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Lin LZ, Wu QY, Zhang JH, Li SJ, Wu WZ, Ruan DD, Wu M, Chen Q, Liao LS, Fang ZT, Luo JW, Li ZA, Li Z, Li H. A pedigree analysis of Rotor hyperbilirubinemia combined with hepatitis B virus infection in a SLCO1B1 and SLCO1B3 gene mutations patient. Heliyon 2024; 10:e33864. [PMID: 39071607 PMCID: PMC11283089 DOI: 10.1016/j.heliyon.2024.e33864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
Background Rotor syndrome (RS, OMIM#237450) is an extremely rare autosomal digenic recessive disorder characterized by mild non-hemolytic hereditary conjugated hyperbilirubinemia, caused by biallelic variation of SLCO1B1 and SLCO1B3 genes that resulted in OATP1B1/B3 dysfunction in the sinusoidal membrane leading to impaired bilirubin reuptake ability of hepatocytes. Methods One RS pedigree was recruited and clinical features were documented. Whole genome second-generation sequencing was used to screen candidate genes and mutations, Sanger sequencing confirmed predicted mutations. Results This study detected a homozygous nonsense variant c.1738C > T (p.R580*) in the coding region of the SLCO1B1 (NM006446) gene in a family with RS and hepatitis B virus infection by Variants analysis and Sanger sequencing, and confirmed by Copy Number Variation (CNV) analysis and Long Range PCR that there was a homozygous insertion of intron 5 of the SLCO1B3 gene into intron 5 of long-interspersed element 1 (LINE1). A few cases of such haplotypes have been reported in East Asian populations. A hepatitis B virus infection with fatty liver disease was indicated by pathology, which revealed mild-moderate lobular inflammation, moderate lobular inflammation, moderate hepatocellular steatosis, and fibrosis stage 1-2 (NAS score: 4 points/S1-2) alterations. Heterozygotes carrying p.R580* and LINE1 insertions were also detected in family members (I1, I2, III2, III3), but they did not develop conjugated hyperbilirubinemia. Conclusion The mutations may be the molecular genetic foundation for the presence of SLCO1B1 c.1738C > T(p.R580*) and SLCO1B3 (LINE1) in this RS pedigree.
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Affiliation(s)
- Li-zhen Lin
- Department of Traditional Chinese Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Traditional Chinese Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Qiu-yan Wu
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Jian-hui Zhang
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Shi-jie Li
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Wei-zhen Wu
- Xiyuan Clinical Medical College of Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Dan-dan Ruan
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Min Wu
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Qian Chen
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Li-sheng Liao
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Zhu-Ting Fang
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Jie-wei Luo
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Zuo-an Li
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Department of Emergency, Fujian provincial hospital, Fuzhou, 350001, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fujian Provincial Institute of Emergency Medicine, Fujian Emergency Medical Center, Fuzhou, 350001, China
| | - Zhou Li
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Hong Li
- Fujian provincial hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Department of Emergency, Fujian provincial hospital, Fuzhou, 350001, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fujian Provincial Institute of Emergency Medicine, Fujian Emergency Medical Center, Fuzhou, 350001, China
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Kojima S, Koyama S, Ka M, Saito Y, Parrish EH, Endo M, Takata S, Mizukoshi M, Hikino K, Takeda A, Gelinas AF, Heaton SM, Koide R, Kamada AJ, Noguchi M, Hamada M, Kamatani Y, Murakawa Y, Ishigaki K, Nakamura Y, Ito K, Terao C, Momozawa Y, Parrish NF. Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk. Nat Genet 2023:10.1038/s41588-023-01390-2. [PMID: 37169872 DOI: 10.1038/s41588-023-01390-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
Mobile genetic elements (MEs) are heritable mutagens that recursively generate structural variants (SVs). ME variants (MEVs) are difficult to genotype and integrate in statistical genetics, obscuring their impact on genome diversification and traits. We developed a tool that accurately genotypes MEVs using short-read whole-genome sequencing (WGS) and applied it to global human populations. We find unexpected population-specific MEV differences, including an Alu insertion distribution distinguishing Japanese from other populations. Integrating MEVs with expression quantitative trait loci (eQTL) maps shows that MEV classes regulate tissue-specific gene expression by shared mechanisms, including creating or attenuating enhancers and recruiting post-transcriptional regulators, supporting class-wide interpretability. MEVs more often associate with gene expression changes than SNVs, thus plausibly impacting traits. Performing genome-wide association study (GWAS) with MEVs pinpoints potential causes of disease risk, including a LINE-1 insertion associated with keloid and fasciitis. This work implicates MEVs as drivers of human divergence and disease risk.
