Shotgun DNA microarrays and stage‐specific gene expression in Plasmodium falciparum malaria

Abstract

SummaryMalaria infects over 200 million individuals and kills 2 million young children every year. Understanding the biology of malarial parasites will be facilitated by DNA microarray technology, which can track global changes in gene expression under different physiological conditions. However, genomes of Plasmodium sp. (and many other important pathogenic organisms) remain to be fully sequenced so, currently, it is not possible to construct gene-speci®c microarrays representing complete malarial genomes. In this study, 3648 random inserts from a Plasmodium falciparum mung bean nuclease genomic library were used to construct a shotgun DNA microarray. Through differential hybridization and sequencing of relevant clones, large differences in gene expression were identi®ed between the blood stage trophozoite form of the malarial parasite and the sexual stage gametocyte form. The present study lengthens our list of stage-speci®c transcripts in malaria by at least an order of magnitude above all previous studies combined. The results offer an unprecedented number of leads for developing transmission blocking agents and for developing vaccines directed at blood stage antigens. A signi®cant fraction of the stage-selective transcripts had no sequence homologues in the current genome data bases, thereby underscoring the importance of the shotgun approach. The malarial shotgun microarray will be useful for unravelling additional important aspects of malaria biology and the general approach may be applied to any organism, regardless of how much of its genome is sequenced.

Exploring the transcriptome of the malaria sporozoite stage

“…Microarrays will be the method of choice for expression analysis in asexual and sexual blood stage parasites where the acquisition of sufficient RNA is not a limitation. Although whole genome microarrays are not yet available, partial arrays from mung bean genomic libraries (37) or blood stage cDNA libraries (38) have been used successfully to study gene expression in blood stages. However, microarray analysis of gene expression in ookinetes, early oocysts, sporozoites, and EEF of mammalian Plasmodia will be difficult because large quantities of these stages are not available.…”

Enlistment of omics technologies in the fight against malaria: Panacea or Pandora's Box?

“…60) Because of the large number of unassigned genes, transcriptomics techniques can be useful in identifying stage and host-specific genes and signaling pathways. 12,61) The asexual blood stages are fully responsible for the clinical symptoms of malaria, and transcriptomic techniques have revealed a coordinated program of gene expression during intraerythrocytic development that should help pinpoint genes critical to this pathway.…”

“…56,64) Therefore, it might be possible to block transmission of the disease by disrupting sexual stage-specific gene regulation. 55,61,63) Microarray data have also demonstrated up-regulation of genes involved in immune evasion, shedding light on potential targets associated with host-pathogen interactions. 65,66) Disease severity is determined in part by the parasite's ability to evade immune recognition and splenic clearance, which is heavily influenced by which var gene is expressed.…”

k-Means Walk: Unveiling Operational Mechanism of a Popular Clustering Approach for Microarray Data

“…An infectious disease with particular reference to malaria is caused by a lethal pathogenic protozoan, Plasmodium falciparum, responsible for major losses and death in Sub-Saharan Africa [4,5]. This disease has attracted intense microarray patronage with large data generation efforts [5][6][7][8][9][10][11][12][13]. In addition, from the effort of Kissinger et al [14] and Bahl et al [15], Plasmodium spp data are now accumulated and integrated into a database called PlasmoDB.…”