. Notre laboratoire s'efforce de comprendre comment les parasites P. falciparum peuvent survivre dans les infections chroniques humaines au cours de la longue saison sèche de 6 mois, en utilisant une collection d'échantillons de sang provenant d'une cohorte de volontaires asymptomatiques en Gambie. Pour explorer comment le parasite perçoit son environnement et s'y adapte, nous mesurons le taux de multiplication du parasite et séquençons son transcriptome. Notre nouveau protocole peut séquencer un transcriptome entier à partir de 1000 cellules. Nous identifierons les gènes associés à la saisonnalité en utilisant des échantillons de saison sèche et humide de la Gambie. En parallèle, nous nous concentrons sur la variation antigénique du parasite en analysant l’expression des gènes var. En résumé, nous ferons progresser notre compréhension de la biologie des parasites et découvrirons les principaux moteurs moléculaires des infections asymptomatiques, une étape essentielle pour permettre l'éradication du paludisme.

 

Nous avons récemment publié nos principaux objectifs dans Trends in Parasitology, voici un résumé vidéo de 2min.

 

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Activités de recherche

 

INTRODUCTION:

Basic facts about malaria:

  • Caused by Plasmodium parasites (unicellular eukaryote)
  • Transmitted by Anopheles mosquitoes
  • Plasmodium parasites spend most of their asexual life inside red blood cells, with a reinvasion cycle every 48 hours.
  • Over half a million deaths per year, mainly children in Sub-Saharan Africa infected with Plasmodium falciparum

Malaria in The Gambia, West Africa

Where malaria transmission is seasonal such as The Gambia in West Africa, this occurs during and immediately after the rains (June-December). During the dry season (January-May) there is no transmission, hardly any clinical case is diagnosed during these dry months, and there are fewer mosquitoes[1,2]. Most of these infections will clear naturally, inducing a parasite population bottleneck (Fig. 1). However some P. falciparum parasites survive by establishing chronic, asymptomatic infections across the whole dry season. These infections are the reservoir from which the seasonal peak will restart at the next transmission season.

Asymptomatic infections: out of sight, out of mindOur current research focuses on P. falciparum asymptomatic infections for three main reasons: 

On any given day, the vast majority of all P. falciparum infections are asymptomatic, yet they have been poorly investigated (Fig 2). Currently, our knowledge of the parasite biology is based on isolates derived from clinical cases, and usually from clonal culture-adapted parasites. How asymptomatic infections differ from clinical cases has hardly ever been investigated, with no genome, epigenome, transcriptome, proteome or phenotypic description of such parasites published to date, due to the technical challenges associated with very low amount of biological material. Today’s technology is at a turning point for addressing these issues.


  1. This reservoir, shown to produce gametocytes and transmit them[4], represents the biggest challenge for malaria eradication. However, clearing all infections would include treating carriers without clinical symptoms who are unlikely to seek treatment. A campaign that would only target clinical cases, the most virulent forms of the parasite, is at risk of inadvertently selecting for a population with an “asymptomatic profile” (i.e. low-parasitaemia, chronic infections), complicating the elimination effort.Asymptomatic infections, a challenge for malaria elimination
  1. Asymptomatic infections as a new model for host-pathogen interactions

Currently, pathogenesis studies typically collect a single blood sample from the patient on its arrival at hospital, giving us only a snapshot of the host-pathogen interaction. I believe we could “record the video” of the host-pathogen interaction with regular blood sampling of the same chronic asymptomatic carrier, to study the evolution of the same infection in real time (Fig 3).

    Figure 3

This is why in The Gambia we recruited a cohort of ~50 volunteers who were asymptomatic carriers at the start of the dry season (December 2016). These individuals were sampled monthly for up to 6 months. Epidemiology results will be described in a separate post.
Understanding how the parasite can survive in a human host for months will help us develop novel genetic surveillance & therapeutic tools.

 

AIMS:

To understand how the parasite is able to survive over the dry season, and start a new epidemic at the following wet season, we will characterize P. falciparum from chronic infections, at the genomic, transcriptomic and phenotypic levels, as well as the associated host immune response. More specifically:

Project 1: Identifying P. falciparum alleles under selection during the dry season

Sequencing of P. falciparum genomes collected during the wet and dry season will identify parasite alleles that are selected for by the parasite population bottleneck due to the lack of transmission in the dry season.

Project 2: Can P. falciparum sense its environment and adapt to it via transcriptional regulation?

2a: We will measure the in vitro parasite multiplication rate to determine whether isolates from asymptomatic infections grow slower than virulent infections.

2b: Using single-cell (sc) RNA-seq, we will compare the transcriptome of parasites collected in dry and wet seasons. Our hypothesis is that at the start of the dry season some subpopulations of parasites switch to a dormant-like state.

Project 3: Can antigenic variation explain chronic infections?

We will record var gene expression switching and its associated immune response monthly over the course of the same infections. This will reveal a long postulated but never formally tested hypothesis that variant surface antigen switching is sufficient for the parasite to evade the host immune system.

 

 

References:

1        Ceesay, S.J. et al. (2008) Changes in malaria indices between 1999 and 2007 in The Gambia: a retrospective analysis. Lancet 372, 1545–54

2        Ceesay, S.J. et al. (2010) Continued decline of malaria in The Gambia with implications for elimination. PLoS One5, 4–13

3        Lindblade, K. a et al. (2013) The silent threat: asymptomatic parasitemia and malaria transmission. Expert Rev. Anti. Infect. Ther. 11, 623–39

4        Stone, W. et al. (2015) Assessing the infectious reservoir of falciparum malaria: Past and future. Trends Parasitol.31, 287–296

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Antoine CLAESSENS
CR INSERM
antoine.claessens[arobase]umontpellier.fr
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