1
|
Cirrincione M, Downing M, Leite K, Dolphin S, Samuta A, Schermer M, Noble K, Walsh B. Assessment of Reader Technologies for Over-the-Counter Diagnostic Testing. IEEE Open J Eng Med Biol 2024; 5:210-215. [PMID: 38606399 PMCID: PMC11008808 DOI: 10.1109/ojemb.2024.3355701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/29/2023] [Accepted: 01/15/2024] [Indexed: 04/13/2024] Open
Abstract
Background: Over-the-counter (OTC) diagnostic testing is on the rise with many in vitro diagnostic tests being lateral flow assays (LFAs). A growing number of these are adopting reader technologies, which provides an alternative to visual readouts for results interpretation, allowing for improved accessibility of OTC diagnostics. As the reader technology market develops, there are many technologies entering the market, but no clear, single solution has yet been identified. The purpose of this research is to identify and discuss important parameters for the assessment of LFA reader technologies for consideration by manufacturers or researchers. Methods: As part of The National Institute of Biomedical Imaging and Bioengineering's Rapid Acceleration of Diagnostics (RADx) Tech program, reader manufacturers were interviewed to investigate the current state of reader technology development through several parameters identified as important industry standards. Readers were categorized by technology type and parameters including cost, detection method, multiplex capabilities, assay type, maturity, and use case were all assessed. Results: Fifteen reader manufacturers were identified and interviewed, and information on a total of 19 technologies was assessed. Reader technology type was found to be predictive of other attributes, whether the reader is smart technology only, a standalone reader, a reader with smart technology required, or a reader with smart technology optional. Conclusions: Pairing reader technology with OTC diagnostic tests is important for improving existing COVID-19 tests and can be utilized in other diagnostics as the OTC use case grows in popularity. Reader technology type, which is predictive of core reader attributes, should be considered when selecting a reader technology for a specific LFA test within the context of regulatory guidance. As diagnostics increase in complexity, readers provide solutions to accessibility challenges, facilitate public health reporting, and ease the transition to multiplex testing, therefore increasing market availability.
Collapse
|
2
|
Jayaseelan VP, Loganathan K, Pandi A, Ramasubramanian A, Kannan B, Arumugam P. Proteolysis-targeting chimeras targeting epigenetic modulators: a promising strategy for oral cancer therapy. Epigenomics 2023; 15:1233-1236. [PMID: 37990892 DOI: 10.2217/epi-2023-0293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Affiliation(s)
- Vijayashree Priyadharsini Jayaseelan
- Clinical Genetics lab, Centre for Cellular & Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu - 600077, India
| | - Kavitha Loganathan
- Department of Oral and Maxillofacial Pathology, Ragas Dental College and Hospital, East Coast Road, Uthandi, Chennai - 600 119. Affiliated to The Tamil Nadu Dr. MGR Medical University, Anna Salai, Guindy, Chennai - 600032, India
| | - Anitha Pandi
- Clinical Genetics lab, Centre for Cellular & Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu - 600077, India
| | - Abilasha Ramasubramanian
- Department of Oral Pathology, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu - 600077, India
| | - Balachander Kannan
- Centre for Cellular & Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu - 600077, India
| | - Paramasivam Arumugam
- Centre for Cellular & Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu - 600077, India
| |
Collapse
|
3
|
Jain K, Marunde MR, Burg JM, Gloor SL, Joseph FM, Poncha KF, Gillespie ZB, Rodriguez KL, Popova IK, Hall NW, Vaidya A, Howard SA, Taylor HF, Mukhsinova L, Onuoha UC, Patteson EF, Cooke SW, Taylor BC, Weinzapfel EN, Cheek MA, Meiners MJ, Fox GC, Namitz KEW, Cowles MW, Krajewski K, Sun ZW, Cosgrove MS, Young NL, Keogh MC, Strahl BD. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. eLife 2023; 12:e82596. [PMID: 37204295 PMCID: PMC10229121 DOI: 10.7554/elife.82596] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/18/2023] [Indexed: 05/20/2023] Open
Abstract
In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
Collapse
Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | | | - Faith M Joseph
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Karl F Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | | | | | | | | | | | | | | | - Spencer W Cooke
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | - Bethany C Taylor
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | - Geoffrey C Fox
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | | | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, Upstate Medical UniversitySyracuseUnited States
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| |
Collapse
|
4
|
