Top Genome Editing Breakthroughs in 2020

Due to the affection of the COVID-19 pandemic, lots of research facilities and institutes were locked down for a long time during 2020. Even though, researchers are trying their best to move their projects forward. Surprisingly, 2020 has been an exciting year for genome editing technologies with lots of breakthroughs. In this article, let’s review some of the most impactful advances in genome editing this year. 

CRISPR-free mitochondrial base editor

Mitochondrial DNA (mtDNA) is the small circular chromosome found inside mitochondria. These organelles found in cells have often been called the powerhouse of the cell (wikipedia.org). Mutations in mtDNA are associated with a range of human diseases. However, precise editing to mitochondrial genomes has been hindered by the challenge of transporting RNAs into mitochondria, including guide RNAs that are required for CRISPR-associated proteins. 

(Image source: National Human Genome Research Institute, NIH)

A team led by Joseph Mougous, PhD, at the University of Washington in Seattle, and David R. Liu, PhD, at Harvard University and the Broad Institute, reported his findings in Nature on 08 July 2020, described how an interbacterial toxin can enable the edit of mitochondria genomes (Beverly Y. Mok et al. Nature; 2020). This collaborating study started from an enzyme named DddA discovered by Mougous lab, which can catalyze the deamination of cytidines within dsDNA. Once recognized that the DddA could be useful for gene editing, Mougous reached out to David Liu, the well-known scientist in genome editing research whose lab has developed several high-efficient base editors. To prevent the deaminase from altering mitochondrial DNA before it reached its target, they split the DddA into two halves which are non-toxic and inactive until brought together on target DNA. By fusing the DddA halves, transcription activator-like effector array proteins, and a uracil glycosylase inhibitor, they developed a new kind of RNA-free DddA-derived cytosine base editors (DdCBEs), which could catalyse C-G to T-A conversions in human mtDNA with high target specificity and product purity. This mitochondrial base editor enables the precise manipulation of mtNDA and have great potential to treat mitochondrial disorders (Beverly Y. Mok et al. Nature; 2020). 

Faster and more efficient base editor

On March 16, a team led by David R. Liu and Jennifer A. Doudna published their research in Nature Biotechnology, reported that they have developed a new adenine base editor (ABE) that is far faster and more efficient than its predecessor (Michelle F. Richter et al., 2020). In this study, the researchers developed and applied a new PACE (Phage-assisted Continuous Evolution) selection method to greatly enhance the activity and compatibility of ABEs with diverse Cas homologs. The resulting evolved ABE8e variant contains eight additional mutations that increase activity 590-fold compared with its predecessor ABE7.10, and offers substantially improved editing efficiencies when paired with a variety of Cas9 or Cas12 homologs. The off-target editing by ABE8e was observed higher compared with ABE7.10 but can be ameliorated by the introduction of an additional mutation. Finally, ABE8e expands the targeting scope, editing efficiency and overall utility of ABEs. 

Only a few months later, Science published the first 3D structure of base editors obtained by the researchers at the University of California, Berkeley. More specifically, the researchers determined a 3.2-angstrom resolution cryo-EM structure of ABE8e in a substrate-bound state (Audrone Lapinaite et al., 2020).

Fig. 1. The 3.2 Å resolution cryo-EM structure of the SpCas9-ABE8e complex. Subunits are colored as follows: SpCas9, gray; sgRNA, purple; TS, teal; NTS, blue; and TadA-8e dimer, red and pink. (Audrone Lapinaite et al., 2020).

This study revealed the secret of why ABE8e catalyzes DNA deamination up to ~1100-fold faster than earlier ABEs. Kinetic and structural data suggest that mutations in ABE8e stabilize DNA substrates in a constrained, transfer RNA–like conformation. Furthermore, ABE8e’s accelerated DNA deamination suggests a previously unobserved transient DNA melting that may occur during double-stranded DNA surveillance by CRISPR-Cas9. On the whole, these results explain the structural and biological base of ABE8e’s outstanding performance in base-editing as Michelle F. Richter et al reported in their work and also provide references for the future design of base editors.