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Affiliation(s)
- Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Mirei Ka
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Next-Generation Precision Medicine Development, Integrative Genomics Laboratory, Graduate School of Medicine, Department of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuka Saito
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Erica H Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sadaaki Takata
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Misaki Mizukoshi
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takeda
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Asami F Gelinas
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Steven M Heaton
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Rie Koide
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Anselmo J Kamada
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Paleovirology Lab, Department of Biology, University of Oxford, Oxford, UK
| | - Michiya Noguchi
- Cell Engineering Division, BioResource Research Center, RIKEN, Tsukuba, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukio Nakamura
- Cell Engineering Division, BioResource Research Center, RIKEN, Tsukuba, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.
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Ramsey LB, Gong L, Lee SB, Wagner JB, Zhou X, Sangkuhl K, Adams SM, Straka RJ, Empey PE, Boone EC, Klein TE, Niemi M, Gaedigk A. PharmVar GeneFocus: SLCO1B1. Clin Pharmacol Ther 2023; 113:782-793. [PMID: 35797228 PMCID: PMC10900141 DOI: 10.1002/cpt.2705] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 11/06/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) is now providing star (*) allele nomenclature for the highly polymorphic human SLCO1B1 gene encoding the organic anion transporting polypeptide 1B1 (OATP1B1) drug transporter. Genetic variation within the SLCO1B1 gene locus impacts drug transport, which can lead to altered pharmacokinetic profiles of several commonly prescribed drugs. Variable OATP1B1 function is of particular importance regarding hepatic uptake of statins and the risk of statin-associated musculoskeletal symptoms. To introduce this important drug transporter gene into the PharmVar database and serve as a unified reference of haplotype variation moving forward, an international group of gene experts has performed an extensive review of all published SLCO1B1 star alleles. Previously published star alleles were self-assigned by authors and only loosely followed the star nomenclature system that was first developed for cytochrome P450 genes. This nomenclature system has been standardized by PharmVar and is now applied to other important pharmacogenes such as SLCO1B1. In addition, data from the 1000 Genomes Project and investigator-submitted data were utilized to confirm existing haplotypes, fill knowledge gaps, and/or define novel star alleles. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by the Clinical Pharmacogenetics Implementation Consortium (CPIC) 2022 guideline on statin-associated musculoskeletal symptoms.
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Affiliation(s)
- Laura B Ramsey
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Seung-Been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Korea
| | - Jonathan B Wagner
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Solomon M Adams
- School of Pharmacy, Shenandoah University, Fairfax, Virginia, USA
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Philip E Empey
- School of Pharmacy and Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Mikko Niemi
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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4
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Cheng YY, Chang KC, Chen PL, Yeung CY, Liou BY, Chen HL. SLCO1B1 and SLCO1B3 genetic mutations in Taiwanese patients with Rotor syndrome. J Formos Med Assoc 2023:S0929-6646(23)00070-0. [PMID: 36964102 DOI: 10.1016/j.jfma.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/26/2023] Open
Abstract
Rotor syndrome is a rare, benign, inherited disorder that is commonly associated with mild hyperbilirubinemia. It is caused by bi-allelic pathological variants in both SLCO1B1 and SLCO1B3 genes, causing defective OATP1B1 and OATP1B3 in the sinusoidal membrane and interrupted bilirubin uptake of the hepatocytes. We report five Taiwanese pediatric and adult patients aged 5-32 years presenting with conjugated hyperbilirubinemia, and were found to have genetic variants of SLCO1B1 and SLCO1B3. Two also had history of prolonged neonatal jaundice. Genetic analysis using panel-based next generation sequencing revealed three patients with homozygous mutations c.1738C>T (p.R580∗) in SLCO1B1 and a transposon LINE-1 insertion in SLCO1B3, one patient with homozygous mutations for another haplotype, c.757C>T (p.R253∗) in SLCO1B1 and c.1747+1G>A in SLCO1B3. Another patient had heterozygous c.1738C>T (p.R580∗) in SLCO1B1 linked with a LINE-1 insertion in SLCO1B3, and heterozygous c.757C>T (p.R253∗) in SLCO1B1 linked with c.1747+1G>A in SLCO1B3. In conclusion, we present the first time of genetic diagnosis of Rotor syndrome in Taiwan. Advanced genetic testing has enhanced the diagnosis of rare diseases with mild symptoms.