Piell KM, Petri BJ, Head KZ, Wahlang B, Xu R, Zhang X, Pan J, Rai SN, de Silva K, Chariker JH, Rouchka EC, Tan M, Li Y, Cave MC, Klinge CM. Disruption of the Mouse Liver Epitranscriptome by Long-term Aroclor 1260 Exposure. Environ Toxicol Pharmacol 2023; 100:104138. [PMID: 37137421 DOI: 10.1016/j.etap.2023.104138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/05/2023]
Abstract
Chronic environmental exposure to polychlorinated biphenyls (PCBs) is associated with non-alcoholic fatty liver disease (NAFLD) and exacerbated by a high fat diet (HFD). Here, chronic (34 wks.) exposure of low fat diet (LFD)-fed male mice to Aroclor 1260 (Ar1260), a non-dioxin-like (NDL) mixture of PCBs, resulted in steatohepatitis and NAFLD. Twelve hepatic RNA modifications were altered with Ar1260 exposure including reduced abundance of 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A), in contrast to increased Am in the livers of HFD-fed, Ar1260-exposed mice reported previously. Differences in 13 RNA modifications between LFD- and HFD- fed mice, suggest that diet regulates the liver epitranscriptome. Integrated network analysis of epitranscriptomic modifications identified a NRF2 (Nfe2l2) pathway in the chronic, LFD, Ar1260-exposed livers and an NFATC4 (Nfatc4) pathway for LFD- vs. HFD-fed mice. Changes in protein abundance were validated. The results demonstrate that diet and Ar1260 exposure alter the liver epitranscriptome in pathways associated with NAFLD.
Collapse
Affiliation(s)
- Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292
| | - Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center
| | - Banrida Wahlang
- University of Louisville Hepatobiology and Toxicology Center
| | - Raobo Xu
- University of Louisville Hepatobiology and Toxicology Center; Department of Chemistry, University of Louisville College of Arts and Sciences
| | - Xiang Zhang
- University of Louisville Hepatobiology and Toxicology Center; Department of Chemistry, University of Louisville College of Arts and Sciences; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
| | - Jianmin Pan
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267
| | - Shesh N Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267
| | - Kalpani de Silva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292
| | - Julia H Chariker
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292
| | - Min Tan
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine; Louisville, KY 40292
| | - Yan Li
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine; Louisville, KY 40292
| | - Matthew C Cave
- University of Louisville Hepatobiology and Toxicology Center; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS); Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine; Louisville, KY 40292; The University of Louisville Superfund Research Center
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS).
| |
Collapse
|
5
|
Alam M, Levin NA, Grant-Kels JM, Elston DM. Letter from the Editors: Advice for JAAD reviewers that may be of interest to authors and readers. J Am Acad Dermatol 2023; 88:785-786. [PMID: 36041553 DOI: 10.1016/j.jaad.2022.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 10/15/2022]
Affiliation(s)
- Murad Alam
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Nikki A Levin
- Department of Dermatology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane M Grant-Kels
- Department of Dermatology, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Dirk M Elston
- Department of Dermatology, Medical University of South Carolina, Charleston, South Carolina
| |
Collapse
|
6
|
Adamopoulos PG, Athanasopoulou K, Daneva GN, Scorilas A. The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses. Int J Mol Sci 2023; 24. [PMID: 36768716 DOI: 10.3390/ijms24032387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Although a plethora of DNA modifications have been extensively investigated in the last decade, recent breakthroughs in molecular biology, including high throughput sequencing techniques, have enabled the identification of post-transcriptional marks that decorate RNAs; hence, epitranscriptomics has arisen. This recent scientific field aims to decode the regulatory layer of the transcriptome and set the ground for the detection of modifications in ribose nucleotides. Until now, more than 170 RNA modifications have been reported in diverse types of RNA that contribute to various biological processes, such as RNA biogenesis, stability, and transcriptional and translational accuracy. However, dysfunctions in the RNA-modifying enzymes that regulate their dynamic level can lead to human diseases and cancer. The present review aims to highlight the epitranscriptomic landscape in human RNAs and match the catalytic proteins with the deposition or deletion of a specific mark. In the current review, the most abundant RNA modifications, such as N6-methyladenosine (m6A), N5-methylcytosine (m5C), pseudouridine (Ψ) and inosine (I), are thoroughly described, their functional and regulatory roles are discussed and their contributions to cellular homeostasis are stated. Ultimately, the involvement of the RNA modifications and their writers, erasers, and readers in human diseases and cancer is also discussed.
