ANNEX 2: MRC workshop - DELEGATE HANDBOOK

MRC Epigenetics workshop

16 – 17 April 2015. The Oakley Court. Windsor. Berkshire. UK

Scientific Steering Committee

MRC Board experts

Professor Mark McCarthy, University of Oxford (Chair) Dr Nessa Carey, PraxisUnico Professor Michael O’Donovan, Cardiff University UK and international experts

Professor Stephan Beck, University College London Dr Jordana Bell, Kings College London Professor Anne Ferguson-Smith, University of Cambridge Professor John Greally, Albert Einstein College of , USA Professor Caroline Relton, University of Bristol

Cover

A wordle of the topics to be covered during this workshop. These topics have been derived from the responses posted by the delegates as part of the pre-workshop survey. Image credits: All delegates!

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Workshop background and aims

Understanding the epigenetic mechanisms, their interactions and alterations in health and disease promises to make a significant contribution to the clinic. High- throughput technologies are enabling genome-wide epigenetic modifications to be mapped on an unprecedented scale. However, several challenges remain including whether such knowledge can be rapidly translated into biomedical applications. The MRC recognises that the UK has considerable strength in mechanistic (), descriptive (genome wide) and functional (cell and model organisms) epigenetic research and better integration of these fields could present a big opportunity and address some of the challenges.

This cross-Board workshop will aim to understand the existing gaps and review the emerging opportunities in epigenetics research; with a view to inform the MRC’s future strategy and help ensure that the balance of MRC investment in the area is appropriately aligned.

Workshop format: pre-workshop survey

Epigenetics is a vast and rapidly expanding field. To keep the workshop focussed on current and key strategic issues, all delegates were asked the following question:

"Within your area of interest1, what are the 3 major challenges in the field of epigenetics, which if addressed appropriately, will present future opportunities in the short- to longer-term (5 - 10 years)"

The survey responses were ‘sorted’ based on similarity2 and loosely grouped together to structure the workshop. We worked around these groupings to format the workshop such that it allows sufficient time to discuss the key issues in the field – as identified by the pre-workshop survey:

Main sessions Breakout sessions Round table

Expert talks Group discussions, Summarising and introducing key further exploring the agreeing on key issues and issues identified recommendations to challengeslenge during main sessions inform future strategy

- 2 plenaryl sessions (Setting the scene, Functional epigenomics) - 3 topical sessions (Mechanisms, Drivers of epigenetic variations, Epigenetics and disease)

1 this may include all methodological fields, for example; experimental, computational, statistical epigenetics and epi-genomics 2 using the automated survey and visualisation platform, Wellsorted (well-sorted.org)

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Pre-workshop survey outcomes: An overview

Below is an overview of the responses (titles only) submitted by the delegates, grouped under the relevant sessions. Corresponding descriptions are listed in session specific sections, to provide context. Each response has been given a unique number so they are easier to find. Session 2: Causes and Plenary 1: Setting the scene consequences of epigenetic variation 1. Retroelements

2. Function of the epigenome 3. Human Epigenomics 31. Proof of causality 4. Use of whole blood epigenetic 32. 'Signatures' of social and profiling in EWAS behavioural experiences 5. DNA and RNA epigenome: 33. Pathways from experiences to complexity and interplay epigenome 6. Higher-order chromatin 34. Health and behavioural structure consequences of epigenetics 7. Methylation vs other types of 35. Ageing epigenetics epigenomic data 36. Environment versus 8. We need to talk about EWAS factors 9. Distinguishing biologically 37. Approaches from determining significant changes cause from effect 10. Targets of Histone Modifying 38. Genetic-epigenetic- environmental variation 39. Disease cohorts, epidemiology Session 1: Focus on mechanisms and functional assay 40. Stem cells and Epigenetics 41. Metabolism and Epigenetics 11. Identifying high-confidence 42. Maternal nutrition and offspring epigenetic changes epigenome 12. Molecular cell classification 43. Effects of epigenome on 13.Epigenetic Inheritance function 14.Transgenerational epigenetic 44. Ascribing function to inheritance epigenomes 15.Peripheral tissues as a proxy for 45. Integrating metabolism, internal organs signaling and epigenetics 16.Transgenerational epigenetic 46. Dietary effects on the inheritance epigenome 17.Epigenetic diversity and cell fate 47. Identifying cause and effect decisions 48. Are epigenetic changes 18. Transgenerational effects instructive? 19.Trans-generational inheritance 49. Encouraging strengthening 20. Identifying a mechanism for causal inference 50. Causal inference 21. How is DNA demethylated 51. Epigenetic information, 22.Addressing tissue specificity environment and disease 23. Neurodisorders:map & validate 52. Epigenetic causality (epi)genetic network 53. Causality 24. Epigenetic memory 54. Cause and effect 25.Tissue and cellular specificity 55. Markers of exposure 26.Brain and periphery 56. The meaning of epigenetic 27. Tissue specificity markers 28.Understanding cellular responses 57. Epigenetics and other 29. Stability and heterogeneity 58. Epigenetics and environmental 30.Are the changes stable? exposure 59. Cause or effect

