The Opisthorchis viverrini genome provides insights into life in the bile duct

Opisthorchiasis is a neglected, tropical disease caused by the carcinogenic Asian liver fluke, Opisthorchis viverrini. This hepatobiliary disease is linked to malignant cancer (cholangiocarcinoma, CCA) and affects millions of people in Asia. No vaccine is available, and only one drug (praziquantel) is used against the parasite. Little is known about O. viverrini biology and the diseases that it causes. Here we characterize the draft genome (634.5 Mb) and transcriptomes of O. viverrini, elucidate how this fluke survives in the hostile environment within the bile duct and show that metabolic pathways in the parasite are highly adapted to a lipid-rich diet from bile and/or cholangiocytes. We also provide additional evidence that O. viverrini and other flukes secrete proteins that directly modulate host cell proliferation. Our molecular resources now underpin profound explorations of opisthorchiasis/CCA and the design of new interventions.

[1]  Z. Halpern,et al.  Bile and plasma lipid composition in non-obese normolipidemic subjects with and without cholesterol gallstones. , 2008, Liver.

[2]  R. Hrabal,et al.  The hairpin stack fold, a novel protein architecture for a new family of protein growth factors , 1996, Nature Structural Biology.

[3]  Y. Awasthi,et al.  Antioxidant role of glutathione S-transferases: protection against oxidant toxicity and regulation of stress-mediated apoptosis. , 2004, Antioxidants & redox signaling.

[4]  Martin Fusek,et al.  Cathepsin D--many functions of one aspartic protease. , 2008, Critical reviews in oncology/hematology.

[5]  S. Huh,et al.  Chromosomes of the liver fluke, Clonorchis sinensis. , 2000, The Korean journal of parasitology.

[6]  J. J. van Hellemond,et al.  Biochemical and evolutionary aspects of anaerobically functioning mitochondria. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[7]  A. Loukas,et al.  Gene discovery for the carcinogenic human liver fluke, Opisthorchis viverrini , 2007, BMC Genomics.

[8]  U. Fölsch,et al.  The amino acid composition of rat bile , 1977, Experientia.

[9]  R. Durbin,et al.  RNA sequence analysis using covariance models. , 1994, Nucleic acids research.

[10]  A. Loukas,et al.  RNA interference targeting cathepsin B of the carcinogenic liver fluke, Opisthorchis viverrini. , 2011, Parasitology international.

[11]  Ross S Hall,et al.  Molecular Changes in Opisthorchis viverrini (Southeast Asian Liver Fluke) during the Transition from the Juvenile to the Adult Stage , 2012, PLoS neglected tropical diseases.

[12]  S. Taylor-Robinson,et al.  Epidemiology, risk factors, and pathogenesis of cholangiocarcinoma. , 2008, HPB : the official journal of the International Hepato Pancreato Biliary Association.

[13]  M. McClelland,et al.  Bile acids mimic oxidative stress induced upregulation of thioredoxin reductase in colon cancer cell lines. , 2002, Carcinogenesis.

[14]  P. Sithithaworn,et al.  Early stage biliary and intrahepatic migration of Opisthorchis viverrini in the golden hamster , 2007, Journal of Helminthology.

[15]  Xuchu Hu,et al.  Molecular characterization of a novel Clonorchis sinensis secretory phospholipase A(2) and investigation of its potential contribution to hepatic fibrosis. , 2009, Molecular and biochemical parasitology.

[16]  J. Dalton,et al.  Fasciola hepatica: a secreted cathepsin L-like proteinase cleaves host immunoglobulin. , 1993, International journal for parasitology.

[17]  R. B. Short,et al.  Chromosomes of nine species of schistosomes. , 1960, The Journal of parasitology.

[18]  H. Ginsberg Lipoprotein physiology. , 1998, Endocrinology and metabolism clinics of North America.

[19]  P. Hotez,et al.  The metastasis‐associated protein‐1 gene encodes a host permissive factor for schistosomiasis, a leading global cause of inflammation and cancer , 2011, Hepatology.