Collapse
|
7
|
Tang L, Xue J, Ren X, Zhang Y, Du L, Ding F, Zhou K, Ma W. Genome-Wide Identification and Expression Analysis of m6A Writers, Erasers, and Readers in Litchi ( Litchi chinensis Sonn.). Genes (Basel) 2022; 13:genes13122284. [PMID: 36553551 PMCID: PMC9777543 DOI: 10.3390/genes13122284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in litchi was performed and 31 litchi m6A regulatory genes were identified in total, including 7 m6A writers, 12 m6A erases, and 12 readers. Phylogeny analysis showed that all three of the kinds of litchi m6A regulatory proteins could be divided into three groups; domains and motifs exhibited similar patterns in the same group. MiRNA target site prediction showed that 77 miRNA target sites were located in 25 (80.6%) litchi m6A regulatory genes. Cis-elements analysis exhibited that litchi m6A regulatory genes were mainly responsive to light and plant hormones, followed by environmental stress and plant development. Expression analysis revealed litchi m6A regulatory genes might play an important role during the peel coloration and fruit abscission of litchi. This study provided valuable and expectable information of litchi m6A regulatory genes and their potential epigenetic regulation mechanism in litchi.
Collapse
Affiliation(s)
- Liwen Tang
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Jiali Xue
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Xingyu Ren
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Yue Zhang
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Liqing Du
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture & Rural Affairs, South Subtropical Crops Research Institute of Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Kaibing Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Wuqiang Ma
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
- Correspondence: ; Tel.: +86-158-1331-3342
| |
Collapse
|
8
|
Navarro IC, Suen KM, Bensaddek D, Tanpure A, Lamond A, Balasubramanian S, Miska EA. Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA. Wellcome Open Res 2022; 7:282. [PMID: 37475875 PMCID: PMC10354459 DOI: 10.12688/wellcomeopenres.17893.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2022] [Indexed: 07/22/2023] Open
Abstract
Background: Methylation of carbon-5 of cytosines (m 5C) is a conserved post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. It can be further modified to yield 5-hydroxymethylcytidine (hm 5C), 5-formylcytidine (f 5C), 2´-O-methyl-5-hydroxymethylcytidine (hm 5Cm) and 2´-O-methyl-5-formylcytidine (f 5Cm). How m 5C, and specially its derivates, contribute to biology mechanistically is poorly understood. We recently showed that m 5C is required for Caenorhabditis elegans development and fertility under heat stress. m 5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. Hence, identifying readers for RNA modifications can enhance our understanding in the biological roles of these modifications. Methods: To contribute to the understanding of how m 5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Potential readers were identified using mass spectrometry. The interaction of two of the putative readers with m 5C was validated using immunoblotting. Results: Our mass spectrometry analyses revealed unique binding proteins for each of the modifications. In silico analysis for phenotype enrichments suggested that hm 5Cm unique readers are enriched in proteins involved in RNA processing, while readers for m 5C, hm 5C and f 5C are involved in germline processes. We validated our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m 5C in vitro. Finally, sequence alignment analysis showed that several of the putative m 5C readers contain the conserved RNA recognition motif (RRM), including ALY-1 and ALY-2. Conclusions: The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m 5C and its derivatives. Furthermore, we demonstrate that ALY-1 and ALY-2 bind to m 5C in C. elegans.
