The CRISPR gene editing technology, born in 2012, may be the most significant scientific breakthrough in the field of life sciences since the 21st century. In 2020, CRISPR gene editing technology was recognized by the Nobel Prize, and this month, the US FDA approved the first CRISPR based gene editing therapy for patients with sickle cell disease (SCD). This indicates that CRISPR can truly and meaningfully address the challenging issues faced by patients.
Nowadays, thousands of CRISPR related research papers are published every year, and the addition of transposase, Fanzor, and epigenome editing has continuously expanded the CRISPR toolbox; The development of delivery tools such as LNP and VLP, as well as the discovery of miniaturized CRISPR systems, have led to the rapid development of gene editing in vivo; CRISPR based gene editing has shown great potential in preclinical and clinical studies of various diseases
At the end of 2023, Bioworld selected the top ten research advances in the field of CRISPR gene editing in 2023 (sorted by the publication time of the selected papers, focusing on breakthroughs in gene editing technology, not including papers that only use CRISPR as a gene editing tool). These research advances include the development, modification, therapeutic application, and safety research of new CRISPR systems.
1. Treating heart disease through base editing
On January 12, 2023, Eric Olson’s team from the University of Texas Southwestern Medical Center published a paper in the Science journal titled “Absorption of CaMKII” δ Research paper on oxidation by CRISPR-Cas9 base editing as a therapy for cardiovascular disease.
This study used a CRISPR-Cas9 based adenine base editor (ABE) to replicate CaMKII in a mouse model δ Two methionines (ATGs) are edited as valine (GTG) to prevent CaMKII δ Overactivation of the heart can protect it from the effects of ischemia-reperfusion injury, promote the recovery of heart function, reduce permanent damage, and it is not too late to seek treatment after a heart attack. It is expected to be developed as a treatment and protection method suitable for a wide range of heart disease patients.
2. The first oral CRISPR drug to prevent and treat bacterial infections
On May 4, 2023, researchers from SNIPR Biome, a gene editing therapy company at the Danish University of Science and Technology, published a research paper titled “Engineering phase with antimicrobial CRISPR – Cas selectively reduce E. coli burden in mice” in the journal Nature Biotechnology.
Antibiotic treatment has adverse effects on the human gut microbiota and can also lead to antibiotic resistance. In this study, the research team screened 162 natural bacteriophages and found that 8 of them showed outstanding performance in targeting Escherichia coli. Then, they modified these bacteriophages through CRISPR gene editing, and designed four CRISPR Cas armed bacteriophages with stronger targeting and clearance capabilities against Escherichia coli.
This study developed the first oral candidate drug based on CRISPR Cas, which can selectively target and eliminate Escherichia coli without affecting other gut microbiota. At present, the drug is undergoing Phase 1 clinical trials aimed at reducing and preventing fatal infections caused by the translocation of Escherichia coli into the bloodstream in patients with hematologic cancers.
3. Developing new base editing tools using AI technology
On June 27, 2023, Gao Caixia’s research team of the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences published a research paper entitled “Discovery of destructive functions by structured protein clustering” in the Cell journal.
This study innovatively utilized AI assisted large-scale protein structure prediction to establish a novel high-throughput protein clustering method based on tertiary structure, achieving in-depth exploration of deaminase functional structures and identifying novel chassis elements that are completely different from known deaminase tools, including 45 single stranded cytosine deaminases (Sdd) and 13 double stranded cytosine deaminases (Ddd), The research team developed a series of novel base editing systems based on these deaminases and tested them in animal and plant cells. Furthermore, through rational protein design and functional validation, a new Sdd6-CBE base editor capable of being delivered by a single adeno-associated virus (AAV) was developed, with a marginal efficiency of up to 43.1% in mouse cell lines, and an Sdd7-CBE base editor with an editing efficiency of up to 22.1% in soybeans.
This study has successfully developed a series of new base editing tools with independent intellectual property rights in China, breaking through the application bottleneck of existing deaminases and demonstrating the broad application prospects of new base editing systems in medicine and agriculture.
4. First discovery of CRISPR like system in eukaryotes
On June 28, 2023, Zhang Feng’s team published a research paper titled “Fanzor is a eucaryotic programmable RNA guided endolucase” in the journal Nature.
The research team has discovered the first RNA guided DNA nuclease in eukaryotes – Fanzor, and more importantly, this novel CRISPR like system can enable editing of the human genome after reprogramming.
In addition, compared to the CRISPR Cas system, the Fanzor system is very compact and easier to deliver to cells and tissues. Moreover, the Fanzor system has no collateral cleavage activity, allowing for more precise genome editing. This latest study also suggests that RNA guided DNA cleavage mechanisms exist in all biological realms.
This study indicates that Fanzor, as a programmable RNA guided DNA nuclease, is widely present in eukaryotes (Fanzor1) and their associated viruses (Fanzor2). Fanzor has a strong nuclear localization signal (NLS), which can enter the nucleus of eukaryotic cells and edit endogenous genes of human cells under fRNA guidance. Moreover, it has no collateral cleavage activity, highlighting the potential application of these widely existing RNA guided nucleases in eukaryotic organisms.
