From reading the code of life to re-writing it: My journey through genomic era
It took three days to complete a sequencing experiment, and at best we could read around two hundred bases with each reaction. I was a graduate student at The Ohio State University, and my lab was on the second floor of Nationwide Children’s Research Institute. It was mid-nineties, and we were using the Sanger method for sequencing. It involved running DNA fragments through a thin gel matrix and reading the sequence of bases through a manual process. It took several days to complete—a significant amount of time and effort as each base had to be read and recorded by hand. Of course, mistakes were common. I still remember the smell of the siliconized glasses used to prevent the gel from sticking after the run was complete. While trying not to tear the thin DNA gel in its transfer to a white paper before drying it, I daydreamed of someday developing a gene therapy for hereditary spherocytosis, the subject of my PhD thesis.
I say dreaming because this was just before the sequencing of the human genome, all three billion bases of it (we have 6 billion bases in total, three billion coming from each parent). The human genome project was an incredible undertaking, especially with the technological limits of the time. However, thanks to the foresight of the Committee on National Strategy for Biotechnology led by Bruce Alberts, gene sequencing technology took priority, which enabled the project’s completion two years ahead of its original plan of 15 years. The total cost was approximately one dollar per base, or three billion dollars in total.
The language of life and re-writing it with CRISPR
On June 26, 2000, during the White House ceremony to announce the completion of the first draft of Human Genome Project, U.S. President Bill Clinton used these words:
“Today, we are learning the language in which God created life. We are gaining ever more awe for the complexity, the beauty, the wonder of God's most divine and sacred gift. With this profound new knowledge, humankind is on the verge of gaining immense, new power to heal. Genome science will have a real impact on all our lives — and even more, on the lives of our children. It will revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases.”
Since then, there have been numerous advances in genomics. I feel grateful and lucky to have witnessed these developments and played a part in molecular life sciences research during this transformative time. In my research, I worked on developing a gene therapy for Neuroblastoma, a childhood cancer of the nervous system, by killing cancer cells through a death inducing gene loaded onto a gutted adenovirus. For Alexander Disease, a lethal neurodegenerative condition, I used RNAi technology to prevent the production of the disease-causing protein. I created multiple transgenic mouse lines by transferring pieces of human DNA into them to study the temporal and spatial expression of these transgenes. In another project, I disrupted or "knocked out” a single gene in mice. This knock-out proved that, in mice, the gene is necessary for the ability to eat solid food. I give these examples not to boast, but to highlight the historic significance of all genomic research in the past twenty years. President Clinton said it very well: this was an “epoch-making triumph of science and reason.” Although he was referring specifically to the Human Genome Project, his statement describes the advances made in all molecular life sciences fields. Because for much of human history, we, as a species, could only observe life and try to understand it through empirical observation. But with the genetic revolution, humanity now and for the first time understands and can manipulate the language of life. The completion of the Human Genome Project fueled this transition.
The Human Genome Project created high hopes for us all. Some media sources went so far as to say that we will cure all genetic diseases within a few decades. In theory, we should have been able to fix or correct mutations and cure diseases such as sickle cell disease (SCD). After all, we knew the mutation that causes it from Vernon Ingram’s work in the 1950s. He showed that SCD is caused by a single amino acid change from glutamine to valine in the beta-globin gene. We now know that a single nucleotide change is the culprit behind this devastating disease. However, progress has been slow despite several attempts to correct disease-causing mutations using gene therapy. Moreover, a few high-profile failures, such as the Jesse Gelsinger case and leukemia causing x-SCID trial, led to a temporary halt in gene therapy trials. A slower, more cautious approach emerged as a result of scrutiny from these setbacks. Advances in the development and improvement of gene therapy vectors played an important role in that rebound.
Targeting diseases such as sickle cell with a single nucleotide change
The discovery of CRISPR genome editing brings us closer to the next steps for gene therapy. Developed by Jennifer Doudna and Emmanuelle Charpentier, for which they won the Nobel, CRISPR is the closest thing to the proverbial pencil scientists have sought to write and re-write the language of life. Its simplicity and precision have revolutionized medical research as it rapidly moves toward clinical application. Victoria Gray’s experience as the first American to participate in CRISPR therapy trials for SCD in 2019 was a tremendous achievement and milestone. She has been disease-free ever since. It is very likely that 2023 will be the year we see the first FDA-approved CRISPR therapeutics: Vertex and CRISPR therapeutics have submitted their CRISPR-mediated ex vivo cell therapy for SCD and beta-thalassemia for FDA approval.
As is the case with any breakthrough, CRISPR is not yet perfect. Off-target effects are still a concern, and cell- or tissue-specific delivery is still a challenge. However, progress is being made by scientists around the world to increase the precision of CRISPR technology.
As researchers continue to explore the vast potential of CRISPR, we can only imagine what the future holds. Yet one thing is certain—this groundbreaking technology has the power to affect every aspect of our lives and change the course of medical history. Although it is still limited to research settings, we are already seeing CRISPR applications in agriculture. CRISPR can improve crop yields and develop crops that are resistant to pests and disease. This could address food insecurity concerns and reduce the environmental impact of agriculture. The technology can also be used in industrial biotechnology to develop new materials in a more sustainable and more efficient manner. In the energy sector, CRISPR can be used to engineer microbes that can produce biofuels from renewable sources. The possibilities seem endless. While the ethical and social implications of some of these possibilities are still under debate, there is no doubt that CRISPR technology has the potential to transform lives in coming decades.
Looking back on the progress made since my graduate school years, it is truly awe-inspiring to see how far we have come. Today a human genome can be sequenced for about $600, one five-millionth of the cost of the first genome sequence! There are already talks about a $100 genome sequence. We have only just entered the era of personalized medicine. I can only imagine what life will be like when the full potential of this new era is realized!
About the Author
Bahri Karacay, PhD, serves as the Commercial Marketing Manager for IDT's CRISPR and Functional Genomics product line. He is also an accomplished author with two bestsellers, "The Secret of Life DNA" and "Happy Brain" (both in Turkish) and more than hundred scientific publications. When he's not at work, Bahri enjoys practicing music and performing with his band TURKANA.