From Bacterial Defense to Human Innovation: The Science and Applications of CRISPR

Fatima Mamedova
Nov 20
10 min read

Updated: Nov 24

From a microscopic bacterium's defense system to genetically modifying babies, CRISPR gives scientists endless opportunities to precisely modify DNA. CRISPR is an innovative gene editing technology that was discovered and developed through investigating bacteria. Scientists discovered that bacteria use a specific system to defend themselves against harmful viruses. This natural immune response system was then experimented with in labs to help edit DNA in humans, plants, and animals, which is now known as the CRISPR technology. The CRISPR technology was co-invented in 2009 by Jennifer Doudna and Emmanuelle Charpentier. Jennifer Doudna, a biochemist at UC Berkeley and Emmanuelle Charpentier, a microbiologist at the Max Plank Institute, worked together to develop a Nobel prize winning CRISPR/Cas 9 system. While the underlying initiative of CRISPR was first discovered by Francisco Mojica in 1995, Doudna and Charpentier are credited for transforming this knowledge into a powerful DNA editing tool.

1.1 The Phage life cycle

The CRISPR-Cas system targets phages, which are viruses that infect bacteria and operate as a defense mechanism. Bacteria evolved CRISPR-Cas to recognize phage DNA and destroy it, protecting the cell from infection. A phage attaches itself to a bacterial cell and injects its viral DNA inside through the cell membrane, which later uses the bacterium's own resources to duplicate itself (Figure 1). When there are too many duplicates cramped inside the bacterium cell, the cell bursts open and frees the phages, letting them infect more bacteria and the cycle repeats itself.

Figure 1. Lytic vs. lysogenic phage infection.

Image from Innovative Genomics Institute/CRISPRpedia, CRISPR in Nature.

1.2 The CRISPR Immune System

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Immune system is a defense mechanism used by many bacteria to protect themselves from phages. This adaptive defense mechanism allows microbes to memories past infections and respond more efficiently and effectively to future attacks.

CRISPR Locus Architecture

The CRISPR locus in a bacterial genome consists of three major components :

Repeats : These are short, identical sequences of DNA that are palindromic, meaning they read the same backwards and forwards. These sequences dont code for proteins but play a structural role in the Array. The role of the repeats is to recognize and process the Array during the production of CRISPR RNAs (crRNAs)
Spacers : Spacers are unique DNA sequences located between the repeats. Each spacer is a fragment of DNA taken from a virus (phage) or other genetic elements that previously infected the bacterium. Spacers act as a genetic memory bank of past infections, serving as a molecular ID tag to recognize and target the threat if it tries to attack again.
Altogether, these repeats and spacers form the CRISPR Array (Figure 2). Over time, as a bacterium encounters new viruses, new spacers are added to the Array near the end, maintaining a chronological record of the history of infections. During immune responses, the spacers guide the system to target and destroy any matching foreign DNA.

Figure 2. CRISPR Array.

Image from Innovative Genomics Institute/CRISPRpedia, CRISPR in Nature

Steps of CRISPR-Cas Immunity

CRISPR-Cas Immunity occurs in three main stages:

Adaptation (Spacer Acquisition)

When a bacterium is infected by a phage, special Cas proteins recognize foreign DNA and cut a short fragment of it. This fragment (called the protospacer) is inserted into the CRISPR array (Figure 3) as a new spacer. This keeps a record of the infection, allowing the bacterium to recognize the same virus in the future.

2. Expression (CRISPR RNA Biogenesis)

The CRISPR array is transcribed into a long RNA molecule (Figure 3) called pre-

crRNA, which is then processed into shorter crRNAs (CRISPR RNAs). Each crRNA

contains one unique spacer that corresponds to a previously encountered phage sequence.

3. Interference

If the same phage infects the bacterium again, the crRNA forms a complex with a Casprotein (Cas 9). The crRNA guides Cas9 to the matching DNA sequence in the invader’s genome. Cas9 then cuts the DNA (Figure 3), effectively destroying the threat before it can harm the cell.

Figure 3. CRISPR-Cas Immunity.

Image from Innovative Genomics Institute/CRISPRpedia, CRISPR in Nature

1.3 Crispr in nature vs technology

In nature, CRISPR helps bacteria fight viruses, however in technology, scientists program CRISPR to target and cut specific genes in other organisms for genetic modification to occur. For example, in its natural role in bacterial immunity, Cas9 acts as a defense protein that cuts and destroys viral DNA, preventing infection. However, in genome editing technology, Cas9 is repurposed to make deliberate and precise cuts at the targeted locations in an organism's genome. Instead of destroying the DNA, the technology allows the Cas9 protein to either disrupt a gene or insert new genetic material.

