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Van Uffelen A, Posadas A, Roosens NHC, Marchal K, De Keersmaecker SCJ, Vanneste K. Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities. Sci Data 2024; 11:864. [PMID: 39127718 PMCID: PMC11316826 DOI: 10.1038/s41597-024-03672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.
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Affiliation(s)
- Alexander Van Uffelen
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Andrés Posadas
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium.
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2
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Lischka A, Eggermann K, Record CJ, Dohrn MF, Laššuthová P, Kraft F, Begemann M, Dey D, Eggermann T, Beijer D, Šoukalová J, Laura M, Rossor AM, Mazanec R, Van Lent J, Tomaselli PJ, Ungelenk M, Debus KY, Feely SME, Gläser D, Jagadeesh S, Martin M, Govindaraj GM, Singhi P, Baineni R, Biswal N, Ibarra-Ramírez M, Bonduelle M, Gess B, Romero Sánchez J, Suthar R, Udani V, Nalini A, Unnikrishnan G, Marques W, Mercier S, Procaccio V, Bris C, Suresh B, Reddy V, Skorupinska M, Bonello-Palot N, Mochel F, Dahl G, Sasidharan K, Devassikutty FM, Nampoothiri S, Rodovalho Doriqui MJ, Müller-Felber W, Vill K, Haack TB, Dufke A, Abele M, Stucka R, Siddiqi S, Ullah N, Spranger S, Chiabrando D, Bolgül BS, Parman Y, Seeman P, Lampert A, Schulz JB, Wood JN, Cox JJ, Auer-Grumbach M, Timmerman V, de Winter J, Themistocleous AC, Shy M, Bennett DL, Baets J, Hübner CA, Leipold E, Züchner S, Elbracht M, Çakar A, Senderek J, Hornemann T, Woods CG, Reilly MM, Kurth I. Genetic landscape of congenital insensitivity to pain and hereditary sensory and autonomic neuropathies. Brain 2023; 146:4880-4890. [PMID: 37769650 PMCID: PMC10689924 DOI: 10.1093/brain/awad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 10/02/2023] Open
Abstract
Congenital insensitivity to pain (CIP) and hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders exclusively or predominantly affecting the sensory and autonomic neurons. Due to the rarity of the diseases and findings based mainly on single case reports or small case series, knowledge about these disorders is limited. Here, we describe the molecular workup of a large international cohort of CIP/HSAN patients including patients from normally under-represented countries. We identify 80 previously unreported pathogenic or likely pathogenic variants in a total of 73 families in the >20 known CIP/HSAN-associated genes. The data expand the spectrum of disease-relevant alterations in CIP/HSAN, including novel variants in previously rarely recognized entities such as ATL3-, FLVCR1- and NGF-associated neuropathies and previously under-recognized mutation types such as larger deletions. In silico predictions, heterologous expression studies, segregation analyses and metabolic tests helped to overcome limitations of current variant classification schemes that often fail to categorize a variant as disease-related or benign. The study sheds light on the genetic causes and disease-relevant changes within individual genes in CIP/HSAN. This is becoming increasingly important with emerging clinical trials investigating subtype or gene-specific treatment strategies.