5. Eliminating excess chromosomes in cancer cells with CRISPR can prevent tumor growth
On July 6, 2023, the Jason Sheltzer team from Yale University published a research paper titled “Oncogene like addition to any human cancer” in the Science journal.
As well known, human cells typically have 23 pairs of chromosomes, but cells may also have extra chromosomes, known as aneuploidy. If we observe normal tissues, 99.9% of cells have a normal number of chromosomes. However, more than 100 years ago, scientists discovered that almost all cancers are aneuploidy, but it has always been unclear what role this phenomenon plays in cancer. People have been debating whether aneuploidy leads to cancer or whether cancer brings aneuploidy.
This study used CRISPR-Cas9 gene editing technology to eliminate the entire chromosome in cancer cells, which is an important technological advancement. Manipulating non diploid chromosomes in this way will enable us to better understand their function. The research results show that cancer cells carrying extra chromosomes rely on these chromosomes for growth, and using CRISPR-Cas9 to eliminate these extra chromosomes can prevent tumor formation. This discovery also suggests that selective targeting of extra chromosomes may provide new avenues for cancer treatment.
6. The evolutionary origin of CRISPR molecular scissors
On September 27, 2023, the team led by Samuel Sternberg from Columbia University published a research paper in the journal Nature titled: Transfer encoded nuclei use guide RNAs to promote their self fish spread.
This study takes our attention back to the past and reveals how the “DNA scissors” in the CRISPR system evolved by looking back at the predecessor of CRISPR-Cas9- the jumping gene (transposon). This study confirms that RNA guided DNA nucleases TnpB and IscB are crucial in preventing permanent loss of transposase TnpA during transposition.
These findings reveal that RNA guided DNA cleavage emerged as a early biochemical activity to promote selfish inheritance and transmission of transposons, which later became used for antiviral defense in the evolutionary process of CRISPR Cas adaptive immunity.
7. Strategies to alleviate T cell chromosome loss caused by CRISPR-Cas9 in clinical practice
On October 3, 2023, Professor Jennifer Doudna, a Nobel laureate in chemistry and a member of the University of California, Berkeley, along with Chun Jimmy Ye from the University of California, San Francisco, Zhang Yuanhao from Stanford University, and Carl June from the University of Pennsylvania, published a research paper titled “Migration of chromosome loss in clinical CRISPR-Cas9-engineered T cells” in the Cell journal.
This study suggests that chromosomal deletion induced by CRISPR-Cas9 gene editing is a common phenomenon, and the resulting defective T cells have disadvantages in adaptability and proliferation, but can still persist for several weeks in vitro culture, which may have adverse effects on clinical applications. In addition, the research team has proposed a new T-cell gene editing scheme that can reduce the occurrence of chromosomal deletions in gene editing and improve clinical safety.
8. A new record of gene edited pig organ xenotransplantation
On October 11, 2023, researchers from eGenesis published a research paper titled “Design and Testing of a Humanized Porcine Donor for Xenotransplantation” in Nature.
This study reports on the surgical design and successful process of transplanting genetically engineered pig kidneys into non-human primates (NHPs). The research team conducted up to 69 gene edits on pigs, including knocking out three genes related to the synthesis of polysaccharide antigens associated with hyperacute rejection reactions, knocking in seven human genes involved in regulating multiple pathways of rejection reactions (inflammation, innate immunity, coagulation, and complement), and knocking out endogenous retroviruses present in the pig genome.
9. A New Method of Virus Antimicrobial CRISPR Cas Immune System
On October 18, 2023, researchers from the University of Copenhagen in Denmark and the University of Otago in New Zealand published a research paper titled “Bacterophases suppress CRISPR Cas immunity using RNA based anti CRISPRs” in the top international academic journal Nature.
This study reveals a novel method for viruses (bacteriophages) to inhibit the bacterial CRISPR Cas immune system – small non coding RNA anti CRISPR (Racr), which is also the first evidence of RNA based anti CRISPR.
The research team stated that this discovery tells us that microbial dynamics in the natural environment can used to enhance the safety of gene editing and have the potential to bring more effective alternatives to antibiotics. This discovery is exciting for the scientific community as it provides us with a deeper understanding of how to prevent bacterial CRISPR Cas defense systems.
10. Using big data algorithms, discover 188 new CRISPR systems at once
On November 23, 2023, Zhang Feng’s team published a research paper in Science titled: Uncovering the Functional Diversity of Rare CRISPR Cas Systems with Deep Terrascale Clustering.
This study developed a new search algorithm based on the Fast Local Sensitive Hash Clustering Algorithm (FLSHcluster), which used to mine three major public databases containing data on various unusual bacteria. 188 novel CRISPR systems identified from these databases, and four of them characterized in detail. These new systems may used to edit mammalian cells, Its off target effect is less than the current CRISPR-Cas9 system, and it may also used for diagnosis or recording intracellular activities.
This study highlights the unprecedented diversity and flexibility of CRISPR, and also indicates that most CRISPR systems are rare and only found in unusual bacteria and archaea. With the continuous growth of databases available for searching, there may be more rare systems discovered