Congrats on a successful defense, Dr. Vockley

Chris Vockley just successfully defended his dissertation "Quantifying eukaryotic gene regulation in hormone response and human disease." Chris was co-advised by Tim Reddy and Brigid Hogan. As a graduate student, Chris developed several high-throughput approaches to study gene regulation in health and disease. He contributed to an impressive six published manuscripts including one lead-author publication. He is also lead author on a seventh manuscript that is currently in press. He was awarded an NIH F31 fellowship and several presentation awards at conferences and retreats. All within five years!

Chris is currently pursuing a postdoctoral and fellowship positions in genomics. Congrats Chris!

 Chris slaving away in the lab!

Chris slaving away in the lab!

Tony awarded NIH F31 Grant

Congratulations to Tony D'Ippolito for receiving a Ruth L. Kirschstein Predoctoral Individual National Research Service Award from the National Institutes of Health!

This grant will support the remainder of Tony's graduate studies with the Reddy lab. He will continue to explore how the glucocorticoid receptor (GR) represses gene transcription. It is well established that the GR can activate gene transcription, but how it represses transcription is less well understood. Tony has identified potential candidate genes that are activated by the GR, and likely result in downstream repression of genes. Tony is looking forward to investigating how GR represses transcription through secondary means.

An exciting summer internship opportunity for Tony...

Lab member Tony D’Ippolito will be interning in Research Triangle Park with BD Technologies’ single cell genomics group this summer. He expects to be involved with a project isolating circulating tumor cells in blood and determining their genomic profiles in order to develop novel diagnostic approaches. We’re excited for this opportunity for Tony, and for new insights and approaches he’ll bring back to his work and the Reddy lab.

 

Congrats To Karl on A successful defense!

The Reddy lab and many other colleagues are excited to celebrate Karl Guo's successful dissertation defense on Wednesday, March 23rd. 

His dissertation, 'Dissecting the Functional Impacts of Non-Coding Genetic Variation' is the result of five years of steady and original work in Duke's Program in Genetics and Genomics.

Tim Reddy served as his advisor, Dr. Ashley Chi as Chair, and Beth Hauser and
Greg Crawford rounded out his committee.

We all join in congratulating Dr. Guo and wishing him well as he moves forward. We trust his work will continue to contribute to better human health.

karl and tim

Reddy lab expands with new grants and projects

We are happy to welcome several new folks to the Reddy lab team.

Alex Barrera is here to support us with all things software-related. He'll help create durable and efficient programming. He'll also help develop visualization tools which are so critical to conveying our research and new findings to others.

Luke Bartelt is joining us on the molecular side of the lab supporting our bacterial culture work to create libraries of DNA.

We also have two new rotation graduate student who contribute to and learn from the lab for a few months as they decide on a focus for their graduate work. Welcome Jacob Hoj and Kyle Moran.

Read about all Reddy lab members, including postdocs, graduate students, and research analysts and lab technicians on our people page.

 

Reddy lab receives Duke Chancellor's Program Project Accelerator grant

Along with Duke collaborators Donald McDonnell, Jeff Marks, and Kris Wood, the Reddy lab has received a $100k grant from Duke's School of Medicine Chancellor's Program Project accelerator.  The grant will fund new research to develop and apply genomics studies to understanding the progression of breast cancer from its earliest roots to invasive tumors. We hope this new research will identify some of the earliest events that lead to tumor development in the breast.   

Nature article Highlights our contributions to the Roadmap Epigenomics Project

A new Nature article, Epigenetics: The genome unwrapped, focuses on the work of the Roadmap Epigenomics Project, a collaboration of more than 90 laboratories, including the Reddy, Gersbach, and Crawford labs. The project investigates what the article calls "one of the central mysteries of biology: how do cells with the same genetic instructions take on wildly different identities?" The article also discusses a recent publication, co-authored by our lab and the Gersbach lab, Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

Pulling the Strings of Our Genomic Puppetmasters

 DURHAM, N.C. -- Duke researchers have developed a new method to precisely control  when genes are turned on and active.

The new technology allows researchers to turn on specific gene promoters and enhancers -- pieces of the genome that control gene activity -- by chemically manipulating proteins that package DNA. This web of biomolecules that supports and controls gene activity is known as the epigenome.

The researchers say having the  ability to steer the epigenome will help them explore the roles that particular promoters and enhancers play in cell fate or the risk for genetic disease and it could provide  a new avenue for gene therapies and guiding stem cell differentiation.

The study appears online April 6 in Nature Biotechnology.

“The epigenome is everything associated with the genome other than the actual genetic sequence, and is just as important as our DNA in determining cell function in healthy and diseased conditions,” said Charles Gersbach, assistant professor of biomedical engineering at Duke. “That becomes immediately obvious when you consider that we have over 200 cell types, and yet the DNA in each is virtually the same. The epigenome determines which genes each cell activates and to what degree.”

This genetic puppetmaster consists of DNA packaging proteins called histones and a host of chemical modifications -- either to these histones or the DNA itself -- that help determine whether a gene is on or off.   

But Gersbach's team didn't have to modify the genes themselves to gain some control.