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Affiliation(s)
- Annette Lischka
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Katja Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Petra Laššuthová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Daniela Dey
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Danique Beijer
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jana Šoukalová
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czechia
| | - Matilde Laura
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander M Rossor
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Radim Mazanec
- Department of Neurology, Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Prague, Czechia
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Pedro J Tomaselli
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Martin Ungelenk
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Karlien Y Debus
- Center for Molecular Biomedicine Institute for Biophysics, Friedrich-Schiller Universität Jena, 07745 Jena, Germany
| | - Shawna M E Feely
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Pediatric Neurology, Seattle Children’s Hospital, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Dieter Gläser
- Center for Human Genetics, Genetikum®, 89231 Neu-Ulm, Germany
| | - Sujatha Jagadeesh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Madelena Martin
- Davis and Davis Children's Hospital, University of California, Sacramento, CA 95817, USA
| | - Geeta M Govindaraj
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Pratibha Singhi
- Pediatric Neurology and Neurodevelopment, Medanta, The Medicity, Gurgaon, Haryana 122 001, India
| | - Revanth Baineni
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Niranjan Biswal
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Marisol Ibarra-Ramírez
- Genetics Department, Hospital Universitario Dr. José Eleuterio González Universidad Autónoma de Nuevo León, 64460 Monterrey, Nuevo León, México
| | - Maryse Bonduelle
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Jette, Brussels, Belgium
| | - Burkhard Gess
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Department of Neurology, University Hospital, Evangelisches Klinikum Bethel, University of Bielefeld, 33617 Bielefeld, Germany
| | | | - Renu Suthar
- Pediatric Neurology and Neurodevelopment Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160 012, India
| | - Vrajesh Udani
- Department of Child Neurology, PD Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra 400 016, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Gopikrishnan Unnikrishnan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Wilson Marques
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Centre de Référence des Maladies Neuromusculaires AOC, 44000 Nantes, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Céline Bris
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Beena Suresh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Vaishnavi Reddy
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Mariola Skorupinska
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Fanny Mochel
- Genetics Department, Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, 75013 Paris, France
| | - Georg Dahl
- Pediatric Neurology, Children’s Hospital of the King’s Daughters in Norfolk, Norfolk, VA 23507, USA
| | - Karthika Sasidharan
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Fiji M Devassikutty
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala 682 041, India
| | - Maria J Rodovalho Doriqui
- Department of Genetics, Hospital Infantil Doutor Juvêncio Mattos, São Luis, Maranhão 65015-460, Brazil
| | - Wolfgang Müller-Felber
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, LMU Campus Innenstadt, University of Munich, 80337 Munich, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, 80337 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Abele
- Neurologie, Praxis für Neurologie und Schlafmedizin, 53359 Rheinbach, Germany
| | - Rolf Stucka
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Saima Siddiqi
- Genomics Group, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
| | - Noor Ullah
- Institute for Paramedical Sciences, Khyber Medical University, Peshawar, KPK 25100, Pakistan
| | | | - Deborah Chiabrando
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center ‘Guido Tarone’, University of Torino, 10124 Turin, Italy
| | - Behiye S Bolgül
- Department of Pedodontics, Faculty of Dentistry, Dicle University, 21200 Diyarbakir, Turkey
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Pavel Seeman
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Angelika Lampert
- Institute of Neurophysiology, Medical Faculty, Uniklinik RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Research Centre Jülich GmbH, and RWTH Aachen University, 52056 Aachen, Germany
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Jonathan de Winter
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | | | - Michael Shy
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - Jonathan Baets
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Enrico Leipold
- Department of Anesthesiology and Intensive Care and CBBM—Center of Brain, Behavior and Metabolism, University of Luebeck, 23562 Luebeck, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Jan Senderek
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
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Biswas A, Kumari A, Gaikwad DS, Pandey DK. Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:550-569. [PMID: 38100404 DOI: 10.1089/omi.2023.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.
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Affiliation(s)
- Aakanksha Biswas
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - Aditi Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
| | - D S Gaikwad
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Dhananjay K Pandey
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, India
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Lu N, Qiao Y, An P, Luo J, Bi C, Li M, Lu Z, Tu J. Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data. Brief Bioinform 2023; 24:bbad275. [PMID: 37529913 DOI: 10.1093/bib/bbad275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown. RESULTS We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras. AVAILABILITY AND IMPLEMENTATION The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.