Collapse
Affiliation(s)
- IC Navarro
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Kin Man Suen
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- School of Molecular and Cellular Biology, University of Leeds, LC Miall Building, Leeds, LS2 9JT, UK
| | - Dalila Bensaddek
- Laboratory for Quantitative Proteomics, Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Bioscience Core Labs, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Arun Tanpure
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Angus Lamond
- Laboratory for Quantitative Proteomics, Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research (UK), Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| |
Collapse
|
9
|
Ignat T, Ayris P, Gini B, Stepankova O, Özdemir D, Bal D, Deyanova Y. Perspectives on Open Science and The Future of Scholarly Communication: Internet Trackers and Algorithmic Persuasion. Front Res Metr Anal 2022; 6:748095. [PMID: 35005422 PMCID: PMC8734967 DOI: 10.3389/frma.2021.748095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
The current digital content industry is heavily oriented towards building platforms that track users' behaviour and seek to convince them to stay longer and come back sooner onto the platform. Similarly, authors are incentivised to publish more and to become champions of dissemination. Arguably, these incentive systems are built around public reputation supported by a system of metrics, hard to be assessed. Generally, the digital content industry is permeable to non-human contributors (algorithms that are able to generate content and reactions), anonymity and identity fraud. It is pertinent to present a perspective paper about early signs of track and persuasion in scholarly communication. Building our views, we have run a pilot study to determine the opportunity for conducting research about the use of "track and persuade" technologies in scholarly communication. We collected observations on a sample of 148 relevant websites and we interviewed 15 that are experts related to the field. Through this work, we tried to identify 1) the essential questions that could inspire proper research, 2) good practices to be recommended for future research, and 3) whether citizen science is a suitable approach to further research in this field. The findings could contribute to determining a broader solution for building trust and infrastructure in scholarly communication. The principles of Open Science will be used as a framework to see if they offer insights into this work going forward.
Collapse
Affiliation(s)
| | - Paul Ayris
- LCCOS - Library, Culture, Collections, Open Science, University College London, London, United Kingdom
| | - Beatrice Gini
- Cambridge University Library (CUL), University of Cambridge, Cambridge, United Kingdom
| | - Olga Stepankova
- CIIRC (Czech Institute of Informatics and Robotics and Cybernetics), BEAT (Biomedical Engineering and Assited Technologies) Department, Czech Technical University in Prague, Prague, Czechia
| | - Deniz Özdemir
- CIIRC (Czech Institute of Informatics and Robotics and Cybernetics), BEAT (Biomedical Engineering and Assited Technologies) Department, Czech Technical University in Prague, Prague, Czechia
| | - Damla Bal
- Scientific Knowledge Services, Munich, Germany
| | | |
Collapse
|
10
|
Qu N, Bo X, Li B, Ma L, Wang F, Zheng Q, Xiao X, Huang F, Shi Y, Zhang X. Role of N6-Methyladenosine (m 6A) Methylation Regulators in Hepatocellular Carcinoma. Front Oncol 2021; 11:755206. [PMID: 34692544 PMCID: PMC8529104 DOI: 10.3389/fonc.2021.755206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Liver cancer is the fifth most common malignant tumor in terms of incidence and the third leading cause of cancer-related mortality globally. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Although great progress has been made in surgical techniques, hepatic artery chemoembolization, molecular targeting and immunotherapy, the prognosis of liver cancer patients remains very poor. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells and regulates various stages of the RNA life cycle. Many studies have reported that the abnormal expression of m6A-related regulators in HCC represent diagnostic and prognostic markers and potential therapeutic targets. In this review, firstly, we introduce the latest research on m6A-related regulators in detail. Next, we summarize the mechanism of each regulator in the pathogenesis and progression of HCC. Finally, we summarize the potential diagnostic, prognostic and therapeutic value of the regulators currently reported in HCC.
Collapse
Affiliation(s)
- Nanfang Qu
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiaotong Bo
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bin Li
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Lei Ma
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Feng Wang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qinghua Zheng
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuhua Xiao
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Fengmei Huang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yuanyuan Shi
- Department of Oncology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuemei Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, China
| |
Collapse
|
11
|
Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. Environ Epigenet 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
Collapse
Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
| |
Collapse
|
12
|
Zhou WM, Liu B, Shavandi A, Li L, Song H, Zhang JY. Methylation Landscape: Targeting Writer or Eraser to Discover Anti-Cancer Drug. Front Pharmacol 2021; 12:690057. [PMID: 34149432 PMCID: PMC8209422 DOI: 10.3389/fphar.2021.690057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer is a major global health challenge for our health system, despite the important pharmacological and therapeutic discoveries we have seen since past 5 decades. The increasing prevalence and mortality of cancer may be closely related to smoking, exposure to environmental pollution, dietary and genetic factors. Despite significant promising discoveries and developments such as cell and biotechnological therapies a new breakthrough in the medical field is needed to develop specific and effective drugs for cancer treatment. On the development of cell therapies, anti-tumor vaccines, and new biotechnological drugs that have already shown promising effects in preclinical studies. With the continuous enrichment and development of chromatin immunoprecipitation sequencing (ChIP-seq) and its derivative technologies, epigenetic modification has gradually become a research hotspot. As key ingredients of epigenetic modification, Writers, Readers, Erasers have been gradually unveiled. Cancer has been associated with epigenetic modification especially methylation and therefore different epigenetic drugs have been developed and some of those are already undergoing clinical phase I or phase II trials, and it is believed that these drugs will certainly assist the treatment in the near future. With respect to this, an overview of anti-tumor drugs targeting modified enzymes and de-modified enzymes will be performed in order to contribute to future research.