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Plenary 2: Functional Session 3: Epigenetics and epigenomics – a critical disease evaluation 83. Targeted 60. Precision (smart) medicine reprogramming 61. Cellular heterogeneity and 84. Epigenetic single-cell analysis interventions 62. Single cell technology 85. Development and 63. Single cell and single disease molecule technologies 86. Chemical Probes 64. Histone Epigenomics 87. Functional role of

65. Sample Collection epigenetic biomarkers 66. Bioinformatics 88. and disease 67. Data crunching capacity drivers and 68. Increasing the coverage of combinations epigenomic data 89. Understanding the 69. Single cell ChIP-Seq consequences of 70. Locus Specific ChIP-seq / disease changes proteomics 90. Translating epigentic 71. Single-cell epigenomics changes into 72. Detection of epigenetic biomarkers marks in single cells 91. Epigenetic changes 73. Technologies for population and based studies progression 74. Functional follow-up of 92. Epigenetic epigenetic signals neurodevelop. 75. In-vivo chromatin structure disorders - animal - nucleosome position models 76. Sequencing 93. Translational potential 77. Technologies for measuring of epigenetic markers methylation 94. Translational potential 78. Data visualisation from of epigenetic markers epigenome to phenome 95. Manipulation 79. Gaps in epigentic 96. Identifying predictive methodology biomarkers 80. Emerging technology for 97. Epigenetics and drugs functional epigenetics 98. Reprogramming 81. Combinatorial Nucleosome 99. Do they matter? Modifications 82. Structures of Chromatin- Associating Complexes

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Agenda Day 1, Thursday 16th April 2015

09:30 Registration open. Networking tea/coffee

11:00 Welcome and workshop context Professor Mark McCarthy, University of Oxford, UK

11:15 Plenary Day 1: Setting the scene

- Interpreting the epigenetics landscape Dr Gavin Kelsey, The Babraham Institute, UK

- Interpreting the results of Epigenome-Wide Association Studies Professor John Greally, Albert Einstein College of Medicine, USA

12:15 Session 1: Focus on mechanisms

- Trans-generational inheritance Professor Vardhman Rakyan, The Blizard Institute QMUL, UK

- Epigenetic heterogeneity in cells Professor Jonathan Mill, University of Exeter Medical School, UK

- What can we learn from animal models? Professor Eric Miska, Gurdon Institute, UK

13:15 Networking lunch

14:00 Session 1 continues (breakout group discussions3)

14:50 Session 2: Causes and consequences of epigenetic variation

- Genetics, epigenetics & the environment Dr Jordana Bell, Kings College London

- Population epigenetics and causal inference Professor Caroline Relton, University of Bristol

15:40 Afternoon tea break

16:00 Session 2 continues (breakout group discussions)

16:50 Workshop mixer

17:30 – 18:30 Round table Day 1

19:30 Dinner

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Day 2, Friday 17th April 2015

Chair welcome and context for Day 2 09:00 Professor Mark McCarthy, University of Oxford, UK

09:15 Plenary Day 2: Functional Epigenomics – a critical evaluation

- Critical evaluation of current technologies Professor Wolf Reik, Babraham Institute & WT Sanger Institute, UK

Critical evaluation of recent world-wide epigenetics initiatives Professor Henk Stunnenberg, Radbound University, The Netherlands

- Panel Q&A4

10:30 Session 3: Epigenetics and disease

- Epigenetic modification: their function and role in disease - Professor Stephan Beck, University College London, UK

- From mechanisms to therapeutics: an industry perspective - Dr Rab Prinjha, GSK Research Centre, GSK UK

11:30 Session 3 continues (breakout group discussions)

12:30 Networking lunch

Round table Day 2 13:15

14:15 Afternoon tea break

14:30 Setting a future agenda MRC cross Board discussions

15:40 Chair closes workshop

3 Details of breakout group arrangements will be displayed at the event, near the registration desk 4 Representatives / participants from all major Epigenetics initiatives (e.g. Blueprint, RoadMap, Encode, GTex, IHEC, Epigenesys) will be present

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Notes

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Plenary 1: Setting the scene

Chair: Professor Mark McCarthy

Session Abstract

In this plenary session, the two speakers were asked to set the scene for the workshop in talks designed to raise some of the key issues that we will discuss in the days ahead. Dr Gavin Kelsey will describe the epigenetic landscape, with an emphasis on the mechanistic contributions of the growing repertoire of epigenomic modifications. Professor John Greally will address some of the challenges associated with the design and interpretation of epigenome wide association studies. Many of the issues raised will be the subject of more intensive discussions later in the meeting .

