See also CRISP gene editing, RNA interference and Gene Delivery. 

Companies: Dark Horse Consulting Group

Gene therapy encompasses the genetic modulation of cells and/or tissue in order to achieve a therapeutic effect. Gene therapy comes in a variety of forms from standard gene replacement strategies (for loss of function abnormalities), to gene silencing strategies (for gain of function abnormalities) and gene editing techniques. In all cases, the therapeutic genetic material is packaged in either a recombinant virus or non-viral vehicle and is delivered to cells via either in vivo or ex vivo routes of admistration. (Henckaerts, “What re the issues associated with developing gene therapies for rare disease and are the current development models working?” Cell & Gene Therapy Insights 2024: 10(5), 773-784)

Cell and gene therapy (CGT) products represent a diverse class of advanced therapies with the potential to treat and cure the underlying cause of a disease. Over the last several years the number of FDA approved CGTs has steadily increased form two products in 2015 to a total of 28 in 2024 (excluding cord blood dervived therapies, off-market and withdrawn licenses). These 38 approvals are spread across 3 major product classes: cell therapies, gene therapies and gene-modified cell therapies. The majority of approved products utilize viral vectors to deliver genetic material, with adeno-associated virus (AAV) being the predominant platform for in vivo gene therapies and lentivirus (LVV) being the predominant modality sued ex vivo for gene modified cell therapies. AAV delivers genetic material that forms episomal DNA in a cell which largely does not integrate into the host genome. This leads to stable expression in non-dividing cells and transient expression in dividing cells, as each cell division will ultimately dilute the episomes. In contrast, LVV delivers its genetic payload into both dividing and non-dividing cells leading to stable expression, and integration is typically random. (Christina Fuentes “Coming of age: an overview of the growing toolbox for gene editing and its use in CGT applications” Cell & Gene therapy insights, 2024; 10(9), 1221-1236).

Ex vivo Gene Therapies:

Ex vivo genome editing (GE) cell and gene therapy (CGTs) are the most advanced in development (i.e., CASGEVY commercial approval) and comprise the majority of GE CGTs in the clinical. In most cases, delivery is achieved via electroporation to the target cells ex vivo while in vivo GE CGTs utilize viral and nonviral delivery platforms. Ex vivo GE CGTs offer an advantage of greater control of editing, as the target cell population can be precisely selected, and analysis of any off-target edits can be performed prior to administration to the patient. (Christina Fuentes “Coming of age: an overview of the growing toolbox for gene editing and its use in CGT applications” Cell & Gene therapy insights, 2024; 10(9), 1221-1236).

Ex vivo gene therapies include adoptive cell strategies that enhance the anti-tumour activity of lymphocytes to target rare blood cancers such as Kymriah and genetically modified CD34+ hematopietic stem cells to treat non-cancer related RD such as Strimvelis, Casgevy and Lenmeldy.

HSCs are the target cell population:

HSCs are a good target cell population in gene therapy due to their ability to repopulate the patient’s body and remain in the system indefinitely. One approach involves extracting the cells from the patient, culturing them ex vivo, genetically modifying them, and re-infusing them into the patient. In the meantime, the patient can receive chemotherpay or a conditioning regimen to create space in the bone marrow for the genetically modified cells. (Charlotte Barker “Advancing ene therapies for beta-hemoglobinopathies with novel genome and epigenome editing tools” Cell & Geen Therapy Insights, 2024: 10(9), 1163-1171).

In vivo Gene Therapies:

In vivo gene therapy involves direct administration (either locally or systemically) of the vectorized therapeutic genetic material with the intention of directly transfecting or transducing cells in situ for therapeutic effect. Vector systems for in vivo gene therapy are selected based on their specific targeting capacity for the intended tissue and their safety profiles. Currently, recombinant AAV has attracted the most attention, with seven AAV based products arleady on the market, including ntoable therapies such as Luxturna (for Leber congenital amaurosis (LCA)) and Zolgensma (for spinal muscular atrophy (SMA)).  (Henckaerts, “What re the issues associated with developing gene therapies for rare disease and are the current development models working?” Cell & Gene Therapy Insights 2024: 10(5), 773-784)

 RNA Therapy

Therapeutic RNA refers to antisense oligonucleotides (ASOs), such as gapmers, which contain DNA nucleotides flanked by RNA, small interfering RNAs (siRNAs) or large RNAs, such as messenger RNA (mRNA). These RNA therapies act by targeting RNA or proteins, by encoding missing or defective proteins, or by mediating DNA or RNA editing. Irrespective of their therapeutic mechanism of action, the large size of some therapeutic RNAs, such as mRNAs, their anionic charge, and their susceptibility to RNases present in both the bloodstream and tissues make it difficult for therapeutic RNA to enter cells efficiently and function on its own. To overcome the barriers to safe and effective RNA delivery, scientists have developed both viral vector and non-viral delivery systems that protect the RNA from degradation, maximize delivery to on-target cells and minimize exposure to off target cells. (Dahlman “Drug delivery systems for RNA therapeutics” Nature Reviews, Genetics, 23 (May 2022).