1.4 Cell - Based vs In - situ therapies

There are two main ways that CRISPR is used for gene therapy:

1. Cell Based therapy involves removing cells from a patient, editing them in a lab and later inserting them back into the patient's body. This method is often used for blood related diseases. The cells are first collected from the patient (e.g., blood or stem cells), and they are later edited or treated in the lab (e.g., using CRISPR to correct a genetic defect), The modified cells are later expanded if needed and infused back into the patient's body. For example, in the CAR-T cell therapy for cancer, T cells are extracted, engineered to recognize cancer cells and later returned to the body to attack tumors.

2. In-situ therapy edits the DNA directly inside the patient's body, without taking the cells out. During and In - Situ therapy, therapeutic agents are injected or administered to the patient. Later, these agents seek out and edit the target cells directly in vivo (Within the body). An example of an In - Situ therapy is the CRISPR therapy for Leber congenital amaurosis (A genetic eye disorder), where CRISPR components are injected directly into the eye.

Existing CRISPR therapies

2.1 First approved CRISPR treatment

Sickle cell disease is a serious inherited blood disorder caused by a mutation in the HBB gene, which provides instructions for making hemoglobin, the protein that is crucial for carrying oxygen throughout the body in red blood cells. A single base change results in the production of hemoglobin S, an abnormal form of hemoglobin. Under low oxygen levels, hemoglobin S molecules stick together, causing red blood cells to become rigid, sticky and crescent shaped. These abnormal cells block blood flow in small vessels, leading to organ damage, increased risk of stroke and severe pain.

2.2 Case study: Sickle cell disease

CRISPR was used to treat sickle cell disease for the first time ever in 2023. The therapy, called Casgevy, was the first CRISPR approved treatment, creating a huge medical breakthrough. Doctors collect stem cells from the patient’s bone marrow and use CRISPR to turn off a gene called BCL11A, which stops the production of fetal haemoglobin (HbF). By switching off this specific gene, patients started making fetal haemoglobin again, which can carry oxygen properly. The edited cells were later returned to the patient's body, where they started producing healthy red blood cells, allowing the patient to no longer require blood transfusions.

2.3 Advantages and Disadvantages

Advantages:

1. CRISPR can potentially cure genetic diseases by fixing the root cause. Unlike

traditional therapies that only treat symptoms, CRISPR edits the actual faulty DNA

sequence responsible for the disease.

2. It's faster and more precise than older gene editing methods. Older techniques such as zinc finger nucleases (ZFNs) and TALENs required custom protein engineering for each target, making them lengthy and too complex, whereas CRISPR only needed a short RNA sequence to guide it to the target, making it faster, more efficient and effective.

3. Some treatments only require a single procedure. Many CRISPR therapies are

designed as one-time treatments, especially ex vivo therapies such as Casgevy for sickle cell disease.

Disadvantages:

1. Treatments are not available to the widespread public. Current CRISPR therapies can cost over 2 million dollars per patient, such as Casgevy and Lyfgenia, making them inaccessible to most people.

2. Can cause unintended edits, called off-target effects. Sometimes, CRISPR cuts DNA at sites that are similar, but not identical to the intended target. These off - target mutations can disrupt other genes, potentially causing unwanted side effects such as cancer, immune problems, or new genetic disorders.

3. Long term safety is still being studied. Because CRISPR is a relatively new technology, researchers are still monitoring patients over time to observe any complications.

Future CRISPR therapies

3.1 Preclinical and clinical trials

Before new CRISPR treatments are allowed for public use, they must pass 2 specific trials.

1. Preclinical trials are done in lab animals and cells to study safety

2. Clinical trials involve human patients and happen in 3 phases:

Phase 1: Is it safe?

Phase 2: Does it work?

Phase 3: Is it better than existing treatments?

3.2 Developing CRISPR therapies

Scientists are developing new CRISPR therapies for many conditions, including:

1. Type 1 Diabetes: Researchers are using CRISPR to edit immune cells, particularly

regulatory T cells, to reduce or eliminate their attack on pancreatic β cells.

2. Blindness: In retinal diseases such as Leber congenital amaurosis (LCA), CRISPR is being used to fix mutations in genes like CEP290 directly in retinal cells via in vivo editing. This approach restores normal CEP290 function, helping to recover

photoreceptor health and vision

3. Muscular dystrophy: For Dunchenne muscular dystrophy (DMD), CRISPR strategie target the DMD gene itself to restore the reading frame of dystrophin, the large muscle protein that is missing in patients.

