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Borges-Monroy R, Chu C, Dias C, Choi J, Lee S, Gao Y, Shin T, Park PJ, Walsh CA, Lee EA. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA 2021; 12:28. [PMID: 34838103 PMCID: PMC8627061 DOI: 10.1186/s13100-021-00256-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available. RESULTS We analyzed WGS data from a cohort of 2288 ASD families from the Simons Simplex Collection by establishing a scalable computational pipeline for retrotransposon insertion detection. We report 86,154 polymorphic retrotransposon insertions-including > 60% not previously reported-and 158 de novo retrotransposition events. The overall burden of de novo events was similar between ASD individuals and unaffected siblings, with 1 de novo insertion per 29, 117, and 206 births for Alu, L1, and SVA respectively, and 1 de novo insertion per 21 births total. However, ASD cases showed more de novo L1 insertions than expected in ASD genes. Additionally, we observed exonic insertions in loss-of-function intolerant genes, including a likely pathogenic exonic insertion in CSDE1, only in ASD individuals. CONCLUSIONS These findings suggest a modest, but important, impact of intronic and exonic retrotransposon insertions in ASD, show the importance of WGS for their analysis, and highlight the utility of specific bioinformatic tools for high-throughput detection of retrotransposon insertions.
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Affiliation(s)
- Rebeca Borges-Monroy
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Caroline Dias
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Genetics, Harvard Medical School, MA, Boston, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yue Gao
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Pediatrics, Harvard Medical School, MA, Boston, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Pediatrics, Harvard Medical School, MA, Boston, USA.
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102
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 800] [Impact Index Per Article: 200.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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103
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Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. Trends Genet 2021; 38:246-257. [PMID: 34711425 DOI: 10.1016/j.tig.2021.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome the read size limit of short-read sequencing. However, analyzing the raw nanopore signal data provides many more opportunities beyond just sequencing genomes and transcriptomes: algorithms that use machine learning approaches to extract biological information from these signals allow the detection of DNA and RNA modifications, the estimation of poly(A) tail length, and the prediction of RNA secondary structures. In this review, we discuss how developments in machine learning methodologies contributed to more accurate basecalling and lower error rates, and how these methods enable new biological discoveries. We argue that direct nanopore sequencing of DNA and RNA provides a new dimensionality for genomics experiments and highlight challenges and future directions for computational approaches to extract the additional information provided by nanopore signal data.
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104
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Liu Y, Rosikiewicz W, Pan Z, Jillette N, Wang P, Taghbalout A, Foox J, Mason C, Carroll M, Cheng A, Li S. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biol 2021; 22:295. [PMID: 34663425 PMCID: PMC8524990 DOI: 10.1186/s13059-021-02510-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/04/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies. RESULTS We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale. We evaluate the per-read and per-site performance of CpG methylation prediction across different genomic contexts, CpG site coverage, and computational resources consumed by each tool. The seven tools exhibit different performances across the evaluation criteria. We show that the methylation prediction at regions with discordant DNA methylation patterns, intergenic regions, low CG density regions, and repetitive regions show room for improvement across all tools. Furthermore, we demonstrate that 5hmC levels at least partly contribute to the discrepancy between bisulfite and nanopore sequencing. Lastly, we provide an online DNA methylation database ( https://nanome.jax.org ) to display the DNA methylation levels detected by nanopore sequencing and bisulfite sequencing data across different genomic contexts. CONCLUSIONS Our study is the first systematic benchmark of computational methods for detection of mammalian whole-genome DNA modifications in nanopore sequencing. We provide a broad foundation for cross-platform standardization and an evaluation of analytical tools designed for genome-scale modified base detection using nanopore sequencing.
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Affiliation(s)
- Yang Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Present address: Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ziwei Pan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA
| | | | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Martin Carroll
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Albert Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
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105
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Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev 2021; 131:988-1004. [PMID: 34592258 DOI: 10.1016/j.neubiorev.2021.09.049] [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: 04/05/2021] [Revised: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.