[20]  R. Andrews,et al.  The zoonotic, fish-borne liver flukes Clonorchis sinensis, Opisthorchis felineus and Opisthorchis viverrini. , 2013, International journal for parasitology.

[21]  D. Parkin,et al.  The global health burden of infection‐associated cancers in the year 2002 , 2006, International journal of cancer.

[22]  S. Hanai,et al.  Genetic and environmental determinants of risk for cholangiocarcinoma via Opisthorchis viverrini in a densely infested area in Nakhon Phanom, northeast Thailand , 2005, International journal of cancer.

[23]  George M. Church,et al.  Heritable genome editing in C. elegans via a CRISPR-Cas9 system , 2013, Nature Methods.

[24]  A. Loukas,et al.  The tumorigenic liver fluke Opisthorchis viverrini--multiple pathways to cancer. , 2012, Trends in parasitology.

[25]  Jian Wang,et al.  Whole-genome sequence of Schistosoma haematobium , 2012, Nature Genetics.

[26]  A. Bateman,et al.  Granulins: the structure and function of an emerging family of growth factors. , 1998, The Journal of endocrinology.

[27]  A. V. Katokhin,et al.  Comparative cytogenetics of opisthorchid species (Trematoda, Opisthorchiidae). , 2012, Parasitology international.

[28]  A. Linde,et al.  Slow earthquakes triggered by typhoons , 2009, Nature.

[29]  D. Keppler,et al.  Substrate specificity of human ABCC4 (MRP4)-mediated cotransport of bile acids and reduced glutathione. , 2006, American journal of physiology. Gastrointestinal and liver physiology.

[30]  C. Pairojkul,et al.  Cholangiocarcinoma: lessons from Thailand , 2008, Current opinion in gastroenterology.

[31]  M. Sánchez-Moreno,et al.  Superoxide dismutase in cestodes. Isoenzymatic characterization and studies of inhibition by a series of benzimidazoles and by pyrimidine derivatives of recent synthesis. , 1987, Arzneimittel-Forschung.

[32]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[33]  J. Boyer,et al.  Bile salt transporters: molecular characterization, function, and regulation. , 2003, Physiological reviews.

[34]  J. Dalton,et al.  Schistosome asparaginyl endopeptidase SM32 in hemoglobin digestion. , 1996, Parasitology today.

[35]  N. Ahmed,et al.  Host-lipidome as a potential target of protozoan parasites. , 2013, Microbes and infection.

[36]  Xiao-yun Wang,et al.  The Carcinogenic Liver Fluke, Clonorchis sinensis: New Assembly, Reannotation and Analysis of the Genome and Characterization of Tissue Transcriptomes , 2013, PloS one.

[37]  L. Moens,et al.  Trematode hemoglobins show exceptionally high oxygen affinity. , 1998, Biophysical journal.

[38]  I. Brook Aerobic and anaerobic microbiology of biliary tract disease , 1989, Journal of clinical microbiology.

[39]  A. Rigotti,et al.  Enrichment of canalicular membrane with cholesterol and sphingomyelin prevents bile salt-induced hepatic damage. , 1999, Journal of lipid research.

[40]  W. Balch,et al.  NPC1/NPC2 function as a tag team duo to mobilize cholesterol , 2008, Proceedings of the National Academy of Sciences.

[41]  Y. Bahk,et al.  A family of cathepsin F cysteine proteases of Clonorchis sinensis is the major secreted proteins that are expressed in the intestine of the parasite. , 2010, Molecular and biochemical parasitology.

[42]  humAn cArcinogens,et al.  [Biological agents]. , 2009, Nihon rinsho. Japanese journal of clinical medicine.

[43]  Aaron Ciechanover,et al.  The ubiquitin–proteasome pathway: on protein death and cell life , 1998, The EMBO journal.

[44]  Helen H. Hobbs,et al.  Identification of Scavenger Receptor SR-BI as a High Density Lipoprotein Receptor , 1996, Science.

[45]  T. Aoki,et al.  Paragonimus westermani possesses aerobic and anaerobic mitochondria in different tissues, adapting to fluctuating oxygen tension in microaerobic habitats. , 2010, International journal for parasitology.