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Affiliation(s)
- Ya-Yuan Cheng
- School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Kai-Chi Chang
- Department of Pediatrics, National Taiwan University Children's Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Yan Yeung
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, MacKay Children's Hospital, Taipei, Taiwan
| | - Bang-Yu Liou
- Department of Pediatrics, National Taiwan University Children's Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Huey-Ling Chen
- Department of Pediatrics, National Taiwan University Children's Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Education and Bioethics, National Taiwan, University College of Medicine, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan.
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5
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Kim YG, Sung H, Shin HS, Kim MJ, Lee JS, Park SS, Seong MW. Intronic LINE-1 insertion in SLCO1B3 as a highly prevalent cause of rotor syndrome in East Asian population. J Hum Genet 2021; 67:71-77. [PMID: 34354231 DOI: 10.1038/s10038-021-00967-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/09/2022]
Abstract
Rotor syndrome is caused by digenic loss-of-function variants in SLCO1B1 and SLCO1B3 but only a few studies have reported co-occurring inactivating variants from both genes. A rotor syndrome-causing long interspersed element-1 (LINE-1) insertion in SLCO1B3 had been reported to be highly prevalent in the Japanese population but there has been no additional report. In spite of its known association with various human diseases, LINE-1 is hard to detect with current sequencing technologies. In this study, we aimed to devise a method to screen the LINE-1 insertion variant and investigate the frequency of this variant in various populations. A chimeric sequence, that was generated by concatenating the reference sequence at the junction and a part of inserted LINE-1 sequence, was searched from 725 raw sequencing data files. In cases containing the chimeric sequence, confirmatory long-range PCR and gap-PCR were performed. In total, 95 (13.1%) of 725 patients were positive for the chimeric sequence, and all were confirmed to have the SLCO1B3 LINE-1 insertion by PCR-based tests. The same chimeric sequence was searched from the 1000 Genomes Project data repository and the carrier frequency was remarkably high in the East Asian populations (10.1%), especially in Southern Han Chinese (18.5%), but almost absent in other populations. This SLCO1B3 LINE-1 insertion should be screened in a population-specific manner under suspicion of Rotor syndrome and the methods proposed in this study would enable this in a simple way.
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Affiliation(s)
- Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hobin Sung
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis. Sci Rep 2021; 11:7571. [PMID: 33828143 PMCID: PMC8026973 DOI: 10.1038/s41598-021-87054-9] [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: 12/05/2020] [Accepted: 03/23/2021] [Indexed: 02/01/2023] Open
Abstract
Solute carrier organic anion transporter 1B3 (SLCO1B3) is an important liver primarily highly expressed gene, its encoded protein (OATP1B3) involved in the transport of multi-specific endogenous and exogenous substances. We previously reported that an EAV-HP inserted mutation (IM+) in the 5' flanking region of SLCO1B3 was the causative mutation of chicken blue eggs, and a further research showed that IM+ significantly reduced the expression of SLCO1B3 in liver. Herein, we confirmed a cholate response element (IR-1) played an important role in activating SLCO1B3 and in vitro experiments showed that the activation of IR-1 can be significantly reduced by the EAV-HP IM+ . We performed transcriptome and proteomic analysis using the same set of IM+ and IM- liver tissues from Yimeng hens (a Chinese indigenous breed) to study the effect of SLCO1B3 and OATP1B3 expression reduction on chicken liver function. The results showed that common differential expression pathways were screened out from both transcriptome and proteome, in which fatty acid metabolism and drug metabolism-cytochrome P450 were significantly enriched in the KEGG analysis. The lipid-related metabolism was weakened in IM+ group, which was validated by serum biochemical assay. We unexpectedly found that EAV-HP fragment was highly expressed in the liver of the IM+ chickens. We cloned the EAV-HP full-length transcript and obtained the complete open reading frame. It is worth noting that there was some immune related differential expressed genes, such as NFKBIZ, NFKBIA, and IL1RL1, which were higher expressed in the IM+ group, which may due to the high expression of EAV-HP. Our study showed that EAV-HP IM+ reduced the expression of SLCO1B3 in liver, resulting in the decrease of fatty metabolism and exogenous substance transport capacity. The mutation itself also expressed in the liver and may be involved in the immune process. The mechanism needs further study.