Collapse
Affiliation(s)
- Wen-Min Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bin Liu
- Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Amin Shavandi
- BioMatter Unit, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Lu Li
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
13
|
Siklos M, Kubicek S. Therapeutic targeting of chromatin: status and opportunities. FEBS J 2021; 289:1276-1301. [PMID: 33982887 DOI: 10.1111/febs.15966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/25/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022]
Abstract
The molecular characterization of mechanisms underlying transcriptional control and epigenetic inheritance since the 1990s has paved the way for the development of targeted therapies that modulate these pathways. In the past two decades, cancer genome sequencing approaches have uncovered a plethora of mutations in chromatin modifying enzymes across tumor types, and systematic genetic screens have identified many of these proteins as specific vulnerabilities in certain cancers. Now is the time when many of these basic and translational efforts start to bear fruit and more and more chromatin-targeting drugs are entering the clinic. At the same time, novel pharmacological approaches harbor the potential to modulate chromatin in unprecedented fashion, thus generating entirely novel opportunities. Here, we review the current status of chromatin targets in oncology and describe a vision for the epigenome-modulating drugs of the future.
Collapse
Affiliation(s)
- Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
14
|
Sivasudhan E, Blake N, Lu ZL, Meng J, Rong R. Dynamics of m6A RNA Methylome on the Hallmarks of Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:642443. [PMID: 33869193 PMCID: PMC8047153 DOI: 10.3389/fcell.2021.642443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
Epidemiological data consistently rank hepatocellular carcinoma (HCC) as one of the leading causes of cancer-related deaths worldwide, often posing severe economic burden on health care. While the molecular etiopathogenesis associated with genetic and epigenetic modifications has been extensively explored, the biological influence of the emerging field of epitranscriptomics and its associated aberrant RNA modifications on tumorigenesis is a largely unexplored territory with immense potential for discovering new therapeutic approaches. In particular, the underlying cellular mechanisms of different hallmarks of hepatocarcinogenesis that are governed by the complex dynamics of m6A RNA methylation demand further investigation. In this review, we reveal the up-to-date knowledge on the mechanistic and functional link between m6A RNA methylation and pathogenesis of HCC.
Collapse
Affiliation(s)
- Enakshi Sivasudhan
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Neil Blake
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Zhi-Liang Lu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Rong Rong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
15
|
Maas MN, Hintzen JCJ, Porzberg MRB, Mecinović J. Trimethyllysine: From Carnitine Biosynthesis to Epigenetics. Int J Mol Sci 2020; 21:E9451. [PMID: 33322546 PMCID: PMC7764450 DOI: 10.3390/ijms21249451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Trimethyllysine is an important post-translationally modified amino acid with functions in the carnitine biosynthesis and regulation of key epigenetic processes. Protein lysine methyltransferases and demethylases dynamically control protein lysine methylation, with each state of methylation changing the biophysical properties of lysine and the subsequent effect on protein function, in particular histone proteins and their central role in epigenetics. Epigenetic reader domain proteins can distinguish between different lysine methylation states and initiate downstream cellular processes upon recognition. Dysregulation of protein methylation is linked to various diseases, including cancer, inflammation, and genetic disorders. In this review, we cover biomolecular studies on the role of trimethyllysine in carnitine biosynthesis, different enzymatic reactions involved in the synthesis and removal of trimethyllysine, trimethyllysine recognition by reader proteins, and the role of trimethyllysine on the nucleosome assembly.