[46]  J. Dalton,et al.  A Family of Helminth Molecules that Modulate Innate Cell Responses via Molecular Mimicry of Host Antimicrobial Peptides , 2011, PLoS pathogens.

[47]  N. LaRusso,et al.  Intrahepatic bile ducts transport water in response to absorbed glucose. , 2002, American journal of physiology. Cell physiology.

[48]  Wei Huang,et al.  The Schistosoma japonicum genome reveals features of host–parasite interplay , 2009, Nature.

[49]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[50]  Jason Mulvenna,et al.  A Granulin-Like Growth Factor Secreted by the Carcinogenic Liver Fluke, Opisthorchis viverrini, Promotes Proliferation of Host Cells , 2009, PLoS pathogens.

[51]  Sang-Haeng Choi,et al.  Developmental Transcriptomic Features of the Carcinogenic Liver Fluke, Clonorchis sinensis , 2011, PLoS neglected tropical diseases.

[52]  John P. Overington,et al.  The genome of the blood fluke Schistosoma mansoni , 2009, Nature.

[53]  R. Maizels,et al.  Immunomodulation by helminth parasites: defining mechanisms and mediators. , 2013, International journal for parasitology.

[54]  Jacqueline A. Keane,et al.  The genomes of four tapeworm species reveal adaptations to parasitism , 2013, Nature.

[55]  Ross S Hall,et al.  Unlocking the Transcriptomes of Two Carcinogenic Parasites, Clonorchis sinensis and Opisthorchis viverrini , 2010, PLoS neglected tropical diseases.

[56]  Ramon Moreno Lessons from Thailand , 1997 .

[57]  Bin Tean Teh,et al.  Exome sequencing of liver fluke–associated cholangiocarcinoma , 2012, Nature Genetics.

[58]  M. Miwa,et al.  Gene expression profiling defined pathways correlated with fibroblast cell proliferation induced by Opisthorchis viverrini excretory/secretory product. , 2006, World journal of gastroenterology.

[59]  A. Zaha,et al.  Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica , 2010, BMC Genomics.

[60]  A. Loukas,et al.  The secreted and surface proteomes of the adult stage of the carcinogenic human liver fluke Opisthorchis viverrini , 2010, Proteomics.

[61]  C. Wongkham,et al.  Chromosomes and karyotype analysis of a liver fluke, Opisthorchis viverrini, by scanning electron microscopy. , 2012, Parasitology international.

[62]  U. Beuers,et al.  The biliary HCO3− umbrella: A unifying hypothesis on pathogenetic and therapeutic aspects of fibrosing cholangiopathies , 2010, Hepatology.

[63]  I. Kang,et al.  Differential Activation of Diverse Glutathione Transferases of Clonorchis sinensis in Response to the Host Bile and Oxidative Stressors , 2013, PLoS neglected tropical diseases.

[64]  Alex Loukas,et al.  Advanced periductal fibrosis from infection with the carcinogenic human liver fluke Opisthorchis viverrini correlates with elevated levels of interleukin‐6 , 2009, Hepatology.

[65]  J. Lobaccaro,et al.  Bile acids: from digestion to cancers. , 2013, Biochimie.

[66]  Jennifer Keiser,et al.  Food-Borne Trematodiases , 2009, Clinical Microbiology Reviews.

[67]  P. Vounatsou,et al.  Efficacy and safety of mefloquine, artesunate, mefloquine-artesunate, tribendimidine, and praziquantel in patients with Opisthorchis viverrini: a randomised, exploratory, open-label, phase 2 trial. , 2011, The Lancet. Infectious diseases.

[68]  G. Núñez,et al.  ML -- a conserved domain involved in innate immunity and lipid metabolism. , 2002, Trends in biochemical sciences.

[69]  E. Furlong,et al.  Transcription factors: from enhancer binding to developmental control , 2012, Nature Reviews Genetics.

[70]  K. Straif,et al.  A review of human carcinogens--Part B: biological agents. , 2009, The Lancet. Oncology.