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Affiliation(s)
- Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengfei An
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Monash University-Southeast University Joint Research Institute, Suzhou 215123, China
| | - Jiajian Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89511, USA
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Wang B, Shao J, Qu L, Xu Q, Zheng D. The sequencing of the key genes and end products in the TLR4 signaling pathway from the kidney of Rana dybowskii exposed to Aeromonas hydrophila. Open Life Sci 2023; 18:20220704. [PMID: 37724117 PMCID: PMC10505344 DOI: 10.1515/biol-2022-0704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/06/2023] [Accepted: 07/30/2023] [Indexed: 09/20/2023] Open
Abstract
Infectious diseases caused by Aeromonas hydrophila (AH) have reduced the populations of Rana dybowskii). However, little is known about the immune response of R. dybowskii against AH infections. The toll-like receptor (TLR) signaling pathway has been identified as a critical component in innate immunity, responsible for identifying pathogen-associated molecular patterns in pathogens. Our study used the next-generation sequencing technique and single-molecule long-read sequencing to determine the structures of transcript isoforms and functions of genes in the kidneys of R. dybowskii, as well as identify and validate the related genes in the TLR4 signaling pathway. In total, 628,774 reads of inserts were identified, including 300,053 full-length non-chimeric reads and 233,592 non-full-length reads. Among the transcriptome sequences, 124 genes were identified as homologs of known genes in the TLR4 pathway especially inflammatory cytokines and receptors. Our findings shed light on the structures and functions of R. dybowskii genes exposed to AH and confirm the presence of both MyD88-dependent and independent pathways in R. dybowskii. Our work reveals how various functional proteins in amphibians at the initial stage of immune response are activated and complete their corresponding functions in a short time.
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Affiliation(s)
- Boju Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin150040, China
| | - Jie Shao
- College of Wildlife Resources, Northeast Forestry University, Harbin150040, China
| | - Lili Qu
- College of Wildlife Resources, Northeast Forestry University, Harbin150040, China
| | - Qing Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin150040, China
| | - Dong Zheng
- College of Wildlife Resources, Northeast Forestry University, Harbin150040, China
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Wang Y, Cai X, Hu S, Qin S, Wang Z, Cao Y, Hou C, Yang J, Zhou W. Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2. Gene 2023; 855:147118. [PMID: 36521669 DOI: 10.1016/j.gene.2022.147118] [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: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.
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Affiliation(s)
- Yongqiang Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Xunhui Cai
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shengnan Hu
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Sidong Qin
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Yixiang Cao
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Chaoliang Hou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Jiangshan Yang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Wei Zhou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
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7
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Khor CC, Winter S, Sutiman N, Mürdter TE, Chen S, Lim JSL, Li Z, Li J, Sim KS, Ganchev B, Eccles D, Eccles B, Tapper W, Zgheib NK, Tfayli A, Ng RCH, Yap YS, Lim E, Wong M, Wong NS, Ang PCS, Dent R, Tremmel R, Klein K, Schaeffeler E, Zhou Y, Lauschke VM, Eichelbaum M, Schwab M, Brauch HB, Chowbay B, Schroth W. Cross-Ancestry Genome-Wide Association Study Defines the Extended CYP2D6 Locus as the Principal Genetic Determinant of Endoxifen Plasma Concentrations. Clin Pharmacol Ther 2023; 113:712-723. [PMID: 36629403 DOI: 10.1002/cpt.2846] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The therapeutic efficacy of tamoxifen is predominantly mediated by its active metabolites 4-hydroxy-tamoxifen and endoxifen, whose formation is catalyzed by the polymorphic cytochrome P450 2D6 (CYP2D6). Yet, known CYP2D6 polymorphisms only partially determine metabolite concentrations in vivo. We performed the first cross-ancestry genome-wide association study with well-characterized patients of European, Middle-Eastern, and Asian descent (n = 497) to identify genetic factors impacting active and parent metabolite formation. Genome-wide significant variants were functionally evaluated in an independent liver cohort (n = 149) and in silico. Metabolite prediction models were validated in two independent European breast cancer cohorts (n = 287, n = 189). Within a single 1-megabase (Mb) region of chromosome 22q13 encompassing the CYP2D6 gene, 589 variants were significantly associated with tamoxifen metabolite concentrations, particularly endoxifen and metabolic ratio (MR) endoxifen/N-desmethyltamoxifen (minimal P = 5.4E-35 and 2.5E-65, respectively). Previously suggested other loci were not confirmed. Functional analyses revealed 66% of associated, mostly intergenic variants to be significantly correlated with hepatic CYP2D6 activity or expression (ρ = 0.35 to -0.52), and six hotspot regions in the extended 22q13 locus impacting gene regulatory function. Machine learning models based on hotspot variants (n = 12) plus CYP2D6 activity score (AS) increased the explained variability (~ 9%) compared with AS alone, explaining up to 49% (median R2 ) and 72% of the variability in endoxifen and MR endoxifen/N-desmethyltamoxifen, respectively. Our findings suggest that the extended CYP2D6 locus at 22q13 is the principal genetic determinant of endoxifen plasma concentration. Long-distance haplotypes connecting CYP2D6 with adjacent regulatory sites and nongenetic factors may account for the unexplained portion of variability.
