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New CRISPR Improvement Allows Multiple Gene Edits and Better Accuracy


Researchers at the Scripps Research Institute Florida campus have refined the already state-of-the-art gene-editing system CRISPR. The new improvements boost the ability of CRISPR to target, cut, and paste genes in human and animal cells and helps to address the concerns of off-target gene mutations raised in a recent study[1].

What is CRISPR?

CRISPR is short for “Clustered Regularly Interspaced Short Palindromic Repeat”, and is a gene editing system that exploits an ancient bacterial immune defense process. Some microbes combat viral infection by sequestering a piece of a virus’ foreign genetic material within its own DNA, to serve as a template.

The next time the viral sequence is encountered by the microbe, it is detected immediately and cut up for disposal with the help of two types of RNA. Molecules called guide RNAs show the location of the invader, and the CRISPR effector proteins act as the scissors that cut it apart and destroy it.

Scientists have hijacked this process to edit genes and allow a cut-and-paste approach to genetic engineering that is both relatively easy as well as very powerful. In just five years, the CRISPR gene editing system has totally revolutionized microbiology, changing what was once a difficult and laborious process using older techniques like zinc fingers and TALENS into a quick and easy system to edit genes.

Ultimately the hope is that genetic engineering will eventually become a useful treatment for diseases including those related to age.

Unfortunately, there are have been some bumps in the road as with all new technology and it has its limitations. Gene therapy currently needs a viral shell to deliver the genetic material to the target. The CRISPR molecule is too large to fit into the viral shell with multiple guide RNAs in the most commonly used viral packaging systems.

Multiple gene targeting

This new study helps to solve this issue by allowing multiple guide RNAs to be packaged in a viral shell [2]. The research team have improved the efficiency of CRISPR by incorporating guide RNAs with “multiplexing” capability.

Guide RNAs are short nucleic acid strings that help guide the CRISPR molecular scissors to their target genes. The new research is particularly exciting as it allows multiple gene targets in a cell to be hit at once by the CRISPR-Cpf1 complex.

This is a hugely important step for CRISPR, because it significantly improves the efficiency of multiple gene edits, or multiple sites on a single gene. This could be particularly valuable when multiple disease related genes or multiple sites of a disease related gene need to be targeted.

The novelty could help treat various diseases

This advance of the CRISPR system may prove helpful to treat diseases like hepatitis B. After the infection, the hepatitis B DNA remains in liver cells and slowly regulates the production of more viruses. This ultimately leads to liver damage, cirrhosis, and potentially even cancer.

Using the CRISPR-Cpf1 system with its “multiplex” ability therapies could digest the viral DNA more efficiently, halting progression of the disease before the liver is damaged beyond repair.

It could also find utility in treating conditions such as muscular dystrophy as it could allow enough gene repairs to be made in muscle cells to restore function. The system allows for much greater scope and quantity of cells in a therapy making this a plausible idea.

Two main types of CRISPR

There are a number of variants of the CRISPR system, but the two most widely used are Cas9 and Cpf1, which have different kinds of molecular scissors. The research team in this study focused on using Cpf1, as it is more accurate in mammalian cells than the better-known Cas9 variant.

The Cpf1 molecule they used, which has been studied on E.coli in previous experiments, was sourced from two kinds of bacteria, Lachnospiraceae bacterium and Acidaminococcus sp. The key property of these molecules is their ability to grab their guide RNAs from a long string of RNA, however, it was uncertain if this would work with the RNA produced by mammalian cells.

The researchers tested this by editing a firefly bioluminescence gene into a cell’s chromosome and the modified CRISPR-Cpf1 system worked as they had hoped it would.

This is good news, because it means researchers can use a simpler delivery system for directing the CRISPR effector protein plus guide RNAs. This will make the CRISPR process more efficient for a variety of gene editing techniques.


As with all new technology, there will be setbacks but we at LEAF believe that the concern about unexpected mutations is simply a bump in the road and not a cause to believe that CRISPR is not suitable for human use in medicine. All pioneering technologies encounter problems, and for each there are solutions.

The Cpf1 protein needs to be researched more thoroughly to understand it better, so that its utility in delivering gene therapy vectors can be improved and expanded upon in the future.

The research world is busy refining and improving the technology, and in the very near future, given the meteoric progress happening in this field, we will soon without a doubt have an exceptionally accurate gene editing system. There is every reason to be pretty breathless and enthusiastic about CRISPR and its potential as a weapon in the war against age-related diseases and more.

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[1] Schaefer, K. A., Wu, W. H., Colgan, D. F., Tsang, S. H., Bassuk, A. G., & Mahajan, V. B. (2017). Unexpected mutations after CRISPR-Cas9 editing in vivo. Nature methods, 14(6), 547-548.

[2]  Zhong, G., Wang. H., Li, Y., Mai, H., Farzan, M. (2017) Cpf1 proteins excise CRISPR RNAs from mRNA transcripts in mammalian cells. Nature chemical biology, doi:10.1038/nchembio.2410.

About the author

Steve Hill

Steve serves on the LEAF Board of Directors and is the Editor in Chief, coordinating the daily news articles and social media content of the organization. He is an active journalist in the aging research and biotechnology field and has to date written over 600 articles on the topic, interviewed over 100 of the leading researchers in the field, hosted livestream events focused on aging, as well as attending various medical industry conferences. His work has been featured in H+ magazine, Psychology Today, Singularity Weblog, Standpoint Magazine, Swiss Monthly, Keep me Prime, and New Economy Magazine. Steve is one of three recipients of the 2020 H+ Innovator Award and shares this honour with Mirko Ranieri – Google AR and Dinorah Delfin – Immortalists Magazine. The H+ Innovator Award looks into our community and acknowledges ideas and projects that encourage social change, achieve scientific accomplishments, technological advances, philosophical and intellectual visions, author unique narratives, build fascinating artistic ventures, and develop products that bridge gaps and help us to achieve transhumanist goals. Steve has a background in project management and administration which has helped him to build a united team for effective fundraising and content creation, while his additional knowledge of biology and statistical data analysis allows him to carefully assess and coordinate the scientific groups involved in the project.
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