Delete and re-write: how CRISPR-Cas9 is changing medicine

Nowadays, medical approaches evolve quite fast, as many investments and efforts are put in place in biomedical sciences research to improve patients' health and therapies success. In recent years, an innovative approach called CRISPR-Cas9 had advanced our success in correcting the development of several genetic diseases. In this article it will be described what CRISPR-Cas9 is, how it works and a recent case study of how this lab technique has been used to remove the extra chromosome in Down syndrome.

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CRISPR-Cas9: what is it?

CRISPR-Cas9 (which is the acronym of Clustered Regularly Interspaced Short Palindromic Repeats - Cas9, where Cas9 is the protein used in this system), is only one of the most recent and advanced technologies in genome/gene editing. Genome editing techniques allow genetic material to be added, removed, or altered at particular locations in the genome (which consists of all the genes expressed in our body).

Although this system was discovered almost forty years ago, it was only in 2012, with the work published by Emmanuelle Charpentier and Jennifer Doudna, that the interest in this molecular technique exploded as the beginning of a new era for gene editing.

CRISPR-Cas9 was adapted from a naturally occurring genome editing system that bacteria use as an immune defense. When infected with viruses, bacteria capture small pieces of the viruses' DNA and insert them into their own DNA in a particular pattern to create segments known as CRISPR arrays. These DNA segments are extremely important, as they allow the bacteria to "remember" the infection developed upon viral infection. If the viruses (even of similar type) attack again, the bacteria produce RNA segments from the CRISPR arrays that recognize and attach to specific regions of the viruses' DNA. These RNA segments are then recognized by Cas9 (or similar enzymes with overlapping role, like Cpf1, for example), which cuts the DNA apart disabling the virus and defending bacteria against it.

This discovery led Charpentier and Doudna to be awarded the Nobel Prize in Chemistry for their work on developing the CRISPR-Cas9 gene-editing tool in 2020.

How does this molecular technique works?

As previously mentioned in this article, the original bacterial molecular mechanism was adapted for gene editing of DNA segments. Scientists developed a system in which they create a small piece of RNA with a short "guide" sequence that binds to a specific target sequence in a cell's DNA. This system is very similar to the RNA segments bacteria produce from the CRISPR array. This guide RNA also attaches to the Cas9 enzyme. When introduced into cells, the guide RNA recognizes the intended DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location, mirroring the process in bacteria. Once the DNA is cut, the cell's own DNA repair machinery can be used to add or delete pieces of genetic material of interest, or to make changes to the DNA by replacing an existing segment with a customized DNA sequence.

Pros and cons of CRISPR-Cas9

The exceptional interest in genome editing is connected to the possibility of prevent and treat many genetic human diseases. Currently, genome editing is used in cells and animal models in research labs to understand diseases. Scientists are still working to determine whether this approach is safe and effective for use in people. It is being explored in research and clinical trials for a wide variety of diseases, including single-gene disorders such as cystic fibrosis, haemophilia, and sickle cell disease. It also holds promise for the treatment and prevention of more complex diseases, such as cancer, heart disease, mental illness, and human immunodeficiency virus (HIV) infection.

Although several positive aspects can be listed for CRISPR-Cas9, some ethical concerns arise when genome editing is used to alter human genomes. Most of the changes introduced with genome editing are limited to somatic cells (for the moment), which are cells other than egg and sperm cells (germline cells). These changes are isolated to only certain tissues and are not passed from one generation to the next, as in general genetic traits are transmitted via germline cells. However, some changes made to genes in egg or sperm cells or to the genes of an embryo could potentially be passed to future generations. Germline cell and embryo genome editing bring up a number of ethical challenges, including whether it would be permissible to use this technology to enhance normal human traits (such as height or intelligence, as this could lead to eugenetics approaches, which aim to improve the mankind genetic features through genetic systems). Based on concerns about ethics and safety, germline cell and embryo genome editing are currently illegal in the majority of the countries, until further studies are released and law has evolved to face these new situations.

A case study: using CRISPR to delete the extra chromosome in Down Syndrome

Down syndrome (DS) is a genetic disorder caused by the presence of an extra copy of human chromosome 21 (HSA21). It is the most common viable chromosomal abnormality, occurring in ∼1 in 700 live births. Extensive research has been conducted to elucidate the clinical features, genetic causes, and cellular characteristics of DS. These studies have been aided by the development of innovative animal models and advancements in prenatal diagnostic techniques, such as preimplantation genetic testing for aneuploidy. Despite these significant strides, a relative paucity of research has addressed the fundamental cause of DS. In a recent scientific study published in 2025, researchers used CRISPR-Cas9 to delete the extra chromosome behind Down syndrome in both germline and somatic cells. It was also observed that the edit not only eliminated the extra chromosome, but also restored normal gene expression. The process involved precisely timed CRISPR-Cas9 edits of an allele specific chromosome and a temporary suppression of the cells’ DNA repair mechanisms to enhance precision and increase the loss of the extra chromosome.

While this breakthrough remains in the lab and could be optimized to for a more effective outcome, it offers a potential pathway toward future therapies for genetic disorders long considered untreatable, where the precision of the molecular approach could make a difference in improving patients' health with minimized downsides.

References

Boti MA, Athanasopoulou K, Adamopoulos PG, Sideris DC, Scorilas A. Recent Advances in Genome-Engineering Strategies. Genes (Basel). 2023 Jan 2;14(1):129. doi: 10.3390/genes14010129. PMID: 36672870. Free full-text available from PubMed Central: PMC9859587.

Gostimskaya I. CRISPR-Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing. Biochemistry (Mosc). 2022 Aug;87(8):777-788. doi: 10.1134/S0006297922080090. PMID: 36171658. Free full-text available from PubMed Central: PMC9377665.

Sharma G, Sharma AR, Bhattacharya M, Lee SS, Chakraborty C. CRISPR-Cas9: A Preclinical and Clinical Perspective for the Treatment of Human Diseases. Mol Ther. 2021 Feb 3;29(2):571-586. doi: 10.1016/j.ymthe.2020.09.028. Epub 2020 Sep 20. PMID: 33238136. Free full-text available from PubMed Central: PMC7854284.

Zheng R, Zhang L, Parvin R, Su L, Chi J, Shi K, Ye F, Huang X. Progress and Perspective of CRISPR-Cas9 Technology in Translational Medicine. Adv Sci (Weinh). 2023 Sep;10(25):e2300195. doi: 10.1002/advs.202300195. Epub 2023 Jun 25. PMID: 37356052. Free full-text available from PubMed Central: PMC10477906.

Hashizume R, Wakita S, Sawada H, et al. Trisomic rescue via allele-specific multiple chromosome cleavage using CRISPR-Cas9 in trisomy 21 cells. PNAS Nexus. 2025;4(2):pgaf022. Published 2025 Feb 18. doi:10.1093/pnasnexus/pgaf022

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