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Soffritti I, D’Accolti M, Bini F, Mazziga E, Di Luca D, Maccari C, Arcangeletti MC, Caselli E. Virus-Induced MicroRNA Modulation and Systemic Sclerosis Disease. Biomedicines 2024; 12:1360. [PMID: 38927567 PMCID: PMC11202132 DOI: 10.3390/biomedicines12061360] [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: 05/16/2024] [Revised: 06/06/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNA sequences that regulate gene expression at the post-transcriptional level. They are involved in the regulation of multiple pathways, related to both physiological and pathological conditions, including autoimmune diseases, such as Systemic Sclerosis (SSc). Specifically, SSc is recognized as a complex and multifactorial disease, characterized by vascular abnormalities, immune dysfunction, and progressive fibrosis, affecting skin and internal organs. Among predisposing environmental triggers, evidence supports the roles of oxidative stress, chemical agents, and viral infections, mostly related to those sustained by beta-herpesviruses such as HCMV and HHV-6. Dysregulated levels of miRNA expression have been found in SSc patients compared to healthy controls, at both the intra- and extracellular levels, providing a sort of miRNA signature of the SSc disease. Notably, HCMV/HHV-6 viral infections were shown to modulate the miRNA profile, often superposing that observed in SSc, potentially promoting pathological pathways associated with SSc development. This review summarizes the main data regarding miRNA alterations in SSc disease, highlighting their potential as prognostic or diagnostic markers for SSc disease, and the impact of the putative SSc etiological agents on miRNA modulation.
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Affiliation(s)
- Irene Soffritti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, 44121 Ferrara, Italy; (I.S.); (M.D.); (F.B.); (E.M.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Maria D’Accolti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, 44121 Ferrara, Italy; (I.S.); (M.D.); (F.B.); (E.M.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Francesca Bini
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, 44121 Ferrara, Italy; (I.S.); (M.D.); (F.B.); (E.M.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Eleonora Mazziga
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, 44121 Ferrara, Italy; (I.S.); (M.D.); (F.B.); (E.M.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Dario Di Luca
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Clara Maccari
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (C.M.); (M.-C.A.)
| | - Maria-Cristina Arcangeletti
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (C.M.); (M.-C.A.)
| | - Elisabetta Caselli
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, 44121 Ferrara, Italy; (I.S.); (M.D.); (F.B.); (E.M.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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Korsnes MS, Korsnes R. Initial refinement of data from video-based single-cell tracking. CANCER INNOVATION 2023; 2:416-432. [PMID: 38090384 PMCID: PMC10686135 DOI: 10.1002/cai2.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/13/2023] [Accepted: 06/01/2023] [Indexed: 10/15/2024]
Abstract
Background Video recording of cells offers a straightforward way to gain valuable information from their response to treatments. An indispensable step in obtaining such information involves tracking individual cells from the recorded data. A subsequent step is reducing such data to represent essential biological information. This can help to compare various single-cell tracking data yielding a novel source of information. The vast array of potential data sources highlights the significance of methodologies prioritizing simplicity, robustness, transparency, affordability, sensor independence, and freedom from reliance on specific software or online services. Methods The provided data presents single-cell tracking of clonal (A549) cells as they grow in two-dimensional (2D) monolayers over 94 hours, spanning several cell cycles. The cells are exposed to three different concentrations of yessotoxin (YTX). The data treatments showcase the parametrization of population growth curves, as well as other statistical descriptions. These include the temporal development of cell speed in family trees with and without cell death, correlations between sister cells, single-cell average displacements, and the study of clustering tendencies. Results Various statistics obtained from single-cell tracking reveal patterns suitable for data compression and parametrization. These statistics encompass essential aspects such as cell division, movements, and mutual information between sister cells. Conclusion This work presents practical examples that highlight the abundant potential information within large sets of single-cell tracking data. Data reduction is crucial in the process of acquiring such information which can be relevant for phenotypic drug discovery and therapeutics, extending beyond standardized procedures. Conducting meaningful big data analysis typically necessitates a substantial amount of data, which can stem from standalone case studies as an initial foundation.
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Affiliation(s)
- Mónica Suárez Korsnes
- Department of Clinical and Molecular MedicineNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Korsnes Biocomputing (KoBio)TrondheimNorway
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Borges A, Castellan F, Irie N. Emergent roles of maternal microchimerism in postnatal development. Dev Growth Differ 2023; 65:75-81. [PMID: 36519824 DOI: 10.1111/dgd.12830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Maternal microchimerism (MMc) is the phenomenon that a low number of cells from the mother persists within her progeny. Despite their regular presence in mammalian pregnancies, the overall cell type repertoire and roles of maternal cells, especially after birth, remain unclear. By using transgenic mouse strains and human umbilical blood samples, recent studies have for the first time characterized and quantified MMc cell type repertoires in offspring, identified the cross-generational influence on fetal immunity, and determined possible factors that affect their presence in offspring. This review summarizes new findings, especially on the maternal cell type repertoires and their potential role in utero, in postnatal life, and long after birth.
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Affiliation(s)
- Alexandria Borges
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Flore Castellan
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Irie
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
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van den Hove DLA, Riemens RJM, Koulousakis P, Pishva E. Epigenome-wide association studies in Alzheimer's disease; achievements and challenges. Brain Pathol 2020; 30:978-983. [PMID: 32654262 PMCID: PMC8018126 DOI: 10.1111/bpa.12880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/27/2020] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) represents a devastating progressive neurodegenerative disease with a complex pathophysiology, affecting millions of people worldwide. Recent epigenome-wide association studies suggest a key role for epigenetic mechanisms in its development and course. Despite the fact that current evidence on the role of epigenetic dysregulation in aging and AD is convincing, the pioneering field of neuroepigenetics is still facing many challenges that need to be addressed to fundamentally increase our understanding about the underlying mechanisms of this neurodegenerative disorder. This perspective paper describes the current state of play for epigenetic research into AD and discusses how new methodological advances in the field of epigenetics and related data science disciplines could further spur the development of novel therapeutic agents and biomarker assays.