Collapse
Affiliation(s)
| | | | | | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.N.M.); (J.C.J.H.); (M.R.B.P.)
| |
Collapse
|
16
|
Li Y, Ge YZ, Xu L, Xu Z, Dou Q, Jia R. The Potential Roles of RNA N6-Methyladenosine in Urological Tumors. Front Cell Dev Biol 2020; 8:579919. [PMID: 33015074 PMCID: PMC7510505 DOI: 10.3389/fcell.2020.579919] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is regarded as the most abundant, prevalent and conserved internal mRNA modification in mammalian cells. M6A can be catalyzed by m6A methyltransferases METTL3, METTL14 and WTAP (writers), reverted by demethylases ALKBH5 and FTO (erasers), and recognized by m6A -binding proteins such as YTHDF1/2/3, IGF2BP1/2/3 and HNRNPA2B1 (readers). Emerging evidence suggests that m6A modification is significant for regulating many biological and cellular processes and participates in the pathological development of various diseases, including tumors. This article reviews recent studies on the biological function of m6A modification and the methylation modification of m6A in urological tumors.
Collapse
Affiliation(s)
- Yang Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Quanliang Dou
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
17
|
Ru W, Zhang X, Yue B, Qi A, Shen X, Huang Y, Lan X, Lei C, Chen H. Insight into m 6A methylation from occurrence to functions. Open Biol 2020; 10:200091. [PMID: 32898471 PMCID: PMC7536083 DOI: 10.1098/rsob.200091] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
RNA m6A methylation is a post-transcriptional modification that occurs at the nitrogen-6 position of adenine. This dynamically reversible modification is installed, removed and recognized by methyltransferases, demethylases and readers, respectively. This modification has been found in most eukaryotic mRNA, tRNA, rRNA and other non-coding RNA. Recent studies have revealed important regulatory functions of the m6A including effects on gene expression regulation, organism development and cancer development. In this review, we summarize the discovery and features of m6A, and briefly introduce the mammalian m6A writers, erasers and readers. Finally, we discuss progress in identifying additional functions of m6A and the outstanding questions about the regulatory effect of this widespread modification.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| |
Collapse
|
18
|
Abstract
Introduction: Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena. Areas covered: We broadly divide this literature into two parts: 'modification-centric' analyses that link histone PTMs to cancer biology; and 'complex-centric' analyses that examine protein-protein interactions that occur de novo as a result of oncogenic mutations. We also discuss proteomic studies of oncohistones. We highlight relevant examples, discuss limitations, and speculate about forthcoming innovations regarding each application. Expert commentary: 'Modification-centric' analyses have been used to further understanding of cancer's histone code and to identify associated therapeutic vulnerabilities. 'Complex-centric' analyses have likewise revealed insights into mechanisms of oncogenesis and suggested potential therapeutic targets, particularly in MLL-associated leukemia. Proteomic experiments have also supported some of the pioneering studies of oncohistone-mediated tumorigenesis. Additional applications of proteomics that may benefit cancer epigenetics research include middle-down and top-down histone PTM analysis, chromatin reader profiling, and genomic locus-specific protein identification. In the coming years, proteomic approaches will remain powerful ways to interrogate the biology of cancer.
Collapse
Affiliation(s)
- Dylan M Marchione
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - John Wojcik
- b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
19
|
Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S. Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. Genes (Basel) 2018; 9:E329. [PMID: 29958477 PMCID: PMC6070936 DOI: 10.3390/genes9070329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Sequence databases and transcriptome-wide mapping have revealed different reversible and dynamic chemical modifications of the nitrogen bases of RNA molecules. Modifications occur in coding RNAs and noncoding-RNAs post-transcriptionally and they can influence the RNA structure, metabolism, and function. The result is the expansion of the variety of the transcriptome. In fact, depending on the type of modification, RNA molecules enter into a specific program exerting the role of the player or/and the target in biological and pathological processes. Many research groups are exploring the role of RNA modifications (alias epitranscriptome) in cell proliferation, survival, and in more specialized activities. More recently, the role of RNA modifications has been also explored in stem cell biology. Our understanding in this context is still in its infancy. Available evidence addresses the role of RNA modifications in self-renewal, commitment, and differentiation processes of stem cells. In this review, we will focus on five epitranscriptomic marks: N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, Pseudouridine (Ψ) and Adenosine-to-Inosine editing. We will provide insights into the function and the distribution of these chemical modifications in coding RNAs and noncoding-RNAs. Mainly, we will emphasize the role of epitranscriptomic mechanisms in the biology of naïve, primed, embryonic, adult, and cancer stem cells.
