Categories
Genomics Precision Medicine

How Modern Genomics has Changed our Approach to Cancer Treatment

Alexia Di Martino—McMaster University Molecular Biology & Genetics 2023

Within our chromosomes, there are billions of nucleotides that are all a part of our genome, the entirety of our DNA. Genomics is the study of the genome. A nucleotide sequence, its precise location, and the gene-gene or gene-protein interactions of specific genes are just a few of the findings that can be discovered through genomics.1 The human body is amazing in its ability to use DNA as a blueprint to direct millions of processes in the body. Of course, our DNA also encodes for the billions of other vital cells – like those of the blood, skin, and brain among other organs – that make up our body on a whole. When cell division goes wrong, though, cells may continue to divide uncontrollably and develop growths that we know as cancer.2

There are two families of genes that influence cancer development. The tumour suppressor gene family has a positive effect on cancerous growth when inactivated or improperly functioning. On the other hand, proto-oncogenes cause cancerous growth when they are mutated and active.3

The Human Genome Project was an advancement in sequencing technology that allowed for a decreased cost of sequencing an organism’s entire genome, as well as improved accuracy of the nucleotides and genes that are sequenced.4 Artificial intelligence and computer algorithms are even further advanced technologies that give researchers the ability to automate pattern-recognition within these sequences. From this, links between a gene’s function in the DNA compared to the patient’s phenotypic presentation of a disease can be made.

Tens of thousands of sequenced genetic mutations have been archived through the amazing work of oncology researchers into genetic libraries. One of these libraries is The Cancer Genome Atlas (TCGA).5 Using a patient’s genome, doctors can refer to these mutated cancer-linked genes to screen patients for susceptibility to a specific cancer.

SOURCE: British Columbia Genome Sciences Centre6

With the knowledge of the patient’s cancerous tumour’s genome, clinicians can identify the exact mechanisms of the cancer cells that causes their proliferation. By comparing the genome of the same patient’s normally functioning ‘germline’ cells to their cancer, researchers can pinpoint the mutated or defective genes responsible for the cancer. They can then recommend better-informed treatments such as pharmaceutical drugs and antibodies targeting certain molecules or pathways of the tumour cells.7 Targeted treatments are much better overall than uninformed therapies. Radiation therapy or stem cell transplants may not be appropriate or as effective in all cases, and can be very expensive. Understanding the genomics of a patient’s cancer could spare them from unnecessarily high medical bills, and more importantly, could have less harmful effects on their body, leading them to being cancer-free more quickly.8

While genomics-driven cancer treatment has been in practice in this way, recent studies into novel gene-editing practices have shown to be promising for the future. In the CRISPR-Cas9 gene editing system, scientists specially design a guide RNA to target a specific DNA fragment. When this guide RNA binds the gene of interest, it associates with a Cas enzyme that cleaves the DNA at that location.9 Scientists may insert a new gene in that cleavage site or perform other modifications depending on their goal.

SOURCE: National Cancer Institute9

Since at least 2017, researchers have been working on using CRISPR-Cas9 on model organisms such as mice and zebrafish in vitro to remove or directly target genes linked to cancer. However, it still poses some challenges when attempting to deliver cancer treatment in vivo.10 These issues are already being studied to create functional and safe delivery of CRISPR-Cas9 gene editing in different tissues in order to accommodate the wide range of cancers seen in patients. As the cancer genome library continues to expand, the CRISPR-Cas9 method of treatment will experience many benefits as well.

The work of biologists in all fields have contributed to this progress – from improved genetic sequencing techniques, to experiments that identify cancer genes, to the assembly of genetic libraries, and everything in between. These advances give every human being a lifesaving advantage in cancer diagnoses. With further research on these gene libraries, scientists will be able to screen the genomes of patients and target cancer-causing genes to inhibit their mechanisms before cancerous cells even get the chance to cause damage.

References

  1. NIH Staff. A brief guide to genomics [Internet]. Genome.gov. 2020 [cited 2022Jan2]. Available from: https://www.genome.gov/about-genomics/fact-sheets/A-Brief-Guide-to-Genomics
  2. Williams GH, Stoeber K. The cell cycle and cancer. The Journal of Pathology. 2011Oct12;226(2):352–64.
  3. Lee EY, Muller WJ. Oncogenes and tumor suppressor genes. Cold Spring Harbor Perspectives in Biology. 2010;2(10).
  4. Hofstatter EW, Bale AE. The promise and pitfalls of Genomics-Driven Cancer Medicine. AMA Journal of Ethics. 2013;15(8):681–6.
  5. NCI Staff. The cancer genome atlas program [Internet]. National Cancer Institute. 2019 [cited 2022Jan2]. Available from: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga/history
  6. BCGSC Staff. Genome sequencing helps prioritize cancer treatment options [Internet]. Genome Sciences Centre. 2020 [cited 2022Jan2]. Available from: https://www.bcgsc.ca/news/genome-sequencing-helps-prioritize-cancer-treatment-options
  7. Mattick JS, Dziadek MA, Terrill BN, Kaplan W, Spigelman AD, Bowling FG, et al. The impact of genomics on the future of Medicine and Health. Medical Journal of Australia. 2014Jul7;201(1):17–20.
  8. Welch JS. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA. 2011Apr20;305(15):1577–84.
  9. NCI Staff. How CRISPR is Changing Cancer Research and Treatment [Internet]. National Cancer Institute. 2020 [cited 2022Jan2]. Available from: https://www.cancer.gov/news-events/cancer-currents-blog/2020/crispr-cancer-research-treatment
  10. Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, et al. Application of the CRISPR/cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Molecular Cancer. 2021;20(1).
Categories
CRISPR Genomics Precision Medicine