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Affiliation(s)
- Manci Li
- University of Minnesota, St. Paul, MN, 55108, United States
| | - Peter A Larsen
- University of Minnesota, St. Paul, MN, 55108, United States.
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106
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Wong JS, Jadhav T, Young E, Wang Y, Xiao M. Characterization of full-length LINE-1 insertions in 154 genomes. Genomics 2021; 113:3804-3810. [PMID: 34534648 DOI: 10.1016/j.ygeno.2021.09.011] [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: 05/17/2021] [Revised: 08/18/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations.
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Affiliation(s)
- Jessica S Wong
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Tanaya Jadhav
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Yilin Wang
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America; Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, United States of America.
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107
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Briggs EM, Mita P, Sun X, Ha S, Vasilyev N, Leopold ZR, Nudler E, Boeke JD, Logan SK. Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. Mob DNA 2021; 12:21. [PMID: 34425899 PMCID: PMC8381588 DOI: 10.1186/s13100-021-00249-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells. RESULTS Here, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5'UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1. CONCLUSION Our optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.
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Affiliation(s)
- Erica M Briggs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Xiaoji Sun
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Cellarity, Cambridge, MA, USA
| | - Susan Ha
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Zev R Leopold
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Susan K Logan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
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108
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Smits N, Rasmussen J, Bodea GO, Amarilla AA, Gerdes P, Sanchez-Luque FJ, Ajjikuttira P, Modhiran N, Liang B, Faivre J, Deveson IW, Khromykh AA, Watterson D, Ewing AD, Faulkner GJ. No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Rep 2021; 36:109530. [PMID: 34380018 PMCID: PMC8316065 DOI: 10.1016/j.celrep.2021.109530] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/28/2023] Open
Abstract
A recent study proposed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2 and do not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolve 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV)-positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions by ONT sequencing. That we find no evidence of SARS-CoV-2 integration suggests that such events are, at most, extremely rare in vivo and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.
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Affiliation(s)
- Nathan Smits
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Gabriela O Bodea
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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109
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Cao M, Zhang C, Zhou L. DNA methylation detection technology and plasma-based methylation biomarkers in screening of gastrointestinal carcinoma. Epigenomics 2021; 13:1327-1339. [PMID: 34369810 DOI: 10.2217/epi-2021-0118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is of paramount importance for the evolution of human cancers. Its high sensitivity and specificity make it a potential biomarker for early cancer screening in the context of an increasing global burden of gastrointestinal (GI) carcinoma. More DNA methylation biomarkers are emerging with the development of liquid biopsy and sensitive DNA methylation detection technology. This review provides an overview of DNA methylation, focusing on the presentation and comparison of 5-methylcytosine detection technologies, and introduces the promising plasma-based cell-free DNA (cfDNA) methylation biomarkers published in recent years for early screening of GI carcinoma. Finally, we summarize and discuss the future of plasma cfDNA methylation markers detection as a clinical tool for early screening of GI carcinoma.
