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Zhang LS, Ju CW, Jiang B, He C. Base-resolution quantitative DAMM-seq for mapping RNA methylations in tRNA and mitochondrial polycistronic RNA. Methods Enzymol 2023; 692:39-54. [PMID: 37925186 PMCID: PMC10882886 DOI: 10.1016/bs.mie.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
The human AlkB family proteins, such as FTO and ALKBH5, are known to mediate RNA m6A demethylation. However, although ALKBH7 localizes in mitochondria and affects metabolism, the detailed biological function and mechanism have remained unknown for years. We developed Demethylation-Assisted Multiple Methylation sequencing (DAMM-seq) to simultaneously detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) methylations in both steady-state RNA and nascent RNA, and discovered that human ALKBH7 demethylates m22G and m1A within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in mitochondrial polycistronic RNA. DAMM-seq quantitatively and sensitively monitors the methylation stoichiometry change at pre-tRNA junctions within nascent mt-RNA, revealing the target region where ALKBH7 regulates RNA processing and local structural switch of polycistronic mt-RNAs. A new RNA demethylase in human cells was characterized through the base-resolution quantification of multiple RNA methylations in nascent mt-RNA, resolving the long-standing question about the functional substrate of ALKBH7.
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Affiliation(s)
- Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States.
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
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Xuan TT, Li GY, Meng SB, Wang ZM, Qu LL. Immunotherapy combined with antiangiogenic agents in patients with advanced malignant pleural mesothelioma: A case report. World J Clin Cases 2022; 10:8284-8290. [PMID: 36159517 PMCID: PMC9403696 DOI: 10.12998/wjcc.v10.i23.8284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/12/2022] [Accepted: 06/26/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Malignant pleural mesothelioma has limited therapeutic options and a poor outcome. Antiangiogenic agents might increase the efficacy of immunotherapy as second-line treatment of advanced-stage malignancies.
CASE SUMMARY A patient with stage IIIB pleural mesothelioma received second-line treatment with a combination of pembrolizumab, bevacizumab and chemotherapy following standard chemotherapy under the guidance of second-generation sequencing. He achieved a partial response after four cycles of treatment with progression-free survival of 5 mo. Pembrolizumab was suspended due to grade 2 immunerelated pneumonia, which was resolved by oral glucocorticoids. However, disease progression was observed after immunotherapy rechallenge and anlotinib therapy. The patient had disease progression, multiorgan dysfuntion and died suddenly in October 2019.
CONCLUSION The combination of immune checkpoint inhibitor, anti-angiogenic agents and chemotherapy showed effective response for advanced pleural mesothelioma, but with adverse reactions.
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Affiliation(s)
- Tian-Tian Xuan
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong Province, China
| | - Guang-Yi Li
- Department of Respiratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong Province, China
| | - Si-Bo Meng
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong Province, China
| | - Zhan-Mei Wang
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong Province, China
| | - Lin-Li Qu
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, Shandong Province, China
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Maxwell SM, Lhakhang TC, Lin Z, Kramer YG, Zhang Y, Wang F, Heguy A, Tsirigos A, Grifo JA, Licciardi F. Investigation of Global Gene Expression of Human Blastocysts Diagnosed as Mosaic using Next-generation Sequencing. Reprod Sci 2022; 29:1597-1607. [PMID: 35304731 DOI: 10.1007/s43032-022-00899-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 02/20/2022] [Indexed: 10/18/2022]
Abstract
Embryos are diagnosed as mosaic if their chromosomal copy number falls between euploid and aneuploid. The purpose of this study was to investigate the impact of mosaicism on global gene expression. This study included 42 blastocysts that underwent preimplantation genetic testing for aneuploidy (PGT-A) and were donated for IRB approved research. Fourteen blastocysts were diagnosed as mosaic with Next-generation Sequencing (NGS). Three NGS diagnosed euploid embryos, and 25 aneuploid embryos (9 NGS, 14 array Comparative Genomic Hybridization, 2 Single Nucleotide Polymorphism array) were used as comparisons. RNA-sequencing was performed on all of the blastocysts. Differentially expressed genes (DEGs) were calculated using DESeq2/3.5 (R Bioconductor Package) with p < 0.05 considered significantly differentially expressed. Pathway analysis was performed on mosaic embryos using EnrichR with p < 0.05 considered significant. With euploid embryo gene expression used as a control, 12 of 14 mosaic embryos had fewer DEGs compared to aneuploid embryos involving the same chromosome. On principal component analysis (PCA), mosaic embryos mapped separately from aneuploid embryos. Pathways involving cell proliferation, differentiation, and apoptosis were the most disrupted within mosaic embryos. Mosaic embryos have decreased disruption of global gene expression compared to aneuploid embryos. This study was limited by the small sample size, lack of replicate samples for each mosaic abnormality, and use of multiple different PGT-A platforms for the diagnosis of aneuploid embryos.
