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Imm J, Pishva E, Ali M, Kerrigan TL, Jeffries A, Burrage J, Glaab E, Cope EL, Jones KM, Allen ND, Lunnon K. Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation. Front Cell Dev Biol 2021; 9:647981. [PMID: 34277599 PMCID: PMC8281298 DOI: 10.3389/fcell.2021.647981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/14/2021] [Indexed: 12/21/2022] Open
Abstract
In development, differentiation from a pluripotent state results in global epigenetic changes, although the extent to which this occurs in induced pluripotent stem cell-based neuronal models has not been extensively characterized. In the present study, induced pluripotent stem cell colonies (33Qn1 line) were differentiated and collected at four time-points, with DNA methylation assessed using the Illumina Infinium Human Methylation EPIC BeadChip array. Dynamic changes in DNA methylation occurring during differentiation were investigated using a data-driven trajectory inference method. We identified a large number of Bonferroni-significant loci that showed progressive alterations in DNA methylation during neuronal differentiation. A gene–gene interaction network analysis identified 60 densely connected genes that were influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity.
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Affiliation(s)
- Jennifer Imm
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Ehsan Pishva
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Muhammadd Ali
- Biomedical Data Science Group, Luxembourg Centre for System Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Talitha L Kerrigan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Aaron Jeffries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Joe Burrage
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for System Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Emma L Cope
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | - Nicholas D Allen
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Katie Lunnon
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Steg LC, Shireby GL, Imm J, Davies JP, Franklin A, Flynn R, Namboori SC, Bhinge A, Jeffries AR, Burrage J, Neilson GWA, Walker EM, Perfect LW, Price J, McAlonan G, Srivastava DP, Bray NJ, Cope EL, Jones KM, Allen ND, Pishva E, Dempster EL, Lunnon K, Mill J, Hannon E. Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons. Mol Brain 2021; 14:98. [PMID: 34174924 PMCID: PMC8236187 DOI: 10.1186/s13041-021-00810-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.
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Affiliation(s)
- Leonard C Steg
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Gemma L Shireby
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jennifer Imm
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan P Davies
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Alice Franklin
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Robert Flynn
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Seema C Namboori
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Akshay Bhinge
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Aaron R Jeffries
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Joe Burrage
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Grant W A Neilson
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Emma M Walker
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Leo W Perfect
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Grainne McAlonan
- Department of Forensic and Neurodevelopmental Sciences, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Behavioural and Developmental Psychiatry, South London and Maudsley NHS Foundation Trust, London, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Nicholas J Bray
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Emma L Cope
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | - Ehsan Pishva
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Emma L Dempster
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK.
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Crawford B, Craig Z, Mansell G, White I, Smith A, Spaull S, Imm J, Hannon E, Wood A, Yaghootkar H, Ji Y, Mullins N, Lewis CM, Mill J, Murphy TM. DNA methylation and inflammation marker profiles associated with a history of depression. Hum Mol Genet 2019; 27:2840-2850. [PMID: 29790996 DOI: 10.1093/hmg/ddy199] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.
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Affiliation(s)
- Bethany Crawford
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Zoe Craig
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Isobel White
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Adam Smith
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Steve Spaull
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Jennifer Imm
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Andrew Wood
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Hanieh Yaghootkar
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Yingjie Ji
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | | | - Niamh Mullins
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK.,Division of Genetics and Molecular Medicine, King's College London, London SE1 9RT, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Therese M Murphy
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
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Abstract
Alzheimer's disease is the most common form of dementia, it is estimated to affect over 40 million people worldwide. Classically, the disease has been characterized by the neuropathological hallmarks of aggregated extracellular amyloid-β and intracellular paired helical filaments of hyperphosphorylated tau. A wealth of evidence indicates a pivotal role for the innate immune system, such as microglia, and inflammation in the pathology of Alzheimer's disease. The over production and aggregation of Alzheimer's associated proteins results in chronic inflammation and disrupts microglial clearance of these depositions. Despite being non-excitable, microglia express a diverse array of ion channels which shape their physiological functions. In support of this, there is a growing body of evidence pointing to the involvement of microglial ion channels contributing to neurodegenerative diseases such as Alzheimer's disease. In this review, we discuss the evidence for an array of microglia ion channels and their importance in modulating microglial homeostasis and how this process could be disrupted in Alzheimer's disease. One promising avenue for assessing the role that microglia play in the initiation and progression of Alzheimer's disease is through using induced pluripotent stem cell derived microglia. Here, we examine what is already understood in terms of the molecular underpinnings of inflammation in Alzheimer's disease, and the utility that inducible pluripotent stem cell derived microglia may have to advance this knowledge. We outline the variability that occurs between the use of animal and human models with regards to the importance of microglial ion channels in generating a relevant functional model of brain inflammation. Overcoming these hurdles will be pivotal in order to develop new drug targets and progress our understanding of the pathological mechanisms involved in Alzheimer's disease.
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Affiliation(s)
- Laura Thei
- Reading School of Pharmacy, University of Reading, Reading, United Kingdom
| | - Jennifer Imm
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Eleni Kaisis
- Reading School of Pharmacy, University of Reading, Reading, United Kingdom
| | - Mark L Dallas
- Reading School of Pharmacy, University of Reading, Reading, United Kingdom
| | - Talitha L Kerrigan
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Imm J. P3‐124: EPIGENOMIC PROFILING OF 33QN1 IPSCS THROUGHOUT NEURONAL DIFFERENTIATION. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.1481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Imm J, Kerrigan TL, Jeffries A, Lunnon K. Using induced pluripotent stem cells to explore genetic and epigenetic variation associated with Alzheimer's disease. Epigenomics 2017; 9:1455-1468. [DOI: 10.2217/epi-2017-0076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
It is thought that both genetic and epigenetic variation play a role in Alzheimer's disease initiation and progression. With the advent of somatic cell reprogramming into induced pluripotent stem cells it is now possible to generate patient-derived cells that are able to more accurately model and recapitulate disease. Furthermore, by combining this with recent advances in (epi)genome editing technologies, it is possible to begin to examine the functional consequence of previously nominated genetic variants and infer epigenetic causality from recently identified epigenetic variants. In this review, we explore the role of genetic and epigenetic variation in Alzheimer's disease and how the functional relevance of nominated loci can be investigated using induced pluripotent stem cells and (epi)genome editing techniques.
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Affiliation(s)
- Jennifer Imm
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Talitha L Kerrigan
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Aaron Jeffries
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
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