3.3 Case Study: HIV

One of the most studied CRISPR therapies for HIV targets the CCR5 gene, which encodes a receptor that HIV uses to enter immune cells. In a 2019 clinical trial in China, CRISPR was used to edit CCR5 in donor stem cells before transplanting them into a patient with both HIV and leukemia. However, although the edited cells were successfully transplanted and caused no off-target effects, the gene editing efficiency was low, and the therapy did not cure HIV. A newer therapy, EBT-101, developed by Excision Biotherapeutics, uses CRISPR to directly remove HIV DNA from infected cells. It is currently in phase 1/2a trials in the US and has shown early signs of promise for curing HIV.

3.4 Case Study: Cancer

In cancer treatment, CRISPR is being used to enhance immune cells. For example, T cells can be edited to remove the PDCD1 gene, which encodes the immune checkpoint protein PD-1. Removing PD-1 prevents cancer cells from “turning off” the immune response. In a 2016-2019 Chinese Phase 1 trial, CRISPR edited T cells were used to treat patients with non - small cell lung cancer. The treatment was safe and showed minimal side effects, although the effectiveness of using this type of CRISPR therapy to shrink tumors was limited.

Ethical considerations of CRISPR

4.1 Off target effects

CRISPR can sometimes hit the wrong target. If it accidentally cuts the wrong DNA in the genome, it could accidentally switch off an essential gene or activate a harmful one. This could lead to different types of diseases, such as cancer. Newer versions of CRISPR, such as “prime editing,”, which is a precise gene editing technique that allows scientists to directly rewrite specific DNA sequences, are being developed to reduce the risks of off-target effects occurring.

4.2 Passing edits to future generations

Editing sperm, eggs, or embryos, means that the changes made by CRISPR can be passed to children and future generations. This raises serious ethical questions such as : What if a gene edit causes problems in the lives of future generations? Should parents be allowed to choose features such as appearance or IQ in their future children? These questions are yet to be answered and are still debated.

4.3 Case study: CRISPR editing babies

In 2018, Chinese scientist He Juankui shocked the scientific community by announcing the birth of the world's first CRISPR-modified babies. Twin girls, Lulu and Nana. He claimed to have edited the CCR5 gene, which encodes a receptor that HIV uses to enter immune cells. By disabling this gene, the goal was to make the twins resistant to HIV.

One major concern of the procedure was the lack of medical necessity. The father was HIV positive, but the risk of HIV transmission could have been more safely and reliably eliminated through existing methods such as sperm washing. Editing the embryos wasn't necessary but rather experimental and risky. However, the most discussed aspect of the therapy was the ethical violation, the edited children could not consent, and the long-term health effects of the edit are unknown. These edits could be passed onto future generations, which means that a single edit will affect entire family trees.

Jennifer Doudna, the co-inventor of CRISPR, described this experiment as a “shocking and unethical breach of scientific conduct” and warned that such reckless use of gene editing could damage public trust and slow down medical processes. As a result of this scandal, He Jiankui was sentenced to three years in prison by Chinese authorities for violating medical regulations.

Conclusion

5.1 Summary

CRISPR is revolutionizing science and medicine by allowing researchers to edit DNA with groundbreaking precision and efficiency. It originated as a natural bacterial immune defense but has been adapted into a powerful tool for treating genetic diseases, infections, and even cancer. CRISPR therapies have already been approved for use in diseases such as sickle cell disease, proving that gene editing is no longer theoretical - it is today's reality and it's making a difference.

5.2 Is CRISPR on the Way to Being Recognized Worldwide?

CRISPR is rapidly gaining global recognition and acceptance, both in research and clinical settings. Dozens of clinical trials are underway around the world, targeting diseases from HIV to cancer to genetic blindness. However, widespread use depends on overcoming challenges like high costs, unequal access and the need for strict ethical guidelines. With continued regulations and research, CRISPR has a huge potential to become globally recognized.

Bibliography

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Active Hearts Association

From Bacterial Defense to Human Innovation: The Science and Applications of CRISPR

Contents:

1. Introduction to CRISPR and how it is now used as a technology

2. Existing CRISPR therapies

3. Future CRISPR therapies

4. Ethical considerations of CRISPR

5. Conclusion

Intro to CRISPR and how it is now used as a technology: