The CEGX Blog

06.06.2017

Epigenetics Experts Interview - Dr Brock Christensen

BrockChristensen.png

Dr Christensen received his B.S. from the University of Wisconsin Madison in Medical Microbiology & Immunology in 2002, and his Ph.D. from the Program in Biological Sciences in Public Health at Harvard University in 2008. He trained as a postdoctoral research associate in molecular epidemiology of cancer at Brown University in the Department of Pathology and Laboratory Medicine. Dr Christensen joined the faculty at Dartmouth in 2011 as an Assistant Professor in the Departments of Community and Family Medicine in the Section of Biostatistics and Epidemiology, and Pharmacology and Toxicology. Dr Christensen has a long-standing interest in epigenetics and his lab’s latest research, published in Nature Communications, describes how the levels of the epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) correlate with prognosis for glioblastoma survival.

We caught up with Brock to find out more about his ground-breaking research and to hear his thoughts on what the future of epigenetics may hold.


Can you give us a brief background on your current research interests

Our research is focused on combining advances in molecular biology, genomics and bioinformatics with the powerful techniques of modern epidemiology and statistics to characterise epigenetic states in human health and disease. Our main interests are to understand the relation of DNA modifications with initiation and progression of cancer on the continuum from normal to pre-invasive and invasive tumours. An aim of our research is to uncover the relation of cytosine modifications with cancer risk factors, prognosis and response to treatment. 

What first ignited your interest in epigenetics? 

As a graduate student, I became interested in epigenetics when I learned about DNA methylation as a mechanism of tumour suppressor gene silencing that can be an alternative to inactivation by mutation. 

What are the main challenges associated with studying DNA modifications and epigenetics, and how are you approaching them?

Understanding the patterns and consequences to gene regulation of DNA modifications in human health and disease forms the basis for our research program. One of the main challenges we face in our work is knowing and adjusting for the potential influence of variation in cell type proportions across the subject specimens used to measure DNA methylation. At the same time, developing methods to overcome these challenges has opened new areas of research that leverage DNA methylation signatures of immune cell types to infer cell type proportions.

What excites you most about the future of epigenetics?

One recent exciting technological development is epigenome editing using CRISPR/dCas9 that has opened a new avenue for interrogating the role of cytosine modifications in chromatin structure and gene expression. If this technology becomes mainstream, it may be possible to more precisely define the mechanisms behind patterns of cytosine modifications and disease states. Another exciting prospect for the future of epigenetics is expansion into the clinical arena for use in biomarker panels.

What techniques do you use in your lab to study epigenetics?

We measure several different epigenetic states in our lab with a variety of techniques. Most often we use genome-scale array-based approaches to measure cytosine modifications, though we often follow up with candidate region approaches such as pyrosequencing. Depending on the cellular context, we may focus on 5-methylcytosine or aim to include measures of 5-hydroxymethylcytosine [using oxidative bisulfite sequencing] as well.

You mention 5hmC, how important do you think it is to study this DNA modification in addition to 5mC? 

It is essential to continue studying 5hmC, particularly resolved at the nucleotide level to better understand its fundamental properties in gene regulation. We are just being to scratch the surface about the unique role of 5hmC in gene regulation and disease. In a recent paper from our group we described the relation of 5hmC with prognosis in patients with glioblastoma and an interpretation of the data is the patients whose 5hmC patterns were furthest from those observed in normal cortex tissue had the poorest outcomes. To better realise the extent of 5hmC marks as potential biomarkers for disease onset and prognosis requires additional investigation in brain and other cancer types. It is exciting that genome scale profiling of 5hmC in both tumour and component normal tissues are beginning to emerge. 

How did you approach the analysis of your oxBS data?

Data analysis can be challenging if analysis and validation plans have not been determined prior to the experiment. Therefore, I ask that my trainees define their analytical steps before starting data analysis. To simultaneously and accurately estimate unmethylated cytosine, 5hmC and 5mC, we developed a novel algorithm called OxyBS. This method applies a maximum likelihood approach to the BS-oxBS array data and explicitly disallows proportion estimates that are not possible biologically. We use this approach in our 5hmC research and have made the software publicly available to the research community on github

What breakthroughs in methodologies do you think are needed to move the field of epigenetics forward?

I’d like to see a number of new breakthroughs to further enhance our knowledge of epigenetics, including increased understanding of RNA modifications, improved methods for cellular deconvolution, and targeted libraries for customised hypothesis-driven research. 

What papers have you read recently that you recommend to other epigenetics researchers?

I highly recommend the recent Cell Stem Cell paper by Farlik et al (2016). It is a nicely structured paper that revealed novel biology about hematopoietic stem cell differentiation by analysing single-cell DNA methylation, integrating diverse epigenomic data sets, and validating findings in an in vitro model. A comprehensive epigenetics paper with an elegant approach. 

What advice would you give any young researchers entering the field of epigenetics today?

Cross-train. Gain experience in both the biology and genome-scale data analysis techniques relevant to epigenetics. The next generation of scientists need to be conversant in both experimental and genome data science techniques.

Where can we find out more about your research?

Lucas Salas, a postdoc in our research group, recently presented some preliminary data on DNA methylation in breast milk at the AACR meeting in Washington.

I’m still trying to get to the Epigenomics of Common Diseases conference held in Cambridge, UK later this year [14-17 November 2017].

For more information about our research, people can visit our lab website.

Find out how CEGX can support your epigenetics biomarker development and research projects.

Author

Stephen Archibald