The State of Gene Therapies

Nima Karimi — McMaster University Health Sciences 2023

As the quest of mankind for optimal health continues,  different avenues for achieving this goal have emerged. One area, in particular, is looking at the role of genes in the pathophysiology of diseases, and consequently, investigating therapeutics that target those genes. Genes are the basic functional unit of heredity (1); in other words, they determine your height, the color of your eye and hair, and many other biological traits. Importantly, alterations of the genes and genome have been consistently linked to many pathological conditions. Cystic fibrosis (CF), sickle-cell anemia, and Huntington’s disease are some of the more prominent examples of genetic disorders (2). As these conditions have led to increased mortality and reduced quality of life, the scientific community has searched for potential therapeutics; one, in particular, being gene therapy.

The first human studies on gene therapy were done in the early 1990s. One such experiment involved the transfer of genes coding for a specific enzyme, to patients with severe combined immunodeficiency, which showed promising results (3). Since then, research into gene therapy has grown considerably. More recently, some studies have used gene therapy to treat CF, a progressive genetic condition that leads to the loss of lung function with no current treatment (4). Interestingly, the use of gene therapy in CF patients have shown to improve lung capacity (3). With CF being one of the most prevalent genetic disorders, the use of gene therapy shows a promising future for the treatment of this condition.

Now you may be wondering to yourself, how is genetic therapy actually done? Generally speaking, gene therapy involves the identification of cell types and DNA sequences that are defective, and then introducing a new DNA sequence containing the functional genes to offset the effects of the disease-causing genetic alterations (5). There are two different approaches to gene therapy (figure 1), and these involve alterations of different types of cells (6). Somatic gene therapy involves the transfer of DNA to different cells in our body that do not produce sperm or eggs. Given that these changes are not in the germline, any DNA alteration cannot be passed on from parents to their children (6). In contrast, germline gene therapy involves the transfer of DNA to cells that produce eggs or sperms, meaning these changes can be inherited (6).

Additionally, various techniques are being used in gene therapy. One such technique is gene augmentation therapy (6). This technique can be used to treat genetic abnormalities  that stem from mutation, where the gene in question does not produce its functional products (6, 7). As shown in figure 2, this therapy adds the DNA containing a functional gene back into the cell that is defective and ultimately, can reverse the abnormality (8). Another technique involves gene inhibition (6). This technique can be used in pathologies in which the overexpression of certain genes is causing the disease. In this approach, the aim is to introduce a new gene that either inhibits the expression of another faulty gene, or interferes with the activity of the product produced by the faulty gene (9), as shown in figure 3.

Overall, it is clear that gene therapy presents a very promising future for the treatment and management of diseases that were once deemed incurable. Today, there are more than 600 genes and cellular therapies that are being researched (10). In the coming years, one could expect the emergence of many genetic therapies for common and rare conditions. This emergence could both provide treatments for patients that lack therapeutics today, and also improve their overall quality of life.

References

1.         Kitcher P. Genes. The British Journal for the Philosophy of Science. 1982;33(4):337-59.

2.         Conrad Stöppler M. Genetic Diseases (Disorder Definition, Types, and Examples): MedicineNet;  [Available from: https://www.medicinenet.com/genetic_disease/article.htm.

3.         Steffin DHM, Hsieh EM, Rouce RH. Gene Therapy: Current Applications and Future Possibilities. Advances in Pediatrics. 2019;66:37-54.

4.         Davis PB. Cystic Fibrosis Since 1938. American Journal of Respiratory and Critical Care Medicine. 2006;173(5):475-82.

5.         Verma IM, Naldini L, Kafri T, Miyoshi H, Takahashi M, Blömer U, et al., editors. Gene Therapy: Promises, Problems and Prospects. Genes and Resistance to Disease; 2000 2000//; Berlin, Heidelberg: Springer Berlin Heidelberg.

6.         What is gene therapy? 2021 [Available from: https://www.yourgenome.org/facts/what-is-gene-therapy.

7.         Frazier S. Embryo Gene Editing: Changing Life As We Know It 2019 [Available from: https://the-gist.org/2019/05/embryo-gene-editing-changing-life-as-we-know-it/.

8.         Nóbrega C, Mendonça L, Matos CA. Gene Therapy Strategies: Gene Augmentation. In: Nóbrega C, Mendonça L, Matos CA, editors. A Handbook of Gene and Cell Therapy. Cham: Springer International Publishing; 2020. p. 117-26.