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Kimura A, Kagawa T, Takei H, Maruo Y, Sakugawa H, Sasaki T, Murai T, Naritaka N, Takikawa H, Nittono H. Rotor Syndrome: Glucuronidated Bile Acidemia From Defective Reuptake by Hepatocytes. Hepatol Commun 2021; 5:629-633. [PMID: 33860121 PMCID: PMC8034574 DOI: 10.1002/hep4.1660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 11/09/2022] Open
Abstract
Organic anion transporting polypeptide (OATP) 1B1 (gene, solute carrier organic anion transporter family member 1B1 [SLCO1B1]) and OATP1B3 (SLCO1B3) serve as transporters for hepatic uptake of important endogenous substances and several commonly prescribed drugs. Inactivation of both proteins together causes Rotor syndrome. How this OATP1B1/1B3 defect disturbs bile acid (BA) metabolism is largely unknown. In this study, we performed detailed BA analysis in 3 patients with genetically diagnosed Rotor syndrome. We found that BAs glucuronidated at the C-3 position (BA-3G) accounted for 50% or more of total BAs in these patients. In contrast but similarly to healthy controls, only trace amounts of BA-3G were detected in patients with constitutional indocyanine green excretory defect (OATP1B3 deficiency) or sodium-taurocholate cotransporting polypeptide (NTCP; gene, solute carrier family 10 member 1 [SLC10A1]) deficiency. Therefore, substantial amounts of BA-3G are synthesized in hepatocytes. The cycling pathway of BA-3G, consisting of excretion from upstream hepatocytes and uptake by downstream hepatocytes by OATP1B1/1B3 may exist to reduce the burden on upstream hepatocytes. Conclusion: Detailed BA analysis revealed glucuronidated bile acidemia in patients with Rotor syndrome. Further exploration of the physiologic role of glucuronidated BAs is necessary.
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Affiliation(s)
- Akihiko Kimura
- Department of Pediatrics and Child HealthKurume University School of MedicineKurumeJapan.,Junshin Clinic Bile Acid InstituteTokyoJapan
| | - Tatehiro Kagawa
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineTokai University School of MedicineIseharaJapan
| | | | - Yoshihiro Maruo
- Department of PediatricsShiga University of Medical ScienceOtsuJapan
| | - Hiroshi Sakugawa
- Department of Internal MedicineHeartlife HospitalNakagusukuJapan
| | - Takahiro Sasaki
- Faculty of Pharmaceutical ScienceHealth Science University of HokkaidoIshikari-TobetsuJapan
| | - Tsuyoshi Murai
- Faculty of Pharmaceutical ScienceHealth Science University of HokkaidoIshikari-TobetsuJapan
| | | | - Hajime Takikawa
- Faculty of Medical TechnologyTeikyo University School of MedicineTokyoJapan
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Dimopoulou D, Lyra V, Dimopoulou A, Papaevangelou V, Fessatou S. Is Hepatobiliary Scintigraphy Sufficient to Diagnose Rotor Syndrome in a 3-Year-Old Boy? J Nucl Med Technol 2021; 49:193-194. [PMID: 33722924 DOI: 10.2967/jnmt.120.257618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/27/2021] [Indexed: 11/16/2022] Open
Abstract
Rotor syndrome (RS) is a benign, inherited, commonly misdiagnosed cause of conjugated hyperbilirubinemia whose identification prevents unnecessary invasive investigations. We present the case of a 3-y-old boy with phenotypic and laboratory findings of RS but negative genetic test results, whose diagnosis was confirmed by hepatobiliary scintigraphy.
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Affiliation(s)
- Dimitra Dimopoulou
- Third Department of Pediatrics, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassiliki Lyra
- Nuclear Medicine Department, Children's Hospital of Athens "Agia Sofia," Athens, Greece; and
| | - Anastasia Dimopoulou
- Department of Paediatric Surgery, Attikon University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassiliki Papaevangelou
- Third Department of Pediatrics, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Smaragdi Fessatou
- Third Department of Pediatrics, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
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9
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Zhou D, Qi S, Zhang W, Wu L, Xu A, Li X, Zhang B, Li Y, Jia S, Wang H, Jia J, Ou X, Huang J, You H. Insertion of LINE-1 Retrotransposon Inducing Exon Inversion Causes a Rotor Syndrome Phenotype. Front Genet 2020; 10:1399. [PMID: 32082363 PMCID: PMC7005217 DOI: 10.3389/fgene.2019.01399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Rotor syndrome, a rare autosomal-recessive genetic disorder characterized by conjugated hyperbilirubinemia, is caused by biallelic pathogenic variants in both SLCO1B1 and SLCO1B3 genes. Long interspersed nuclear elements (LINEs) make up about 17% of the human genome and insertion of LINE-1 in genes can result in genetic diseases. In the current study, we examined SLCO1B1 and SLCO1B3 genes in two Chinese patients diagnosed with Rotor syndrome based on laboratory tests. In one patient, a novel exon 4 inversion variant was identified. This variant may have been induced by LINE-1 retrotransposon insertion into SLCO1B3 intron 3, and was identified using genome walking. Splicing assay results indicated that the exon inversion, resulting in SLCO1B3 exon 4 (122 bp) exclusion in the mature mRNA, might generate a premature termination codon. Here, we describe an exon inversion contributing to the molecular etiology of Rotor syndrome. Our results may inform future diagnoses and guide drug prescriptions and genetic counseling.
