Stories of IHEC

Christoph Bock

What are your major research activities/interests?

Our goal is to understand the epigenetic basis of cancer, and to develop epigenetic approaches to personalized therapy. Toward this goal, we pursue three lines of research: (i) to develop high-throughput technologies for cancer epigenome analysis (read more); (ii) to establish the diagnostic utility of DNA methylation patterns as epigenetic biomarkers (read more); and (iii) to study the anticancer effects of epigenetic drugs, with the perspective of enabling rational design of patient-specific combination therapies (read more).

Why do you find epigenomics such an interesting field of research?

Recent research has shown that all cancers exhibit epigenetic alterations. Because the epigenome is so closely linked to the regulation of cell state, this important finding suggests that cancer should be regarded as a disease of messed-up cell states. If this is true, we may be able to develop entirely new approaches to cancer therapy that are aimed at stabilizing the epigenomes of precancerous cells or to try and reprogram the epigenomes of those cells that have already made the transition to cancer.

What is the most exciting thing about being a part of IHEC?

The work of my lab is inherently high-throughput, as we combine experimental and computational methods to dissect the epigenetic basis of cancer. We very much profit from (and contribute to) the technology development and standardization efforts that are being performed in IHEC. With all of IHEC’s ongoing projects, a global map of the human epigenome is now on the horizon, which will for the first time allow us to systematically navigate the epigenetic landscape in health and disease.

How do you see the future of epigenomics research unfolding/ evolving?

Large-scale epigenome mapping continues to gain momentum as biomedical researchers are increasingly realizing the many ways in which the epigenome contributes to diseases such as cancer and autoimmune disorders, and potentially to many more types of diseases. Furthermore, new research topics are already emerging on the horizon, such as the development of new epigenetic drugs, personalized cancer therapies, targeted epigenome editing and epigenetic cancer prevention.

Christoph-Bock
Project:

BLUEPRINT

Institution:

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
Max Planck Institute for Informatics, Saarbrücken, Germany

Position:

Principal Investigator (CeMM)
Guest Professor (MedUniWien)
Adjunct Group Leader (MPI-INF)

Field of Research:

Epigenomics, Bioinformatics and Personalized Cancer Therapy

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Iñaki Martin-Subero

What are your major research activities/ interests?

The main activity of our laboratory is to characterize the epigenome of normal and neoplastic lymphoid cells. In particular, we are characterizing the epigenome of B cells at different maturation stages and of various B-cell neoplasias. Our main goals are: a) to better understand the mechanisms of cell differentiation, b) to obtain new insights into the molecular mechanisms underlying cancer, and c) to identify epigenetic biomarkers leading to a better diagnosis and prognosis of patients suffering with lymphoid malignancies.

Why do you find epigenomics such an interesting field of research?

I did my PhD in genetics of lymphoid malignancies. During my postdoctoral training in Kiel (Germany) I became strongly interested in epigenomics and I took a firm decision of becoming an epigeneticist. Studying the dynamic epigenome offers an unique opportunity to understand how the genome communicate with its surroundings, both during physiological and pathological conditions. Epigenomics is very much interdisciplinary and is involved multiple aspects of life such as development and cell differentiation, tumoral and non-tumoral diseases, aging, psychology, ecology and evolution.

What is the most exciting thing about being a part of IHEC?

Due to the dynamic nature of the epigenome, IHEC is a very challenging project. At the personal level, being part of this international endeavor is an honor. Professionally, it offers the opportunity interact with the world experts in the field, which is a privilege and a continuous source of learning and inspiration. The research made in the context of IHEC is at the edge of our knowledge. Analyzing and interpreting epigenomic data generated at a genome-wide scale requires a high dose of creative thinking. Exciting indeed!

How do you see the future of epigenomics research unfolding/ evolving?

I think that the future of the discipline will be marked both by new technical approaches and by new ways of thinking about the data. For instance, new sequencing technologies, single cell whole-epigenome analysis, techniques to study whole-genome interactions with high resolution and perhaps also techniques for detecting epigenomic marks in vivo. We will also have to define the precise role(s) of each epigenetic mark and how they influence each other. Furthermore, analyzing the mechanisms of epigenetic inheritance and determining which genomic regions are susceptible to changes mediated by life style factors may also be relevant for the future.

Inaki-Martin
Project:

BLUEPRINT

Institution:

University of Barcelona
Institut d'investigacions Biomèdiques August Pi i Sunyer

Position:

Ramon y Cajal tenure track researcher

Field of Research:

Epigenomics of Normal and Neoplastic Lymphoid Cells

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Annaick Carles

What are your major research activities/ interests?

