NIDDK Workshop: Towards a Functional Understanding of the Diabetic Genome 2018

Recently, members of the T2D Knowledge Portal team were fortunate to participate in a fascinating workshop hosted by the NIDDK: Towards a Functional Understanding of the Diabetic Genome. Speakers highlighted the diversity of ongoing research projects that aim to translate disease-associated variants into functional insights in type 2 diabetes.

The workshop featured presentations on multiple data types that can provide clues about the mechanisms by which sequence variants affect T2D risk. Many of these offer insights into transcriptional regulation: epigenomic chromatin modifications; tissue-specific RNA levels; eQTLs; transcription factor binding sites; long-range interactions between chromosomes that bring promoters and enhancers into proximity; and regulatory pathways. Others focus on downstream processes such as protein-protein interactions, biochemical pathways, and metabolomics.

It will be crucial to integrate all of these data types with genetic association data in order to get a complete picture of how particular genomic regions influence T2D biology, and at the T2DKP we are working towards incorporating as many of these data types as possible.

Although the presentations in this workshop were diverse, some common themes were evident. One was that although the insulin-secreting beta cells in pancreatic islets are hugely significant to T2D, and most T2D risk variants influence insulin secretion, current research projects are confirming and underscoring the importance of other tissues. Fat, liver, skeletal muscle (which comprises 40% of human body weight), and brain are all intimately involved in the development of T2D.

Another common theme for ongoing T2D research is that things may often be much more complicated than they first appear. A single genomic region associated with T2D risk may harbor multiple independent causal variants, each potentially having different regulatory effects, possibly affecting different tissues, and causing varied phenotypic consequences. Even if these variants alter a protein-coding sequence, they may not act through their effects on that sequence. These genetically complicated regions, such as those elucidated in FTO or TCF7L2, may be more common than we previously thought.

A third overall conclusion from the workshop is that model organism research can accelerate the investigation of candidate genes. The short life cycles of Drosophila and zebrafish, and the versatile genetic tools available for these systems, allow for rapid and systematic interrogation of gene function. Zebrafish glucose and lipid metabolism have much in common with those processes in human cells, and with their transparent bodies, zebrafish literally give us a window into pancreatic development.  In addition to being a well-developed model system, the mouse offers much greater genetic diversity than human, with about 40 million SNPs in the mouse genome as compared to about 10 million in the human genome.

At the T2DKP, efforts to integrate many of these data types are in progress, and integration of others is being planned. We continue to work towards making the T2DKP a comprehensive resource for the T2D research community, to help accelerate the translation of variant associations into knowledge about disease mechanisms and identification of potential drug targets.

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Many of the presentations at the workshop featured web resources of potential interest to T2D researchers, listed below. The T2DKP is connected with the first, the Diabetes Epigenome Atlas. We are interested providing better connections between the T2DKP and other relevant resources. If you would be particularly interested in seeing links from the T2DKP to one of the resources below, or if you know of a resource that would be informative, we would love to hear your suggestions!

• Diabetes Epigenome Atlas (formerly T2DREAM): provides genomic and epigenomic data relevant to T2D

• Capture HiC Plotter (CHiCP): web application for visually integrating human population genetic data with promoter capture Hi-C data

• HaploReg: explore annotations of the noncoding genome at variants on haplotype blocks

• ExPecto: tissue-specific gene expression effect predictions for human mutations

• DeepSea: predict the cell type-specific epigenetic state of a sequence and the chromatin effects of sequence variants

• GeNets: unified web platform for network-based analyses of genetic data

• Attie Lab Diabetes Database: gene expression and diabetes-related clinical phenotypes in mouse

• DCell: a deep neural network simulating cell structure and function

Bringing the power of epigenomics to the T2DKP

Until recently, all of the results displayed in the Type 2 Diabetes Knowledge Portal (T2DKP) were based on genetic association data: the significance with which variants, or SNPs, occur in people’s genomes in conjunction with a disease or trait.

This information is hugely important for pinpointing regions of the genome that contribute to disease risk. It is now relatively straightforward to identify these regions, but it is still a large challenge to discover the mechanisms by which they act—especially for variants that are outside of coding sequences, without an obvious effect on the sequence of a particular protein. These non-coding variants, the most commonly seen in genetic association studies, are likely to affect tissue-specific gene regulation that could potentially be important to the disease process.

How can we overcome this challenge to find clues about the effects of these non-coding variants? Epigenomic data to the rescue!