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Affiliation(s)
- Mengjiao Cao
- Department of Biochemistry, Department of the Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chuanfeng Zhang
- Department of Biochemistry, Department of the Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Linfu Zhou
- Department of Biochemistry, Department of the Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
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110
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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111
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Onodera A, González-Avalos E, Lio CWJ, Georges RO, Bellacosa A, Nakayama T, Rao A. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol 2021; 22:186. [PMID: 34158086 PMCID: PMC8218415 DOI: 10.1186/s13059-021-02384-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1, DNA demethylation can occur through "passive," replication-dependent dilution when cells divide. A distinct, replication-independent ("active") mechanism of DNA demethylation involves excision of 5fC and 5caC by the DNA repair enzyme thymine DNA glycosylase (TDG), followed by base excision repair. RESULTS Here by analyzing inducible gene-disrupted mice, we show that DNA demethylation during primary T cell differentiation occurs mainly through passive replication-dependent dilution of all three oxi-mCs, with only a negligible contribution from TDG. In addition, by pyridine borane sequencing (PB-seq), a simple recently developed method that directly maps 5fC/5caC at single-base resolution, we detect the accumulation of 5fC/5caC in TDG-deleted T cells. We also quantify the occurrence of concordant demethylation within and near enhancer regions in the Il4 locus. In an independent system that does not involve cell division, macrophages treated with liposaccharide accumulate 5hmC at enhancers and show altered gene expression without DNA demethylation; loss of TET enzymes disrupts gene expression, but loss of TDG has no effect. We also observe that mice with long-term (1 year) deletion of Tdg are healthy and show normal survival and hematopoiesis. CONCLUSIONS We have quantified the relative contributions of TET and TDG to cell differentiation and DNA demethylation at representative loci in proliferating T cells. We find that TET enzymes regulate T cell differentiation and DNA demethylation primarily through passive dilution of oxi-mCs. In contrast, while we observe a low level of active, replication-independent DNA demethylation mediated by TDG, this process does not appear to be essential for immune cell activation or differentiation.
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Affiliation(s)
- Atsushi Onodera
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Institute for Global Prominent Research, Chiba University, 1-33, Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Present address: Department of Microbial Infection and Immunity, Ohio State University, 460 W 12th Ave, Columbus, OH, 43210, USA
| | - Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Alfonso Bellacosa
- Cancer Signaling and Epigenetics Program & Cancer Epigenetics Institute, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
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112
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McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nat Commun 2021; 12:3586. [PMID: 34117247 PMCID: PMC8196195 DOI: 10.1038/s41467-021-23918-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.
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Affiliation(s)
- Torrin L McDonald
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Christopher P Castro
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Camille Mumm
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jessica A Switzenberg
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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113
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Zhang J, Xie S, Xu J, Liu H, Wan S. Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing. Front Genet 2021; 12:672804. [PMID: 34122526 PMCID: PMC8188482 DOI: 10.3389/fgene.2021.672804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
Cancer is a complex disease, driven by a combination of genetic and epigenetic alterations. DNA and RNA methylation modifications are the most common epigenetic events that play critical roles in cancer development and progression. Bisulfite converted sequencing is a widely used technique to detect base modifications in DNA methylation, but its main drawbacks lie in DNA degradation, lack of specificity, or short reads with low sequence diversity. The nanopore sequencing technology can directly detect base modifications in native DNA as well as RNA without harsh chemical treatment, compared to bisulfite sequencing. Furthermore, CRISPR/Cas9-targeted enrichment nanopore sequencing techniques are straightforward and cost-effective when targeting genomic regions are of interest. In this review, we mainly focus on DNA and RNA methylation modification detection in cancer with the current nanopore sequencing approaches. We also present the respective strengths, weaknesses of nanopore sequencing techniques, and their future translational applications in identification of epigenetic biomarkers for cancer detection and prognosis.
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Affiliation(s)
- Junjie Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Shuilian Xie
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Jingxiang Xu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Hui Liu
- Institute of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
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114
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Jansz N, Faulkner GJ. Endogenous retroviruses in the origins and treatment of cancer. Genome Biol 2021; 22:147. [PMID: 33971937 PMCID: PMC8108463 DOI: 10.1186/s13059-021-02357-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous retroviruses (ERVs) are emerging as promising therapeutic targets in cancer. As remnants of ancient retroviral infections, ERV-derived regulatory elements coordinate expression from gene networks, including those underpinning embryogenesis and immune cell function. ERV activation can promote an interferon response, a phenomenon termed viral mimicry. Although ERV expression is associated with cancer, and provisionally with autoimmune and neurodegenerative diseases, ERV-mediated inflammation is being explored as a way to sensitize tumors to immunotherapy. Here we review ERV co-option in development and innate immunity, the aberrant contribution of ERVs to tumorigenesis, and the wider biomedical potential of therapies directed at ERVs.
