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

Abstract

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.

Figure 1. Processes proposed to take place during the establishment of Opisthorchis viverrini in the bile duct and the subsequent pathogenesis of biliary disease and associated cholangiocarcinoma.

This proposal integrates salient information from the present study (*) and considers published literature. Metastasis-associated protein 1-mediated fibrosis and transformation of cell cycle progress are linked to: transforming growth factor-beta (TGF-beta) and epidermal growth factor receptor (EGFR)-mediated cell proliferation, associated with an upregulation in Toll-like receptor 4 (TLR4), TGF-beta-stimulated clone 22 homologue (TSC22D1) and EGFR pathway substrate 8 (EPS8); cell cycle activation and cytokinesis associated with an upregulation in dual specificity protein kinase TTK (TTK), serine/threonine kinase 6 (STK6), CDC28 protein kinase regulatory subunit 2 (CKS2), budding uninhibited by benzimidazoles 1 mitotic checkpoint serine/threonine kinase (BUB1 and BUB1B), cell division cycle 20 (CDC20), protein regulator of cytokinesis 1 (PRC1), kinesin family member 2C (KIF2C); and endogenous/exogenous xenobiotic metabolism associated with an upregulation in UDP glucuronosyltransferase 1 family, polypeptide A10 (UGT1A10); UGT 2 family B11 (UGT2B11), carbohydrate sulphotransferase 4 (CHST4) and sulphotransferase family, cytosolic, 1C, member 1 (SULT1C1). Chronic opisthorchiasis is linked to genetic alterations in tumour protein 53 (TP53: 44.4% cases), mothers against decapentaplegic homologue 4 (SMAD4; 16.7%), Kirsten rat sarcoma viral oncogene (KRAS; 16.7%), histone-lysine N-methyltransferase (MLL3; 14.8%), roundabout homologue 2 (ROBO2; 9.3%), guanine nucleotide-binding protein (GNAS; 9.3%) and ring finger protein 43 (RFN43; 9.3%).

Figure 2. Opisthorchis viverrini biological pathways linked to life in the human bile duct.

O. viverrini genes (boxed) associated with responses to environmental stressors or the processing of abundant nutrients found within the bile duct. Genes unique to opisthorchiids (that is, found in O. viverrini and Clonorchis sinensis) or gene families, which have expanded within this group of flukes are shown in red. Pathways required for the degradation and uptake of micelles, including very-low (VLDL), low (LDL), intermediate (IDL) and high density lipoproteins (HDL), are represented by blue arrows.

Figure 3. Opisthorchis viverrini and Clonorchis sinensis proteins with at least one granulin domain.

(a) Alignment of the amino acid sequences translated from O. viverrini and C. sinensis protein-coding regions of putative progranulin (PGRN) and granulin (GRN-1 and GRN-2) genes, displaying the structural organization of the signal peptide and cysteine-rich granulin domain/s (InterProScan ID: IPR000118). Conserved granulin domain residues are highlighted in yellow. (b) Amino acid logos of conserved granulin domains encoded within O. viverrini and C. sinensis granulins (GRN-1 and GRN-2; one granulin domain each), PGRN (eight domains per protein) and human PGRN (seven granulin domains). Logo is coloured on the basis of amino acid chemistry, where amino acid residues are grouped by colour, depending on their chemical characteristics, so that polar residues (G, S, T, Y and C) are green, neutral (Q and N) are purple, basic (K, R and H) are blue, acidic (D and E) are red and hydrophobic (A, V, L, I, P, W, F and M) are black. Residue height denotes the measure of uncertainty for each residue (in bits per symbol). (c) Alignment of the predicted mature opisthorchiid-specific granulin proteins.