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Affiliation(s)
- Susan M Maxwell
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA. .,Northwell Health Fertility of New York City, 210A East 64th St., Floor 1, New York, NY, 10065, USA.
| | - Tenzin C Lhakhang
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - Ziyan Lin
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - Yael G Kramer
- Hackensack Meridian Health, 40 Prospect Ave, Hackensack, NJ, 07601, USA
| | - Yutong Zhang
- Genome Technology Center, New York University Langone Health, 550 First Ave., MSB 308, New York, NY, 10016, USA
| | - Fang Wang
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Langone Health, 550 First Ave., MSB 308, New York, NY, 10016, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - James A Grifo
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
| | - Frederick Licciardi
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
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Liu D, Zhou H, Xu T, Yang Q, Mo X, Shi D, Ai J, Zhang J, Tao Y, Wen D, Tong Y, Ren L, Zhang W, Xie S, Chen W, Xing W, Zhao J, Wu Y, Meng X, Ouyang C, Jiang Z, Liang Z, Tan H, Fang Y, Qin N, Guan Y, Gai W, Xu S, Wu W, Zhang W, Zhang C, Wang Y. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine 2021; 74:103649. [PMID: 34814051 PMCID: PMC8608867 DOI: 10.1016/j.ebiom.2021.103649] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Shotgun metagenomics has been used clinically for diagnosing infectious diseases. However, most technical assessments have been limited to individual sets of reference standards, experimental workflows, and laboratories. METHODS A reference panel and performance metrics were designed and used to examine the performance of shotgun metagenomics at 17 laboratories in a coordinated collaborative study. We comprehensively assessed the reliability, key performance determinants, reproducibility, and quantitative potential. FINDINGS Assay performance varied significantly across sites and microbial classes, with a read depth of 20 millions as a generally cost-efficient assay setting. Results of mapped reads by shotgun metagenomics could indicate relative and intra-site (but not absolute or inter-site) microbial abundance. INTERPRETATION Assay performance was significantly impacted by the microbial type, the host context, and read depth, which emphasizes the importance of these factors when designing reference reagents and benchmarking studies. Across sites, workflows and platforms, false positive reporting and considerable site/library effects were common challenges to the assay's accuracy and quantifiability. Our study also suggested that laboratory-developed shotgun metagenomics tests for pathogen detection should aim to detect microbes at 500 CFU/mL (or copies/mL) in a clinically relevant host context (10^5 human cells/mL) within a 24h turn-around time, and with an efficient read depth of 20M. FUNDING This work was supported by National Science and Technology Major Project of China (2018ZX10102001).
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Affiliation(s)
- Donglai Liu
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Haiwei Zhou
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Teng Xu
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province and College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dawei Shi
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Jingwen Ai
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology. Beijing 100029
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
| | - Shumei Xie
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong 510000, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen 518083, China
| | - Wanli Xing
- School of Medicine Tsinghua University, Beijing, China; CapitalBio Technology Co., Ltd., Yizhuang Biomedical Park Beijing, China
| | - Jinyin Zhao
- Dalian GenTalker Clinical Laboratory, Dalian 116635, China
| | - Yilan Wu
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, China
| | - Xianfa Meng
- Guangzhou Kingmed Diagnostics, Guangzhou, Guangdong 510330, China
| | - Chuan Ouyang
- Hangzhou MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Zhi Jiang
- Genskey Medical Technology, Co., Ltd., Beijing 102206, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou 510663, China
| | - Haiqin Tan
- Hangzhou IngeniGen XunMinKang Biotechnology Co., Ltd., Hangzhou 311121, China
| | - Yuan Fang
- Dinfectome Inc, Shanghai 201321, China
| | - Nan Qin
- Realbio Genomics Institute, Shanghai 201114, China
| | | | - Wei Gai
- WillingMed Technology Beijing Co., Ltd., Beijing, China
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China.
| | - Chuntao Zhang
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Youchun Wang
- National Institutes for Food and Drug Control, Beijing 100050, China.