Collapse
Affiliation(s)
- Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Chiara Argentati
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Martina Bazzucchi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
| |
Collapse
|
20
|
Yang AY, Kim H, Li W, Kong ANT. Natural compound-derived epigenetic regulators targeting epigenetic readers, writers and erasers. Curr Top Med Chem 2016; 16:697-713. [PMID: 26306989 PMCID: PMC4955582 DOI: 10.2174/1568026615666150826114359] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/10/2015] [Indexed: 12/21/2022]
Abstract
Post-translational modifications can affect gene expression in a long-term manner without changes in the primary nucleotide sequence of the DNA. These epigenetic alterations involve dynamic processes that occur in histones, chromatin-associated proteins and DNA. In response to environmental stimuli, abnormal epigenetic alterations cause disorders in the cell cycle, apoptosis and other cellular processes and thus contribute to the incidence of diverse diseases, including cancers. In this review, we will summarize recent studies focusing on certain epigenetic readers, writers, and erasers associated with cancer development and how newly discovered natural compounds and their derivatives could interact with these targets. These advances provide insights into epigenetic alterations in cancers and the potential utility of these alterations as therapeutic targets for the future development of chemopreventive and chemotherapeutic drugs.
Collapse
Affiliation(s)
| | | | | | - Ah-Ng Tony Kong
- Rutgers, The State University of New Jersey, Ernest Mario School of Pharmacy, Room 228, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA.
| |
Collapse
|
21
|
Allia E, Ronco G, Coccia A, Luparia P, Macrì L, Fiorito C, Maletta F, Deambrogio C, Tunesi S, De Marco L, Gillio-Tos A, Sapino A, Ghiringhello B. Interpretation of p16(INK4a) /Ki-67 dual immunostaining for the triage of human papillomavirus-positive women by experts and nonexperts in cervical cytology. Cancer Cytopathol 2014; 123:212-8. [PMID: 25534957 DOI: 10.1002/cncy.21511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/25/2014] [Accepted: 12/01/2014] [Indexed: 11/09/2022]
Abstract
BACKGROUND The triage of human papillomavirus (HPV)-positive women is needed to avoid overreferral to colposcopy. p16(INK4a) immunostaining is an efficient triage method. p16(INK4a) /Ki-67 dual staining was introduced mainly to increase reproducibility and specificity compared with stand-alone p16(INK4a) staining. METHODS Within a pilot project, HPV-positive women were referred to colposcopy if cytology was abnormal or unsatisfactory or HPV testing was still positive after 1 year. For 500 consecutive women, a slide obtained during colposcopy was immunostained for p16(INK4a) /Ki-67 and independently interpreted by 7 readers without previous experience with dual staining. Four of these readers were experts in cervical pathology and 3 were not. Kappa values for multiple raters, sensitivity, and specificity for cervical intraepithelial neoplasia type 2-positive histology were computed. Because women with normal cytology were underrepresented, estimates for all HPV-positive women were obtained as weighted means of cytology-specific estimates. RESULTS The overall kappa for HPV-positive women was 0.70 (95% confidence interval [95% CI], 0.60-0.77). Kappa values were not found to be significantly different between expert and nonexpert readers with regard to cervical cytology but were significantly increased (P =. 0066) after consensus discussion. The overall specificity estimate for HPV-positive women was 64.0% (95% CI, 57.4%-70.2%): 66.7% (95% CI, 59.8%-73.0%) for experts and 60.5% (95% CI, 59.8%-73.0%) for nonexperts. Among women with abnormal cytology, the sensitivity was 85.5% (95% CI, 77.9%-90.8%): 85.8% (95% CI, 77.9%-91.2%) for experts and 85.1% (95% CI, 76.6%-90.9%) for nonexperts. CONCLUSIONS p16(INK4a) /Ki-67 immunostaining demonstrated good reproducibility and specificity when triaging HPV-positive women. Dual-staining interpretation can be performed, after short training, even by staff who are not experts in cervical cytology. This allows HPV-based screening with triage to be performed in settings in which such expert staff is not available.
Collapse
Affiliation(s)
- Elena Allia
- Center for Cervical Cancer Screening, AO City of Health and Science, Turin, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|