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Affiliation(s)
- Daniel L. A. van den Hove
- Department of Psychiatry and NeuropsychologySchool for Mental Health and Neuroscience (MHeNs)Maastricht UniversityMaastrichtthe Netherlands
- Division of Molecular PsychiatryLaboratory of Translational NeuroscienceCenter of Mental HealthDepartment of PsychiatryUniversity of WürzburgWürzburgGermany
| | - Renzo J. M. Riemens
- Department of Psychiatry and NeuropsychologySchool for Mental Health and Neuroscience (MHeNs)Maastricht UniversityMaastrichtthe Netherlands
- Institute of Human GeneticsJulius Maximilians UniversityWürzburgGermany
| | - Philippos Koulousakis
- Department of Psychiatry and NeuropsychologySchool for Mental Health and Neuroscience (MHeNs)Maastricht UniversityMaastrichtthe Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and NeuropsychologySchool for Mental Health and Neuroscience (MHeNs)Maastricht UniversityMaastrichtthe Netherlands
- College of Medicine and HealthUniversity of Exeter Medical SchoolExeter UniversityExeterUK
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Morovic W, Budinoff CR. Epigenetics: A New Frontier in Probiotic Research. Trends Microbiol 2020; 29:117-126. [PMID: 32409146 DOI: 10.1016/j.tim.2020.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
Research into the benefits of probiotics has progressed beyond interventional studies to identifying the underlying molecular mechanisms. Health-promoting effector molecules produced by probiotics are well documented and have been linked to specific genes and even individual nucleotides. However, the factors controlling the expression of these molecules are poorly understood and we argue that epigenetic influences likely play an important role in mediating the health-promoting attributes of probiotics. Here, we review established epigenetic regulation of important microbial genetic systems involved in health promotion, safety, and industrialization to provide evidence that the same regulation occurs in probiotic organisms. We advocate for studies combining genomic and meta-epigenomic data to better understand the mode of action of probiotics, their associated microbiomes, and their effects on consumers.
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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9
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Green HLH, Brewer AC. Dysregulation of 2-oxoglutarate-dependent dioxygenases by hyperglycaemia: does this link diabetes and vascular disease? Clin Epigenetics 2020; 12:59. [PMID: 32345373 PMCID: PMC7189706 DOI: 10.1186/s13148-020-00848-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clinical, social and economic burden of cardiovascular disease (CVD) associated with diabetes underscores an urgency for understanding the disease aetiology. Evidence suggests that the hyperglycaemia associated with diabetes is, of itself, causal in the development of endothelial dysfunction (ED) which is recognised to be the critical determinant in the development of CVD. It is further recognised that epigenetic modifications associated with changes in gene expression are causal in both the initiation of ED and the progression to CVD. Understanding whether and how hyperglycaemia induces epigenetic modifications therefore seems crucial in the development of preventative treatments. A mechanistic link between energy metabolism and epigenetic regulation is increasingly becoming explored as key energy metabolites typically serve as substrates or co-factors for epigenetic modifying enzymes. Intriguing examples are the ten-eleven translocation and Jumonji C proteins which facilitate the demethylation of DNA and histones respectively. These are members of the 2-oxoglutarate-dependent dioxygenase superfamily which require the tricarboxylic acid metabolite, α-ketoglutarate and molecular oxygen (O2) as substrates and Fe (II) as a co-factor. An understanding of precisely how the biochemical effects of high glucose exposure impact upon cellular metabolism, O2 availability and cellular redox in endothelial cells (ECs) may therefore elucidate (in part) the mechanistic link between hyperglycaemia and epigenetic modifications causal in ED and CVD. It would also provide significant proof of concept that dysregulation of the epigenetic landscape may be causal rather than consequential in the development of pathology.
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Affiliation(s)
- Hannah L H Green
- School of Cardiovascular Medicine & Sciences, King's College London British Heart Foundation Centre of Research Excellence, London, UK
| | - Alison C Brewer
- School of Cardiovascular Medicine & Sciences, King's College London British Heart Foundation Centre of Research Excellence, London, UK.
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Jacques M, Hiam D, Craig J, Barrès R, Eynon N, Voisin S. Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review. Epigenetics 2019; 14:633-648. [PMID: 31046576 PMCID: PMC6557592 DOI: 10.1080/15592294.2019.1614416] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 12/20/2022] Open
Abstract
Exercise training is continually challenging whole-body homeostasis, leading to improvements in performance and health. Adaptations to exercise training are complex and are influenced by both environmental and genetic factors. Epigenetic factors regulate gene expression in a tissue-specific manner and constitute a link between the genotype and the environment. Moreover, epigenetic factors are emerging as potential biomarkers that could predict the response to exercise training. This systematic review aimed to identify epigenetic changes that have been reported in skeletal muscle following exercise training in healthy populations. A literature search of five databases (PUBMED, MEDLINE, CINHAL, SCOPUS and SportDiscuss) was conducted in November 2018. Articles were included if they examined epigenetic modifications (DNA methylation, histone modifications and non-coding RNAs) in skeletal muscle, following either an acute bout of exercise, an exercise intervention in a pre/post design, or a case/control type of study. Twenty-two studies met the inclusion criteria. Several epigenetic markers including DNA methylation of genes known to be differentially expressed after exercise and myomiRs were reported to be modified after exercise. Several epigenetic marks were identified to be altered in response to exercise, with potential influence on skeletal muscle metabolism. However, whether these epigenetic marks play a role in the physiological impact of exercise is unclear. Exercise epigenetics is still a very young research field, and it is expected that in the future the causality of such changes will be elucidated via the utilization of emerging experimental models able to target the epigenome.
