The ‘Genomic Revolution’ and its Impact on Medical Research

Rehma Chandaria

The sequencing of the human genome held great promise for better
disease treatment and a concomitant reduction in animal experiments.
Neither promise has been adequately fulfilled.

In 1953, four scientists — James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin — uncovered the double helix structure of DNA, the molecule that carries genetic information in all living beings. In the 60 years since then, the ways in which we study and manipulate genes has changed considerably. In 2001, the human genome was sequenced, providing hope that common and serious conditions, such as Alzheimer’s disease and heart disease, could be predicted before they manifested clinically, and that personalised treatments for many other human conditions could be found. However, a decade on from this historic scientific achievement,  questions were raised about the lack of real clinical progress made from this vast genetic knowledge.1,2 In part, this is due to unrealistic expectations and the difficulties involved in translating discoveries made in the laboratory to clinical products that can benefit patients.

The sequencing of the human genome and better technologies for studying human genetics came with the expectation that we would no longer have to rely on animals to learn about human diseases and to find treatments. However, in reality, there has been a sharp increase in the use of genetically-modified animals, which has been responsible for the overall increase in animal procedures undertaken in the UK3 and elsewhere, in recent years.

So what actually has been achieved as a result of the ‘genomic revolution’, and what future progress can we realistically expect to see? Furthermore, is the use of animals still justified in this genomics era?

Some examples of successes arising from the genomic revolution

New research technologies

Since 1953, and particularly accelerated after the launch of the Human Genome Project in 1990, there have been significant advances in the research techniques used to study genes. Some particular highlights include the development of the Polymerase Chain Reaction (PCR) in 1985, and progress made in sequencing methods which means that the precise order of bases in DNA can now be obtained quickly and efficiently. PCR is still routinely used by researchers across the globe, to amplify a small amount of DNA to  generate millions of copies of a particular gene.

Understanding and treating genetically inherited diseases

The individual genes responsible for causing many inheritable diseases have been identified as a result of the genomic revolution. Consequently, gene therapy is now a possibility, where a faulty gene is corrected by inactivation or replacement with a functional version of the gene. In 2012,  Glybera became the first gene therapy treatment to be approved  in Europe.4 The treatment involves the delivery of an intact copy of the faulty gene in the rare inherited genetic disorder, lipoprotein lipase deficiency. Many other gene therapy treatments are in human clinical trials, although it is still an experimental
technique with several hurdles to be overcome before it can be considered as a widespread treatment option.

Cancer

Cancer usually occurs as a result of mutations in the genetic sequence,5 and therefore diagnosis and personalised treatment of cancer is one of the primary successes of the genomic revolution. The genome sequencing of different cancers has revealed common mutations and patterns which determine how cancers develop.6 Mutations in genes such as BRCA1 have been identified as increasing the risk of developing breast cancer, meaning that preventative action, such as surgery to remove the breasts, can be offered to carriers of these mutations. Treatments have been developed against cancers with particular genetic profiles. For example, trastuzumab (Herceptin) is a drug mainly used to treat breast cancer, but it is only effective against cancers which overexpress the HER2 protein.7 Another example of this selective treatment is the drug gefitinib, which is only active against the 10–15% of lung cancers that carry EGFR mutations.8

Why have more treatments not been developed since the human genome was sequenced?

Of the 14,000 genes sequenced to date, only around 3800 are associated with a genetic condition that arises when the gene is faulty.9 The most common human diseases are not caused by a single gene defect, but are associated with multiple genes, each one having a small contributing effect. Other important contributing factors include influences such as diet, gender, ethnicity, age and environment, and epigenetics. Epigenetics refers to changes to the DNA molecules and the protein with which the DNA is associated to form chromatin. These epigenetic changes affect whether particular genes are switched on or off. Although every cell in the body of an organism has identical DNA, due to epigenetic modifications the characteristics of a liver cell, for example, are very different to those of a nerve cell. In addition, DNA interacts with other molecules in cells, such as RNA, signalling molecules and receptors. These complicating factors mean that someone can appear to have the genetic features of a disease such as diabetes mellitus, but not express it clinically. Therefore the idea of predicting and preventing diseases based on a person’s genetic make-up continues to be much further away than initially was hoped.

Genetically-altered animals

Since the human genome was sequenced, there has been a large increase in the use of genetically altered animals, and in particular mice, with the aim of learning about the roles of individual genes in whole animals. A genetically-altered animal has been bred or engineered to mutate, remove or insert a gene of interest. However, as the complexities already described above suggest, it is not always possible to find out the role of a gene in humans just by altering it in a mouse. Interactions with the environment and other components in a cell mean that the effects can vary greatly between species.10 In  fact, there are even examples of gene knockouts having different effects in different strains of mice.11 Therefore, we have to question whether data from genetically-altered mice can really provide insights into complex genetic interactions in humans. This is particularly relevant because of the inefficient process by which the desired genetic alterations are achieved, which results in large numbers of animals being bred but not used in experiments. There are several steps in the breeding procedure at which surplus animals are produced. The gene of interest (transgene) is constructed by using recombinant DNA technology, and then inserted into embryos which are implanted into female mice with the hope that they become pregnant and give birth to mice carrying the transgene. However, only 25% of the animals will contain the transgene, and even fewer will prove to be satisfactory for further study.12 Furthermore, extensive cross-breeding and back-crossing is required to produce animals with a homozygous genetic background in which both copies of the gene are correctly modified. The majority of the animals produced in these steps will not contain the correct genotype, are therefore considered surplus to requirements and are usually killed.13 Data from The Netherlands indicate that the number of animals that are bred but not used is almost equal to the number of animals used in experiments.14 This number of surplus animals continues to increase, due to the ongoing rise in the use of genetically-altered animals.

There are different levels of understanding human biology: the whole body, which has historically been studied by using non-human animals; tissue and organs; the cellular level; and the molecular level — which is where genomics is focused. To fully grasp how diseases develop, and to find new treatments, we need to understand the processes that happen at every level, and not just molecular processes. Despite the great successes of the genomic revolution, it is important to realise that work on genes is not the be all and end-all of biomedical research. There are complex systems and processes that occur in the body which are not related to genetics. Examples of this at the cellular and tissue levels are post-translational modifications, which occur to proteins after  they have been produced, and interactions with the extracellular matrix that surrounds cells, providing mechanical and biochemical cues that influence how cells behave. With this in mind, it is crucial to maintain efforts in all areas and at all levels of biology, rather than looking at genes and genomics in isolation. It is also vital that this is done by using scientifically- valid approaches, which provide results that are relevant to humans. This will not be achieved by using animals, and especially not genetically-modified animals. Very exciting progress has been made by biologists who have successfully used mathematical approaches to integrate data provided by in vitro techniques and thereby usefully simulate and predict physiological responses in vivo.15 This suggests that a more-complete understanding of human disease can be obtained by using human tissues and by investing in research across different levels.

Conclusions

From improvements in laboratory research technologies, to increased knowledge of genetic contributions to disease and genetic therapies, much has been achieved as the result of the genomic revolution. However, the resulting clinical outcome seen by patients has been much smaller than was anticipated, due to difficulties in translating research into actual treatments. This is due to the complex nature of how genes interact with other factors contributing to disease, as well as an over-reliance on animal models that are inherently different to the humans we are trying to treat. However, if the scientific community is able to turn its focus to human-based research, then the future prospects for new drugs and therapies to improve human health will be much greater.

Rehma Chandaria
FRAME
Russell & Burch House
96–98 North Sherwood Street
Nottingham NG1 4EE
UK
E-mail: science@frame.org.uk

References

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