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Hildebrandt A, Kirchner B, Nolte-'t Hoen ENM, Pfaffl MW. miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples. J Mol Biol 2021; 433:167070. [PMID: 34052284 DOI: 10.1016/j.jmb.2021.167070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized, membrane-enclosed vesicles released by cells for intercellular communication. EVs are involved in pathological processes and miRNAs in EVs have gained interest as easily accessible biomolecules in liquid biopsies for diagnostic purposes. To validate potential miRNA biomarker, transcriptome analyses must be carried out to detect suitable reference miRNAs. miREV is a database with over 400 miRNA sequencing data sets and helps the researcher to find suitable reference miRNAs for their individual experimental setup. The researcher can put together a specific sample set in miREV, which is similar to his own experimental concept in order to find the most suitable references. This allows to run validation experiments without having to carry out a complex and costly transcriptome analysis priorly. Additional read count tables of each generated sample set are downloadable for further analysis. miREV is freely available at https://www.physio.wzw.tum.de/mirev/.
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Masamune A, Kotani H, Sörgel FL, Chen JM, Hamada S, Sakaguchi R, Masson E, Nakano E, Kakuta Y, Niihori T, Funayama R, Shirota M, Hirano T, Kawamoto T, Hosokoshi A, Kume K, Unger L, Ewers M, Laumen H, Bugert P, Mori MX, Tsvilovskyy V, Weißgerber P, Kriebs U, Fecher-Trost C, Freichel M, Diakopoulos KN, Berninger A, Lesina M, Ishii K, Itoi T, Ikeura T, Okazaki K, Kaune T, Rosendahl J, Nagasaki M, Uezono Y, Algül H, Nakayama K, Matsubara Y, Aoki Y, Férec C, Mori Y, Witt H, Shimosegawa T. Variants That Affect Function of Calcium Channel TRPV6 Are Associated With Early-Onset Chronic Pancreatitis. Gastroenterology 2020; 158:1626-1641.e8. [PMID: 31930989 DOI: 10.1053/j.gastro.2020.01.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND & AIMS Changes in pancreatic calcium levels affect secretion and might be involved in development of chronic pancreatitis (CP). We investigated the association of CP with the transient receptor potential cation channel subfamily V member 6 gene (TRPV6), which encodes a Ca2+-selective ion channel, in an international cohort of patients and in mice. METHODS We performed whole-exome DNA sequencing from a patient with idiopathic CP and from his parents, who did not have CP. We validated our findings by sequencing DNA from 300 patients with CP (not associated with alcohol consumption) and 1070 persons from the general population in Japan (control individuals). In replication studies, we sequenced DNA from patients with early-onset CP (20 years or younger) not associated with alcohol consumption from France (n = 470) and Germany (n = 410). We expressed TRPV6 variants in HEK293 cells and measured their activity using Ca2+ imaging assays. CP was induced by repeated injections of cerulein in TRPV6mut/mut mice. RESULTS We identified the variants c.629C>T (p.A210V) and c.970G>A (p.D324N) in TRPV6 in the index patient. Variants that affected function of the TRPV6 product were found in 13 of 300 patients (4.3%) and 1 of 1070 control individuals (0.1%) from Japan (odds ratio [OR], 48.4; 95% confidence interval [CI], 6.3-371.7; P = 2.4 × 10-8). Twelve of 124 patients (9.7%) with early-onset CP had such variants. In the replication set from Europe, 18 patients with CP (2.0%) carried variants that affected the function of the TRPV6 product compared with 0 control individuals (P = 6.2 × 10-8). Variants that did not affect the function of the TRPV6 product (p.I223T and p.D324N) were overrepresented in Japanese patients vs control individuals (OR, 10.9; 95% CI, 4.5-25.9; P = 7.4 × 10-9 for p.I223T and P = .01 for p.D324N), whereas the p.L299Q was overrepresented in European patients vs control individuals (OR, 3.0; 95% CI, 1.9-4.8; P = 1.2 × 10-5). TRPV6mut/mut mice given cerulein developed more severe pancreatitis than control mice, as shown by increased levels of pancreatic enzymes, histologic alterations, and pancreatic fibrosis. CONCLUSIONS We found that patients with early-onset CP not associated with alcohol consumption carry variants in TRPV6 that affect the function of its product, perhaps by altering Ca2+ balance in pancreatic cells. TRPV6 regulates Ca2+ homeostasis and pancreatic inflammation.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Hiroshi Kotani
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Franziska Lena Sörgel
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Jian-Min Chen
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Reiko Sakaguchi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Emmanuelle Masson
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France; CHU Brest, Service de Génétique, Brest, France
| | - Eriko Nakano
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tatsuya Hirano
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tetsuya Kawamoto
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Atsuki Hosokoshi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Lara Unger
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Maren Ewers
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Helmut Laumen
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany