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Affiliation(s)
- Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Jeffrey Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
- Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
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11
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Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
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Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
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12
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Massaia A, Chaves P, Samari S, Miragaia RJ, Meyer K, Teichmann SA, Noseda M. Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart. Front Cardiovasc Med 2018; 5:167. [PMID: 30525044 PMCID: PMC6258739 DOI: 10.3389/fcvm.2018.00167] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/29/2018] [Indexed: 12/21/2022] Open
Abstract
The recent development of single cell gene expression technologies, and especially single cell transcriptomics, have revolutionized the way biologists and clinicians investigate organs and organisms, allowing an unprecedented level of resolution to the description of cell demographics in both healthy and diseased states. Single cell transcriptomics provide information on prevalence, heterogeneity, and gene co-expression at the individual cell level. This enables a cell-centric outlook to define intracellular gene regulatory networks and to bridge toward the definition of intercellular pathways otherwise masked in bulk analysis. The technologies have developed at a fast pace producing a multitude of different approaches, with several alternatives to choose from at any step, including single cell isolation and capturing, lysis, RNA reverse transcription and cDNA amplification, library preparation, sequencing, and computational analyses. Here, we provide guidelines for the experimental design of single cell RNA sequencing experiments, exploring the current options for the crucial steps. Furthermore, we provide a complete overview of the typical data analysis workflow, from handling the raw sequencing data to making biological inferences. Significantly, advancements in single cell transcriptomics have already contributed to outstanding exploratory and functional studies of cardiac development and disease models, as summarized in this review. In conclusion, we discuss achievable outcomes of single cell transcriptomics' applications in addressing unanswered questions and influencing future cardiac clinical applications.
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Affiliation(s)
- Andrea Massaia
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Patricia Chaves
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sara Samari
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Kerstin Meyer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sarah Amalia Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Michela Noseda
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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13
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The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors. Genes (Basel) 2018; 9:genes9110552. [PMID: 30428628 PMCID: PMC6265908 DOI: 10.3390/genes9110552] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/27/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022] Open
Abstract
Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m6A) is the most frequent, especially among mRNAs. m6A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells’ epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m6A-related players: the so-called writers, readers and erasers. These proteins modulate m6A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms—kidney, bladder, prostate and testicular cancer—for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m6A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies.
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14
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Strzelecka PM, Ranzoni AM, Cvejic A. Dissecting human disease with single-cell omics: application in model systems and in the clinic. Dis Model Mech 2018; 11:dmm036525. [PMID: 30401698 PMCID: PMC6262815 DOI: 10.1242/dmm.036525] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Probing cellular population diversity at single-cell resolution became possible only in recent years. The popularity of single-cell 'omic' approaches, which allow researchers to dissect sample heterogeneity and cell-to-cell variation, continues to grow. With continuous technological improvements, single-cell omics are becoming increasingly prevalent and contribute to the discovery of new and rare cell types, and to the deciphering of disease pathogenesis and outcome. Animal models of human diseases have significantly facilitated our understanding of the mechanisms driving pathologies and resulted in the development of more efficient therapies. The application of single-cell omics to animal models improves the precision of the obtained insights, and brings single-cell technology closer to the clinical field. This Review focuses on the use of single-cell omics in cellular and animal models of diseases, as well as in samples from human patients. It also highlights the potential of these approaches to further improve the diagnosis and treatment of various pathologies, and includes a discussion of the advantages and remaining challenges in implementing these technologies into clinical practice.
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Affiliation(s)
- Paulina M Strzelecka
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Anna M Ranzoni
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
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15
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Yim M, Shaw D. Achieving greater efficiency and higher confidence in single‐cell cloning by combining cell printing and plate imaging technologies. Biotechnol Prog 2018; 34:1454-1459. [DOI: 10.1002/btpr.2698] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/23/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Mandy Yim
- Cell Culture, Pharma Technical DevelopmentGenentech, Inc. 1 DNA Way South San Francisco California, 94080
| | - David Shaw
- Cell Culture, Pharma Technical DevelopmentGenentech, Inc. 1 DNA Way South San Francisco California, 94080
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16
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A Simple Method for Visualization of Locus-Specific H4K20me1 Modifications in Living Caenorhabditis elegans Single Cells. G3-GENES GENOMES GENETICS 2018; 8:2249-2255. [PMID: 29724885 PMCID: PMC6027889 DOI: 10.1534/g3.118.200333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, advances in next-generation sequencing technologies have enabled genome-wide analyses of epigenetic modifications; however, it remains difficult to analyze the states of histone modifications at a single-cell resolution in living multicellular organisms because of the heterogeneity within cellular populations. Here we describe a simple method to visualize histone modifications on the specific sequence of target locus at a single-cell resolution in living Caenorhabditis elegans, by combining the LacO/LacI system and a genetically-encoded H4K20me1-specific probe, “mintbody”. We demonstrate that Venus-labeled mintbody and mTurquoise2-labeled LacI can co-localize on an artificial chromosome carrying both the target locus and LacO sequences, where H4K20me1 marks the target locus. We demonstrate that our visualization method can precisely detect H4K20me1 depositions on the her-1 gene sequences on the artificial chromosome, to which the dosage compensation complex binds to regulate sex determination. The degree of H4K20me1 deposition on the her-1 sequences on the artificial chromosome correlated strongly with sex, suggesting that, using the artificial chromosome, this method can reflect context-dependent changes of H4K20me1 on endogenous genomes. Furthermore, we demonstrate live imaging of H4K20me1 depositions on the artificial chromosome. Combined with ChIP assays, this mintbody-LacO/LacI visualization method will enable analysis of developmental and context-dependent alterations of locus-specific histone modifications in specific cells and elucidation of the underlying molecular mechanisms.