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Affiliation(s)
- Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Clinical Pharmacology, SingHealth, Singapore, Singapore
| | - Stefan Winter
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Natalia Sutiman
- Clinical Pharmacology Laboratory, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
| | - Thomas E Mürdter
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Sylvia Chen
- Clinical Pharmacology Laboratory, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
| | - Joanne Siok Liu Lim
- Clinical Pharmacology Laboratory, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
| | - Zheng Li
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Jingmei Li
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Kar Seng Sim
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Boian Ganchev
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Diana Eccles
- Faculty of Medicine, Cancer Sciences Academic Unit and University of Southampton Clinical Trials Unit, University of Southampton, Southampton, UK.,University Hospital Southampton National Health Service Foundation Trust, Southampton, UK
| | - Bryony Eccles
- Faculty of Medicine, Cancer Sciences Academic Unit and University of Southampton Clinical Trials Unit, University of Southampton, Southampton, UK.,University Hospital Southampton National Health Service Foundation Trust, Southampton, UK
| | - William Tapper
- Faculty of Medicine, Cancer Sciences Academic Unit and University of Southampton Clinical Trials Unit, University of Southampton, Southampton, UK.,University Hospital Southampton National Health Service Foundation Trust, Southampton, UK
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Arafat Tfayli
- Hematology-Oncology Division, Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Yoon Sim Yap
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Elaine Lim
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Mabel Wong
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Nan Soon Wong
- OncoCare Cancer Centre, Mount Elizabeth Novena Medical Centre, Singapore, Singapore
| | - Peter Cher Siang Ang
- OncoCare Cancer Centre, Mount Elizabeth Novena Medical Centre, Singapore, Singapore
| | - Rebecca Dent
- Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Kathrin Klein
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Elke Schaeffeler
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany.,Image-Guided and Functionally Instructed Tumor Therapies Cluster of Excellence (iFIT), University of Tübingen, Tübingen, Germany
| | - Yitian Zhou
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Volker M Lauschke
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany.,Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Michel Eichelbaum
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Image-Guided and Functionally Instructed Tumor Therapies Cluster of Excellence (iFIT), University of Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, University of Tübingen, Tübingen, Germany.,Department of Biochemistry and Pharmacy, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Partner Site Tübingen, Tübingen, Germany
| | - Hiltrud B Brauch
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany.,Image-Guided and Functionally Instructed Tumor Therapies Cluster of Excellence (iFIT), University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Partner Site Tübingen, Tübingen, Germany
| | - Balram Chowbay
- Clinical Pharmacology, SingHealth, Singapore, Singapore.,Clinical Pharmacology Laboratory, Division of Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore.,Centre for Clinician-Scientist Development, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Werner Schroth
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University Tübingen, Tübingen, Germany
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8
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Liu M, Han Z, Zhi Y, Ruan Y, Cao G, Wang G, Xu X, Mu J, Kang J, Dai F, Wen X, Zhang Q, Li F. Long-read sequencing reveals oncogenic mechanism of HPV-human fusion transcripts in cervical cancer. Transl Res 2023; 253:80-94. [PMID: 36223881 DOI: 10.1016/j.trsl.2022.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022]