11:15 Main session, Westminster suite (60 min)

- Interpreting the epigenetics landscape (25 min) Dr Gavin Kelsey, The Babraham Institute, UK

- Interpreting the results of Epigenome-Wide Association Studies (25 min) Professor John Greally, Albert Einstein College of Medicine, USA

- Brief Q & A (10 min)  Note taker: Dr Claire Newland

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Session specific survey outcomes (descriptive)

# Title Description

1. Retroelements They make up nearly half of mammalian genomes and yet how they influence normal gene function and disease is very poorly understood

2. Function of the We know many epigenetic marks, and many have been epigenome mapped onto the genome, but we understand little about their significance at a molecular level

3. Human We need a more comprehensive analysis of epigenetic Epigenomics signatures of different cell/tissue types in healthy and diseased states. Both on DNA (CpG methylation -better coverage) and histone levels (poorly understood)

4. Use of whole blood How appropriate is whole blood for EWAS of different epigenetic profiling diseases? 1/ Is the aim to identify disease mechanisms or in EWAS biomarkers? 2/ Value of computational tools for cell heterogeneity correction 3/ Establishing tissue specific/shared effects at EWAS signals

5. DNA and RNA Novel DNA modifications, their abundance, function and epigenome: metabolism. The epigenetic world of RNA - more complex complexity and than the world of DNA modifications, but still largely interplay unexplored (modifications, abundance, biological roles?)

6. Higher-order What regulates the formation and specificity of long- range chromatin chromatin interactions? structure

7. Methylation vs Is methylation special? Or is it historical that so much other types of research focuses on methylation rather than other epigenomic data mechanisms of epigenomic control. Should we be looking for more holistic approaches to assessing epigenomic changes?

8. We need to talk What makes an EWAS study worthwhile? Sample size, use of about EWAS blood as tissue, 450K vs other assays, methylation vs other epigenomic profiles, prospective design, replication, validation, causal inference. Can we come up with some practical recommendations?

9. Distinguishing Epigenomic profiling will always find changes if you look hard biologically enough but how do we know which changes have any significant changes biological significance. Ties in to bigger issue of which histone modifications, in which combinations, are really most relevant

10 Targets of Histone The identification of the histone and non-histone targets of Modifying Enzymes specific histone modifying enzymes will provide important insights regarding the post- translational control of interlinked nuclear processes

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Session 1: Focus on mechanisms

Chair: Professor Anne Ferguson-Smith

Session Abstract In this session we will explore transgenerational epigenetic phenomena and the possible mechanisms underlying them through consideration of mammalian and non- mammalian models. Strengths and limitations of these models will be considered and comparison of data generated in pursuit of mechanism will facilitate discussion into the relative merits of DNA methylation, small RNA mediated mechanisms and other mechanisms, in transgenerational inheritance. Epigenetic variability, within and between individuals and tissues, can now be measured more accurately. Here, we will discuss such epigenetic heterogeneity, consider relationships between genotype and epi-genotype and the functional implications of epigenetic variability in normal and environmentally compromised contexts.

12:15 Main session, Westminster suite (506 min)

- Trans-generational inheritance (20 min) Professor Vardhman Rakyan, The Blizard Institute QMUL, UK

- Epigenetic heterogeneity in cells (20 min) Professor Jonathan Mill, University of Exeter Medical School, UK

- What can we learn from animal models? (10 min) Professor Eric Miska, Gurdon Institute, UK

- Brief Q & A (10 min)

13:15 Networking lunch

14:00 Breakout sessions, Westminster and Marlborough suites (50 min) - Breakout group 1 Expert facilitators: Professor Andrew Prentice, Professor Anne Ferguson-Smith Note taker: Dr Des Walsh

- Breakout group 2 Expert facilitators: Dr Petra Hajkova, Professor Richard Meehan, Note taker: Dr Joe McNamara

Hot and cold buffet lunch will be served in The Scullery

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Session specific survey outcomes (descriptive)

# Title Description

11. Identifying high- If the hypothesis tested is that cells have undergone epigenetic confidence alterations, then differences in the epigenetic regulator that are the epigenetic consequence of confounding DNA, transcriptional, cell subtype or other changes sources of variability have to be excluded.

12. Molecular cell If cell subtypes are better discriminated by epigenomic assays than by classification histology or cell surface markers, and cell subtype variability influences the interpretation of epigenetic assays, we need to re-classify cell subtypes using these molecular assays.