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Affiliation(s)
- Donghu Zhou
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Saiping Qi
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Wei Zhang
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Lina Wu
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Anjian Xu
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Xiaojin Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Bei Zhang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Yanmeng Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Siyu Jia
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Hejing Wang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Jidong Jia
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Xiaojuan Ou
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Jian Huang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Hong You
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
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12
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Chen HL, Wu SH, Hsu SH, Liou BY, Chen HL, Chang MH. Jaundice revisited: recent advances in the diagnosis and treatment of inherited cholestatic liver diseases. J Biomed Sci 2018; 25:75. [PMID: 30367658 PMCID: PMC6203212 DOI: 10.1186/s12929-018-0475-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/03/2018] [Indexed: 12/17/2022] Open
Abstract
Background Jaundice is a common symptom of inherited or acquired liver diseases or a manifestation of diseases involving red blood cell metabolism. Recent progress has elucidated the molecular mechanisms of bile metabolism, hepatocellular transport, bile ductular development, intestinal bile salt reabsorption, and the regulation of bile acids homeostasis. Main body The major genetic diseases causing jaundice involve disturbances of bile flow. The insufficiency of bile salts in the intestines leads to fat malabsorption and fat-soluble vitamin deficiencies. Accumulation of excessive bile acids and aberrant metabolites results in hepatocellular injury and biliary cirrhosis. Progressive familial intrahepatic cholestasis (PFIC) is the prototype of genetic liver diseases manifesting jaundice in early childhood, progressive liver fibrosis/cirrhosis, and failure to thrive. The first three types of PFICs identified (PFIC1, PFIC2, and PFIC3) represent defects in FIC1 (ATP8B1), BSEP (ABCB11), or MDR3 (ABCB4). In the last 5 years, new genetic disorders, such as TJP2, FXR, and MYO5B defects, have been demonstrated to cause a similar PFIC phenotype. Inborn errors of bile acid metabolism also cause progressive cholestatic liver injuries. Prompt differential diagnosis is important because oral primary bile acid replacement may effectively reverse liver failure and restore liver functions. DCDC2 is a newly identified genetic disorder causing neonatal sclerosing cholangitis. Other cholestatic genetic disorders may have extra-hepatic manifestations, such as developmental disorders causing ductal plate malformation (Alagille syndrome, polycystic liver/kidney diseases), mitochondrial hepatopathy, and endocrine or chromosomal disorders. The diagnosis of genetic liver diseases has evolved from direct sequencing of a single gene to panel-based next generation sequencing. Whole exome sequencing and whole genome sequencing have been actively investigated in research and clinical studies. Current treatment modalities include medical treatment (ursodeoxycholic acid, cholic acid or chenodeoxycholic acid), surgery (partial biliary diversion and liver transplantation), symptomatic treatment for pruritus, and nutritional therapy. New drug development based on gene-specific treatments, such as apical sodium-dependent bile acid transporter (ASBT) inhibitor, for BSEP defects are underway. Short conclusion Understanding the complex pathways of jaundice and cholestasis not only enhance insights into liver pathophysiology but also elucidate many causes of genetic liver diseases and promote the development of novel treatments.
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Affiliation(s)
- Huey-Ling Chen
- Departments of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, 17F, No. 8, Chung Shan S. Rd, Taipei, 100, Taiwan. .,Department of Medical Education and Bioethics, National Taiwan University College of Medicine, No. 1, Jen Ai Rd Section 1, Taipei, 100, Taiwan. .,Hepatitis Research Center, National Taiwan University Hospital, Changde St. No.1, Zhongzhen Dist., Taipei 100, Taiwan.
