There has been increasing interest in epigenetic research due to the possible effects it can have on modifying gene expression in vivo.

Epigenetic Editing Approaches

Gene editing involves directly altering the sequence of a gene. All epigenetic modification techniques must contain a DNA binding molecule and an active epigenetic modification molecule. These modifications first require DNA to be cut using an endonuclease to make a double-stranded break and then allow the two ends of the DNA to repair. During this repair process, the DNA in the vicinity of the cut undergoes replacement by a new sequence using a template delivered into the target cell along with an endonuclease. Three of the most widely studied DNA binding molecules are zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs), and deactivated Cas9 (dCas9).[1]

Zinc Finger Proteins (ZFP)

Zinc finger proteins are fused to a DNA cleavage domain to make zinc finger nucleases. These nucleases cause double-stranded breaks at a very specific targeted DNA sequence, which can then disrupt that specific sequence due to errors during the non-homologous repair end-joining pathway, thereby permanently disrupting the targeted gene. The zinc finger nucleases are highly individualized for their respective DNA sequences, and a new one must be engineered for each specific site, making this process too laborious and expensive.[3] 

Transcription Activator-Like Effectors (TALE)

These proteins are produced by a plant pathogen Xanthomonas that is capable of altering plant gene expression. They can be modified to have endonuclease activity by combining the TALE with a DNA cleavage domain, making a transcription activator-like effector nuclease. They work similarly to zinc finger nucleases, and their clinical application is also limited due to the necessity of creating new proteins for each target site.[4]

Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)/ Cas9

CRISPR arrays are regions of DNA in bacterial genomes that are used to store genetic information of infecting viruses so that the bacteria can transcribe the sequence into RNA upon reinfection with that specific virus to eventually cleave the homologous region in the viral genome. One of the endonucleases used by this system is called CRISPR-associated protein 9, or Cas9. Cas9 can be guided to any chosen DNA sequence by changing the sequence of the guide RNA to match the DNA sequence of interest.[5]

Currently Under Investigation

One technique currently under investigation is the generation of hematopoietic stem and progenitor cells (HSPCs) that lack the CCR5 receptor to provide HIV resistant T cells in an HIV infected individual.[3][6] Another technique is silencing the HER2/Neu oncogene using a zinc finger fusion protein via histone methylation.[1] Clinical trials for using CRISPR gene editing for cancers such as melanoma, synovial sarcoma, and multiple myeloma are also currently ongoing at the University of Pennsylvania.[7] 

Current FDA Approved Drugs

Hypomethylating Agents

Azacytidine and decitabine are the two FDA approved drugs that inhibit DNA methyltransferases and result in reduced DNA methylation. Azacytidine was approved for the treatment of myelodysplastic syndromes by the FDA in 2004, and decitabine received approval for the treatment of myelodysplastic syndromes in 2006.[8]

Histone Deacetylase Inhibitors

Histone deacetylation leads to the repression of a specific gene. Drugs that inhibit deacetylation, known as histone deacetylase inhibitors (HDACi’s), lead to decreased histone deacetylation and ultimately increased gene expression. There are four HDACi’s currently approved by the FDA. Vorinostat obtained approval in 2006 for the treatment of cutaneous t-cell lymphoma.[9] Romidepsin is a natural HDACi isolated from bacterial fermentation of Chromobacterium violaceum and was approved in 2009 for the treatment of cutaneous t-cell lymphoma.  Belinostat received approval in 2014, and panobinostat approval came in 2015, both under the FDA’s accelerated approval program, for the treatment of relapsed peripheral t-cell lymphoma and relapsed multiple myeloma, respectively.[10] Many other HDACi’s are currently under investigation.[11]

Gene Therapy

Gene therapy refers to a process of introducing a gene, known as a transgene, and is presently being studied for various disorders, such as disorders of the eyes, hemophilia, cystic fibrosis, sickle cell disease, and thalassemia, and as cancer therapy.

Ocular Gene Therapy

Leber’s congenital amaurosis 2 (LCA2) is an autosomal recessive early-onset retinal degeneration caused by mutations in the RPE65 gene. Mutations in this gene result in the defective formation of the visual pigments including rhodopsin and cone opsin leading to dysfunctional photoreceptor function and loss of vision. Gene therapy for vision loss associated with this condition called voretigene neparvovex has been developed, which consists of an adeno-associated virus combined with the RPE65 gene, was investigated and subsequently, FDA approved in December 2017 for the treatment of biallelic RPE65 mutation-associated retinal dystrophy. It directly delivers a normal copy of the RPE65 gene into retinal cells and is the first gene therapy approved by the FDA for an inherited disorder.[12]