13. Epigenetic This is at present a very controversial topic. Although the potential Inheritance implications are significant, truly convincing mechanistic or epidemiological data are lacking in mammals and almost non-existent for humans

14. Transgenerational Many publications and great public interest, but usually lacking in epigenetic rigour. Is this field supported by robust evidence or a passing fad? inheritance

15. Peripheral tissues To what extent can we use easily accessible peripheral tissues (blood, as a proxy for saliva, etc) as a proxy for tissues that cannot be collected longitudinally internal organs during life (brain, pancreas, etc). To what extent is inter-individual variation shared across tissues?

16. Transgenerational It is becoming apparent that transgenerational epigenetic inheritance epigenetic probably exists in mammals. But it is unclear what the underlying inheritance mechanisms are especially in the face of global erasure of epigenetic information in the germ line

17. Epigenetic Epigenetics is associated with stable memory but recent work shows diversity and cell that epigenetic mechanisms have the potential to generate diversity of fate decisions between cells. This may contribute to cellular diversity in development, ageing, and disease

18. Transgenerational Especially in the field of neurological or behavioural outcomes, effects understanding of exactly how pervasive such effects are and whether there is really an epigenetic basis to transmission

19. Trans- Reliable model systems are required to dissect out the relevance of TGI generational phenomena, what is its genetic basis and what is the transmissible inheritance factor? Recent profiling studies in inbred mice tend to rule out a direct role for DNA modification in this process?

20. Identifying a There is plenty of evidence suggesting that changes induced by mechanism for experience (eg fear, malnutrition) can be inherited but efforts to heritability understand a biochemical mechanism have not been rigorous

21. How is DNA Neurones possibly provide the best evidence for the existence of an demethylated active DNA demethylation process yet we still don't understand how it is brought about

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22. Addressing tissue Epidemiological studies are limited by a reliance on surrogate (non- specifcity target) tissues. Methods to improve inter-tissue comparison of epigenomic features would be beneficial. Investment in computational approaches to use available reference data is needed

23. Neurodisorders:m Neurological disorders have chromatin regulators as major ap & validate predisposing hubs. Bioinformatics can define the linked (epi)genetic (epi)genetic networks . We should validate and test these maps with throughput cell network culture and in vivo with in model organisms

24. Epigenetic In the complex epigenetic code what are the key epigenetic memory modifications that contribute to epigenetic memory and the stability of cell fate? How are these affected in disease? Do they constitute a barried in epigenetic reprogramming?

25. Tissue and cellular There is a wide-held view that DNA methylation changes are tissue and specificity cell-specific. Many clinical samples contain a mixture of cells. Are mixed tissue/cell samples worth analysing e.g. whole blood?

26. Brain and In applications to the neuroscience board, it is not periphery infrequent to see proposals to apply some form of methylation profiling of a peripheral tissue in the hope that it indexes changes in (some bit of) the CNS. What is evidence?

27. Tissue specificity Epigenetic markers can differ between tissues, and between cell types in the same tissue

28. Understanding The effects of epigenetic pharmacological mediators vary dramatically cellular responses in different cell types and the reasons are unclear

29. Stability and Robust techniques are needed for single cell analyses of chromatin that heterogeneity will allow study of the dynamic nature of epigenetic changes and heterogeneity within populations of cells

30. Are the changes Are epigenetic changes stable over time and reproducible in a given stable? disease?

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Notes

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Session 2: Causes and consequences of epigenetic variation

Chairs: Dr Jordana Bell, Professor Mark McCarthy

Session Abstract

Much work has focused on identifying the factors that influence epigenetic variability and its biomedical significance. Population-based approaches have been applied to identify novel associations between epigenetic marks and genetic variants, environmental exposures, as well as and disease outcomes, providing mechanistic insights, but often facing issues of bias, confounding and reverse causation in epigenetic epidemiology. Methods for causal inference can be applied to epigenetics to solve some of these problems. This session will seek to define current knowledge regarding the genetic and non-genetic factors that influence epigenetic variation and the extent to which a mechanistic understanding has been supported by analyses of causal inference.

14:50 Main session, Westminster suite (50 min) - Genetics, epigenetics & the environment (20 min) Dr Jordana Bell, Kings College London

- Population epigenetics and causal inference (20 min) Professor Caroline Relton, University of Bristol

- Brief Q & A (10 min) 15:40 Afternoon tea break (20 min)

16:00 Breakout sessions, Westminster and Marlborough suites (50 min)

- Breakout group 1 Expert facilitators: Dr Karen Lilycrop, Professor Mark McCarthy Note taker: Dr Jacqui Oakley

- Breakout group 2 Expert facilitators: Dr Jordana Bell, Professor Adrian Bird Note taker: Dr Kate Adcock

16:50 Workshop mixer5 (40 min)

Please return to the Westminster suite at 17:30 for the Round table to be Chaired by Professor Michael O’Donovan. Session Chairs / expert facilitators will report back - details will be provided at the event.

