1
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Sohail I, Hassan MU, Schmid D, Chiba P. The noncanonical nucleotide binding site 1 of the bile salt export pump is optimized for proper function of the transporter. Cell Biol Int 2024; 48:638-646. [PMID: 38328902 DOI: 10.1002/cbin.12136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/19/2023] [Accepted: 01/28/2024] [Indexed: 02/09/2024]
Abstract
The bile salt export pump (ABCB11/BSEP) is a hepatocyte plasma membrane-resident protein translocating bile salts into bile canaliculi. The sequence alignment of the four full-length transporters of the ABCB subfamily (ABCB1, ABCB4, ABCB5 and ABCB11) indicates that the NBD-NBD contact interface of ABCB11 differs from that of other members in only four residues. Notably, these are all located in the noncanonical nucleotide binding site 1 (NBS1). Substitution of all four deviant residues with canonical ones (quadruple mutant) significantly decreased the transport activity of the protein. In this study, we mutated two deviant residues in the signature sequence to generate a double mutant (R1221G/E1223Q). Furthermore, a triple mutant (E502S/R1221G/E1223Q) was generated, in which the deviant residues of the signature sequence and Q-loop were mutated concurrently to canonical residues. The double and triple mutants showed 80% and 60%, respectively, of the activity of wild-type BSEP. As expected, an increasing number of mutations gradually impair transport as an intricate network of interactions within the ABC proteins ensures proper functioning.
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Affiliation(s)
- Imran Sohail
- Department of Zoology, Government College University Lahore, Lahore, Pakistan
- Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Mahmood Ul Hassan
- Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore, Pakistan
| | - Diethart Schmid
- Institute of Physiology, Medical University of Vienna, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
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2
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Liu H, Irobalieva RN, Kowal J, Ni D, Nosol K, Bang-Sørensen R, Lancien L, Stahlberg H, Stieger B, Locher KP. Structural basis of bile salt extrusion and small-molecule inhibition in human BSEP. Nat Commun 2023; 14:7296. [PMID: 37949847 PMCID: PMC10638440 DOI: 10.1038/s41467-023-43109-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
BSEP (ABCB11) is an ATP-binding cassette transporter that is expressed in hepatocytes and extrudes bile salts into the canaliculi of the liver. BSEP dysfunction, caused by mutations or induced by drugs, is frequently associated with severe cholestatic liver disease. We report the cryo-EM structure of glibenclamide-bound human BSEP in nanodiscs, revealing the basis of small-molecule inhibition. Glibenclamide binds the apex of a central binding pocket between the transmembrane domains, preventing BSEP from undergoing conformational changes, and thus rationalizing the reduced uptake of bile salts. We further report two high-resolution structures of BSEP trapped in distinct nucleotide-bound states by using a catalytically inactivated BSEP variant (BSEPE1244Q) to visualize a pre-hydrolysis state, and wild-type BSEP trapped by vanadate to visualize a post-hydrolysis state. Our studies provide structural and functional insight into the mechanism of bile salt extrusion and into small-molecule inhibition of BSEP, which may rationalize drug-induced liver toxicity.
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Affiliation(s)
- Hongtao Liu
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | | | - Julia Kowal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Kamil Nosol
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Rose Bang-Sørensen
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Loïck Lancien
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Bruno Stieger
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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3
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In Vitro Rescue of the Bile Acid Transport Function of ABCB11 Variants by CFTR Potentiators. Int J Mol Sci 2022; 23:ijms231810758. [PMID: 36142670 PMCID: PMC9502978 DOI: 10.3390/ijms231810758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
ABCB11 is responsible for biliary bile acid secretion at the canalicular membrane of hepatocytes. Variations in the ABCB11 gene cause a spectrum of rare liver diseases. The most severe form is progressive familial intrahepatic cholestasis type 2 (PFIC2). Current medical treatments have limited efficacy. Here, we report the in vitro study of Abcb11 missense variants identified in PFIC2 patients and their functional rescue using cystic fibrosis transmembrane conductance regulator potentiators. Three ABCB11 disease-causing variations identified in PFIC2 patients (i.e., A257V, T463I and G562D) were reproduced in a plasmid encoding an Abcb11-green fluorescent protein. After transfection, the expression and localization of the variants were studied in HepG2 cells. Taurocholate transport activity and the effect of potentiators were studied in Madin–Darby canine kidney (MDCK) clones coexpressing Abcb11 and the sodium taurocholate cotransporting polypeptide (Ntcp/Slc10A1). As predicted using three-dimensional structure analysis, the three variants were expressed at the canalicular membrane but showed a defective function. Ivacaftor, GLP1837, SBC040 and SBC219 potentiators increased the bile acid transport of A257V and T463I and to a lesser extent, of G562D Abcb11 missense variants. In addition, a synergic effect was observed when ivacaftor was combined with SBC040 or SBC219. Such potentiators could represent new pharmacological approaches for improving the condition of patients with ABCB11 deficiency due to missense variations affecting the function of the transporter.