| | - Masayuki X Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Volodymyr Tsvilovskyy
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Petra Weißgerber
- Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, Homburg, Germany
| | - Ulrich Kriebs
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Claudia Fecher-Trost
- Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, Homburg, Germany
| | - Marc Freichel
- Pharmakologisches Institut, Universität Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research, partner site Heidelberg, Germany
| | - Kalliope N Diakopoulos
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Alexandra Berninger
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marina Lesina
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Kentaro Ishii
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Tsukasa Ikeura
- Department of Gastroenterology and Hepatology, Kansai Medical University, Hirakata, Japan
| | - Kazuichi Okazaki
- Department of Gastroenterology and Hepatology, Kansai Medical University, Hirakata, Japan
| | - Tom Kaune
- Department of Internal Medicine I, Martin Luther University, Halle (Saale), Germany
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin Luther University, Halle (Saale), Germany
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yasuhito Uezono
- Cancer Pathophysiology Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Hana Algül
- Mildred Scheel Chair of Tumor Metabolism and Comprehensive Cancer Center Munich at the Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Claude Férec
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France; CHU Brest, Service de Génétique, Brest, France
| | - Yasuo Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Heiko Witt
- Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, Paediatric Nutritional Medicine, Technische Universität München, Freising, Germany
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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7
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Tang L, Yang F, He X, Xie H, Liu X, Fu J, Xi H, Lu X, Liu C, Song Z, Qu J, Zhao J, Gu F. Efficient cleavage resolves PAM preferences of CRISPR-Cas in human cells. Cell Regen 2019; 8:44-50. [PMID: 31709036 PMCID: PMC6833347 DOI: 10.1016/j.cr.2019.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) of bacterial adaptive immunity have been adopted as a powerful and versatile tool for manipulation of the genome. This paradigm has been widely applied in biological research and treatments of animal or cellular disease models. A critical feature of CRISPR-Cas is the protospacer adjacent motif (PAM), which dictates the DNA target recognition mechanism of Cas proteins. While, direct identifying functional PAM sequences in human cells remains a challenge. Here, we developed a positive screen system termed PAM-DOSE (PAM Definition by Observable Sequence Excision) to delineate the functional PAMs in human cells. Specifically, the PAM libraries for CRISPR-Cas (SpCas9, SpCas9-NG, FnCas12a, AsCas12a, LbCas12a and MbCas12a) were generated and the corresponding CRISPR-Cas mediated cleaved fragments with functional PAM in human cells were harvested for DNA sequencing, which could be tracked and visualized with either florescence microscopy or flow cytometry analysis. With this system, we identified the functional PAMs of CRISPR-Cas members. We also found that spacer sequence affects the PAM preference of Cas proteins. This method will facilitate identification of functional PAMs for Cas-mediated human genome editing applications.
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Affiliation(s)
- Lianchao Tang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Fayu Yang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Xiaoxue He
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Haihua Xie
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Xiaoyu Liu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Junhao Fu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Haitao Xi
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027 China
| | - Xiaosheng Lu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027 China
| | - Changbao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027 China
| | - Zongming Song
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
- Henan Provincial People's Hospital, Henan Eye Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, Henan 450003 China
| | - Jia Qu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
| | - Junzhao Zhao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027 China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang 325027 China
- Corresponding author. Eye Hospital, Wenzhou Medical University, 270 Xueyuan West Road, Wenzhou, Zhejiang 325027, China.
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Shin D, Won KH, Song KD. In silico approaches to discover the functional impact of non-synonymous single nucleotide polymorphisms in selective sweep regions of the Landrace genome. Asian-Australas J Anim Sci 2018; 31:1980-1990. [PMID: 29879810 PMCID: PMC6212746 DOI: 10.5713/ajas.18.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 05/29/2018] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome. METHODS Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. RESULTS Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. CONCLUSION The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.