New hypercompact genome editor has advances in cellular delivery

On 17 July 2020, a team led by Jennifer A. Doudna published a paper in Science describing a new  CRISPR-Cas system, comprising a single small protein CasΦ (~70Kda), a CRISPR array, encoded exclusively in the genomes of huge bacteriophages. The unusually small size of CasΦ and its lack of co-occurring genes raised the question of whether this system could function as a bona fide CRISPR-Cas system. To examine this new system’s ability and potential to work as a genome editing tool, researchers at Doudna lab investigated three divergent CasΦ orthologs from metagenomics assemblies and demonstrated that this system is active in vitro and in human and plant cells with expanded target recognition capabilities relative to other CRISPR-Cas proteins. They also demonstrated that CasΦ uses a single active site for both CRISPR RNA (crRNA) processing and crRNA-guided DNA cutting, which is unexpected and particularly meaningful to create new function modules for genome manipulation (Patrick Pausch et al., 2020). 

Considering the super small size of CasΦ and minimal requirements for PAM sequence, it has advantages especially for cellular delivery and a wider range of targets in the genome. Furthermore, more studies in vitro and in vivo will focus on investigating the efficiency and off-target effects of this new CRISPR-Cas system. 

CRISPR takes in cancer immunotherapy

According to the article published in Nature reviews drug discovery titled “Gene-editing pipeline takes off”, in the past year and a half alone, at least 11 gene editing programmes entered the clinic in the US or EU. And 6 of these rely on CRISPR–Cas-based editors. With the clinical-stage pipeline now spanning ex vivo, immuno-oncology and in vivo applications, the genome-editing pipeline is taking form (Asher Mullard, 2020). On 28 Feb 2020, researchers at University of Pennsylvania reported a phase 1 clinical trial to assess the safety and feasibility of CRISPR-Cas9 gene edited T cells in three patients with refractory cancer. In this study, the researchers removed T lymphocytes from patients and used CRISPR-Cas9 to disrupt three genes (TRAC, TRBC, and PDCD1) with the goal of improving antitumor immunity. The engineered cells were administered to patients and were well tolerated, with durable engraftment observed for the study duration. These encouraging observations pave the way for future trials to study CRISPR-engineered cancer immunotherapies (Edward A. Stadtmauer et al., 2020). 

New viable CRISPR-Cas12b system for plant genome engineering

CRISPR has had a profound impact on agriculture and researchers have applied this handy precision genome-editing tool in different crops for making them more resilient to pests and climate changes as well as for improving flavor and nutrition.

This year, a new CRISPR-Cas12b system becomes viable for genome engineering in plants. This study led by Dr. Yiping Qi, assistant professor of Plant Science at the University of Maryland was published in Nature Plants on 09 March 2020. This is the first time CRISPR-Cas12b was demonstrated viable in plants and becomes the third promising CRISPR system after Cas9 and Cas12a for plant genome editing (Meiling Ming et al., 2020). CRISPR-Cas12b has advances over CRISPR-Cas12a particularly when gene activation is the goal. Additionally, it retains all the positives that were inherent in CRISPR-Cas12a for plants, including the ability to customize cuts and gene regulation across a broad range of applications. Qi and his lab also successfully applied the engineered CRISPR-Cas12b system for multiplexed genome editing. The initial work in this paper was conducted in rice while the researchers are trying to develop applications to additional crops and explore more genome editing systems to further enhance and improve plant genome engineering (ScienceDaily.com).

Discussion

We are impressed of what genome editing has achieved this year, and excited to see what will come in the coming years. Will more efficient systems be discovered or developed? Will we see more clinical trials for different diseases? Will genome edited vegetables or meat be available in the supermarket shelves? Let’s wait and stay tuned. 

Which breakthrough in genome editing area has impressed you? How will genome editing technology change our lives? Leave us a comment below. The best comments will have chances to win a $20 amazon gift card!

Related articles

Glycosylase base editors enable C-to-A and C-to-G base changes

Rapid Multicopy Chromosomal Integration Renovates the Way Cell Factories are Built

CRISPR-CasФ: A new all-in-one hypercompact genome editor