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4
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Balasubramaniyan N, Devereaux MW, Orlicky DJ, Sokol RJ, Suchy FJ. miR-199a-5p inhibits the Expression of ABCB11 in Obstructive Cholestasis. J Biol Chem 2021; 297:101400. [PMID: 34774795 PMCID: PMC8665360 DOI: 10.1016/j.jbc.2021.101400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
ATP-binding cassette, subfamily B member 11 (ABCB11) is an efflux transporter for bile acids on the liver canalicular membrane. The expression of this transporter is reduced in cholestasis; however, the mechanisms contributing to this reduction are unclear. In this study, we sought to determine whether miR-199a-5p contributes to the depletion of ABCB11/Abcb11 in cholestasis in mice. In a microRNA (miRNA) screen of mouse liver after common bile duct ligation (CBDL), we found that miR-199a-5p was significantly upregulated by approximately fourfold. In silico analysis predicted that miR-199a-5p would target the 3′-untranslated region (3′-UTR) of ABCB11/Abcb11 mRNA. The expression of ABCB11-3′-UTR luciferase construct in Huh-7 cells was markedly inhibited by cotransfection of a miRNA-199a-5p mimic, which was reversed by an miRNA-199a-5p mimic inhibitor. We also show treatment of mice after CBDL with the potent nuclear receptor FXR agonist obeticholic acid (OCA) significantly increased Abcb11 mRNA and protein and decreased miR-199a-5p expression. Computational mapping revealed a well-conserved FXR-binding site (FXRE) in the promoter of the gene encoding miR-199a-5, termed miR199a-2. Electromobility shift, chromatin immunoprecipitation, and miR199a-2 promoter-luciferase assays confirmed that this binding site was functional. Finally, CBDL in mice led to depletion of nuclear repressor NcoR1 binding at the miR199a-2 promoter, which facilitates transcription of miR199a-2. In CBDL mice treated with OCA, NcoR1 recruitment to the miR199a-2 FXRE was maintained at levels found in sham-operated mice. In conclusion, we demonstrate that miR-199a-5p is involved in regulating ABCB11/Abcb11 expression, is aberrantly upregulated in obstructive cholestasis, and is downregulated by the FXR agonist OCA.
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Affiliation(s)
| | - Michael W Devereaux
- Department of Pediatrics, Digestive Health Institute, Children's Hospital Colorado
| | - David J Orlicky
- Department of Pathology, University of Colorado School of Medicine, 13123 East 16(th) Avenue, Aurora, Colorado 80045
| | - Ronald J Sokol
- Department of Pediatrics, Digestive Health Institute, Children's Hospital Colorado
| | - Frederick J Suchy
- Department of Pediatrics, Digestive Health Institute, Children's Hospital Colorado.
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5
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Yeh HI, Yu YC, Kuo PL, Tsai CK, Huang HT, Hwang TC. Functional stability of CFTR depends on tight binding of ATP at its degenerate ATP-binding site. J Physiol 2021; 599:4625-4642. [PMID: 34411298 DOI: 10.1113/jp281933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/13/2021] [Indexed: 01/28/2023] Open
Abstract
Opening of the cystic fibrosis transmembrane conductance regulator (CFTR) channel is coupled to the motion of its two nucleotide-binding domains: they form a heterodimer sandwiching two functionally distinct ATP-binding sites (sites 1 and 2). While active ATP hydrolysis in site 2 triggers rapid channel closure, the functional role of stable ATP binding in the catalysis-incompetent (or degenerate) site 1, a feature conserved in many other ATP-binding cassette (ABC) transporter proteins, remains elusive. Here, we found that CFTR loses its prompt responsiveness to ATP after the channel is devoid of ATP for tens to hundreds of seconds. Mutants with weakened ATP binding in site 1 and the most prevalent disease-causing mutation, F508del, are more vulnerable to ATP depletion. In contrast, strengthening ligand binding in site 1 with N6 -(2-phenylethyl)-ATP, a high-affinity ATP analogue, or abolishing ATP hydrolysis in site 2 by the mutation D1370N, helps sustain a durable function of the otherwise unstable mutant channels. Thus, tight binding of ATP in the degenerate ATP-binding site is crucial to the functional stability of CFTR. Small molecules targeting site 1 may bear therapeutic potential to overcome the membrane instability of F508del-CFTR. KEY POINTS: During evolution, many ATP-binding cassette transporters - including the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, whose dysfunction causes cystic fibrosis (CF) - lose the ability to hydrolyse ATP in one of the two ATP-binding sites. Here we show that tight ATP binding at this degenerate site in CFTR is central for maintaining the stable, robust function of normal CFTR. We also demonstrate that membrane instability of the most common CF-causing mutant, F508del-CFTR, can be rescued by strengthening ATP binding at CFTR's degenerate site. Our data thus explain an evolutionary puzzle and offer a potential therapeutic strategy for CF.