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Affiliation(s)
- Donghyun Shin
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896,
Korea
| | - Kyung-Hye Won
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896,
Korea
| | - Ki-Duk Song
- Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896,
Korea
- The Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896,
Korea
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9
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Zhao WL, Wu YH, Li HF, Li SY, Fan SY, Wu HL, Li YJ, Lü YL, Han J, Zhang WC, Zhao Y, Li GL, Qiao XD, Ren HT, Zhu YC, Peng B, Cui LY, Guan HZ. [Clinical experience and next-generation sequencing analysis of encephalitis caused by pseudorabies virus]. Zhonghua Yi Xue Za Zhi 2018; 98:1152-1157. [PMID: 29690727 DOI: 10.3760/cma.j.issn.0376-2491.2018.15.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To detect potential pathogens including pseudorabies virus in patients with encephalitis of unknown etiology in China and describe novel encephalitic entities. Methods: Patients with clinically suspected infectious encephalitis were enrolled in a multicenter study to identify the pathogens in PUMCH Encephalitis Program.Next-generation sequencing(NGS) of cerebrospinal fluid (CSF) was used in patients with encephalitis of unknown etiology enrolled from 2016 to 2017.The patients diagnosed as PRV encephalitis were studied to describe this novel entity. Results: The four patients(3 male, 1 male, 38-54 years old) had occupational exposure to raw park when working in the production or marketing of pork and at least one got injured during pork-cutting.Two of them were confirmed with NGS of CSF, and anti-PRV antibodies were positive in 3 patients whose serum was available for serological analysis.They all presented with an acute onset of fever, convulsion, loss of consciousness and respiratory failure within 1 to 4 days and rapidly deteriorated even on extensive treatment.All the patients needed ICU admission and 3 needed mechanical ventilation.Two patients also had bilateral retinitis.Neuroimaging revealed symmetric gray matter lesions including limbic system, basal ganglia and midbrain without obvious hemorrhage.Lumbar puncture revealed elevated intracranial pressure and lymphocytic pleocytosis [(6-64)×10(6)/L] of CSF.The patients failed to response to the treatment of acyclovir combined with intravenous immunoglobulin and steroids.Modified Rankin Score was 3, 5, 5 and 6 (died) for the 4 patients respectively on last follow-up. Conclusions: PRV could be a cause of severe encephalitis.The patients with suspected pseudorabies encephalitis (PRE) need to be tested for PRV DNA timely.Severe encephalitis with bilateral involvement of limbic system, basal ganglion, thalamus and midbrain in patient with occupational exposure indicate this emerging infectious encephalitis.
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Affiliation(s)
- W L Zhao
- Department of Neurology, the Affiliated Hospital of Chifeng University, Chifeng, Inner Mongolia Autonomous Region 024005, China
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10
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Abstract
UNLABELLED Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. LAY ABSTRACT Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and bioinformatics tools to be able to store and analyze large amounts of data. To address this need, we have developed the High-performance Integrated Virtual Environment, or HIVE. HIVE uses a combination of distributed cloud storage and distributed cloud computations to provide a platform that is both rapid and responsive to support the growing and increasingly diverse scientific and regulatory needs of FDA scientists in their evaluation of NGS in research and ultimately for evaluation of NGS data in regulatory submissions.
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Affiliation(s)
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, FDA, Bethesda, MD
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Zhao Q, Yang J, Li L, Cao D, Yu M, Shen K. Germline and somatic mutations in homologous recombination genes among Chinese ovarian cancer patients detected using next-generation sequencing. J Gynecol Oncol 2017; 28:e39. [PMID: 28541631 PMCID: PMC5447142 DOI: 10.3802/jgo.2017.28.e39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/21/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To define genetic profiling of homologous recombination (HR) deficiency in Chinese ovarian cancer patients. METHODS we have applied next-generation sequencing to detect deleterious mutations through all exons in 31 core HR genes. Paired whole blood and frozen tumor samples from 50 Chinese women diagnosed with epithelial ovarian carcinomas were tested to identify both germline and somatic variants. RESULTS Deleterious germline HR-mutations were identified in 36% of the ovarian cancer patients. Another 5 patients had only somatic mutations. BRCA2 was most frequently mutated. Three out of the 5 somatic mutations were in RAD genes and a wider distribution of other HR genes was involved in non-serous carcinomas. BRCA1/2-mutation carriers had favorable platinum sensitivity (relative risk, 1.57, p<0.05), resulting in a 100% remission probability and survival rate. In contrast, mutations in other HR genes predicted poor prognosis. However, multivariate analysis demonstrated that platinum sensitivity and optimal cytoreduction were the independent impact factors influencing survival (hazards ratio, 0.053) and relapse (hazards ratio, 0.247), respectively. CONCLUSION our results suggest that a more comprehensive profiling of HR defect than merely BRCA1/2 could help elucidate tumor heterogeneity and lead to better stratification of ovarian cancer patients for individualized clinical management.
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Affiliation(s)
- Qianying Zhao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxin Yang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Yu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Abstract
Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multiple subjects, leading to a posterior probability of ASM. We flag SNPs with high posterior probabilities of ASM by accounting for multiple comparisons based on posterior false discovery rates. Applying the Bayesian approach to the in-house prostate cell line data, we identify 269 SNPs as candidates of ASM. A simulation study is carried out to demonstrate the quantitative performance of the proposed approach.
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