Abstract
Integration of high-risk human papillomavirus (HPV) into the host genome is a crucial event for the development of cervical cancer, however, the underlying mechanism of HPV integration-driven carcinogenesis remains unknown. Here, we performed long-read RNA sequencing on 12 high-grade squamous intraepithelial lesions (HSIL) and cervical cancer patients, including 3 pairs of cervical cancer and corresponding para-cancerous tissue samples to investigate the full-length landscape of cross-species genome integrations. In addition to massive unannotated isoforms, transcriptional regulatory events, and gene chimerism, more importantly, we found that HPV-human fusion events were prevalent in HPV-associated cervical cancers. Combined with the genome data, we revealed the existence of a universal transcription pattern in these fusion events, whereby structurally similar fusion transcripts were generated by specific splicing in E6 and a canonical splicing donor site in E1 linking to various human splicing acceptors. Highly expressed HPV-human fusion transcripts, eg, HPV16 E6*I-E7-E1SD880-human gene, were the key driver of cervical carcinogenesis, which could trigger overexpression of E6*I and E7, and destroy the transcription of tumor suppressor genes CMAHP, TP63 and P3H2. Finally, evidence from in vitro and in vivo experiments demonstrates that the novel read-through fusion gene mRNA, E1-CMAHP (E1C, formed by the integration of HPV58 E1 with CMAHP), existed in the fusion transcript can promote malignant transformation of cervical epithelial cells via regulating downstream oncogenes to participate in various biological processes. Taken together, we reveal a previously unknown mechanism of HPV integration-driven carcinogenesis and provide a novel target for the diagnosis and treatment of cervical cancer.
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Affiliation(s)
- Min Liu
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiqiang Han
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Zhi
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangxu Cao
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangxue Wang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinxin Xu
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Fangping Dai
- Genome-decoding Biomedical Technology Co., Ltd, Nantong, China
| | - Xuejun Wen
- Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA
| | - Qingfeng Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai, China.
| | - Fang Li
- Department of Obstetrics and Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
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9
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Lu N, Qiao Y, Lu Z, Tu J. Chimera: The spoiler in multiple displacement amplification. Comput Struct Biotechnol J 2023; 21:1688-1696. [PMID: 36879882 PMCID: PMC9984789 DOI: 10.1016/j.csbj.2023.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Multiple displacement amplification (MDA) based on isothermal random priming and high fidelity phi29 DNA polymerase-mediated processive extension has revolutionized the field of whole genome amplification by enabling the amplification of minute amounts of DNA, such as from a single cell, generating vast amounts of DNA with high genome coverage. Despite its advantages, MDA has its own challenges, one of the grandest being the formation of chimeric sequences (chimeras), which presents in all MDA products and seriously disturbs the downstream analysis. In this review, we provide a comprehensive overview of current research on MDA chimeras. We first reviewed the mechanisms of chimera formation and chimera detection methods. We then systematically summarized the characteristics of chimeras, including overlap, chimeric distance, chimeric density, and chimeric rate, as found in independently published sequencing data. Finally, we reviewed the methods used to process chimeric sequences and their impacts on the improvement of data utilization efficiency. The information presented in this review will be useful for those interested in understanding the challenges with MDA and in improving its performance.