| | - Shang-Hsin Wu
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, No. 7 Chung Shan S. Rd, Taipei 100, Taiwan
| | - Shu-Hao Hsu
- Graduate Institute of Anatomy and Cell Biology, Nationatl Taiwan University College of Medicine, No. 1 Jen Ai Rd Section 1, Taipei 100, Taiwan
| | - Bang-Yu Liou
- Departments of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, 17F, No. 8, Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Hui-Ling Chen
- Hepatitis Research Center, National Taiwan University Hospital, Changde St. No.1, Zhongzhen Dist., Taipei 100, Taiwan
| | - Mei-Hwei Chang
- Departments of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, 17F, No. 8, Chung Shan S. Rd, Taipei, 100, Taiwan.,Hepatitis Research Center, National Taiwan University Hospital, Changde St. No.1, Zhongzhen Dist., Taipei 100, Taiwan
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13
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Kaneko J, Kokudo T, Inagaki Y, Hasegawa K. Innovative treatment for hepatocellular carcinoma (HCC). Transl Gastroenterol Hepatol 2018; 3:78. [PMID: 30505965 DOI: 10.21037/tgh.2018.10.04] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
Indocyanine green (ICG) is not new in the field of liver surgery. Early studies performed in the 1980s and 1990s revealed the value of the ICG clearance test in predicting post-hepatectomy morbidity and mortality. ICG clearance and retention tests are crucial for determining precise liver function before liver surgery and offer several benefits for safe surgery. Whereas ICG is well-known and has long history in medicine, recent progress in infrared light technology over the last decade has highlighted another feature of ICG. For example, ICG fluorescence-guided surgery may change the next generation of liver surgery. In the near future, ICG with near-infrared (NIR) light photodynamic therapy (PDT) is expected to become a new treatment method for hepatocellular carcinoma (HCC). Furthermore, several aspects of the mechanisms of ICG accumulation in HCC cells have been revealed by important basic research studies. New imaging technologies and mechanistic findings keep ICG in the spotlight. In this article, we review three recently described topics of ICG which may contribute to the development of innovative and new treatments method for HCC, fluorescence-guided surgery, mechanism of ICG accumulation in HCC cells, PDT for HCC.
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Affiliation(s)
- Junichi Kaneko
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Division of Artificial Organ and Transplantation, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Kokudo
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Division of Artificial Organ and Transplantation, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoshinori Inagaki
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Division of Artificial Organ and Transplantation, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kiyoshi Hasegawa
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Division of Artificial Organ and Transplantation, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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14
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Posbergh CJ, Kalla SE, Sutter NB, Tennant BC, Huson HJ. Mutation responsible for congenital photosensitivity and hyperbilirubinemia in Southdown sheep. Am J Vet Res 2018; 79:538-545. [PMID: 29688779 DOI: 10.2460/ajvr.79.5.538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify the genetic cause for congenital photosensitivity and hyperbilirubinemia (CPH) in Southdown sheep. ANIMALS 73 Southdown sheep from a CPH research flock and 48 sheep of various breeds from commercial flocks without CPH. PROCEDURES Whole-genome sequencing was performed for a phenotypically normal Southdown sheep heterozygous for CPH. Heterozygous variants within Slco1b3 coding exons were identified, and exons that contained candidate mutations were amplified by PCR assay methods for Sanger sequencing. Blood samples from the other 72 Southdown sheep of the CPH research flock were used to determine plasma direct and indirect bilirubin concentrations. Southdown sheep with a plasma total bilirubin concentration < 0.3 mg/dL were classified as controls, and those with a total bilirubin concentration ≥ 0.3 mg/dL and signs of photosensitivity were classified as mutants. Sanger sequencing was used to determine the Slco1b3 genotype for all sheep. Genotypes were compared between mutants and controls of the CPH research flock and among all sheep. Protein homology was measured across 8 species to detect evolutionary conservation of Slco1b. RESULTS A nonsynonymous mutation at ovine Chr3:193,691,195, which generated a glycine-to-arginine amino acid change within the predicted Slco1b3 protein, was significantly associated with hyperbilirubinemia and predicted to be deleterious. That amino acid was conserved across 7 other mammalian species. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested a nonsynonymous mutation in Slco1b3 causes CPH in Southdown sheep. This disease appears to be similar to Rotor syndrome in humans. Sheep with CPH might be useful animals for Rotor syndrome research.