A private dinner will be served in the Gloucester suite at 19:30

5 Oakleaf lounge and conservatory in the main building. MRC staff will guide

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Session specific survey outcomes (descriptive)

Session 2: Causes and consequences of epigenetic variation

# Title Description

31. Proof of causality Demonstration that epigenetic modifications are causally involved in , including disease.

32. 'Signatures' of What are (lasting) epigenetic signatures of adverse social and life experiences? To what extent do signatures of behavioural different experiences (e.g. poverty, harsh experiences parenting, etc) overlap? Are there critical life- course periods for experiences to get biologically embedded?

33. Pathways from Where evidence exists for lasting epigenetic signatures of experience experiences to outside the skin, what are the pathways and mechanisms involved? epigenome

34. Health and What are the subsequent consequences for health and behaviour of behavioural embedded experiential epigenetic changes? Where these exist what consequences of are the pathways? epigenetics

35. Ageing The single most accurate predictor of human age is DNA methylation - epigenetics the epigenetic ageing clock. But what are the molecular origins of the clock and what are the functional consequences? At present we have no idea

36. Environment Does the environment affect the epigenome in a meaningful way? versus Again, huge interest () but hardly any evidence for transcription biologically significant effects. Sequence-specific DNA binding factors on the other hand do affect the epigenome

37. Approaches from What are the optimal strategies for determining causality in epigenetic determining cause epidemiology, especially in disorders that manifest in internal tissues from effect such as the brain and are associated with changes in cellular composition (e.g. Alzheimer's disease)?

38. Genetic- Up to now, only one or a few epigenomes of one particular cell type epigenetic- have been generated. Although this is very important as a first environmental resource, it clearly is limited as it does not provide insight into variation variation

39. Disease cohorts, To gain insight into the etiology of disease and the identification of the epidemiology and drivers in multifactorial diseases, genome-epigenome of well-defined functional assay disease cohorts along with functional studies possible metabolites, microbiome....

40. Stem cells and Integrating epigenetic, genetic and cell signalling signals in the Epigenetics regulation of usage during early cell fate decisions

41. Metabolism and Deciphering novel cross-talk(s) between epigenetic and metabolic

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Epigenetics switches at key developmental transitions

42. Maternal nutrition Does a mother's nutrient status (especially at conception) modify her and offspring offspring's epigenome? What are the critical nutrients/pathways? Can epigenome these be modified to improve birth and lifelong outcomes?

43. Effects of How do we most efficiently study epigenotype/ relationships? epigenome on function

44. Ascribing function To achieve targeted epigenetic therapies, it is crucial to determine to epigenomes which parts of a given epigenome are functionally relevant to a phenotype, as well as which are the "driver" and "passenger" components of the epigenetic portfolio

45. Integrating Examples of mechanistic links between metabolism, signaling and metabolism, epigenetics are few but promising. Expanding these studies would signaling and provide an environmental perspective on how to control our epigenetics epigenomes

46. Dietary effects on A real understanding of the extent to which and the mechanisms by the epigenome which factors such as diet might influence epigenetic information/mechanisms at the single-gene level with long-term consequences

47. Identifying cause It is not possible to identify if disease-associated methylation changes and effect are a cause or consequence of the disease. Longitudinal analysis of non-diseased tissue from unaffected individuals are needed to over come this

48. Are epigenetic Recent epigenomic data sets do not address 'cause or consequence'? changes Do epigenetic alterations in perturbed cells/tissues/ organisms reflect instructive? the outcome of signalling or (GRNs) pathways?

49. Encouraging There is an increasing abundance of association studies in the field of strengthening epigenetics. These studies are inevitably vulnerable to confounding and causal inference reverse causation. Strengthening causal inference through the use of a variety of methods should be encouraged

50. Causal inference Methodological approaches to causal inference in human population- based epigenomic datasets across multiple study designs. To include: causal inference methods, longitudinal studies, meQTL/environmental exposures/discordant twin studies

51. Epigenetic Interaction between epigenome and environment: what type of information, epigenetic information can be perturbed? Effect on transgenerational environment and inheritance. Epigenetic component of disease ; variability between disease epigenomes : within individual vs between individuals

52. Epigenetic Distinguishing between cause and effect in the relationship between causality epigenetic changes and transcriptional control

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53. Causality Unlike genetic associations, epigenetic associations could be bidirectional. This can be difficult to disentangle and therefore limit their value. Also if they are simply an intermediary step to effects on gene expression why not just study the later?

54. Cause and effect What sort of things are measures of methylation sensitive to. In psychiatry, numerous changes in all sorts of things have been reported, usually effects of disorder rather than causes. Can we avoid the mistakes of the past?