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Affiliation(s)
- Han-I Yeh
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ying-Chun Yu
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Pei-Lun Kuo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Kuang Tsai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsin-Tuan Huang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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6
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Sohail MI, Dönmez-Cakil Y, Szöllősi D, Stockner T, Chiba P. The Bile Salt Export Pump: Molecular Structure, Study Models and Small-Molecule Drugs for the Treatment of Inherited BSEP Deficiencies. Int J Mol Sci 2021; 22:E784. [PMID: 33466755 PMCID: PMC7830293 DOI: 10.3390/ijms22020784] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The bile salt export pump (BSEP/ABCB11) is responsible for the transport of bile salts from hepatocytes into bile canaliculi. Malfunction of this transporter results in progressive familial intrahepatic cholestasis type 2 (PFIC2), benign recurrent intrahepatic cholestasis type 2 (BRIC2) and intrahepatic cholestasis of pregnancy (ICP). Over the past few years, several small molecular weight compounds have been identified, which hold the potential to treat these genetic diseases (chaperones and potentiators). As the treatment response is mutation-specific, genetic analysis of the patients and their families is required. Furthermore, some of the mutations are refractory to therapy, with the only remaining treatment option being liver transplantation. In this review, we will focus on the molecular structure of ABCB11, reported mutations involved in cholestasis and current treatment options for inherited BSEP deficiencies.
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Affiliation(s)
| | - Yaprak Dönmez-Cakil
- Department of Histology and Embryology, Faculty of Medicine, Maltepe University, Maltepe, 34857 Istanbul, Turkey;
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, 13A, 1090 Vienna, Austria;
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, 13A, 1090 Vienna, Austria;
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, 10, 1090 Vienna, Austria
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7
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Stockner T, Gradisch R, Schmitt L. The role of the degenerate nucleotide binding site in type I ABC exporters. FEBS Lett 2020; 594:3815-3838. [PMID: 33179257 PMCID: PMC7756269 DOI: 10.1002/1873-3468.13997] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/26/2020] [Accepted: 10/15/2020] [Indexed: 12/18/2022]
Abstract
ATP‐binding cassette (ABC) transporters are fascinating molecular machines that are capable of transporting a large variety of chemically diverse compounds. The energy required for translocation is derived from binding and hydrolysis of ATP. All ABC transporters share a basic architecture and are composed of two transmembrane domains and two nucleotide binding domains (NBDs). The latter harbor all conserved sequence motifs that hallmark the ABC transporter superfamily. The NBDs form the nucleotide binding sites (NBSs) in their interface. Transporters with two active NBSs are called canonical transporters, while ABC exporters from eukaryotic organisms, including humans, frequently have a degenerate NBS1 containing noncanonical residues that strongly impair ATP hydrolysis. Here, we summarize current knowledge on degenerate ABC transporters. By integrating structural information with biophysical and biochemical evidence of asymmetric function, we develop a model for the transport cycle of degenerate ABC transporters. We will elaborate on the unclear functional advantages of a degenerate NBS.