Dr. Kyle Gaulton of the University of California at San Diego researches the transcriptional regulatory networks involved in type 2 diabetes by using epigenomic data in concert with genetic association data. He explains, "Regulatory elements control gene production and function, and are often highly specialized across cell and tissues and located far away from the genes they regulate. Molecular epigenomic hallmarks of gene regulation such as histone and DNA modifications, nucleosome depletion, chromatin conformation and DNA-protein interactions can pinpoint the precise genomic locations of regulatory elements. High-resolution epigenome maps of regulatory elements in pancreatic islets, liver, muscle, adipose and many other human tissues can then enable annotation of non-coding genetic variants and their potential gene regulatory functions. These maps are thus an invaluable component of determining how type 2 diabetes associated non-coding variants influence disease pathogenesis."

A recent paper from Dr. Gaulton and colleagues (Gaulton, KJ, et al. (2015) Nat Genet. 47:1415) illustrates the power of integrating these two data types. By combining information on transcription factor binding sites and tissue-specific chromatin states with genetic fine-mapping of T2D-associated loci, the authors elicidated the molecular mechanisms behind the effects of some T2D-associated variants, uncovering the role of the FOXA2 transcription factor in glucose homeostasis in T2D-relevant tissues.

Now, the T2DKP facilitates this type of analysis by presenting both genetic association and epigenomic data on Gene and Variant pages. We described the display of epigenomic data on Variant pages in a recent blog post. On Gene pages, epigenomic data are integrated into the LocusZoom display.

Locations of variants associated with T2D and chromatin states in pancreatic islets, across the SLC30A8 gene (partial view)

Below the plot of variant associations, chromatin states are displayed by default for the major T2D-relevant tissues. Using the pull-down menu at the top of the plot, you can choose from a diverse set to display other tissues and cell types. All of the details on how to use this interactive plot are included in our Gene Page guide.

This is only the first step for epigenomic data in the T2DKP. In the future, we plan to include additional types of epigenomic data that indicate chromatin accessibility and conformation. We will also add functionality; for example, for any given variant, you will be able to search for the tissues in which enhancer regions overlap the location of that variant.

As we actively develop this aspect of the T2DKP, we welcome your suggestions!

New clues about variant effects: epigenomic data now available in the Portal

The T2D Knowledge Portal aggregates a wealth of genetic association data identifying variants that are associated with type 2 diabetes and related traits. These identifications show us that something within these genomic regions contributes to the risk of developing T2D. That’s an important first step, but in order to make use of this information to develop new T2D treatments, we need to figure out exactly what is causing the effect and how it relates to the disease process.

If a variant lies within a gene and changes a protein sequence, it can be relatively straightforward to formulate testable hypotheses about its effects. But most of the variants that are significantly associated with T2D—and with complex diseases in general—lie within noncoding regions of the genome and are likely to affect regulation of genes that could be far removed from the chromosomal position of the variant. It can be difficult to find clues about which genes are affected by these distant, noncoding changes, but now, we present a new type of data in the T2DKP that can help address this challenge.

The pattern of epigenetic modifications within a genomic region can provide important clues about its regulatory role. The distribution of these position-specific and tissue-specific marks—for example, covalent modifications of the histone proteins that package DNA—is characteristic of elements such as enhancers or transcription start sites. The Roadmap Epigenomics Consortium has developed methods for detecting these modifications genome-wide (hence the term “epigenomics”) and integrating their positional data, using the ChromHMM algorithm, to categorize genomic regions into “chromatin states”. The presence of these states in a given genomic region in different tissue types can give hints about whether that region might be involved in regulation of specific genes or pathways.

Now, you can view the tissue-specific chromatin states spanning the position of each variant on Variant pages within the Portal. We have incorporated epigenomic data from a study (Varshney et al., 2017) in which the locations of 13 distinct chromatin states were determined across a diverse set of cell lines and tissues, including pancreatic islets. The new “Epigenomic annotations” section of each Variant page (see an example) presents information about chromatin states in three different ways.

1. An interactive table listing chromatin states in this region, the tissue or cell line in which they were observed, and their genomic coordinates. Filter the table by chromatin state or by tissue to find states of particular interest.

2. A matrix displaying chromatin states by tissue type. This graphic gives a quick indication of chromatin states that are present in this region, across the whole panel of tissues.

3. A graphic showing the positions of chromatin states relative to the position of the variant.

These new features represent only the first phase of incorporating this new data type into the Portal. In the future, we will be adding more of these data along with more versatile interfaces for exploring them. Please check out our new epigenomic annotations and send us your feedback!