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Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia. .,Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia.
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115
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Siudeja K, van den Beek M, Riddiford N, Boumard B, Wurmser A, Stefanutti M, Lameiras S, Bardin AJ. Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J 2021; 40:e106388. [PMID: 33634906 PMCID: PMC8090852 DOI: 10.15252/embj.2020106388] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore long-read sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.
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Affiliation(s)
- Katarzyna Siudeja
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marius van den Beek
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Nick Riddiford
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Benjamin Boumard
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Annabelle Wurmser
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marine Stefanutti
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Sonia Lameiras
- ICGex Next‐Generation Sequencing PlatformInstitut CuriePSL Research UniversityParisFrance
| | - Allison J Bardin
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
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116
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Kojima S, Kamada AJ, Parrish NF. Virus-derived variation in diverse human genomes. PLoS Genet 2021; 17:e1009324. [PMID: 33901175 PMCID: PMC8101998 DOI: 10.1371/journal.pgen.1009324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/06/2021] [Accepted: 03/25/2021] [Indexed: 11/19/2022] Open
Abstract
Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. We detected non-germline SVs derived from squirrel monkey retrovirus (SMRV), human immunodeficiency virus 1 (HIV-1), and human T lymphotropic virus (HTLV-1); these variants are attributable to infection of the sequenced lymphoblastoid cell lines (LCLs) or their progenitor cells and may impact gene expression results and the biosafety of experiments using these cells. In addition, we detected new heritable SVs derived from human herpesvirus 6 (HHV-6) and human endogenous retrovirus-K (HERV-K). We report the first solo-direct repeat (DR) HHV-6 likely to reflect DR rearrangement of a known full-length endogenous HHV-6. We used linkage disequilibrium between single nucleotide variants (SNVs) and variants in reads that align to HERV-K, which often cannot be mapped uniquely using conventional short-read sequencing analysis methods, to locate previously-unknown polymorphic HERV-K loci. Some of these loci are tightly linked to trait-associated SNVs, some are in complex genome regions inaccessible by prior methods, and some contain novel HERV-K haplotypes likely derived from gene conversion from an unknown source or introgression. These tools and results broaden our perspective on the coevolution between viruses and humans, including ongoing virus-to-human gene transfer contributing to genetic variation between humans.
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Affiliation(s)
- Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Anselmo Jiro Kamada
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- * E-mail:
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117
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Marshall JN, Lopez AI, Pfaff AL, Koks S, Quinn JP, Bubb VJ. Variable number tandem repeats - Their emerging role in sickness and health. Exp Biol Med (Maywood) 2021; 246:1368-1376. [PMID: 33794697 PMCID: PMC8239992 DOI: 10.1177/15353702211003511] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding the mechanisms regulating tissue specific and stimulus inducible
regulation is at the heart of understanding human biology and how this
translates to wellbeing, the ageing process, and disease progression.
Polymorphic DNA variation is superimposed as an extra layer of complexity in
such processes which underpin our individuality and are the focus of
personalized medicine. This review focuses on the role and action of repetitive
DNA, specifically variable number tandem repeats and
SINE-VNTR-Alu domains, highlighting their role in
modification of gene structure and gene expression in addition to their
polymorphic nature being a genetic modifier of disease risk and progression.
Although the literature focuses on their role in disease, it illustrates their
potential to be major contributors to normal physiological function. To date,
these elements have been under-reported in genomic analysis due to the
difficulties in their characterization with short read DNA sequencing methods.
However, recent advances in long read sequencing methods should resolve these
problems allowing for a greater understanding of their contribution to a host of
genomic and functional mechanisms underlying physiology and disease.
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Affiliation(s)
- Jack Ng Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ana Illera Lopez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
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