I am operating a next-generation sequencing data quality control analysis pipeline dedicated to genome wide DNA methylation data. It generates integrated genome browse tracks for visualization and further data analysis. DNA methylation is an epigenetic mark known to be deregulated across different types of cancer. My research aims to participate in the understanding of the epigenetic regulation of gene expression in normal development and human diseases.

Why do you find epigenomics such an interesting field of research?

Epigenomics is crucial to high throughput biology. Management and analysis of those large volumes of data pose considerable computational challenges. For example, the new coming oxidative bisulfite sequencing technology that can distinguish between methylation and hydroxymethylation of DNA cytosine will require specific computational development interesting to me. Analyzing these epigenomics data is exploring a fascinating new layer of gene expression regulation.

What is the most exciting thing about being a part of IHEC?

Being part of IHEC offers me the great opportunity to work in collaboration with leading edge research groups and creates a very stimulating discussion environment. The high quality reference epigenomes generated with state-of-the-art next-generation sequencing technologies as part of IHEC is a huge and very exciting source of knowledge.

How do you see the future of epigenomics research unfolding/ evolving?

Data quality control and uniformly processed data are very important for biological interpretation of the data, extraction of epigenetics signatures and future discoveries. Epigenomics research plays an essential role in the understanding of human disease susceptibility and is a great promise for prevention, detection and therapy of human diseases associated to epigenetics modifications. In particular the new area of single cell epigenetics will likely have important significance in biomedical research. 

Annaick-Carles
Name:

Annaick Carles

Institution:

University of British Columbia

Position:

Computational Biologist

Field of Research:

Bioinformatics, Next-Generation Sequencing Data Management and Quality Control Analysis

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Joost Martens

What are your major research activities/ interests?    

My research focuses on uncovering the molecular structures that underlie transcriptional and epigenetic regulation during development and disease. Using  state-of-the-art technologies I aim to deepen our understanding on transcriptional regulation and to unravel the molecular complexity of the epigenome during normal and perturbed blood development.

Why do you find epigenomics such an interesting field of research?

The epigenome  can explain how to use the information stored in the DNA to develop into different cell types and provides a frame that correlates a person’s actions, the environmental input,  with its future life. As such, knowledge on the packaging of DNA during normal development as well as in disease  has great promise for the development of drugs targeting these packaging mechanism in disease therapy.

What is the most exciting thing about being a part of IHEC?

IHEC creates a framework that offers its participants to act at the forefront of epigenomic research in the world. It facilitates interaction with leading scientists in the field of epigenetics/epigenomics world-wide and allows access to state-of-the-art methodologies and analysis.

How do you see the future of epigenomics research unfolding/ evolving?

Abnormal epigenetic regulation is a feature of most, if not all  diseases.  Knowledge on disease specific  epigenetic alterations  will improve patient stratification and guide choices of existing treatments as well as trigger the development of new therapeutic approaches for intervention. In the long run it might even have the potential to be used for monitoring disease risk, allowing to treat patients preventatively before disease arises.

Joost-Martens
Project:

BLUEPRINT

Institution:

Radboud University Nijmegen

Position:

Assistant professor

Field of Research:

Transcriptional and Epigenetic Regulation in Normal and Aberrant Hematopoiesis

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Alexander Meissner

What are your major research activities/ interests?    

We use genomic tools to study developmental and stem cell biology with a particular interest in the role of epigenetic regulation. The term epigenetic refers to stable modifications of the chromatin and DNA that do not alter the primary nucleotide sequence. We have pioneered next generation sequencing technologies to study the epigenome in normal development and disease.

Why do you find epigenomics such an interesting field of research?

The global epigenetic makeup of a cell is a powerful indicator of its developmental state and potential. Over the past years we have seen that during stem cell differentiation and reprogramming epigenome data provide substantially more insights about the regulatory dynamics than gene expression.

What is the most exciting thing about being a part of IHEC?

The epigenomic space is vast and it takes a significant effort to capture a reasonable fraction of it. Only a well-organized and concerted effort can accomplish this. The maximize the general usability of the data it is important to use comparable standards and procedures.

How do you see the future of epigenomics research unfolding/ evolving?

A major advance for the field has been increases in sequencing throughput. In parallel new technical approaches have further refined the ways of mapping epigenetic modifications. Both will continue to improve, but likely a major accelerator for biomedical research will be the widespread and routine utilization of the publically available data.

Alexander-Meissner
Project:

NIH Roadmap

Institution:

Harvard University/Broad Institute

Position:

Associate Professor

Field of Research:

Stem Cells and Epigenomics

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Chiba Hatsune

What are your major research activities/ interests?    

I'm conducting research on whole genome DNA methylation of human germ cells and preimplantation embryos. I am interested in genomic imprinting in humans, and hope to reveal germ cell specific DNA methylation during gametogenesis. I am also researching DNA methylation and exome in sperm from oligospermic patients. I would like to elucidate differences of DNA methylation pattern between normal sperm and oligospermia.