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17
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Kumar N, Hori Y, Kikuchi K. Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. CHEM REC 2018; 18:1672-1680. [PMID: 29863802 DOI: 10.1002/tcr.201800039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
The epigenetic modification of DNA involves the conversion of cytosine to 5-methylcytosine, also known as DNA methylation. DNA methylation is important in modulating gene expression and thus, regulating genome and cellular functions. Recent studies have shown that aberrations in DNA methylation are associated with various epigenetic disorders or diseases including cancer. This stimulates great interest in the development of methods that can detect and visualize DNA methylation. For instance, fluorescent proteins (FPs) in conjugation with methyl-CpG-binding domain (MBD) have been employed for live-cell imaging of DNA methylation. However, the FP-based approach showed fluorescence signals for both the DNA-bound and -unbound states and thus differentiation between these states is difficult. Synthetic-molecule/protein hybrid probes can provide an alternative to overcome this restriction. In this article, we discuss the synthetic-molecule/protein hybrid probe that we developed recently for live-cell imaging of DNA methylation, which exhibited fluorescence enhancement only after binding to methylated DNA.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
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18
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Geoepidemiology and (epi-)genetics in primary biliary cholangitis. Best Pract Res Clin Gastroenterol 2018; 34-35:11-15. [PMID: 30343705 DOI: 10.1016/j.bpg.2018.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
Abstract
Primary biliary cholangitis (PBC) is a rare female preponderant chronic autoimmune cholestatic liver disease, characterized by intrahepatic ductopenia and progressive fibrosis. During last decades incidence and prevalence showed an increasing rate which vary widely worldwide demonstrating an important interaction between environmental and genetic factors. Heritability suggested by familial occurrence and monozygotic twins concordance have been confirmed in more studies. Epigenetics mechanisms such as histone modification and DNA methylation can partially explain predisposition and inheritance of this disease. Nevertheless, an association with specific class II human leukocyte antigen (HLA) variants have been reported, showing an increase risk in susceptibility. More recently, data regarding a strong protective association between PBC and HLA alleles confirmed this association. After recent genome-wide association studies (GWAS), a more intricate interaction between PBC and the HLA region has been shown. Furthermore, GWAS also identified several immune-related-genes implicated. More genome-wide association studies on this disease are needed to reach a complete and systematic knowledge of this disease. In this review we discuss more recent issued data on geoepidemiology of PBC and the role of (epi-)genetic mechanisms in its pathogenesis.
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19
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Abstract
Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell analysis, especially in the RNA sequencing field. Every improvement increases sensitivity and throughput. Collecting a large amount of data also stimulates the development of new approaches for bioinformatic analysis and interpretation. However, the essential requirement for any analysis is the collection of single cells of high quality. The single-cell isolation must be fast, effective, and gentle to maintain the native expression profiles. Classical methods for single-cell isolation are micromanipulation, microdissection, and fluorescence-activated cell sorting (FACS). In the last decade several new and highly efficient approaches have been developed, which not just supplement but may fully replace the traditional ones. These new techniques are based on microfluidic chips, droplets, micro-well plates, and automatic collection of cells using capillaries, magnets, an electric field, or a punching probe. In this review we summarize the current methods and developments in this field. We discuss the advantages of the different commercially available platforms and their applicability, and also provide remarks on future developments.
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20
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Carbonell A, Fueyo R, Izquierdo-Bouldstridge A, Moreta C, Jordan A. Epigenetic mechanisms in health and disease: BCEC 2017. Epigenetics 2018; 13:331-341. [PMID: 29384431 DOI: 10.1080/15592294.2018.1434391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC). Jordi Bernués, Marian Martínez-Balbás, and Ferran Azorín were also part of the scientific committee. In 22 talks and 51 posters, researchers presented their latest results in the fields of histone variants, epigenetic regulation, and chromatin 3D organization to an audience of around 250 participants from 16 countries. This year, a broad number of talks focused on the epigenetic causes and possible related treatments of complex diseases such as cancer. Participants at the 2017 BCEC elegantly closed the series, discussing progress made in the field of epigenetics and highlighting its role in human health and disease.
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Affiliation(s)
- Albert Carbonell
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain.,b Institute for Research in Biomedicine, IRB Barcelona , The Barcelona Institute for Science and Technology , Baldiri i Reixac, 10, 08028 Barcelona , Catalonia , Spain
| | - Raquel Fueyo
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Andrea Izquierdo-Bouldstridge
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Cristina Moreta
- c Germans Trias i Pujol Research Institute (IGTP) , Can Ruti Campus , 08916 , Badalona , Catalonia , Spain
| | - Albert Jordan
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
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21
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Nakato R, Shirahige K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Brief Bioinform 2017; 18:279-290. [PMID: 26979602 PMCID: PMC5444249 DOI: 10.1093/bib/bbw023] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 02/06/2023] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.
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Affiliation(s)
- Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Japan
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22
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Yeo SK, Guan JL. Breast Cancer: Multiple Subtypes within a Tumor? Trends Cancer 2017; 3:753-760. [PMID: 29120751 DOI: 10.1016/j.trecan.2017.09.001] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/31/2017] [Accepted: 09/11/2017] [Indexed: 12/19/2022]
Abstract
Breast cancer is a heterogeneous disease, and stratification of tumors is paramount to achieve better clinical outcomes. While it is common to stratify and treat breast tumors as a single entity, insights from studies on intratumoral heterogeneity and cancer stem cells raise the possibility that multiple breast cancer subtypes may coexist within a tumor. A role for plasticity in driving dynamic conversions between breast cancer subtypes is proposed, and the clinical implications include a need for combinatorial therapeutic strategies that account for the discrete disease entities and their plasticity. Accordingly, the advent of single-cell technologies will be crucial in enabling the diagnosis and stratification of distinct disease subtypes down to the cellular level.
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Affiliation(s)
- Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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23
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Roubroeks JAY, Smith RG, van den Hove DLA, Lunnon K. Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases. J Neurochem 2017; 143:158-170. [PMID: 28805248 DOI: 10.1111/jnc.14148] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022]
Abstract
Recent studies have suggested a role for epigenetic mechanisms in the complex etiology of various neurodegenerative diseases. In this review, we discuss advances that have been made toward understanding the role of epigenetic processes in neurodegenerative disorders, with a particular focus on Alzheimer's disease, where the most extensive studies have been undertaken to date. We provide a brief overview of DNA modifications, followed by a summarization of studies of DNA modifications in Alzheimer's disease and other neurodegenerative diseases.