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15
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Kagawa T, Adachi Y. Reply. Hepatology 2017; 66:676. [PMID: 28437871 DOI: 10.1002/hep.29233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/17/2017] [Indexed: 12/07/2022]
Affiliation(s)
- Tatehiro Kagawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
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16
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Kagawa T, Adachi Y, Hashimoto N, Mitsui H, Ohashi T, Yoneda M, Hasegawa I, Hirose S, Tsuruya K, Anzai K, Mine T. Loss of organic anion transporting polypeptide 1B3 function causes marked delay in indocyanine green clearance without any clinical symptoms. Hepatology 2017; 65:1065-1068. [PMID: 27863442 PMCID: PMC5324621 DOI: 10.1002/hep.28950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/07/2016] [Accepted: 11/17/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Tatehiro Kagawa
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine, Tokai University School of MedicineIseharaJapan
| | - Yukihiko Adachi
- Ueno City General HospitalIgaJapan,Present address: Mitaki General Hospital, Ikuwa‐cho 458‐1Yokkaichi512‐0911Japan
| | | | | | - Tomohiko Ohashi
- Division of Hepatology and PancreatologyDepartment of Internal Medicine, Aichi Medical UniversityNagakuteJapan
| | - Masashi Yoneda
- Division of Hepatology and PancreatologyDepartment of Internal Medicine, Aichi Medical UniversityNagakuteJapan
| | - Izumi Hasegawa
- Department of Gastroenterology and HepatologyJapan Community Health Care Organization, Chukyo HospitalNagoyaJapan
| | - Shunji Hirose
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine, Tokai University School of MedicineIseharaJapan
| | - Kota Tsuruya
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine, Tokai University School of MedicineIseharaJapan
| | - Kazuya Anzai
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine, Tokai University School of MedicineIseharaJapan
| | - Tetsuya Mine
- Division of Gastroenterology and HepatologyDepartment of Internal Medicine, Tokai University School of MedicineIseharaJapan
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17
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STRÁNECKÝ V, NEŘOLDOVÁ M, HODAŇOVÁ K, HARTMANNOVÁ H, PIHEROVÁ L, ZEMÁNKOVÁ P, PŘISTOUPILOVÁ A, VRABLÍK M, ADÁMKOVÁ M, KMOCH S, JIRSA M. Large Copy-Number Variations in Patients With Statin-Associated Myopathy Affecting Statin Myopathy-Related Loci. Physiol Res 2016; 65:1005-1011. [DOI: 10.33549/physiolres.933284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Some patients are susceptible to statin-associated myopathy (SAM) either because of genetic variations affecting statin uptake and metabolism, or because they predispose their carriers to muscular diseases. Among the frequent variants examined using the genome-wide association study approach, SLCO1B1 c.521T>C represents the only validated predictor of SAM in patients treated with high-dose simvastatin. Our aim was to ascertain the overall contribution of large copy-number variations (CNVs) to SAM diagnosed in 86 patients. CNVs were detected by whole genome genotyping using Illumina HumanOmni2.5 Exome BeadChips. Exome sequence data were used for validation of CNVs in SAM-related loci. In addition, we performed a specific search for CNVs in the SLCO1B region detected recently in Rotor syndrome subjects. Rare deletions possibly contributing to genetic predisposition to SAM were found in two patients: one removed EYS associated previously with SAM, the other was present in LARGE associated with congenital muscular dystrophy. Another two patients carried deletions in CYP2C19, which may predispose to clopidogrel-statin interactions. We found no common large CNVs potentially associated with SAM and no CNVs in the SLCO1B locus. Our findings suggest that large CNVs do not play a substantial role in the etiology of SAM.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - M. JIRSA
- Laboratory of Experimental Hepatology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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18
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Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res 2016; 45:D68-D73. [PMID: 27924012 PMCID: PMC5210629 DOI: 10.1093/nar/gkw925] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022] Open
Abstract
LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potentially active L1 retrotransposons from the reference genome sequences of 17 mammals. The current release of the human genome, GRCh38, contains 146 putatively active L1 elements or full length intact L1 elements (FLIs). The newest versions of the mouse, GRCm38 and the rat, Rnor_6.0, genomes contain 2811 and 492 FLIs, respectively. Most likely reflecting the current level of completeness of the genome project, the latest reference sequence of the common chimpanzee genome, PT 2.19, only contains 19 FLIs. Of note, the current assemblies of the dog, CF 3.1 and the sheep, OA 3.1, genomes contain 264 and 598 FLIs, respectively. Further developments in the new version of L1Base include an updated website with implementation of modern web server technologies. including a more responsive design for an improved user experience, as well as the addition of data sharing capabilities for L1Xplorer annotation.