Why do you find epigenomics such an interesting field of research?

When I was an undergraduate student in 2005, I participated in a workshop about epigenetics at the National Institute of Genetics in Mishima, Japan. In that workshop, many people and groups presented leading edge and interesting topics. I was impressed that epigenetic mechanisms influence all biological phenomenon and we inherit not only genetic information but also epigenetic information on imprinted genes from our parents.

What is the most exciting thing about being a part of IHEC?

I am able to obtain a lot of brand new information about epigenetics. I also have many opportunities to partake in active discussion with excellent scientists.

How do you see the future of epigenomics research unfolding/ evolving?

Improvements of next generation sequencers and methodology of chromatin immunoprecipitation will permit epigenetic analysis on a small scale. I hope to reveal a histone modification map of mammalian oocytes and define standard epigenomic profiles at the single-cell level in the future, so that we can elucidate epigenetic dynamics in early embryogenesis and gametogenesis. These epigenomics researches will also contribute to the innovative progression of infertility treatments in the future.

Chiba-Hatsune
Project:

CREST/IHEC

Institution:

Tohoku University

Position:

Research Associate

Field of Research:

Genomic Imprinting, Gametogenesis, Early Development

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Jacob M. Hooker

What are your major research activities/ interests?

My research group uses molecular imaging (largely positron emission tomography) to study the function and dysfunction chemical interactions in the human body.  Our work tends to focus on neuroscience applications of new imaging technologies that enable us to visual the brain’s response to a stimulus, whether it is a drug, the environment, or a behavior.   For example (in collaboration with clinicians) we are studying neurochemistry and neurobiology related to schizophrenia, ALS, pain, and more recently autism.  What is unique about my lab is our ability to carry a concept from basic chemistry all the way through human neuroimaging in a short amount of time. 

Why do you find epigenomics such an interesting field of research?

I am fascinated by the adaptive responses, good and bad, of the human body.  In medicine we often focus on the causes of an endophenotype or perhaps biomarkers that might correlate with an endophenotype.  Epigenomics (at least for my lab) is a new way of thinking about medicine that gives us some hope that we can ‘rescue’ biological dysfunction closer to the genes contributing to disease that we are, for lack of a better phrase and for the moment, stuck with.  I am excited to develop tools that provide a new way to literally ‘look at’ processes that control gene expression.  We have started by developing tools to image chromatin-modifying machinery, but the concepts we are developing can be expanded to other areas within epigenomics.

What is the most exciting thing about being a part of IHEC?

Being part of IHEC is exciting because its exposes me to brilliant people in the field who I can learn from, dream with and collaborate. 

How do you see the future of epigenomics research unfolding/ evolving?

My hope is that epigenomics research leads to new and creative ways of thinking about disease and ultimately treating it.  Once we determine what ‘normal’ epigenomics means (if there is such a thing) then we can begin developing ways to modulate and control dysfunction.  The extent to which our epigenome is flexible and how much that flexibility allows us to change disease outcomes are yet to be seen.

Jacob-Hooker
Project:

NIH Roadmap

Institution:

Martinos Center for Biomedical Imaging, MGH
Harvard Medical School

Position:

Director of Radiochemistry
Assistant Professor

Field of Research:

Molecular Imaging, Neuroscience, Chemistry

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Genta Nagae

What are your major research activities/ interests?

My research focuses on genome-wide profiling of DNA methylation for a variety of human cell types. During appropriate cellular differentiation, programs are required for each cell to control the correct gene sets at the right time. I am particularly interested in how to accurately change and faithfully keep this program. These questions are linked with my other interests, how this regulatory network is disrupted and results in the initiation and progression of human diseases.

Why do you find epigenomics such an interesting field of research?

The quality of epigenomic profiles depends on the genomic technologies. When I was a graduate student, the breakthrough for genome-wide mapping of DNA methylation and histone modification was reported. And now, the technologies have greatly improved upto one-base or one –chromosome resolution. So, it is time to clarify the epigenetic landscapes of human cells, which are the fundamental information to understand cell fate commitment and lineage specification during development.

What is the most exciting thing about being a part of IHEC?

The more we analyzed the epigenomes, the more we realized the complicated and elaborate system that regulates gene expression networks. We are now able to share the moment to look at this human epigenome milestone as the first witnesses. When we discuss face-to-face with the experts in IHEC is the most exciting time for me.

How do you see the future of epigenomics research unfolding/ evolving?