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Affiliation(s)
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Devon, UK
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands.,Laboratory of Translational Neuroscience, Division of Molecular Psychiatry, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Devon, UK
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24
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Wang L, Livak KJ, Wu CJ. High-dimension single-cell analysis applied to cancer. Mol Aspects Med 2017; 59:70-84. [PMID: 28823596 DOI: 10.1016/j.mam.2017.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/10/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
High-dimension single-cell technology is transforming our ability to study and understand cancer. Numerous studies and reviews have reported advances in technology development. The biological insights gleaned from single-cell technology about cancer biology are less reviewed. Here we focus on research studies that illustrate novel aspects of cancer biology that bulk analysis could not achieve, and discuss the fresh insights gained from the application of single-cell technology across basic and clinical cancer studies.
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Affiliation(s)
- Lili Wang
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Kenneth J Livak
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Catherine J Wu
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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25
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Poulin JF, Tasic B, Hjerling-Leffler J, Trimarchi JM, Awatramani R. Disentangling neural cell diversity using single-cell transcriptomics. Nat Neurosci 2017; 19:1131-41. [PMID: 27571192 DOI: 10.1038/nn.4366] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/22/2016] [Indexed: 12/12/2022]
Abstract
Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies.
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Affiliation(s)
| | - Bosiljka Tasic
- Department of Molecular Genetics, Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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26
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Tsou PS, Sawalha AH. Unfolding the pathogenesis of scleroderma through genomics and epigenomics. J Autoimmun 2017; 83:73-94. [PMID: 28526340 DOI: 10.1016/j.jaut.2017.05.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/12/2022]
Abstract
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated. The non-HLA genes associated with SSc are involved in various functions, with the most robust associations including genes for B and T cell activation and innate immunity. Other pathways include genes involved in extracellular matrix deposition, cytokines, and autophagy. Among these genes, IRF5, STAT4, and CD247 were replicated most frequently while SNPs rs35677470 in DNASE1L3, rs5029939 in TNFAIP3, and rs7574685 in STAT4 have the strongest associations with SSc. In addition to genetic predisposition, it became clear that environmental factors and epigenetic influences also contribute to the development of SSc. Epigenetics, which refers to studies that focus on heritable phenotypes resulting from changes in chromatin structure without affecting the DNA sequence, is one of the most rapidly expanding fields in biomedical research. Indeed extensive epigenetic changes have been described in SSc. Alteration in enzymes and mediators involved in DNA methylation and histone modification, as well as dysregulated non-coding RNA levels all contribute to fibrosis, immune dysregulation, and impaired angiogenesis in this disease. Genes that are affected by epigenetic dysregulation include ones involved in autoimmunity, T cell function and regulation, TGFβ pathway, Wnt pathway, extracellular matrix, and transcription factors governing fibrosis and angiogenesis. In this review, we provide a comprehensive overview of the current findings of SSc genetic susceptibility, followed by an extensive description and a systematic review of epigenetic research that has been carried out to date in SSc. We also summarize the therapeutic potential of drugs that affect epigenetic mechanisms, and outline the future prospective of genomics and epigenomics research in SSc.
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Affiliation(s)
- Pei-Suen Tsou
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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27
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Application of single-cell technology in cancer research. Biotechnol Adv 2017; 35:443-449. [PMID: 28390874 DOI: 10.1016/j.biotechadv.2017.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 12/24/2022]
Abstract
In this review, we have outlined the application of single-cell technology in cancer research. Single-cell technology has made encouraging progress in recent years and now provides the means to detect rare cancer cells such as circulating tumor cells and cancer stem cells. We reveal how this technology has advanced the analysis of intratumor heterogeneity and tumor epigenetics, and guided individualized treatment strategies. The future prospects now are to bring single-cell technology into the clinical arena. We believe that the clinical application of single-cell technology will be beneficial in cancer diagnostics and treatment, and ultimately improve survival in cancer patients.
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28
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Delgado-Morales R, Esteller M. Opening up the DNA methylome of dementia. Mol Psychiatry 2017; 22:485-496. [PMID: 28044062 PMCID: PMC5378809 DOI: 10.1038/mp.2016.242] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/02/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Dementia is a complex clinical condition characterized by several cognitive impairments that interfere with patient independence in executing everyday tasks. Various neurodegenerative disorders have dementia in common among their clinical manifestations. In addition, these diseases, such as Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies and frontotemporal dementia, share molecular alterations at the neuropathological level. In recent years, the field of neuroepigenetics has expanded massively and it is now clear that epigenetic processes, such as DNA methylation, are mechanisms involved in both normal and pathological brain function. Despite the persistent methodological and conceptual caveats, it has been reported that several genes fundamental to the development of neurodegenerative disorders are deregulated by aberrant methylation patterns of their promoters, and even common epigenetic signatures for some dementia-associated pathologies have been identified. Therefore, understanding the epigenetic mechanisms that are altered in dementia, especially those associated with the initial phases, will allow us not only to understand the etiopathology of dementia and its progression but also to design effective therapies to reduce this global public health problem. This review provides an in-depth summary of our current knowledge about DNA methylation in dementia, focusing exclusively on the analyses performed in human brain.
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Affiliation(s)
- R Delgado-Morales
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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29
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Abstract
For several decades, we have known that epigenetic regulation is disrupted in cancer. Recently, an increasing body of data suggests epigenetics might be an intersection of current cancer research trends: next generation sequencing, immunology, metabolomics, and cell aging. The new emphasis on epigenetics is also related to the increasing production of drugs capable of interfering with epigenetic mechanisms and able to trigger clinical responses in even advanced phase patients. In this review, we will use myeloid malignancies as proof of concept examples of how epigenetic mechanisms can trigger or promote oncogenesis. We will also show how epigenetic mechanisms are related to genetic aberrations, and how they affect other systems, like immune response. Finally, we will show how we can try to influence the fate of cancer cells with epigenetic therapy.
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Affiliation(s)
- Maximilian Stahl
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Nathan Kohrman
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Steven D. Gore
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Tae Kon Kim
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Amer M. Zeidan
- Department of Internal Medicine, Section of Hematology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Thomas Prebet
- Department of Internal Medicine, Section of Hematology, Yale Cancer Center at Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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31
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Riba J, Gleichmann T, Zimmermann S, Zengerle R, Koltay P. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing. Sci Rep 2016; 6:32837. [PMID: 27596612 PMCID: PMC5011771 DOI: 10.1038/srep32837] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/16/2016] [Indexed: 01/11/2023] Open
Abstract
The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry.