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Affiliation(s)
- Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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10
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Feng J, Li Y, Zhang J, Zhang M, Zhang X, Shahzad K, Guo L, Qi T, Tang H, Wang H, Qiao X, Lin Z, Xing C, Wu J. Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:930131. [PMID: 35800603 PMCID: PMC9253813 DOI: 10.3389/fpls.2022.930131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Hybrid utilization has proficiently increased crop production worldwide. The cytoplasmic male sterility (CMS) system has emerged as an efficient tool for commercial hybrid cotton seed production. The restorer line with dominant Rf2 gene can restore the fertility of the CMS-D8 sterile line. However, the molecular mechanism of fertility restoration remains unclear in CMS-D8 cotton that limits wider utilization of three-line hybrid breeding. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to understand fertility restoration mechanism of CMS-D8 cotton. In total, 228,106 full-length non-chimeric transcriptome sequences were obtained from anthers of developing flowering buds. The analysis results identified 3,174 novel isoforms, 2,597 novel gene loci, 652 long non-coding RNAs predicted from novel isoforms, 7,234 alternative splicing events, 114 fusion transcripts, and 1,667 genes with alternative polyadenylation. Specially, two novel genes associated with restoration function, Ghir_D05.742.1 and m64033_190821_201011/21103726/ccs were identified and showed significant higher levels of expression in restorer line than sterile and maintainer lines. Our comparative full-length transcriptome analysis provides new insights into the molecular function of Rf2 fertility restorer gene. The results of this study offer a platform for fertility restoration candidate gene discovery in CMS-D8 cotton.
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Affiliation(s)
- Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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11
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Lischka A, Lassuthova P, Çakar A, Record CJ, Van Lent J, Baets J, Dohrn MF, Senderek J, Lampert A, Bennett DL, Wood JN, Timmerman V, Hornemann T, Auer-Grumbach M, Parman Y, Hübner CA, Elbracht M, Eggermann K, Geoffrey Woods C, Cox JJ, Reilly MM, Kurth I. Genetic pain loss disorders. Nat Rev Dis Primers 2022; 8:41. [PMID: 35710757 DOI: 10.1038/s41572-022-00365-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/05/2023]
Abstract
Genetic pain loss includes congenital insensitivity to pain (CIP), hereditary sensory neuropathies and, if autonomic nerves are involved, hereditary sensory and autonomic neuropathy (HSAN). This heterogeneous group of disorders highlights the essential role of nociception in protecting against tissue damage. Patients with genetic pain loss have recurrent injuries, burns and poorly healing wounds as disease hallmarks. CIP and HSAN are caused by pathogenic genetic variants in >20 genes that lead to developmental defects, neurodegeneration or altered neuronal excitability of peripheral damage-sensing neurons. These genetic variants lead to hyperactivity of sodium channels, disturbed haem metabolism, altered clathrin-mediated transport and impaired gene regulatory mechanisms affecting epigenetic marks, long non-coding RNAs and repetitive elements. Therapies for pain loss disorders are mainly symptomatic but the first targeted therapies are being tested. Conversely, chronic pain remains one of the greatest unresolved medical challenges, and the genes and mechanisms associated with pain loss offer new targets for analgesics. Given the progress that has been made, the coming years are promising both in terms of targeted treatments for pain loss disorders and the development of innovative pain medicines based on knowledge of these genetic diseases.
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Affiliation(s)
- Annette Lischka
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Christopher J Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jan Senderek
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.