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Affiliation(s)
- Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ralph Gradisch
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
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8
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Goda K, Dönmez-Cakil Y, Tarapcsák S, Szalóki G, Szöllősi D, Parveen Z, Türk D, Szakács G, Chiba P, Stockner T. Human ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion. PLoS Genet 2020; 16:e1009016. [PMID: 33031417 PMCID: PMC7544095 DOI: 10.1371/journal.pgen.1009016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/29/2020] [Indexed: 11/28/2022] Open
Abstract
Several ABC exporters carry a degenerate nucleotide binding site (NBS) that is unable to hydrolyze ATP at a rate sufficient for sustaining transport activity. A hallmark of a degenerate NBS is the lack of the catalytic glutamate in the Walker B motif in the nucleotide binding domain (NBD). The multidrug resistance transporter ABCB1 (P-glycoprotein) has two canonical NBSs, and mutation of the catalytic glutamate E556 in NBS1 renders ABCB1 transport-incompetent. In contrast, the closely related bile salt export pump ABCB11 (BSEP), which shares 49% sequence identity with ABCB1, naturally contains a methionine in place of the catalytic glutamate. The NBD-NBD interfaces of ABCB1 and ABCB11 differ only in four residues, all within NBS1. Mutation of the catalytic glutamate in ABCB1 results in the occlusion of ATP in NBS1, leading to the arrest of the transport cycle. Here we show that despite the catalytic glutamate mutation (E556M), ABCB1 regains its ATP-dependent transport activity, when three additional diverging residues are also replaced. Molecular dynamics simulations revealed that the rescue of ATPase activity is due to the modified geometry of NBS1, resulting in a weaker interaction with ATP, which allows the quadruple mutant to evade the conformationally locked pre-hydrolytic state to proceed to ATP-driven transport. In summary, we show that ABCB1 can be transformed into an active transporter with only one functional catalytic site by preventing the formation of the ATP-locked pre-hydrolytic state in the non-canonical site. ABC transporters are one of the largest membrane protein superfamilies, present in all organisms from archaea to humans. They transport a wide range of molecules including amino acids, sugars, vitamins, nucleotides, peptides, lipids, metabolites, antibiotics, and xenobiotics. ABC transporters energize substrate transport by hydrolyzing ATP in two symmetrically arranged nucleotide binding sites (NBSs). The human multidrug resistance transporter ABCB1 has two active NBSs, and it is generally believed that integrity and cooperation of both sites are needed for transport. Several human ABC transporters, such as the bile salt transporter ABCB11, have one degenerate NBS, which has significantly reduced ATPase activity. Interestingly, unilateral mutations affecting one of the two NBSs completely abolish the function of symmetrical ABC transporters. Here we engineered an ABCB1 variant with a degenerate, ABCB11-like NBS1, which can nevertheless transport substrates. Our results indicate that ABCB1 can mediate active transport with a single active site, questioning the validity of models assuming strictly alternating catalysis.
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Affiliation(s)
- Katalin Goda
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Yaprak Dönmez-Cakil
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Histology and Embryology, Faculty of Medicine, Maltepe University, Maltepe, Istanbul, Turkey
| | - Szabolcs Tarapcsák
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Gábor Szalóki
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
| | - Zahida Parveen
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Dóra Türk
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
- Institute of Cancer Research, Medical University of Vienna, Borschkegasse, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
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9
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Zhang C, Zhang B, Meng D, Ge C. Comprehensive analysis of DNA methylation and gene expression profiles in cholangiocarcinoma. Cancer Cell Int 2019; 19:352. [PMID: 31889904 PMCID: PMC6933876 DOI: 10.1186/s12935-019-1080-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The incidence of cholangiocarcinoma (CCA) has risen in recent years, and it has become a significant health burden worldwide. However, the mechanisms underlying tumorigenesis and progression of this disease remain largely unknown. An increasing number of studies have demonstrated crucial biological functions of epigenetic modifications, especially DNA methylation, in CCA. The present study aimed to identify and analyze methylation-regulated differentially expressed genes (MeDEGs) involved in CCA tumorigenesis and progression by bioinformatics analysis. METHODS The gene expression profiling dataset (GSE119336) and gene methylation profiling dataset (GSE38860) were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified using the limma packages of R and GEO2R, respectively. The MeDEGs were obtained by overlapping the DEGs and DMGs. Functional enrichment analyses of these genes were then carried out. Protein-protein interaction (PPI) networks were constructed using STRING and visualized in Cytoscape to determine hub genes. Finally, the results were verified based on The Cancer Genome Atlas (TCGA) database. RESULTS We identified 98 hypermethylated, downregulated genes and 93 hypomethylated, upregulated genes after overlapping the DEGs and DMGs. These genes were mainly enriched in the biological processes of the cell cycle, nuclear division, xenobiotic metabolism, drug catabolism, and negative regulation of proteolysis. The top nine hub genes of the PPI network were F2, AHSG, RRM2, AURKB, CCNA2, TOP2A, BIRC5, PLK1, and ASPM. Moreover, the expression and methylation status of the hub genes were significantly altered in TCGA. CONCLUSIONS Our study identified novel methylation-regulated differentially expressed genes (MeDEGs) and explored their related pathways and functions in CCA, which may provide novel insights into a further understanding of methylation-mediated regulatory mechanisms in CCA.