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Affiliation(s)
- J Riba
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - T Gleichmann
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - S Zimmermann
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - R Zengerle
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - P Koltay
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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32
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Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B. Resolving early mesoderm diversification through single-cell expression profiling. Nature 2016; 535:289-293. [PMID: 27383781 PMCID: PMC4947525 DOI: 10.1038/nature18633] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
Abstract
In mammals, specification of the three major germ layers occurs during gastrulation, when cells ingressing through the primitive streak differentiate into the precursor cells of major organ systems. However, the molecular mechanisms underlying this process remain unclear, as numbers of gastrulating cells are very limited. In the mouse embryo at embryonic day 6.5, cells located at the junction between the extra-embryonic region and the epiblast on the posterior side of the embryo undergo an epithelial-to-mesenchymal transition and ingress through the primitive streak. Subsequently, cells migrate, either surrounding the prospective ectoderm contributing to the embryo proper, or into the extra-embryonic region to form the yolk sac, umbilical cord and placenta. Fate mapping has shown that mature tissues such as blood and heart originate from specific regions of the pre-gastrula epiblast, but the plasticity of cells within the embryo and the function of key cell-type-specific transcription factors remain unclear. Here we analyse 1,205 cells from the epiblast and nascent Flk1(+) mesoderm of gastrulating mouse embryos using single-cell RNA sequencing, representing the first transcriptome-wide in vivo view of early mesoderm formation during mammalian gastrulation. Additionally, using knockout mice, we study the function of Tal1, a key haematopoietic transcription factor, and demonstrate, contrary to previous studies performed using retrospective assays, that Tal1 knockout does not immediately bias precursor cells towards a cardiac fate.
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Affiliation(s)
- Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Yosuke Tanaka
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | | | - John C. Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
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Korte M, Schmitz D. Cellular and System Biology of Memory: Timing, Molecules, and Beyond. Physiol Rev 2016; 96:647-93. [PMID: 26960344 DOI: 10.1152/physrev.00010.2015] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The storage of information in the mammalian nervous systems is dependent on a delicate balance between change and stability of neuronal networks. The induction and maintenance of processes that lead to changes in synaptic strength to a multistep process which can lead to long-lasting changes, which starts and ends with a highly choreographed and perfectly timed dance of molecules in different cell types of the central nervous system. This is accompanied by synchronization of specific networks, resulting in the generation of characteristic "macroscopic" rhythmic electrical fields, whose characteristic frequencies correspond to certain activity and information-processing states of the brain. Molecular events and macroscopic fields influence each other reciprocally. We review here cellular processes of synaptic plasticity, particularly functional and structural changes, and focus on timing events that are important for the initial memory acquisition, as well as mechanisms of short- and long-term memory storage. Then, we cover the importance of epigenetic events on the long-time range. Furthermore, we consider how brain rhythms at the network level participate in processes of information storage and by what means they participating in it. Finally, we examine memory consolidation at the system level during processes of sleep.
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Affiliation(s)
- Martin Korte
- Zoological Institute, Division of Cellular Neurobiology, Braunschweig, Germany; Helmholtz Centre for Infection Research, AG NIND, Braunschweig, Germany; and Neuroscience Research Centre, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dietmar Schmitz
- Zoological Institute, Division of Cellular Neurobiology, Braunschweig, Germany; Helmholtz Centre for Infection Research, AG NIND, Braunschweig, Germany; and Neuroscience Research Centre, Charité Universitätsmedizin Berlin, Berlin, Germany
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34
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Kidd CDA, Thompson PJ, Barrett L, Baltic S. Histone Modifications and Asthma. The Interface of the Epigenetic and Genetic Landscapes. Am J Respir Cell Mol Biol 2016; 54:3-12. [PMID: 26397168 DOI: 10.1165/rcmb.2015-0050tr] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Complex lung diseases, such as asthma, are influenced by both genetic predisposition and environmental stimuli. The epigenetic landscape of such diseases is attracting increasing interest and research. Epigenetics broadly covers the transient and the inheritable changes to gene expression that are not directly due to changes in nucleotide sequences. Epigenetic mechanisms could have significant impact on asthma-related allergic, immune, and regulatory pathways, as well as on the generation of biomarkers and the heritable transmission of asthma phenotypes. Recent technological advances have allowed mapping of the epigenome and analysis of genome-wide epigenetic contributors to disease. As a result, ground-breaking observations regarding histone post-translational modifications in a number of immunological diseases have emerged. In this review, we look beyond the biological information coded by DNA and review the epigenetic modifications made to histones, with evidence suggesting a role for their modification in asthma.
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Affiliation(s)
- Courtney D A Kidd
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Philip J Thompson
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and.,3 Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia, Perth, Western Australia, Australia
| | - Lucy Barrett
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Svetlana Baltic
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
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35
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Roussis IM, Guille M, Myers FA, Scarlett GP. RNA Whole-Mount In situ Hybridisation Proximity Ligation Assay (rISH-PLA), an Assay for Detecting RNA-Protein Complexes in Intact Cells. PLoS One 2016; 11:e0147967. [PMID: 26824753 PMCID: PMC4732756 DOI: 10.1371/journal.pone.0147967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
Techniques for studying RNA-protein interactions have lagged behind those for DNA-protein complexes as a consequence of the complexities associated with working with RNA. Here we present a method for the modification of the existing In Situ Hybridisation-Proximity Ligation Assay (ISH-PLA) protocol to adapt it to the study of RNA regulation (rISH-PLA). As proof of principle we used the well-characterised interaction of the Xenopus laevis Staufen RNA binding protein with Vg1 mRNA, the complex of which co-localises to the vegetal pole of Xenopus oocytes. The applicability of both the Stau1 antibody and the Locked Nucleic Acid probe (LNA) recognising Vg1 mRNA were independently validated by whole-mount Immunohistochemistry and whole-mount in situ hybridisation assays respectively prior to combining them in the rISH-PLA assay. The rISH-PLA assay allows the identification of a given RNA-protein complex at subcellular and single cell resolution, thus avoiding the lack of spatial resolution and sensitivity associated with assaying heterogenous cell populations from which conventional RNA-protein interaction detection techniques suffer. This technique will be particularly usefully for studying the activity of RNA binding proteins (RBPs) in complex mixtures of cells, for example tissue sections or whole embryos.