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12
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Long J, Sun L, Gong F, Zhang C, Mao A, Lu Y, Li J, Liu E. Third-generation sequencing: A novel tool detects complex variants in the α-thalassemia gene. Gene 2022; 822:146332. [PMID: 35181504 DOI: 10.1016/j.gene.2022.146332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Thalassemia is a monogenic disorder with a high carrier rate in the southern region of China. Most laboratories currently follow the protocol of testing hematologic indicators in individuals with positive hematologic indicators and then using the hot-spot mutation test kit. A novel thalassemia gene test is performed if there is a mismatch between the hematology and hot-spot mutation test results. However, due to the large population in southern China, some individuals carry complex α-globin gene cluster (CAGC) variants in NG_000006.1, which are difficult to detect using conventional thalassemia genetic analysis protocols, leading to missed or false genetic test results for individuals carrying these complex α-globin gene cluster variants. When an individual carries a complex α-thalassemia gene variant, and an individual carries a β- thalassemia gene variant, there may be clinical symptoms that might complicate clinical consultation and prenatal diagnosis if not accurately detected. Third-generation sequencing (TGS) enables long-read single-molecule sequencing with high detection accuracy, and long-length DNA chain reads in high-fidelity reads mode. TGS can be used to analyze high homology and rich GC DNA sequences. RESULTS Four samples that showed abnormalities in the thalassemia genetic test were studied using TGS, revealing that they carried genotypes with complex α-globin gene cluster variants, one of which was a complex variant αα anti3.7 α anti3.7 α 17.2. CONCLUSIONS TGS detects complex α-globin gene cluster variants. This study may provide a reference protocol for the use of TGS for the detection of complex α-globin gene cluster variants. TGS can reveal individuals with complex α-thalassemia genotypes in the population and improve the accuracy of genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Ju Long
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China.
| | - Lei Sun
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Feifei Gong
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Chenghong Zhang
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Aiping Mao
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Yulin Lu
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Jiaqi Li
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Enqi Liu
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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13
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Affiliation(s)
| | | | | | | | | | | | | | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (M.R.); (P.Z.); (D.J.); (X.Y.); (Y.L.); (Z.Y.)
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14
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Brady MM, Meyer AS. Cataloguing the proteome: Current developments in single-molecule protein sequencing. BIOPHYSICS REVIEWS 2022; 3:011304. [PMID: 38505228 PMCID: PMC10903494 DOI: 10.1063/5.0065509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/13/2022] [Indexed: 03/21/2024]
Abstract
The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.
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Affiliation(s)
- Morgan M. Brady
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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Sun D, Li X, Yin Z, Hou Z. The Full-Length Transcriptome Provides New Insights Into the Transcript Complexity of Abdominal Adipose and Subcutaneous Adipose in Pekin Ducks. Front Physiol 2021; 12:767739. [PMID: 34858212 PMCID: PMC8631521 DOI: 10.3389/fphys.2021.767739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
Abstract
Adipose tissues have a central role in organisms, and adipose content is a crucial economic trait of poultry. Pekin duck is an ideal model to study the mechanism of abdominal and subcutaneous adipose deposition for its high ability of adipose synthesis and deposition. Alternative splicing contributes to functional diversity in abdominal and subcutaneous adipose. However, there has been no systematic analysis of the dynamics of differential alternative splicing of abdominal and subcutaneous adipose in Pekin duck. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to explore the transcriptional complexity of abdominal and subcutaneous adipose in Pekin ducks. In total, 143,931 and 111,337 full-length non-chimeric transcriptome sequences of abdominal and subcutaneous adipocytes were obtained from 41.78 GB raw data, respectively. These data led us to identify 19,212 long non-coding RNAs (lncRNAs) and 74,571 alternative splicing events. In addition, combined with the next-generation sequencing technology, we correlated the structure and function annotation with the differential expression profiles of abdominal and subcutaneous adipose transcripts. This study identified lots of novel alternative splicing events and major transcripts of transcription factors related to adipose synthesis. STAT3 was reported as a vital gene for adipogenesis, and we found that its major transcript is STAT3-1, which may play a considerable role in the process of adipose synthesis in Pekin duck. This study greatly increases our understanding of the gene models, genome annotations, genome structures, and the complexity and diversity of abdominal and subcutaneous adipose in Pekin duck. These data provide insights into the regulation of alternative splicing events, which form an essential part of transcript diversity during adipogenesis in poultry. The results of this study provide an invaluable resource for studying alternative splicing and tissue-specific expression.