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Affiliation(s)
- Cheng Zhang
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Bingye Zhang
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Di Meng
- Department of Gerontology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Chunlin Ge
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
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10
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Wen X, Hu Y, Zhang X, Wei X, Wang T, Yin S. Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus. BMC Genomics 2019; 20:563. [PMID: 31286856 PMCID: PMC6615287 DOI: 10.1186/s12864-019-5915-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Understanding of the cold-tolerance mechanisms of this species is still limited. Integrated application of multi-omics research can provide a wealth of information to help us improve our understanding of low-temperature tolerance in fish. RESULTS To gain a comprehensive and unbiased molecular understanding of cold-tolerance in T. fasciatus, we characterized mRNA-seq and metabolomics of T. fasciatus livers using Illumina HiSeq 2500 and UHPLC-Q-TOF MS. We identified 2544 up-regulated and 2622 down-regulated genes in the liver of T. fasciatus. A total of 40 differential metabolites were identified, including 9 down-regulated and 31 up-regulated metabolites. In combination with previous studies on proteomics, we have established an mRNA-protein-metabolite interaction network. There are 17 DEMs (differentially-expressed metabolites) and 14 DEGs-DEPs (differentially co-expressed genes and proteins) in the interaction network that are mainly involved in fatty acids metabolism, membrane transport, signal transduction, and DNA damage and defense. We then validated a number of genes in the interaction network by qRT-PCR. Additionally, a number of SNPs (single nucleotide polymorphisms) were revealed through the transcriptome data. These results provide key information for further understanding of the molecular mechanisms of T. fasciatus under cold stress. CONCLUSION The data generated by integrated application of multi-omics can facilitate our understanding of the molecular mechanisms of fish response to low temperature stress. We have not only identified potential genes and SNPs involved in cold tolerance, but also show that some nutrient metabolites may be added to the diet to help the overwintering of T. fasciatus.
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Affiliation(s)
- Xin Wen
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Yadong Hu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Xinyu Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Xiaozhen Wei
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Tao Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Shaowu Yin
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
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11
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Zhou J, Yao Y, Huang X, Chen D, Zhang T, Zhang Y. Association between bile salt export pump polymorphisms and intrahepatic cholestasis of pregnancy susceptibility: a meta-analysis of case-control studies. Gynecol Endocrinol 2019; 35:179-183. [PMID: 30614300 DOI: 10.1080/09513590.2018.1512570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The purpose of this meta-analysis was to investigate the relationship between bile salt export pump (BSEP) polymorphisms and intrahepatic cholestasis of pregnancy (ICP) susceptibility. Retrieved studies from Pubmed, EMBASE, Web of Science, Cochrane Library and CBM databases about BSEP polymorphisms and ICP susceptibility were included. Odds ratio (OR) and 95% confidence interval (CI) and publication bias were calculated. Ten related case-control studies on BSEP polymorphisms and ICP susceptibility were included. The pooled results showed a significant association between BSEP rs2287622 polymorphism and ICP risk in Asian population (OR >1, p < .01 for A vs. a and AA vs. Aa/aa) and general population (OR >1, p < .05 for A vs. a, Aa vs. aa, AA/Aa vs. aa), and a borderline statistical significance was found between BSEP rs473351 polymorphism and ICP susceptibility (OR = 1.66, p < .05), and no statistical significance was found in D482G or rs853782 polymorphisms and ICP risk (all p > .05). Additionally, no publication bias was found in these studies (all p > .05). Our current meta-analysis indicated that BSEP rs2287622 polymorphism could increase the susceptibility of ICP in Asians and in general populations, while rs473351, D482G, and rs853782 polymorphisms were not obviously associated with ICP risk, but it needs further larger study with ethnicity and various etiologies.
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Affiliation(s)
- Jie Zhou
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
| | - Ying Yao
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
| | - Xiaoping Huang
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
| | - Daozhen Chen
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
| | - Ting Zhang
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
| | - Yan Zhang
- a Department of Pharmacy , Wuxi Maternal and Child Health Hospital , Wuxi , Jiangsu Province , China
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