55. Markers of Are there robust measures that remain stable in adulthood that may exposure index exposures to various postulated risk factors for psychiatric disorder (childhood trauma/maternal infection etc etc) that can be used in historical samples

56. The meaning of Epigenetic markers can be measures of exposure, mechanisms or epigenetic disease; in any individual study, it can often be unclear which of these markers variables are being measured

57. Epigenetics and Relating epigenetic markers to the corresponding markers in other other omics 'levels' of omics (e.g. transcriptomics, metabolomics)

58. Epigenetics and Establishing the effects of environmental exposure on the epigenetic environmental landscape. Do specific environmental exposures generate specific exposure signatures? Is the signature in tissue different? How quantitative and lasting is it and can it be used as a biomarker?

59. Cause or effect Are epigenetic changes cause or effect?

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Plenary Day 2: Functional Epigenomics – a critical evaluation

Chairs: Professor John Greally

Session Abstract

Our speakers for this session share the same interests in epigenomic technology development and its practical application. Professor Reik will begin with a description of the current and emerging technologies that give us insights into the many ways in which the epigenome can be studied, the kinds of information generated and the insights offered. Professor Stunnenberg will then take the discussion further to describe how large, coordinated projects1 that study multiple facets of epigenomic organization can generate combinatorial information that enhances our insights into genomic physiology. A unifying theme for the two talks will be the applications of these technologies to understand human diseases and other phenotypes, in terms of sample requirements, costs and informative-ness of the results obtained. The goal is to create a foundation for subsequent discussion by the broader group of participants about how best to design epigenomics research project .

Chair welcome and context for Day 2 09:00 Professor Mark McCarthy, University of Oxford, UK

09:15 Main session, Westminster suite (1hr 15 min)

- Critical evaluation of current technologies (30 min) Professor Wolf Reik, Babraham Institute & WT Sanger Institute, UK

- Critical evaluation of recent world-wide epigenetics initiatives (30 min) Professor Henk Stunnenberg, Radbound University, The Netherlands

- Panel Q&A6 (15 min)

Note taker: Dr Nathan Richardson

6 Representatives / participants from all major Epigenetics initiatives (e.g. Blueprint, RoadMap, Encode, GTex, IHEC, Epigenesys) will be present

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Session specific survey outcomes (descriptive)

# Title Description

60. Precision In vivo epigenome monitoring and intervention. (smart) medicine

61. Cellular How are analyses of "bulk" tissue confounded by cellular heterogeneity heterogeneity? What are the possibilities of undertaking and single-cell single-cell analyses in a systematic way - e.g. isolating single analysis neurons and undertaking methylomic analysis

62. Single cell Single cell approaches and development of other technology complementary/orthogonal approaches will be essential to dissect the heterogeneity within affected tissues/cell types

63. Single cell and The epigenome varies between tissues and as recent work single molecule shows also between cells. Single cell epigenomics methods technologies together with new bioinformatics approaches are needed to unravel heterogeneity at the cell and molecule level

64. Histone There is little data on how epigenetic signatures on the Epigenomics level (histones) is linked to which genes. CHIPSeq is the only methodology to do this and it is limited to histone marks with good antibodies. Need tech to link with MS histone proteomics

65. Sample Optimal biological sample collection suitable for population Collection based studies

66. Bioinformatics User-friendly introductions to use of epigenetic data from NIH Roadmap, Encode, Blueprint, etc

67. Data crunching The quantities of data that will be produced present huge capacity bioinformatic and IT challenges. Are we able to cope?

68. Increasing the Epigenomic profiling excludes a substantial proportion of the coverage of genome, namely retroelements. These have been extensively epigenomic data shown to play important regulatory roles, but their impact in disease underestimated. Novel technologies are needed to map them

69. Single cell ChIP- Technology to enable disease tissue derived single cell ChIP- Seq seq and RNAseq

70. Locus Specific Technology to enable locus ChIP and analysis by proteomics ChIP-seq / (open discovery) of locus specific protein complexes and their proteomics response to signalling, gene induction, repression etc.