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Affiliation(s)
- Dandan Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoqin Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhongtao Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhuocheng Hou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Li J, Yu N, Li X, Cui M, Guo Q. The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer. Front Oncol 2021; 11:759894. [PMID: 34745998 PMCID: PMC8566994 DOI: 10.3389/fonc.2021.759894] [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: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/30/2022] Open
Abstract
Tumorigenesis refers to the process of clonal dysplasia that occurs due to the collapse of normal growth regulation in cells caused by the action of various carcinogenic factors. These “successful” tumor cells pass on the genetic templates to their generations in evolutionary terms, but they also constantly adapt to ever-changing host environments. A unique peculiarity known as intratumor heterogeneity (ITH) is extensively involved in tumor development, metastasis, chemoresistance, and immune escape. An understanding of ITH is urgently required to identify the diversity and complexity of the tumor microenvironment (TME), but achieving this understanding has been a challenge. Single-cell sequencing (SCS) is a powerful tool that can gauge the distribution of genomic sequences in a single cell and the genetic variability among tumor cells, which can improve the understanding of ITH. SCS provides fundamental ideas about existing diversity in specific TMEs, thus improving cancer diagnosis and prognosis prediction, as well as improving the monitoring of therapeutic response. Herein, we will discuss advances in SCS and review SCS application in tumors based on current evidence.
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Affiliation(s)
- Jing Li
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Nan Yu
- Department of Pharmacy, Qingdao Eighth People's Hospital, Qingdao, China
| | - Xin Li
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengna Cui
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qie Guo
- Department of Clinical Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao, China
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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Tedersoo L, Albertsen M, Anslan S, Callahan B. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology. Appl Environ Microbiol 2021; 87:e0062621. [PMID: 34132589 PMCID: PMC8357291 DOI: 10.1128/aem.00626-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. Int J Mol Sci 2021; 22:4707. [PMID: 33946766 PMCID: PMC8125562 DOI: 10.3390/ijms22094707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.
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Affiliation(s)
- Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
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Bolz HJ. Diagnostic Analyses of Retinal Dystrophy Genes: Current Status and Perspective. Klin Monbl Augenheilkd 2021; 238:261-266. [PMID: 33784789 DOI: 10.1055/a-1386-5361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the past decade, novel high-throughput DNA sequencing technologies have revolutionised both research and diagnostic testing for monogenic disorders. This applies particularly to genetically very heterogeneous disorders like retinal dystrophies (RDs). Next-generation sequencing (NGS) today is considered as reliable as Sanger sequencing, which had been the gold standard for decades. Today, comprehensive NGS-based diagnostic testing reveals the causative mutations in the majority of RD patients, with important implications for genetic counselling for recurrence risks and personalised medical management (from interdisciplinary surveillance to prophylactic measures and, albeit yet rare, [gene] therapy). While DNA sequencing is - in most cases - no longer the diagnostic bottleneck, one needs to be aware of interpretation pitfalls and dead ends. The advent of new (NGS) technologies will solve some of these issues. However, specialised medical geneticists who are familiar with the peculiarities of certain RD genes and closely interact with ophthalmologists will remain key to successful RD research and diagnostic testing for the benefit of the patients. This review sheds light on the current state of the field, its challenges and potential solutions.
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Affiliation(s)
- Hanno Jörn Bolz
- Humangenetik, Senckenberg Zentrum für Humangenetik, Frankfurt, Germany.,Humangenetik, University Hospital of Cologne, Cologne, Germany
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Kairov U, Molkenov A, Rakhimova S, Kozhamkulov U, Sharip A, Karabayev D, Daniyarov A, H Lee J, D Terwilliger J, Akilzhanova A, Zhumadilov Z. Whole-genome sequencing data of Kazakh individuals. BMC Res Notes 2021; 14:45. [PMID: 33541395 PMCID: PMC7863413 DOI: 10.1186/s13104-021-05464-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/28/2021] [Indexed: 11/22/2022] Open
Abstract
Objectives Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region. Data description Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.
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Affiliation(s)
- Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aigul Sharip
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Daniyar Karabayev
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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