Completing the human epigenome reference map is not only the first goal but also the start line for the next step. By this reference map, we will find lots of epigenetic marks significantly linked to disease. Overwriting the epigenetic marks on the specific loci is really challenging research at the moment. However, it has great potential to cure many diseases due to epigenetic aberrations, in the future.

Genta-Nagae
Project:

CREST/IHEC

Institution:

Research Center for Advanced Science and Technologies, the University of Tokyo

Position:

Assistant Professor

Field of Research:

Epigenomics, DNA methylation, Cellular Differentiation

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Fumihito Miura

What are your major research activities/ interests?

I studied chemistry as an undergraduate and genomic science at graduate school. I also developed informatics skills during my past jobs. Using this knowledge and skills, I would like to develop some key technologies that can bring great advances in the field of in epigenomics. Recently, we have developed a highly sensitive technique for template preparation of DNA methylome analysis, and this technique is used by some IHEC researchers. Now we are working on developing efficient technologies to detect 5-hydroxymethyl cytosine.

Why do you find epigenomics such an interesting field of research?

Epigenomics research sometimes requires knowledge not only in biology but also several related fields of science such as chemistry, informatics and engineering. Many papers produced by authors of different backgrounds are being seen in this field. I think there is still a lot of room for researchers to become pioneers in one of the areas of epigenomics using their expertise. In addition to scientific interest, this makes epigenomics an exciting field of science.

What is the most exciting thing about being a part of IHEC?

Since IHEC activity is cooperatively executed by many researchers, I can have several great opportunities to meet many front-end researchers in regular meetings. It is so exciting for me because I can feel the emotions and ideas of individual researchers very closely.

How do you see the future of epigenomics research unfolding/ evolving?

It is difficult for anyone to say definitely where epigenomics research will go. However, it is certain that, with the unprecedented comprehensive epigenetic data produced by projects like IHEC, we will be able to understand many biological phenomena more deeply and clearly. It is also certain that epigenomics research produces more and more sequencing data, and shortage of free storage space in our hard drives may soon occur.

Fumihito-Miura
Project:

CREST/IHEC

Institution:

Graduate School of Science, The University of Tokyo

Position:

Project Assistant Professor

Field of Research:

Genome Science, Genome Technology

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Cydney Nielsen

What are your major research activities/ interests?

I create software to visualize and analyze biological datasets such as those produced by the IHEC. Visualization is a powerful aid to data interpretation. For example, a street map provides an immediate overview of an area, which would be difficult to obtain from a text table of street addresses or GPS coordinates. IHEC produces a vast data resource and visualization will play a key role in helping to translate these datasets into biological insights.

Why do you find epigenomics such an interesting field of research?

The cells in your body generally all share the same DNA sequence, and yet they display a vast array of morphologies and functions. Understanding how the same genetic material is interpreted in diverse cell types is a fascinating biological question that lies at the heart of epigenomics. Answering it would not only improve our understanding of basic cell function, but would likely inform innovative new treatments of disease.

What is the most exciting thing about being a part of IHEC?

A large-scale international effort like IHEC creates research opportunities not imaginable in any individual laboratory. The wealth of data that will result from such a global combined effort is most exciting to me and I look forward to being a part of making this data resource accessible and interpretable.

How do you see the future of epigenomics research unfolding/ evolving?

Epigenomics holds great potential to improve our understanding of diverse diseases. As our basic understanding of the epigenetic patterning in normal cells increases, so will our ability to identify, interpret, and therapeutically target epigenetic factors in disease.

Cydney-Nielsen
Name:

Cydney Nielsen

Institution:

University of British Columbia and British Columbia Cancer Agency

Position:

Research Associate

Field of Research:

Computational Biology and Data Visualization

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Wei Chen

What are your major research activities/ interests?

Using functional and medical genomics approaches, we aim to understand the molecular mechanisms underlying differental layers of gene regulation and their important roles in human diseases. 

Why do you find epigenomics such an interesting field of research?

I find epigenomics research particularly interesting because 1) it can explain largely how gene expression could be regulated at the transcriptonal level; 2) in contrast to genetic defect, epigenetic deregulation is likely to be reversibe, therefore the research in this field might more easily lead to therapeutic intervention. 

What is the most exciting thing about being a part of IHEC?

In IHEC, groups with the expertise in different areas, such as technology/method development, computational biology, clinical science and etc, work together, which is essential for the success of such integrative study.

How do you see the future of epigenomics research unfolding/ evolving?

In the future, epigenomics research will be more integrated with the research into other layers of gene regulation, such as cell metabolism, cell signalling and post-transcriptional regulation, only then we will grasp a full picture about gene regulation in living organisms. 

Wei-Chen
Name:

Wei Chen

Institution:

Max-Delbrueck-Center for Molecular Medicine

Position:

Group Leader

Field of Research:

Functional and Medical Genomics

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