# Isogenic human disease models

Isogenic human disease models are a family of cells that are selected or engineered to accurately model the genetics of a specific patient population, in vitro. They are provided with a genetically matched 'normal cell' to provide an isogenic system to research disease biology and novel therapeutic agents. They can be used to model any disease with a genetic foundation. Cancer is one such disease for which isogenic human disease models have been widely used.

## Historical models

Human isogenic disease models have been likened to 'patients in a test-tube', since they incorporate the latest research into human genetic diseases and do so without the difficulties and limitations involved in using non-human models.
Historically, cells obtained from animals, typically mice, have been used to model cancer-related pathways. However, there are obvious limitations inherent in using animals for modelling genetically determined diseases in humans. Despite a large proportion of genetic conservation between humans and mice, there are significant differences between the biology of mice and humans that are important to cancer research. For example, major differences in telomere regulation enable murine cells to bypass the requirement for telomerase upregulation, which is a rate-limiting step in human cancer formation. As another example, certain ligand-receptor interactions are incompatible between mice and humans. Additionally, experiments have demonstrated important and significant differences in the ability to transform cells, compared with cells of murine origin. For these reasons, it remains essential to develop models of cancer that employ human cells.

## Targeting vectors

Isogenic cell lines are created via a process called homologous gene-targeting. Targeting vectors that utilize homologous recombination are the tools or techniques that are used to knock-in or knock-out the desired disease-causing mutation or SNP (single nucleotide polymorphism) to be studied. Although disease mutations can be harvested directly from cancer patients, these cells usually contain many background mutations in addition to the specific mutation of interest, and a matched normal cell line is typically not obtained. Subsequently, targeting vectors are used to 'knock-in' or 'knock out' gene mutations enabling a switch in both directions; from a normal to cancer genotype; or vice versa; in characterized human cancer cell lines such as HCT116 or Nalm6.
There are several gene targeting technologies used to engineer the desired mutation, the most prevalent of which are briefly described, including key advantages and limitations, in the summary table below.
| Technique | Gene Knock-In | Gene Knock-out |
| rAAV (recombinant adeno-associated virus vectors) | Targeted insertions or modifications are created within endogenous genes; and so are subject to: The correct gene-regulation mechanisms; and Accurately reflect the disease events found in real patients. rAAV can introduce subtle point mutations, SNPs as well as small insertions with high efficiency. Moreover, many peer reviewed studies have shown that rAAV does not introduce any confounding off target genomic events. Appears to be the preferred method being adopted in academia, Biotech and Pharma on a precision versus time versus cost basis.| | Gene knockouts are at the endogenous locus, and thus are definitive, stable and patient relevant. No confounding off-target effects are elicited at other genomic loci. It requires a 2- step process: Generate a heterozygous KO Generate a bi-allelic knockout by targeting the second allele. This process can therefore generate 3 genotypes (+/+; -/+ and -/-); enabling therefore the analysis of haplo-insufficient gene function. Current limitation is the need to sequentially target single alleles making generation of knock-out cell lines a two-step process.| |
| Plasmid-based homologous recombination | Insertion is at the endogenous locus and has all the above benefits, but it is very inefficient. It also requires a promoterless drug selection strategy entailing bespoke construct generation. A large historical bank of cell lines has been generated using this method which has been displaced by other methods since the mid-1990s. | Deletion is at endogenous locus and has all the above benefits, but it is inefficient. It also requires a promoterless drug selection strategy that entails bespoke construct generation |
| Flip-in | This is an efficient technique that allows the directed insertion of 'ectopic' transgenes at a single pre-defined genomic locus (integration via a FLP recombinase site). This is not a technique for modifying an endogenous locus. Transgenes will usually be under the control of an exogenous promoter, or a partially defined promoter-unit in the incorrect genomic location. Their expression will therefore not be under the same genomic and epigenetic regulation as the endogenous loci, which limits the utility of these systems for studying gene-function. They are however, good for eliciting rapid and stable exogenous gene expression. | Not applicable |
| Zinc-Finger Nucleases (ZFNs) | ZFNs have been reported to achieve high rates of genetic knock-outs within a target endogenous gene. If ZFNs are co-delivered with a transgene construct homologous to the target gene, genetic knock-in's or insertions can also be achieved. One potential drawback is that any off-target double strand breaks could lead to random off-target gene insertions, deletions and wider genomic instability; confounding the resulting genotype. However, no measurable increase in the rate of random plasmid integration was observed in human cells efficiently edited with ZFNs that target a composite 24 bp recognition site | ZFNs are sequence-directed endonucleases which enable the rapid and highly efficient (up to 90% in a bulk cell population) disruption of both alleles of a target gene, although user- defined or patient relevant loss of-function alterations have not been reported at similar frequencies. Off target deletions or insertions elsewhere in the genome are a significant concern. The speed advantage of obtaining a biallelic KO in one step is also partially mitigated if one still needs to derive a clonal cell line to study gene function in a homogenous cell-population. |
| Meganucleases | Meganucleases are operationally analogous to ZFN's. There are limitations inherent in their use such as the meganuclease vector design which can take up to 9 months and cost tens of thousands of dollars. This makes meganucleases more attractive in high-value applications such as gene therapy, agrobiotechnology and engineering of bioproducer lines. | |

## Homologous recombination in cancer cell disease models

Homologous recombination (HR) is a kind of genetic recombination in which genetic sequences are exchanged between two similar segments of DNA. HR plays a major role in eukaryotic cell division, promoting genetic diversity through the exchange between corresponding segments of DNA to create new, and potentially beneficial combinations of genes.
HR performs a second vital role in DNA repair, enabling the repair of double-strand breaks in DNA which is a common occurrence during a cell's lifecycle. It is this process which is artificially triggered by the above technologies and bootstrapped in order to engender 'knock-ins' or 'knockouts' in specific genes 5, 7.
A recent key advance was discovered using AAV-homologous recombination vectors, which increases the low natural rates of HR in differentiated human cells when combined with gene-targeting vectors-sequences.
* Diagram of a typical rAAV vector (source: https://www.horizondiscovery.com/gene-editing/raav)

## Commercialization

Factors leading to the recent commercialization of isogenic human cancer cell disease models for the pharmaceutical industry and research laboratories are twofold.
Firstly, successful patenting of enhanced targeting vector technology has provided a basis for commercialization of the cell-models which eventuate from the application of these technologies.
Secondly, the trend of relatively low success rates in pharmaceutical RnD and the enormous costs have created a real need for new research tools that illicit how patient sub-groups will respond positively or be resistant to targeted cancer therapeutics based upon their individual genetic profile.