Oligonucleotide drugs, such as ASOs and siRNAs, that utilize enzymes endogenous to eukaryotic cells, such as RNAse H1 or the RNA induced silencing complex (RISC), respectively, facilitate delivery by not requiring the delivery of large enzymes. (Dahlman “Drug delivery systems for RNA therapeutics” Nature Reviews, Genetics, 23 (May 2022).

Although different RNA payloads can have different biochemical mechanisms of action, all of them must avoid clearance by off-target organs, must access the correct tissue, must interact with the desired cell type in a complex tissue microenviorment, must be taken up by endocytosis, and must exit the endosome, without eliciting a deleterious immune response. Although small oligonucleotide RNA therapeutics, including ASOs, siRNAs, and ADAR oligonucleotides, can be modified using stable chemistries and delivered using conjugates, mRNA based and DNA based therapeutics require a vehicle for entry into the cell. To facilitate this process, scientifists have developed several RNA delivery systems using a range of materials, including polymers and LNPs. (Dahlman “Drug delivery systems for RNA therapeutics” Nature Reviews, Genetics, 23 (May 2022)).

RNA Interference (RNAi): (See outline)

Companies: Alnylam Pharmaceuticals

RNAi is emerging as a strategy for treating a range of genetic disorders. Its therapeutic efficacy is based on gene silencing wherein a synthetic siRNA takes advantage of machinery in the cell to inhibit specific mRNA expression. Unlike genome editing which make changes to the cell’s DNA, the effect of RNAi is not permanent, providing an extra layer of safety in the clinic. The approach has been used to treat liver fibrosis where siRNA loaded lipid nanoparticles are used to deactivate hepatic stellate cells (HSCs). The siRNA maket is estimated to surpass 67 billion by 2036. (Nnenna Ohaka “Aptamer shares jump 23% following siRNA deal with AstraZeneca”, Tides Global, July 16, 2024).

siRNA interferes with mature mRNA, which is easier to acheive than nuclear delivery. (Dahlman “Drug delivery systems for RNA therapeutics” Nature Reviews, Genetics, 23 (May 2022)

mRNA:

Another type of RNA therapeutic is mRNA, which can encode proteins that have therapeutic activity. Because of their size, mRNAs are in vitro transcribed and cannot currently be made with site specific chemical modifications using solid state synthesis. mRNA can be used to replace protein, using replacement therapies, to reduct protein levels, using Cas9 cutting approaches, or to repair protein mutations at the DNA level, using base editing. (Dahlman “Drug delivery systems for RNA therapeutics” Nature Reviews, Genetics, 23 (May 2022)).

Rare Diseases and Gene Therapy:

RD is an umbrella term used to group a road range of individual diseases that share the common trait of having a low point prevalence within a population. There are an estimated 7k forms of RD. One of the key therapeutic modalities opted for the development of new treatments for RD is gene therapy. Despite the unmet medical needs and clear rationale for gene therapy in a great many different forms of RD, the number of gene therapy products available in the clinic remains relatively low. From a specific in vivo gene therapy perspective, hundreds of clinical trails utilizing AAV based gene therapy strategies have been undertaken for a variety of indications, yet the number of in vivo gene therapies on the market is still in single digits. The case for ex vivo gene therapies is arguably better, but the nature of these medicines often limits them to rare, oncology and immunodeficiency related indications, restricting the number of RD indications with which they are applicable. Currently, as little as 5% of all RDs have pharmacological intervention options, leaving the remaining 95% with no access to established drug based treatments. One of the reasons for this disparity can be attributed to the complex commercialization models associated with developing pharmaceutical agents that target small patient populations. another problem associated with RD drug development is the lack of characterization within the diseases themselves. Of the 7k odd RDs, only 355 of them have a code in the existing International Classifcation of Diseases (ICD).  (Henckaerts, “What are the issues associated with developing gene therapies for rare disease and are the current development models working?” Cell & Gene Therapy Insights 2024: 10(5), 773-784))

Ophan Drug Act (OdA): was created in an attempt to provide incentivization for the development of new drugs for RDs. The act deployed tax incentives, enhanced patent protection and marketing rights, and clinical research subsidies to spur the pharmaceutical industry into action.