Gene Therapy

Gene therapy is a collection of medical approaches that try to treat disease by changing genetic information in cells rather than just treating symptoms or supplying missing products from the outside. In this chapter, the focus is on what is unique about gene therapy: its goals, main strategies, methods of delivery, major applications, and the special risks and ethical questions that arise.

Basic Idea and Goals of Gene Therapy

In classical medicine, drugs usually act on proteins, cells, or organs. In gene therapy, the target is one step "upstream": the DNA (or sometimes RNA) that encodes proteins.

Typical goals are:

• Replace a faulty or missing gene with a functional copy
• Add a new gene to confer a useful function (e.g., resistance to a virus, ability to recognize cancer cells)
• Silence or inactivate a harmful gene (e.g., an overactive oncogene)
• Correct a mutation in the original gene sequence itself

Gene therapy aims ideally at long‑lasting or permanent improvement after a limited number of treatments, because the genetic change can persist as cells divide.

Two major therapeutic targets are distinguished:

• Somatic gene therapy: changes in body cells (e.g., blood cells, liver cells). Effects are limited to the treated individual and are currently the only form used in humans.
• Germline gene therapy: changes in egg cells, sperm cells, or very early embryos, so that the modification is inherited by future generations. This is widely considered ethically unacceptable and is prohibited in many countries.

Main Strategies in Gene Therapy

1. Gene Addition (Supplementation)

Here a functional copy of a gene is delivered into cells that lack it or possess a defective version. The new gene usually integrates into the genome or persists as an extra piece of DNA and is expressed alongside the defective original.

Typical use:

• Monogenic recessive diseases, where a single working copy of the gene can restore enough function, e.g., some forms of:
• Severe combined immunodeficiency (SCID)
• Inherited retinal diseases
• Certain metabolic disorders in the liver

The original faulty gene is not removed or repaired; its effect is simply compensated.

2. Gene Silencing (Inhibiting Gene Expression)

Sometimes, disease results from too much of a certain gene product or from a harmful version that needs to be turned off rather than replaced.

Two broad approaches:

• RNA-targeting strategies
  These reduce the amount of the messenger RNA (mRNA) that is produced or survives. Examples:
• Small interfering RNA (siRNA)
• Short hairpin RNA (shRNA)
• Antisense oligonucleotides (short, synthetic strands complementary to mRNA)

These molecules bind specific mRNAs and either mark them for degradation or block their translation into protein.

• Gene inactivation at the DNA level
  Targeted breaks in DNA can disrupt a gene so that it no longer produces a functional product (for example, by introducing small insertions or deletions that shift the reading frame).

Gene silencing strategies are being explored for:

• Certain cancers (silencing oncogenes)
• Viral infections (silencing viral genes or host factors needed by viruses)
• Dominant genetic diseases caused by a toxic protein

3. Gene Correction and Genome Editing

Instead of adding a new gene elsewhere, genome editing aims to directly correct the existing gene in its natural location.

Modern tools:

• CRISPR–Cas systems
  A guide RNA directs the Cas enzyme to a specific DNA sequence through base pairing; the enzyme then cuts, and the cell's repair machinery modifies the sequence. With additional components, specific corrections can be introduced (e.g., changing one base to another).
• Other nucleases (used before CRISPR became common):
• Zinc-finger nucleases (ZFNs)
• TALENs (Transcription Activator-Like Effector Nucleases)

Editing strategies:

• Knock-out: inactivate a gene (similar outcome to gene silencing but at DNA level)
• Knock-in: insert a functional gene into a defined safe location
• Precise correction: repair a mutation so that the native gene works again

Genome editing is particularly attractive because:

• It can permanently correct a mutation
• It can be designed to act only at specific positions in the genome

However, unintended cuts at other locations (off‑target effects) and incomplete editing present significant safety challenges.

Delivery of Genetic Material: Vectors and Methods

Gene therapy depends critically on how the genetic material is delivered into target cells. DNA and RNA do not easily cross cell membranes on their own and are rapidly degraded in the body. To solve this, vectors and other methods are used.

Viral Vectors

Modified viruses are frequently used because viruses are naturally adapted to insert genetic material into host cells.

Commonly used viral vectors:

• Adeno-associated viruses (AAV)
• Small DNA viruses
• Low disease-causing potential in humans
• Often do not integrate into the genome but remain as separate DNA in the nucleus
• Can drive long-term gene expression in non-dividing cells (e.g., muscle, liver, retina)
• Have a limited cargo capacity (only relatively short genes fit)
• Lentiviral vectors (derived from retroviruses such as HIV)
• Integrate their DNA into the host genome
• Can infect both dividing and non-dividing cells
• Allow stable, long-lasting expression and are widely used in modified immune cells (e.g., CAR-T cells)
• Integration carries a risk of disrupting host genes (insertional mutagenesis)
• Adenoviral vectors
• Do not integrate into the host genome; exist as episomes (separate DNA)
• Can carry larger genetic payloads
• Often provoke stronger immune responses, typically leading to short-term expression

In all cases, viruses used in gene therapy are genetically modified to remove genes needed for replication or pathogenicity, and to insert therapeutic sequences instead. They are thus designed to deliver genes without causing active infection.

Non-viral Delivery Methods

Non-viral methods avoid using viruses and generally have lower immunogenicity, but often also lower efficiency.

Important approaches:

• Lipid nanoparticles (LNPs)
• Tiny fat-like vesicles that encapsulate DNA or RNA
• Can fuse with cell membranes and release their cargo
• Used, for example, in some RNA-based therapies and vaccines
• Can be chemically modified to improve stability and targeting
• Physical methods
• Electroporation: applying short electric pulses to cells to temporarily open pores in the membrane, allowing DNA/RNA entry
• Gene gun (particle bombardment): microscopic particles coated with DNA are shot into tissues
• Hydrodynamic injection (in experimental animals): rapid injection of a large volume of solution, forcing DNA into liver cells
• Receptor-mediated uptake
  DNA or RNA is attached to molecules (e.g., antibodies, sugars, peptides) that bind specifically to certain receptors, which bring the genetic material into the cell by endocytosis.

Each target tissue (e.g., muscle, eye, liver, bone marrow) may require a tailored combination of vector type, route of administration, and dosage.

In Vivo vs Ex Vivo Gene Therapy

Two main treatment formats are distinguished:

• In vivo gene therapy
• The vector or genetic material is delivered directly into the patient's body (e.g., injected into the bloodstream, directly into the eye, or into a particular organ).
• Target cells are modified inside the body.
• Advantages: no cell culture step, suitable for tissues that are difficult to remove.
• Challenges: harder to control exactly which cells are modified and to manage systemic effects.
• Ex vivo gene therapy
• Patient cells are removed, genetically modified in the laboratory, tested and expanded, and then reinfused.
• Often used for:
• Blood-forming stem cells from bone marrow
• T lymphocytes (e.g., in cancer immunotherapy)
• Advantages: cells can be quality‑checked before re‑infusion; better control over which cells are modified.
• Challenges: technically complex and expensive, suitable mostly for cells that can be taken out and reimplanted.

Examples of Gene Therapy Applications

Gene therapy is still a relatively young field, but several therapies have been approved, and many more are under investigation.

Inherited Monogenic Diseases

These are disorders caused by mutations in a single gene, making them promising initial targets.

Examples (general types, not exhaustive):

• Immune deficiencies
• Forms of SCID due to mutations in genes essential for lymphocyte function
• Approaches include ex vivo gene addition into hematopoietic stem cells using retroviral or lentiviral vectors
• Inherited retinal diseases
• Mutations in genes required for photoreceptor function
• A well-known application is a therapy for a specific retinal dystrophy, where a functional gene is delivered via AAV injected under the retina
• Goal: slow or partially reverse vision loss
• Metabolic liver diseases
• For example, certain enzyme deficiencies where the liver is the primary site of disease
• In vivo gene therapy using AAV targeted to liver cells aims to provide a functioning enzyme

Hemophilia

Hemophilia A and B are bleeding disorders caused by deficiencies in clotting factors (factor VIII or IX). Gene therapy strategies deliver functional copies of the relevant gene into liver cells so they start producing the missing clotting factor themselves.

Features:

• Typically in vivo AAV-mediated delivery
• Long-term expression can reduce or eliminate the need for frequent factor infusions
• Potential issues with immune responses to the vector or the newly produced factor, and gradual decline of expression over years

Cancer Gene Therapy

Gene therapy approaches in cancer often reprogram the patient's own immune cells to better recognize and attack tumor cells.

Major example:

• CAR-T cell therapy (Chimeric Antigen Receptor T cells)
• T cells are collected from the patient (ex vivo approach).
• A gene is introduced (often via a lentiviral vector) encoding a synthetic receptor that specifically recognizes a molecule on tumor cells.
• The modified T cells are expanded and reinfused to attack the cancer.

Other cancer-related strategies:

• Introducing genes that:
• Make tumor cells more visible to the immune system
• Sensitize tumor cells to specific drugs or radiation
• Produce toxic substances locally within tumors

Gene therapy in cancer often overlaps with immunotherapy and targeted therapy.

Gene Therapy for Viral Infections

The idea here is to:

• Directly target viral genomes within infected cells (e.g., using genome editing tools)
• Modify host cells to be resistant to infection (for instance, altering receptors that viruses use to enter cells)

Research includes attempts to:

• Disable integrated HIV DNA in patient cells
• Make blood-forming stem cells resistant to HIV so that newly formed immune cells are less susceptible

These applications are still largely experimental.

Safety Risks and Limitations

Despite its potential, gene therapy involves significant biological risks that must be carefully controlled.

Insertional Mutagenesis

When vectors integrate into the host genome (e.g., some retroviral or lentiviral vectors), there is a possibility that:

• The insertion occurs near or within important genes (e.g., tumor suppressor genes, cell-cycle regulators).
• This can lead to uncontrolled cell growth and tumor formation.

Past clinical trials have shown that such events can occur, especially when:

• Integration sites cluster in regions controlling cell division.
• Strong promoters from vectors accidentally activate nearby oncogenes.

This has led to:

• Development of safer vectors with reduced tendency to integrate in risky genomic regions.
• Use of self-inactivating designs, and targeting strategies to more "neutral" loci.

Immune Reactions

The immune system can respond to:

• The viral vector itself
• The newly produced protein (especially when the patient's immune system has never encountered a functional version before)

Consequences:

• Reduced effectiveness of treatment (rapid clearance of vector or modified cells)
• Inflammation or more serious immune-mediated complications

To manage this, clinicians may:

• Screen for pre-existing immunity to specific viral vectors
• Use immunosuppressive drugs around the time of treatment
• Adjust vector type and dosing strategies

Off-target Effects in Genome Editing

Genome editing tools like CRISPR–Cas are highly specific but not perfect.

Potential problems:

• Unintended cuts at similar DNA sequences elsewhere (off-target sites)
• Unpredicted deletions, insertions, or rearrangements around the cut site
• Mosaicism (only some cells are edited; others remain unmodified)

These effects can alter genes not intended to be changed, possibly leading to new diseases, including cancer, or altering critical cell functions.

Limited Targeting and Duration

Not all tissues are equally accessible:

• Solid organs such as the brain or pancreas are hard to reach uniformly.
• The vector may not penetrate deeply into all parts of a large tissue or organ.

Duration of effect:

• In non-dividing cells, a single treatment may provide long‑term benefit.
• In rapidly dividing cells (e.g., in growing children or some tissues), non-integrating vectors are diluted as cells divide.

This can mean:

• Need for repeat treatments
• Necessity of integrating vectors or editing approaches for lasting effect

Manufacturing and Cost

Gene therapies are complex biological products:

• Manufacturing highly purified, consistent viral vectors or nanoparticles is technically demanding.
• Ex vivo cell manipulations require specialized facilities and strict quality control.

As a result:

• Many gene therapies are extremely expensive.
• Access can be limited by healthcare system resources and regulatory approvals.

Ethical and Social Aspects of Gene Therapy

Gene therapy raises questions not only of safety and efficacy but also of how such powerful technologies should be used in society.

Somatic vs Germline Interventions

Most countries allow somatic gene therapy for severe diseases under strict regulations, but germline modifications are widely prohibited.

Reasons for caution about germline interventions:

• Changes are heritable and affect individuals who cannot consent (future generations).
• Long-term, multi-generational effects cannot be fully predicted.
• Risk of "enhancement" uses (altering traits for non-medical reasons, such as appearance, intelligence, or physical performance).

Therapy vs Enhancement

A key ethical distinction is between:

• Therapy: treating serious diseases or disabilities to restore or approximate normal function.
• Enhancement: altering normal traits beyond typical human variation for perceived benefit or preference.

Concerns:

• Social pressure to enhance certain traits
• Deepening inequalities if only some groups have access to enhancements
• Changing conceptions of normality and disability

Many regulatory frameworks currently restrict gene therapy to clear medical indications.

Justice, Access, and Global Inequality

Given the high cost of many gene therapies, there are issues of:

• Fair access: who can actually receive such treatments?
• Global inequality: wealthier countries and patients are more likely to benefit, while rare genetic diseases and advanced cancers exist worldwide.
• Opportunity costs: resources used for extremely expensive single-patient therapies vs. more basic public health measures that help many.

Discussions about pricing, public funding, and intellectual property are central in policy debates.

Consent and Information

Because gene therapy is relatively new and complex:

• Patients must receive clear, understandable information about potential benefits, risks, alternatives, and uncertainties.
• For pediatric applications, decisions are made by parents or guardians, raising questions about how to balance risks and benefits in children.

Long-term follow-up studies are usually required to monitor late effects, which also raise questions about:

• Data protection
• Responsibility for long-term care and monitoring

Future Perspectives

Gene therapy is rapidly developing. Likely future directions include:

• More precise and safer editing tools
• Improved CRISPR variants with reduced off-target activity
• Base editors and prime editors capable of changing specific nucleotides without creating double-strand breaks
• Better targeting of specific tissues
• Engineering of viral capsids and nanoparticles to home in on particular cell types
• Local delivery techniques to the brain, heart, or other difficult organs
• Broadening indications
• From rare monogenic diseases to more common conditions such as heart disease, neurodegenerative disorders, and certain forms of diabetes, if clear genetic targets are found
• Combination therapies
• Gene therapy plus traditional drugs, small-molecule inhibitors, or immunotherapies to enhance effect and reduce doses
• Regulatory evolution
• As knowledge grows, frameworks will likely adapt, balancing patient protection with enabling innovation

Gene therapy thus represents a profound shift in medicine: instead of solely treating the consequences of genetic errors, it strives to change the underlying information itself. Its further development will depend not only on scientific progress but also on careful ethical reflection and socially responsible regulation.