9.         James W. Towards Gene-Inhibition Therapy: A Review of Progress and Prospects in the Field of Antiviral Antisense Nucleic Acids and Ribozymes. Antiviral Chemistry and Chemotherapy. 1991;2(4):191-214.

10.       Dorholt M. We’re on the Verge of a Breakthrough for Gene Therapies 2021 [Available from: https://www.evernorth.com/articles/the-history-and-future-of-gene-therapy.

Categories
Genomics

Unfolding the Code of Cancers Using the Next Generation Sequencing

Christie Siu—McMaster University Honours Life Sciences 2023

By accessing multiple genes in a single assay to identify causative  mutation, next-generation sequencing provides a more efficient and  deeper look into molecular underpinnings of patients’ tumors. 

Not so long ago, it seemed mapping and understanding the entire human genome  sequence was one of the most expensive and time-consuming studies to accomplish. The  Human Genome Project, initiated in 1990, took a total of 13 years and about $3 billion  USD to determine and study the complete human genome, by using the traditional DNA  sequencing technique—”Sanger sequencing.” Yet, the advent of next-generation  sequencing (NGS) has made a great impact on clinical and molecular biological  research, more specifically—cancer research, leading to the molecular age of cancer. 

Before the 1990s, DNA sequencing was accomplished in an “old fashioned” way by adding agarose gel  and targeted genomic bases manually. Later, the Sanger sequencing technique was introduced into the  biological market and allowed researchers to process long DNA fragments at one time. And the  researching technique evolved, Next-generation sequencing has altered the way that sequencing was  ever performed. Although the invention of the Sanger sequencing did allow researchers to map out the  entire human genome sequence, it is unexpectedly costly and time-consuming for diseases diagnosis  and implantation of treatments of patients, especially individuals that are aware or not aware that, they  themselves are suffering from cancers (1). 

Cancer is one of the most leading cause of death worldwide. According to the National Cancer Institute,  there are related deaths in 2018. In addition the the enormous number of cases that can be studies,  cancers are generically complex and requires high-accuracy targeting specific variants and activation  pathways. Undoubtedly, the success of the Human Genome Project, along with the increased  affordability of sequencing, has implanted the wide use of genomic data to assist in cancer diagnosis and  medicine precision. The development of Next-generation sequencing, once thought to be a novelty,  allows researchers to capture and process a massive amount of genomic information about a cancer in  the shortest time one can imagine- taking only about 4 hours to complete a run (2).

Global Cancer | HEAT: Health Evaluations + applied Therapeutics
SOURCE: GLOBOCAN 2018
Individuals in both the developed and developing countries experience cancers, while most patients  were concentrated in Europe and Asia (3). 

Next-generation Sequencing VS Sanger Sequencing  

In principle, the concepts behind the two DNA sequencing techniques are similar. Both of NGS and  Sanger sequencing requires addition of DNA polymerase to the fluorescent nucleotide according to a  growing DNA template strand, while each nucleotide is identified by their fluorescent tag. But in NGS,  DNA fragments are massively parallel, which allows tones of fragments to be sequencing in just a single  trial. Whereas sanger sequencing sanger sequencing only produces one forward and reverse read of a  single fragment, and in other words, researchers have to be determinant when deciding which DNA  fragment, they are interested in.

When Do I Use Sanger Sequencing vs NGS? - Behind the Bench
SOURCE: Natalie Gurson, ThermoFisher Scientific
The fundamental approach of identifying target DNA sequence in NGS and Sanger sequencing is  similar, but their sequencing volume are different. While only a single DNA fragment can be  sequenced at a time in Sanger sequencing, and alternatively, NGS is massively parallel, millions of  fragments can be translated into genes simultaneously in a single run. 

Compared to the traditional way of sequencing, NGS offers high accuracy, sensitivity, and speed in  genomic investigation (4), as it only requires as little as 5% of the DNA sequences from a tumor sample,  and it can reduce the need to preform multiple tests to examine causative mutation within a patient.

References

1. Vincenza Precone, Valentina Del Monaco, Maria Valeria Esposito, Fatima Domenica Elisa De Palma,  Anna Ruocco, Francesco Salvatore, Valeria D’Argenio. Cracking the Code of Human Diseases Using Next Generation Sequencing: Applications, Challenges, and Perspectives. *BioMed Research International*,  vol. 2015, Article ID 161648, 15 pages, 2015. Available from: https://www.hindawi.com/journals/bmri/2015/161648/.

2. Gurson N. When Do I Use Sanger Sequencing vs NGS? – Behind the Bench [Internet]. Behind the  Bench. 2021 [cited 11 March 2021]. Available from: https://www.thermofisher.com/blog/behindthebench/when-do-i-use-sanger-sequencing-vs-ngs-seq-it out-7/.

3. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018:  GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J  Clin. 2018;68(6):394–424. 

4. NGS vs. Sanger sequencing. (n.d.). Retrieved March 11, 2021, from https://www.illumina.com/science/technology/next-generation-sequencing/ngs-vs-sanger sequencing.html.