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Affiliation(s)
- Ioannis M. Roussis
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Matthew Guille
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Fiona A. Myers
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
| | - Garry P. Scarlett
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, United Kingdom
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36
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Veith N, Ziehr H, MacLeod RAF, Reamon-Buettner SM. Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines. BMC Biotechnol 2016; 16:6. [PMID: 26800878 PMCID: PMC4722726 DOI: 10.1186/s12896-016-0238-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recombinant cell lines developed for therapeutic antibody production often suffer instability or lose recombinant protein expression during long-term culture. Heterogeneous gene expression among cell line subclones may result from epigenetic modifications of DNA or histones, the protein component of chromatin. We thus investigated in such cell lines, DNA methylation and the chromatin environment along the human eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) promoter in an antibody protein-expression vector which was integrated into the Chinese hamster ovary (CHO) cell line genome. RESULTS We analyzed four PT1-CHO cell lines which exhibited losses of protein expression at advanced passage number (>P35) growing in adherent conditions and in culture medium with 10 % FCS. These cell lines exhibited different integration sites and transgene copy numbers as determined by fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR), respectively. By qRT-PCR, we analyzed the recombinant mRNA expression and correlated it with DNA methylation and with results from various approaches interrogating the chromatin landscape along the EEF1A1 promoter region. Each PT1-CHO cell line displayed specific epigenetic signatures or chromatin marks correlating with recombinant mRNA expression. The cell line with the lowest recombinant mRNA expression (PT1-1) was characterized by the highest nucleosome occupancy and displayed the lowest enrichment for histone marks associated with active transcription. In contrast, the cell line with the highest recombinant mRNA expression (PT1-55) exhibited the highest numbers of formaldehyde-assisted isolation of regulatory elements (FAIRE)-enriched regions, and was marked by enrichment for histone modifications H3K9ac and H3K9me3. Another cell line with the second highest recombinant mRNA transcription and the most stable protein expression (PT1-7) had the highest enrichments of the histone variants H3.3 and H2A.Z, and the histone modification H3K9ac. A further cell line (PT1-30) scored the highest enrichments for the bivalent marks H3K4me3 and H3K27me3. Finally, DNA methylation made a contribution, but only in the culture medium with reduced FCS or in a different expression vector. CONCLUSIONS Our results suggest that the chromatin state along the EEF1A1 promoter region can help predict recombinant mRNA expression, and thus may assist in selecting desirable clones during cell line development for protein production.
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Affiliation(s)
- Nathalie Veith
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Holger Ziehr
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Roderick A F MacLeod
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Stella Marie Reamon-Buettner
- Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625, Hannover, Germany.
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37
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Gomez D, Swiatlowska P, Owens GK. Epigenetic Control of Smooth Muscle Cell Identity and Lineage Memory. Arterioscler Thromb Vasc Biol 2015; 35:2508-16. [PMID: 26449751 PMCID: PMC4662608 DOI: 10.1161/atvbaha.115.305044] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022]
Abstract
Vascular smooth muscle cells (SMCs), like all cells, acquire a cell-specific epigenetic signature during development that includes acquisition of a unique repertoire of histone and DNA modifications. These changes are postulated to induce an open chromatin state (referred to as euchromatin) on the repertoire of genes that are expressed in differentiated SMC, including SMC-selective marker genes like Acta2 and Myh11, as well as housekeeping genes expressed by most cell types. In contrast, genes that are silenced in differentiated SMC acquire modifications associated with a closed chromatin state (ie, heterochromatin) and transcriptional silencing. Herein, we review mechanisms that regulate epigenetic control of the differentiated state of SMC. In addition, we identify some of the major limitations in the field and future challenges, including development of innovative new tools and approaches, for performing single-cell epigenetic assays and locus-selective editing of the epigenome that will allow direct studies of the functional role of specific epigenetic controls during development, injury repair, and disease, including major cardiovascular diseases, such as atherosclerosis, hypertension, and microvascular disease, associated with diabetes mellitus.
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MESH Headings
- Animals
- Cardiovascular Diseases/genetics
- Cardiovascular Diseases/metabolism
- Cardiovascular Diseases/pathology
- Cardiovascular Diseases/physiopathology
- Cell Differentiation/genetics
- Cell Lineage/drug effects
- Chromatin Assembly and Disassembly
- Embryonic Stem Cells/metabolism
- Embryonic Stem Cells/pathology
- Epigenesis, Genetic
- Epigenomics/methods
- Gene Expression Regulation, Developmental
- Genetic Markers
- Humans
- Muscle Development/genetics
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phenotype
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Affiliation(s)
- Delphine Gomez
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Pamela Swiatlowska
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Gary K Owens
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville.