71. Single-cell Reliable methods that could allow protein occupancy or epigenomics chromatin state data to be obtained at the ultra- low/single cell level to complement DNA methylation and transcription data

72. Detection of The nervous system is composed of many cell types and the

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epigenetic gene expression in each neurone is modified exquisitely and is marks in single potentially long lasting (years). Currently we are not able to cells probe the role of epigenetic marks in these changes

73. Technologies for There is currently a heavy reliance on the Illumina 450 population BeadChip which is often criticised and has well recognised based studies limitations. However it remains the most cost-effective option in population-based studies. Investment in alternatives is needed

74. Functional Gene expression follow up and functional genomic annotation follow-up of of epigenetic signals epigenetic signals

75. In-vivo Development of methods for measuring nucleosome positions chromatin in small cell numbers. Preferably this should be done in vivo structure - rather than in culture, and should be with minimal or no cell nucleosome isolation position

76. Sequencing Single-molecule epigenetic sequencing

77. Technologies for What's the forward path here. Better arrays? targeted measuring sequencing? whole genome sequencing? methylation

78. Data Integration of data analysis and bioinformatic methods to visualisation allow visualisation of the epigenome in the context of from epigenome phenotype and systems biology to phenome

79. Gaps in Identify gaps in epigenetic methods e.g. Single cell epigentic epigenomes or in situ hybridisation based gene specific methodology methylation; finding alternatives to cross- linking immunoprecipitations (ChIPseq)

80. Emerging To allow functional probing of epigenetic marks methods are technology for needed for targeted methylation/demethylation and histone functional modifification epigenetics

81. Combinatorial While recent developments in have Nucleosome advanced our understanding of combinatorial histone Modifications modifications on the same variant sequence, it has been difficult to describe co-existing modifications present at the nucleosome level

82. Structures of Structural data for multimeric chromatin-associating Chromatin- complexes will elucidate how combinatorial modifications Associating encode information to localise activity Complexes

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Notes

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Session 3: Epigenetics and disease

Chairs: Professor Stephan Beck, Professor Caroline Relton

Session Abstract

Now that first 100 of the planned 1000 IHEC reference epigenomes have been published, we can assess if and how this resource can best be leveraged to uncover the role of epigenetics in disease. Building on the discussion of the causes and consequences of epigenetic variation we will turn to current developments to work out the mechanism and functions of epigenetic drivers in disease. Many of the complex study design issues that face the investigation of the determinants of epigenetic variation apply to elucidating their causal influence on disease. Indeed, disease itself is highly likely to perturb the epigenome. The epigenome does not exist in isolation and consideration of other molecular parameters is essential to enhance our understanding of the mechanistic role of the epigenome in normal development and disease. In addition to the role of epigenetic mechanisms in disease itself there is considerable scope to utilise epigenetic information as a biomarker of disease risk, prognosis or treatment response. An overview of epigenetic modifications and their function and role in disease will set the scene. We will then consider how this knowledge can help us move from mechanisms to therapeutics .

10:30 Main session, Westminster suite (60 min)

- Epigenetic modification: their function and role in disease (25 min) Professor Stephan Beck, University College London, UK

- From mechanisms to therapeutics: an industry perspective (25 min) Dr Rab Prinjha, GSK Medicines Research Centre, GSK UK

- Brief Q & A (10 min)

11:30 Breakout sessions, Westminster and Marlborough suites (60 min) - Breakout group 1 Expert facilitators: Professor Caroline Relton, Professor Chas Bountra Note taker: Dr Georgina Drury

- Breakout group 2 Expert facilitators: Professor Stephan Beck, Dr John Marioni Note taker: Dr Rob Buckle

12:30 Networking lunch

Hot and cold buffet lunch will be served in The Scullery

Please return to the Westminster suite at 13:15 for the Round table to be Chaired by Dr Nessa Carey. Session Chairs / expert facilitators will report back - details will be provided at the event.

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Session specific survey outcomes (descriptive)

# Title Description

83. Targeted Ability to reprogram epigenome at will with high specificity reprogramming and low off target effects.

84. Epigenetic Amelioration of disease states mediated by epigenetic interventions dysregulation may require sequence-specific rather than global interventions, and may need to act upon mosaic dysregulated subpopulations of cells, two substantial targeting challenges.

85. Development Further exploring epigenetic-based link(s) between early and disease embryogenesis and diseases

86. Functional role of Defining the functional role of epigenetic marks in different contexts epigenetic throughout the genome. What are correlations between epigenetic biomarkers marks and gene expression, DNA repair and DNA synthesis? Do epigenetic changes drive gene expression or vice versa?

87. Chemical Probes There is limited access to good small molecule modulators of epigenetic proteins and miRNAs. Although research is active in the area of inhibitors, only a small percentage of the potentially druggable epigenome is addressed

88. Genetics and Systematic identification of epigenetic target gene contribution disease drivers to disease pathogenesis and combinations

89. Understanding Methylation analysis of many diseases has identified hundreds the or thousands of disease-associated CpG sites. We focus on consequences of sites within/near genes already associated with the disease, disease changes but could learn more about disease by looking at the unknown sites

90. Translating Identifying the CpG sites that have a functional consequence epigentic on disease pathology and translating these into biomarkers for changes into diagnosis, prognosis and clinical trials biomarkers

91. Epigenetic As is the case for somatic mutations, the majority of cancer- changes and specific epigenetic changes are likely to be passengers. cancer Hypermethylation affecting cancer genes, even frequently, progression does not necessarily drive cancer.