“Next to every gene is a DNA sequence called a promoter that controls its activity,” explained Gersbach. “But there’s also many other pieces of the genome called enhancers that aren’t next to any genes at all, and yet they play a critical role in influencing gene activity too.”  

Timothy Reddy, assistant professor of biostatistics and bioinformatics at Duke, has spent the better part of a decade mapping millions of these enhancers across the human genome. There has not, however, been a good way to find out exactly what each one does. An enhancer might affect a gene next door or several genes across the genome -- or maybe none at all.

To activate these enhancers and see what they do, Reddy thought perhaps he could chemically alter the histones at the enhancers to turn them on.

“There are already drugs that will affect enhancers across the whole genome, but that’s like scorching the earth,” said Reddy. “I wanted to develop tools to go in and modify very specific epigenetic marks in very specific places to find out what individual enhancers are doing.”

Reddy found that specificity by teaming up with Gersbach, his neighbor within Duke’s Center for Genomic and Computational Biology, who specializes in a gene-targeting system called CRISPR. Originally discovered as a natural antiviral system in bacteria, researchers have hijacked the system over the past few years and are now using it to cut and paste DNA sequences in the human genome. 

For this epigenome editing application, Gersbach silenced the DNA-cutting mechanism of CRISPR and used it solely as a targeting system to deliver an enzyme (acetyltransferase) to specific promoters and enhancers.

“It’s like we use CRISPR to find a genetic address so that we can alter the DNA’s packaging at that specific site,” said Reddy. 

Gersbach and Reddy put their artificial epigenetic agent to the test by targeting a few well-studied gene promoters and enhancers. While these histone modifications have long been associated with gene activity, it wasn’t clear if they were enough to turn genes on. And though Gersbach and Reddy had previously used other technologies to activate gene promoters, they had not successfully activated enhancers. 

To the duo’s great surprise, not only did the agent activate the gene promoters, it turned on the adjacent genes better than their previous methods. Equally surprising was that it worked on enhancers as well: they could turn on a gene -- or even families of genes -- by targeting enhancers at distant locations in the genome -- something that their previous gene activators could not do.

But the real excitement from their results is an emerging ability to probe millions of potential enhancers in a way never before possible.

“Some genetic diseases are straightforward -- if you have a mutation within a particular gene, then you have the disease,” said Isaac Hilton, postdoctoral fellow in the Gersbach Lab and first author of the study. “But many diseases, like cancer, cardiovascular disease or neurodegenerative conditions, have a much more complex genetic component. Many different variations in the genome sequence can affect your risk of disease, and this genetic variation can occur in these enhancers that Tim has identified, where they can change the levels of gene expression. With this technology, we can explore what exactly it is that they’re doing and how it relates to disease or response to drug therapies.” 

Gersbach added, “Not only can you start to answer those questions, but you might be able to use this technique for gene therapy to activate genes that have been abnormally silenced or to control the paths that stem cells take toward becoming different types of cells. These are all directions we will be pursuing in the future.”

This work was supported by the National Institutes of Health (R01DA036865, U01HG007900, DP2OD008586, P30AR066527) and the National Science Foundation (CBET-1151035).

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"Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers," Isaac B Hilton, Anthony M D’Ippolito, Christopher M Vockley, Pratiksha I. Thakore, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach. Nature Biotechnology, April 6, 2015. DOI: 10.1038/nbt.3199

 

Radio In Vivo interview available online

Ernie Hood's show Radio In Vivo featured our work to understand regulatory mechanisms contributing to human disease. The conversation ranged from genome editing to correct disease mutations, our work on the genomics of gene regulation project, and the recent discovery of a novel human hexokinase. The full interview is available online on the Radio In Vivo website:

http://radioinvivo.org/2015/03/11/gene-regulation/

Genome editing to correct muscular dystrophy paper published

Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.

Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA

The CRISPR/Cas9 genome-editing platform is a promising technology to correct the genetic basis of hereditary diseases. The versatility, efficiency and multiplexing capabilities of the CRISPR/Cas9 system enable a variety of otherwise challenging gene correction strategies. Here, we use the CRISPR/Cas9 system to restore the expression of the dystrophin gene in cells carrying dystrophin mutations that cause Duchenne muscular dystrophy (DMD). We design single or multiplexed sgRNAs to restore the dystrophin reading frame by targeting the mutational hotspot at exons 45-55 and introducing shifts within exons or deleting one or more exons. Following gene editing in DMD patient myoblasts, dystrophin expression is restored in vitro. Human dystrophin is also detected in vivo after transplantation of genetically corrected patient cells into immunodeficient mice. Importantly, the unique multiplex gene-editing capabilities of the CRISPR/Cas9 system facilitate the generation of a single large deletion that can correct up to 62% of DMD mutations.