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38
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Affiliation(s)
- Tessy Korthout
- Division of Gene Regulation; Netherlands Cancer Institute (NKI); Amsterdam The Netherlands
| | - Giulia Emanuelli
- Cardiovascular Division, James Black Centre (BHF Centre of Excellence); King's College London; UK
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Semrau S, van Oudenaarden A. Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools. Annu Rev Cell Dev Biol 2015; 31:317-45. [DOI: 10.1146/annurev-cellbio-100814-125300] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Alexander van Oudenaarden
- Hubrecht Institute, 3584 CT Utrecht, The Netherlands;
- University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CG Utrecht, The Netherlands
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40
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Januar V, Desoye G, Novakovic B, Cvitic S, Saffery R. Epigenetic regulation of human placental function and pregnancy outcome: considerations for causal inference. Am J Obstet Gynecol 2015; 213:S182-96. [PMID: 26428498 DOI: 10.1016/j.ajog.2015.07.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic mechanisms, often defined as regulating gene activity independently of underlying DNA sequence, are crucial for healthy development. The sum total of epigenetic marks within a cell or tissue (the epigenome) is sensitive to environmental influence, and disruption of the epigenome in utero has been associated with adverse pregnancy outcomes. Not surprisingly, given its multifaceted functions and important role in regulating pregnancy outcome, the placenta shows unique epigenetic features. Interestingly however, many of these are only otherwise seen in human malignancy (the pseudomalignant placental epigenome). Epigenetic variation in the placenta is now emerging as a candidate mediator of environmental influence on placental functioning and a key regulator of pregnancy outcome. However, replication of findings is generally lacking, most likely due to small sample sizes and a lack of standardization of analytical approaches. Defining DNA methylation "signatures" in the placenta associated with maternal and fetal outcomes offers tremendous potential to improve pregnancy outcomes, but care must be taken in interpretation of findings. Future placental epigenetic research would do well to address the issues present in epigenetic epidemiology more generally, including careful consideration of sample size, potentially confounding factors, issues of tissue heterogeneity, reverse causation, and the role of genetics in modulating epigenetic profile. The importance of animal or in vitro models in establishing a functional role of epigenetic variation identified in human beings, which is key to establishing causation, should not be underestimated.
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Affiliation(s)
- Vania Januar
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Silvija Cvitic
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Pediatrics, University of Melbourne, Parkville, Australia.
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41
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Perspective on unraveling the versatility of ‘co-repressor’ complexes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1051-6. [DOI: 10.1016/j.bbagrm.2015.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/01/2023]
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42
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Tsang JS. Utilizing population variation, vaccination, and systems biology to study human immunology. Trends Immunol 2015; 36:479-93. [PMID: 26187853 PMCID: PMC4979540 DOI: 10.1016/j.it.2015.06.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/27/2022]
Abstract
The move toward precision medicine has highlighted the importance of understanding biological variability within and across individuals in the human population. In particular, given the prevalent involvement of the immune system in diverse pathologies, an important question is how much and what information about the state of the immune system is required to enable accurate prediction of future health and response to medical interventions. Towards addressing this question, recent studies using vaccination as a model perturbation and systems-biology approaches are beginning to provide a glimpse of how natural population variation together with multiplexed, high-throughput measurement and computational analysis can be used to uncover predictors of immune response quality in humans. Here I discuss recent developments in this emerging field, with emphasis on baseline correlates of vaccination responses, sources of immune-state variability, as well as relevant features of study design, data generation, and computational analysis.
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Affiliation(s)
- John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Get to Understand More from Single-Cells: Current Studies of Microfluidic-Based Techniques for Single-Cell Analysis. Int J Mol Sci 2015. [PMID: 26213918 PMCID: PMC4581168 DOI: 10.3390/ijms160816763] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This review describes the microfluidic techniques developed for the analysis of a single cell. The characteristics of microfluidic (e.g., little sample amount required, high-throughput performance) make this tool suitable to answer and to solve biological questions of interest about a single cell. This review aims to introduce microfluidic related techniques for the isolation, trapping and manipulation of a single cell. The major approaches for detection in single-cell analysis are introduced; the applications of single-cell analysis are then summarized. The review concludes with discussions of the future directions and opportunities of microfluidic systems applied in analysis of a single cell.
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Wills QF, Mead AJ. Application of single-cell genomics in cancer: promise and challenges. Hum Mol Genet 2015; 24:R74-84. [PMID: 26113645 PMCID: PMC4571998 DOI: 10.1093/hmg/ddv235] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 12/13/2022] Open
Abstract
Recent advances in single-cell genomics are opening up unprecedented opportunities to transform cancer genomics. While bulk tissue genomic analysis across large populations of tumour cells has provided key insights into cancer biology, this approach does not provide the resolution that is critical for understanding the interaction between different genetic events within the cellular hierarchy of the tumour during disease initiation, evolution, relapse and metastasis. Single-cell genomic approaches are uniquely placed to definitively unravel complex clonal structures and tissue hierarchies, account for spatiotemporal cell interactions and discover rare cells that drive metastatic disease, drug resistance and disease progression. Here we present five challenges that need to be met for single-cell genomics to fulfil its potential as a routine tool alongside bulk sequencing. These might be thought of as being challenges related to samples (processing and scale for analysis), sensitivity and specificity of mutation detection, sources of heterogeneity (biological and technical), synergies (from data integration) and systems modelling. We discuss these in the context of recent advances in technologies and data modelling, concluding with implications for moving cancer research into the clinic.
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Affiliation(s)
- Quin F Wills
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK and
| | - Adam J Mead
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK, NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LE, UK
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Seco-Hidalgo V, Osuna A, Pablos LMD. To bet or not to bet: deciphering cell to cell variation in protozoan infections. Trends Parasitol 2015; 31:350-6. [PMID: 26070403 DOI: 10.1016/j.pt.2015.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/11/2015] [Accepted: 05/13/2015] [Indexed: 11/16/2022]
Abstract
Some of the most crucial phenotypic aspects of parasites, such as an antigen-coated surface, parasite sexual differentiation, virulence, and drug resistance, rely on adaptive plasticity and/or stochastic events. At a population level, cell to cell variability represents an avenue for rapid response to drastic changes in the environment. Single cell approaches can be used to unravel the different strategies used by parasites to survive in the context of regulated transcriptional control (apicomplexa) or in its absence (kinetoplastids).
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Affiliation(s)
- Víctor Seco-Hidalgo
- Biochemistry and Molecular Parasitology Research Group, Department of Parasitology, University of Granada, Campus de Fuentenueva, Granada, Spain
| | - Antonio Osuna
- Biochemistry and Molecular Parasitology Research Group, Department of Parasitology, University of Granada, Campus de Fuentenueva, Granada, Spain
| | - Luis Miguel De Pablos
- Biochemistry and Molecular Parasitology Research Group, Department of Parasitology, University of Granada, Campus de Fuentenueva, Granada, Spain; Centre for Immunology and Infection (CII), Biology Department, University of York, York, UK.
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