92. Epigenetic We require circuit and neuron/cell-level models to understand neurodevelop. the role of epigenetic/chromatin regulators in disorders - neurodevelopmental and neuropsychiatric disorders. Genetic animal models animal models (including fly) will be very powerful for this

93. Translational Epigenetic and genetically identified proteins are likely to potential of represent better targets for drug discovery, for many cancer,

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epigenetic inflammatory, metabolic and neuro-psychiatric diseases. But markers how do we more rapidly prioritise targets for drug discovery?

94. Translational How do we more rapidly evaluate drug targeting mechanisms potential of in order to alleviate concerns regarding safety and tolerability? epigenetic markers

95. Manipulation Are epigenetic changes ever going to be amenable to selective manipulation or simply remain a tool towards understanding disease mechanisms?

96. Identifying Need to find ropbust biomarkers for patients most likely to predictive benefit from epigenetic drugs, and also to monitor their biomarkers responses, in the relevant tissues or to find reliable surrogate tissue markers

97. Epigenetics and How do drugs, e.g. anti-cancer drugs alter the epigenetic drugs landscape. How does this relate top therapeutic outcome e.g. efficacy and side effects. Does this contribute to drug resistance? Do the changes provide biomarkers?

98. Reprogramming Need to better understand how epigenetic marks are established and maintained particularly during development and reprogramming (in germ cells and iPS cells)and how this fails in disease. Can they be used as biomarkers and is there potential for therapy?

99. Do they matter? How can we build confidence that epigenetic changes are a target for pharma companies?

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Notes

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Delegate list and biographies

Participants include invited experts from the UK, EU and abroad, as well as, industry representatives. Relevant experts from all the four MRC Boards will also be present; to enable the key messages to be translated to, and embedded in, the future MRC strategy. Delegate biographies and contact details are provided in the next section.

Dr Veronique Azuara, Professor Charles Bangham, Imperial College London Professor Stephan Beck, UCL Dr Jordana Bell, Kings College London Dr Adrian Bird, University of Edinburgh Dr Nicoletta Bobola, University of Manchester Professor Chas Bountra, SGC Dr Miguel Branco, Queen Mary University of London Dr Paul Brennan, SGC, University of Oxford Professor Robert Brown, Imperial College London Dr Nessa Carey, PraxisUnico Professor Cyrus Cooper, University of Southampton Professor John Danesh, University of Cambridge Professor George Davey-Smith, University of Bristol Dr Peter DiMaggio, Imperial College London Professor Anne Ferguson-Smith, University of Cambridge Professor Amanda Fisher, Imperial College London Dr John Greally, Albert Einstein College of Medicine, USA Dr Petra Hajkova, Imperial College London Dr John Hobcraft, University of York Dr Gavin Kelsey, Babraham Institute Professor Tony Kouzarides, Gurdon Institute Professor Karen Lillycrop, University of Southampton Professor David Lomas, UCL Professor John Marioni, EBI Professor Mark McCarthy, University of Oxford Professor Richard Meehan, University of Edinburgh Professor Jonathan Mill, King's College London Professor Eric Miska, Gurdon Institute Professor Adrian Moore, Riken Brain Science Institute, Japan Professor Michael O’Donovan, Cardiff University Professor Marco Oggioni, University of Leicester

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Professor Neil Pearce, LSHTM Professor Andrew Prentice, LSHTM Dr Rab Prinjha, GSK Professor Vardhman Rakyan, Queen Mary University of London Profesor Wolf Reik, Babraham Institute Professor Caroline Relton, University of Bristol Dr Louise Reynard, Newcastle University Professor Nilesh Samani, UniveUsity of Leicester Dr Matt Silver, LSHTM Professor Alison Sinclair, University of Sussex Professor Tim Spector, Kings College London Professor Henk Stunnenberg, Nijmagen NL Dr Martin Turner, Babraham Institute Dr Andrew Ward, University of Bath Dr Nigel Williams , Cardiff University Professor Roland Wolf, University of Dundee Dr Ian Wood, University of Leeds Dr Marina Zvartau-Hind, GSK

Research Council Staff

Dr Kate Adcock, MRC Dr Naomi Beaumont, ESRC Dr Rob Buckle, MRC Dr Georgina Drury, MRC Dr Neha Issar-Brown, MRC Dr Louisa Jenkin, BBSRC Dr Joe McNamara, MRC Dr Claire Newland, MRC Dr Jacqui Oakley, MRC Mrs Helen Page, MRC Dr Nathan Richardson, MRC Dr Des Walsh, MRC

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