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Affiliation(s)
- Tobias Penzkofer
- Department of Radiology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
| | - Richard Badge
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Stefan Mundlos
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,The Jackson Laboratory for Genomic medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Tomasz Zemojtel
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
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19
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Identification of Cryptic Novel α-Galactosidase A Gene Mutations: Abnormal mRNA Splicing and Large Deletions. JIMD Rep 2016; 30:63-72. [PMID: 27255140 DOI: 10.1007/8904_2015_475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/20/2015] [Accepted: 06/11/2015] [Indexed: 03/17/2023] Open
Abstract
Anderson-Fabry (FD) disease is an inborn error of metabolism caused by a deficiency of α-galactosidase A (GLA), a lysosomal enzyme. Many male FD patients display a classic FD phenotype; however, some female patients have neither reduced leukocyte GLA enzyme activity level nor FD symptoms. Thus, GLA gene analysis is especially important for diagnosing suspected FD in female subjects. In this study, we revealed 4 novel GLA gene mutations in 5 independent families using GLA cDNA analysis and multiplex ligation-dependent probe amplification (MLPA) analysis. These distinct mutations included a large deletion mutation from intron 1 to exon 5 (c.195-471_c.691del5.5k, corresponding to g.8508_g.14069del5.5k), an insertion mutation of splicing enhancer sequence in intron 4 (c.639+329_c.639+330ins113, corresponding to g.12627_g.12628ins113), an insertion mutation of retrotransposon L1 in exon 4 (c.634_c.635, corresponding to g.12293_g.12294), and a non-SNP deep intronic point mutation in intron 3 (c.547+395G>C, corresponding to g.11727G>C). It is difficult to detect these mutations with direct sequencing of only the exonic element. When exonic mutations are not found in the GLA gene from suspected FD patients, GLA cDNA and MLPA analyses should be performed to detect large deletion/insertion and intronic mutations including transcription abnormalities.
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20
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 437] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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21
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Wong KC. How to apply clinical cases and medical literature in the framework of a modified "failure mode and effects analysis" as a clinical reasoning tool--an illustration using the human biliary system. J Med Case Rep 2016; 10:85. [PMID: 27048215 PMCID: PMC4822271 DOI: 10.1186/s13256-016-0850-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/25/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clinicians use various clinical reasoning tools such as Ishikawa diagram to enhance their clinical experience and reasoning skills. Failure mode and effects analysis, which is an engineering methodology in origin, can be modified and applied to provide inputs into an Ishikawa diagram. METHOD The human biliary system is used to illustrate a modified failure mode and effects analysis. The anatomical and physiological processes of the biliary system are reviewed. Failure is defined as an abnormality caused by infective, inflammatory, obstructive, malignancy, autoimmune and other pathological processes. The potential failures, their effect(s), main clinical features, and investigation that can help a clinician to diagnose at each anatomical part and physiological process are reviewed and documented in a modified failure mode and effects analysis table. Relevant medical and surgical cases are retrieved from the medical literature and weaved into the table. RESULTS A total of 80 clinical cases which are relevant to the modified failure mode and effects analysis for the human biliary system have been reviewed and weaved into a designated table. The table is the backbone and framework for further expansion. Reviewing and updating the table is an iterative and continual process. The relevant clinical features in the modified failure mode and effects analysis are then extracted and included in the relevant Ishikawa diagram. CONCLUSIONS This article illustrates an application of engineering methodology in medicine, and it sows the seeds of potential cross-pollination between engineering and medicine. Establishing a modified failure mode and effects analysis can be a teamwork project or self-directed learning process, or a mix of both. Modified failure mode and effects analysis can be deployed to obtain inputs for an Ishikawa diagram which in turn can be used to enhance clinical experiences and clinical reasoning skills for clinicians, medical educators, and students.
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Affiliation(s)
- Kam Cheong Wong
- Bathurst Rural Clinical School, Western Sydney University, Bathurst, NSW, Australia. .,School of Rural Health, University of Sydney, Orange, NSW, Australia. .,George Street Medical Practice, Bathurst, NSW, Australia.
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22
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Gazzo AM, Daneels D, Cilia E, Bonduelle M, Abramowicz M, Van Dooren S, Smits G, Lenaerts T. DIDA: A curated and annotated digenic diseases database. Nucleic Acids Res 2015; 44:D900-7. [PMID: 26481352 PMCID: PMC4702791 DOI: 10.1093/nar/gkv1068] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/05/2015] [Indexed: 02/07/2023] Open
Abstract
DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest.
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Affiliation(s)
- Andrea M Gazzo
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Dorien Daneels
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Elisa Cilia
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
| | - Maryse Bonduelle
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Marc Abramowicz
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium
| | - Sonia Van Dooren
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Avenue JJ Crocq 15, 1020 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium AI lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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