Link to full article

Discovery of novel hexokinase published in Nature Communications

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1

Cong (Karl) Guo, Anton E. Ludvik, Michelle E. Arlotto, M. Geoffrey Hayes, Loren L. Armstrong, Denise M. Scholtens, Christopher D. Brown, Christopher B. Newgard, Thomas C. Becker, Brian T. Layden, William L. Lowe  & Timothy E. Reddy

Maternal glucose levels during pregnancy impact the developing fetus, affecting metabolic health early and later in life. Both genetic and environmental factors influence maternal metabolism, but little is known about the genetic mechanisms that alter glucose metabolism during pregnancy. Here we report that haplotypes previously associated with gestational hyperglycemia in the third trimester disrupt regulatory element activity and reduce expression of the nearby HKDC1 gene. We further find that experimentally reducing or increasing HKDC1 expression reduces or increases hexokinase activity, respectively, in multiple cellular models; and that purified HKDC1 protein has hexokinase activity in vitro. Together, these results suggest a novel mechanism of gestational glucose regulation in which the effects of genetic variants in multiple regulatory elements alter glucose homeostasis by coordinately reducing expression of the novel hexokinase HKDC1.

Link to the full article.

Genomics of Gene Regulation Grant funded by the NHGRI

Our genomes encode the blueprint for life. Buried in the genome are both the building blocks ("genes") and instructions on when and where each gene is to be used. There is now strong evidence that changing when and where genes are used is both a major component of evolution, and also can be a major contributor to disease risk.

The Duke/Princeton Genomics of Gene Regulation project will seek to reveal new insights into how genes are regulated by focusing on a single and well-controlled system, the glucocorticoid response. The glucocorticoid response has dual roles in the human body, controlling both metabolism and the immune system. It is one of the reasons you get hungry at the same time every day, and also the way your body prioritizes certain functions over others in times of extreme stress. For example, glucocorticoids act to reduce inflammation if you are being chased by a tiger. This makes sense, as you don't want sore knees to be the reason the tiger was able to catch and eat you. It is this anti-inflammatory activity of glucocorticoids (think: cortisone cream, prednisone) that also makes them among the most widely used drugs today.

The major goal of this project is to figure out all of the part of the genome that determine how genes are used in response to glucocorticoids; and then to figure out how all of those pieces talk to each other. In the end, we will use this information to see if we can change the way cells respond to these drugs. In other words, can we make a modified glucocorticoid response that is better at reducing inflammation, but doesn't impact metabolism quite so much?

This project is one of five projects funded simultaneously by the National Human Genome Research Institute (NHGRI) with the common goal of learning how genes are turned on and off. You can read all about these projects at the official NHGRI press release. We are extremely excited to be starting in on this project, and look for our data hitting the public repositories in the coming months!

This project leverages synergy between investigators at Duke (Reddy, Crawford, Gersbach, and Hartemink) and Princeton (Engelhardt). The investigative team is highly multidisciplinary, spanning several schools and departments within Duke, and synergy between the investigators will allow for close connections between generating data, building and refining network models, and ultimately reprogramming the glucocorticoid response.

Osteoarthritis study with Farsh Guilak and Charlie Gersbach to be funded by NIAMS

Osteoarthritis (OA) is a major cause of disability, and the risk for developing OA is enhanced by the presence of particular genetic variants. This R21 project will examine how genetic variation is linked to cartilage loss during OA by generating cartilage tissue from stem cells that have been modified to contain the gene variant of interest. The eventual goal is to develop drugs that are specifically matched to patients based on their genetic profile. 

 
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"High risk/high impact" seed grant to study gut colonization with John Rawls

The Duke Institute for Genome Sciences and Policy (IGSP) and the Duke Center for the Genomics of Microbial Systems (GeMS) awarded a seed grant to fund a new collaboration with the Rawls lab to study how bacteria have evolved to live inside our intestines. Gut bacteria play a fundamental role in our ability to digest food and resist infection. Many now think that being able to manipulate the gut microbiome may have therapeutic benefits. To better understand how bacteria thrive in the gut, this multidisciplinary effort combines new approaches for culturing symbiotic bacteria, high-throughput genomics, and computational techniques. As a result of this effort, we hope to gain better control over the gut bacteria, which is a step towards our long term goal of manipulating those communities for therapeutic benefit.

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Cell-type specific TF binding site paper published in Molecular Cell

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

Jason Gertz, Daniel Savic, Katherine E. Varley, E. Christopher Partridge, Alexias Safi, Preti Jain, Gregory M. Cooper, Timothy E. Reddy, Gregory E. Crawford, Richard M. Myers 

Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms that govern cell-type-specific transcription factor binding, we used an integrative approach to study estrogen receptor α (ER). We found that ER exhibits two distinct modes of binding. Shared sites, bound in multiple cell types, are characterized by high-affinity estrogen response elements (EREs), inaccessible chromatin, and a lack of DNA methylation, while cell-specific sites are characterized by a lack of EREs, co-occurrence with other transcription factors, and cell-type-specific chromatin accessibility and DNA methylation. These observations enabled accurate quantitative models of ER binding that suggest tethering of ER to one-third of cell-specific sites. The distinct properties of cell-specific binding were also observed with glucocorticoid receptor and for ER in primary mouse tissues, representing an elegant genomic encoding scheme for generating cell-type-specific gene regulation.

Link to full text (opens in new window).

Source: http://www.sciencedirect.com/science/artic...