Executive Summary

Epigenetic regulation of gene transcription has emerged as the key biological determinant of cellular differentiation and has been demonstrated to play significant pathogenic roles in a number of human diseases. This regulation is mediated by selective, enzyme-catalyzed, covalent modification of DNA and of proteins (especially histones) that control the conformational transition between transcriptionally active and inactive states of chromatin.

Disruption of the enzymatic activity of disease-associated epigenetic enzymes offers a clear mechanism for pharmacologic intervention in diseases such as cancer, inflammatory diseases, metabolic diseases and neurodegenerative diseases. At Epizyme, we are focused on discovering novel, small molecule drugs that act as selective inhibitors of key epigenetic enzymes and can thus fulfill unmet needs in human medicine.

It is well understood today that the hereditary blueprint of our cells is stored in the form of chromosomes, made up of individual genes that are themselves composed of DNA. The DNA of each gene encodes the information needed for the production of a specific protein that is needed for the structure and/or function of cells.

The process of protein expression involves two key steps: transcription of the DNA sequence of the gene to a molecule of messenger RNA (mRNA) and then translation of the mRNA structure into the amino acid sequence of the protein product.

There are tens of thousands of individual proteins, hence, tens of thousands of individual genes, required for every cell of the human body. Hence, a large amount of DNA must be stored in the relatively small volume of the cell nucleus.

The Chromatin Structure
To accommodate this mass of genetic material within the nucleus, DNA is packaged into a condensed structure referred to as chromatin. Chromatin is actually composed of a combination of DNA, proteins (mainly proteins known as histones) and some RNA. The histones form disc-like structures around which portions of the DNA wraps itself to form structural units, called nucleosomes, resembling beads along a string (Figure 1).

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Figure 1 - The increasing structural complexity of genetic information from the double-helical structure of DNA (left) through nucleosome and chromatin structures (middle) to the chromosome (right).

Heterochromatin

The chromatin can fold upon itself to compact the nucleosomes, forming a highly condensed structure, referred to as heterochromatin. This provides an effective mechanism for storing a large quantity of DNA in a very small volume. But there’s a problem. In order for genes to be transcribed into mRNA molecules, portions of the gene (referred to as promoter regions) need to interact with particular proteins, such as transcription factors that initiate the process of mRNA transcription.In the condensed heterochromatin structure these promoter regions are largely inaccessible to the transcription factors; hence protein production is inhibited. Therefore, to initiate protein production (also referred to as gene expression) the heterochromatin structure needs to be relaxed in a specific and controlled manner, so as to expose the promoter regions of particular genes that need to be transcribed at specific times and under specific conditions during the lifetime of a cell.

Euchromatin

This more relaxed chromatin structure is referred to as euchromatin. The transition from heterochromatin to euchromatin is accomplished by changing the structure of the nucleosomes by adding or removing small chemical units (e.g., acetyl groups, methyl groups, phosphate groups and ubiquitin groups) at specific locations on the histones. These modifications, which result in chromatin relaxation, are performed by selective enzymes within the cell.

Every cell in the human body contains the full complement of genes that constitute the human genome. Yet, in any given cell, certain genes are transcribed to produce their protein products, and other genes are kept silent, unable to produce the proteins that they encode. This is why some cells become liver cells, some brain cells, others blood cells and the like.

These differences in gene expression pattern - from cell type to cell type - can be inherited, despite the fact that no differences (mutations) exist in the DNA of the cell genome. Thus, the control of cell fate depends upon factors beyond simply the genetics of the cell.

The processes that control this differential outcome of gene expression are collectively known as epigenetics (meaning, “beyond genetics”). Aberrant changes in epigenetic control of gene expression patterns is also one of the main reasons why some cells become malformed, leading to illnesses like cancer, inflammation and other diseases.

There are many examples in our everyday lives where common inputs result in differential outcomes, depending on specific control mechanisms. Consider, for example, how a talented musician can produce a wide variety of music on a guitar. A particular piece of music is encoded by the sequence and timing of notes, that are typically transcribed onto sheet music. The guitarist translates the sheet music by spatial and temporal modifications to the guitar strings; that is, he/ she holds down different strings, at different frets, at different times to produce the music (Figure 2A/B).

Figure 2 A&B - (A) Music is encoded in the form of notations on sheet music, that define the notes to be played and the tempo at which they are played. (B) A guitarist translates the sheet music into audible music by spatial and temporal control of the guitar strings. In a like manner, gene transcription is spatially and temporally controlled by epigenetic modifications, catalyzed by specific enzymes.

In an analogous manner, gene expression is spatially and temporally controlled within cells by specific modifications of the DNA and of the histone proteins. For example, adding small chemical units, such as methyl groups, at specific locations on the histones can change the structure of the chromatin (as described above) in precise ways, thus signaling the cell to turn on or turn off transcription of particular genes.

The selective addition of methyl groups to specific sites on the histones is controlled by the action of a unique family of enzymes known as the histone methyltransferases (HMTs). Once the methyl group has been deposited on the histone site, the affected genes continue to be regulated (turned on or off) until this chemical unit is removed by other enzymes, known as histone demethylases. In a like manner, other enzyme classes can decorate DNA and histones with other chemical species (Figure 3) and still other enzymes can remove these species to provide temporal control of gene regulation.

Figure 3 - Schematic of the nucleosome, illustrating the types of post-translational modifications that can occur on the histone tails and the enzymes responsible for these modification reactions.

The orchestrated collection of epigenetic activities must be tightly controlled in order for cell growth and differentiation to proceed flawlessly. When these controls are disrupted by increased expression and/or activity of the enzymes responsible for DNA and histone modification disease states result.

In human cancers, for example, there is a growing body of evidence to suggest that dysregulated epigenetic enzyme activity contributes to the uncontrolled cell proliferation associated with this devastating disease. Hence, blocking the aberrant action of specific epigenetic enzymes offers a clear way to treat such cancers.

Beyond cancer, there is growing evidence for a role of epigenetic enzymes in a number of other human diseases, including metabolic diseases (such as diabetes), inflammatory diseases (such as Crohn’s disease), neurodegenerative diseases (such as Alzheimer’s disease) and cardiovascular diseases.