Research review articleProgress on the transcriptomics of carcinogenic liver flukes of humans—Unique biological and biotechnological prospects
Introduction
Compounded by a massive global food shortage, parasitic worms are one of the world's greatest challenges. Literally billions of people are infected with worms, which have a comparable socio-economic burden to that of diabetes or lung cancer in disability adjusted life years (DALYs) (World Health Organization, 2004). Liver flukes (Platyhelminthes: Trematoda: Digenea) are particularly important food-borne worms of humans (Keiser and Utzinger, 2009). Clonorchis sinensis and Opisthorchis viverrini (Opisthorchiidae) cause the diseases called clonorchiasis and opisthorchiasis, respectively, which have a substantial public health impact mainly in countries of the Asia Pacific (Lun et al., 2005, Sripa et al., 2007). Both parasites severely affect tens of millions of people, and ~ 600 million people are at risk of infection (Keiser and Utzinger, 2005, Sripa et al., 2007). Despite control efforts, their prevalence can be as high as 70% in some Asian countries (Sithithaworn and Haswell-Elkins, 2003, Lun et al., 2005). Chronic infections are mainly linked to cholangitis and associated problems in the liver, most importantly, bile duct cancer (= cholangiocarcinoma, CCA) (Lun et al., 2005, Sripa et al., 2007, Shin et al., 2010). Although, theoretically, infections could be prevented by persuading people to consume cooked fish, clonorchiasis and opisthorchiasis persist in endemic regions (Sripa et al., 2007, Keiser and Utzinger, 2009). Control relies mainly on treating infected people with praziquantel (an anthelmintic compound). It appears that humans develop only a limited degree of immunity against opisthorchiid liver flukes (see Wongratanacheewin et al., 2003), such that they frequently become re-infected (Sithithaworn et al., 2002, Lun et al., 2005). Although there has also been a focus on developing alternative control methods (Keiser et al., 2006, Keiser et al., 2009), no vaccines or new drugs are yet available.
Fundamental molecular biological investigations are needed to underpin the development of novel methods of diagnosis, treatment and control. However, to date, most molecular studies of flukes have focused on human blood flukes (schistosomes). Complementing the nuclear genome sequencing of schistosomes (Berriman et al., 2009, Liu et al., 2009) have been sustained efforts to establish in vitro systems for functional genomic analyses (Brindley and Pearce, 2007, Kalinna and Brindley, 2007, Ndegwa et al., 2007, Morales et al., 2008, Rinaldi et al., 2009). This is in stark contrast to the situation for other flukes, for which the potential to explore transcriptomes and gene function is only now being realized (McGonigle et al., 2008, Rinaldi et al., 2008). Despite their major socio-economic impact, no draft or complete nuclear genomic sequence is available for liver flukes, and transcriptomic data have been scant. However, recent investigations provide exciting new prospects to explore biological pathways in various socio-economically important liver flukes, with a view toward biotechnological outcomes. In the present article, we provide a concise account of the biology of C. sinensis and O. viverrini and the diseases that these parasites cause; refer to the current treatment in humans; indicate the need for novel intervention strategies; and, importantly, report on recent progress on the transcriptomics of these carcinogenic liver flukes using next-generation sequencing and bioinformatic technologies. We also emphasize the prospects that transcriptomes provide for future -omic explorations and efforts toward developing improved methods for the control of these flukes and the diseases that they cause.
Section snippets
Biology of carcinogenic liver flukes and associated diseases
The life histories of C. sinensis and O. viverrini are similar (Yoshitaka and Dawes, 1967, Kaewkes, 2003, Upatham and Viyanant, 2003), involving an aquatic snail (order Mesogastropoda), in which asexual reproduction takes place, and freshwater cyprinid fishes or palaemonid shrimps (for C. sinensis only) as intermediate hosts (Fig. 1). Piscivorous mammals, including humans, canids and felids, act as definitive hosts, in which sexual reproduction occurs. Infections are prevalent in geographical
Cholangiocarcinoma and the need for novel intervention strategies
Chronic clonorchiasis or opisthorchiasis is associated with hepatobiliary damage, inflammation, periductal fibrosis and/or cellular responses to antigens from the infecting fluke (Sripa et al., 2007) and predisposes to CCA (Thamavit et al., 1978, Kim, 1984, Lee et al., 1993). Chronic hepatobiliary damage is considered to be multi-factorial, arising from a continued irritation of the bile duct epithelium by adult flukes, particularly their suckers, metabolites and excreted/secreted molecules (
Next-generation approaches for the sequencing and assembly/annotation of the transcriptomes of carcinogenic flukes
Recently, Young et al. (2010a) utilized 454 sequencing (Roche) from normalized cDNA libraries and a semi-automated bioinformatic platform to assemble and annotate non-redundant sequence datasets representative of the adult transcriptomes of C. sinensis and O. viverrini. Briefly, nucleotide sequences (> 500,000 per species) were assembled de novo and specifically clustered with similar protein coding domains. Redundancy was reduced by clustering sequences, if their predicted proteins aligned over
Major prospects for future -omic research of carcinogenic flukes — biological and biotechnological implications
Two studies conducted recently (Young et al., 2010a, Young et al., 2010b) provide a first, deep insight into the transcriptomes of carcinogenic liver flukes. For C. sinensis and O. viverrini, 50,000 unique sequences were identified. Comparative analyses revealed that most sequences (> 85%) produced for each species were new, thus expanding current databases (Cho et al., 2006, Laha et al., 2007, Cho et al., 2008, Ju et al., 2009) and providing a resource to research groups investigating molecular
Acknowledgements
Current research was supported by the Australian Research Council (RBG) and an Endeavour Fellowship (NDY).
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