Unlocking the Potential of Multi-Omics in Precision Medicine: A Conversation with Kazusa DNA Research Institute

CHIBA, Japan, Dec. 7, 2023 /PRNewswire/ — The integration of multi-omics approaches offers a comprehensive panorama for advancing our comprehension of biology. It now plays a more important role in understanding the roots of diseases, and in expediting precision medicine and catalyzing advancements in drug development. MGI interviewed Dr. Yoshinori Hasegawa, Ph.D., Group Leader and Chief Scientist at the Laboratory of Gene Sequencing Analysis, Department of Applied Genetics, Kazusa DNA Research Institute.

Dr. Hasegawa has a very unique background in which, while he was a student at the Faculty of Science at Niigata University, he conducted research on courtship methods of Japanese black salamanders (Hynobius nigrescens) and the fertilization capabilities of egg sacs in water, and at the Graduate School of Science at Hiroshima University, he studied regional dialectical variations of frog calls made by male frogs to appeal to females.

“Whether it’s amphibian research, or the research I do in my current position, they both involve using science to explore unexplored fields. In order to discover something new and to find its cause, I can draw from various methods because I was involved in research in different fields.

I believe that’s something that works to my advantage now.”

Kazusa DNA Research Institute

Group Leader and Senior Researcher at the Laboratory of Gene Sequencing Analysis, Department of Applied Genetics

Yoshinori Hasegawa, Ph.D., Doctor of Science

Completed doctoral course at Hiroshima University Graduate School of Science in 1999, received Ph.D. in Science. Joined Kazusa DNA Research Institute in 2009 after working at the Ehime University Faculty of Engineering, the RIKEN Genome Science Research Center, and the Fujita Health University Institute of Comprehensive Medical Sciences. Current position from April 2021.

Q: Please tell us about Kazusa DNA Research Institute.

Kazusa DNA Research Institute was established in 1994 as a DNA research institute with the aim of contributing to society through DNA research in the fields of medicine, agriculture, industry, and education. The institute is unique in that it’s supported not by the national government but by Chiba Prefecture, and in the extremely short time since its opening, it has produced many world-class research results in plant and human DNA research. In particular, it’s known for having decoded the entire genome sequence of Arabidopsis thaliana in 2000, the first time such a genome had been decoded in higher plants.

Q: What kind of research are you doing at the Department of Applied Genetics, where you currently work?

The Department of Applied Genetics consists of four groups, the Laboratory of Plant DNA Analysis, the Laboratory of Biomolecule Analysis, the Laboratory of Clinical Omics Research, and the Laboratory of Gene Sequencing Analysis, to which I belong. Our research activities are varied and include whole genome sequencing projects aimed at improving numerous plant varieties for the advancement of agriculture, and more recently, we’ve been involved in research focused on multi-omics analysis.

Q: Can you tell us about ‘multi-omics analysis?’

The term ‘multi-omics analysis’ refers to analysis across multiple omics data types within omics analysis. To be more specific, it’s an analysis that combines genomics, transcriptomics, metabolite analysis such as metabolomics and lipidomics, as well as proteomics, for a single sample, applying omics analysis at each level to analyze the relationship between each in addition to independent omics analysis.

Multi-omics analysis provides information that could not be seen in a single omics analysis and has been applied for a variety of purposes, such as the elucidation of human diseases including their causes, as well as the prediction and treatment of diseases and symptoms.

Our institute is developing various support measures for the actual use of omics analysis not only in basic research but also in clinical and industrial settings, utilizing the analysis technologies and know-how that we’ve cultivated over the years. For example, we conduct joint research with doctors at university hospitals on treatments for intractable diseases, and then provide the results to pharmaceutical companies to advance them into clinical trials.

Q: What other research is being conducted by the Department of Applied Genetics?

In addition to the collaborative research on cures for intractable diseases I mentioned earlier, I myself am conducting research utilizing human artificial chromosomes and our patented new site-specific recombination systems, as well as research using our own high-quality gene clones.

Q: What are the specific types of research you do?

Our laboratory has tens of thousands of clones, mainly long full-length genes. We put them into cells in various combinations and investigate how they work.

For example, say, in one cell it’s important that expression for genes a, b, and c occur simultaneously, while in another cell it’s important that a, b, and c are expressed in sequence.

We prevent the expression of gene b in cells where expression of genes a, b, and c need to occur. As a result, this may cause disease symptoms. Conversely, adding b to a cell in which b is not expressed will return it to a normal state. In this way, we can examine the function of each gene by intentionally inducing certain cells to express mutations, or by restoring those originally expressing mutations to their normal state, as a way of comparing the normal and abnormal functions of genes.

We expect that the results of such research will be very useful in elucidating the causes of diseases that have not been successfully elucidated until now, and will further contribute to personalized medicine.

Q: We understand that Kazusa DNA Research Institute also offers contract-based genomic/genetic analysis services, but what kind of service is this?

In fact, about 70% to 80% of our work is contract-based genomic/genetic analysis.

Analytical instruments are expensive these days, with many costing JPY100 million or more, and they require large quantities of expensive reagents, placing a heavy monetary burden on a single university or researcher. But it allows many samples to be analyzed at once, thereby reducing costs.
Currently, more than half of the analysis requests we receive are from universities, not only from medical schools, but also from agricultural, science, and engineering faculties.

The turnaround time for it varies depending on the request, but is usually about 8 weeks, and in some cases it’s 4 weeks or 2 weeks for expedited services.

Our contract-based genomic/genetic analysis services are available not only for large-scale samples, but also for samples that are difficult to analyze. For example, we have the knowledge, experience, and technology to analyze DNA that has been degraded, or samples that are too small to be analyzed by other contracted research companies. We call “Kazusa Pride,” the way we carry out it with a sense of pride.

Q: We would like to know why you chose MGI’s products.

The main reason is the cost-effectiveness compared to other companies’ products.

Q: Can you tell us about the quality of the data?

We currently have a DNBSEQ-G400 sequencer from MGI.

We believe that the quality of data obtained from these instruments are as good as or better than that of other companies. MGI’s equipment contributes especially to the quality of our contracted services, which is a part of our “Kazusa Pride” (laughs).

We also understand that MGI has released a smaller instrument, the DNBSEQ-G99, and we hope that they will develop an instrument with medium-sized specifications in the future. Recently, MGI has been developing applications that meet our needs, such as single-cell analysis, and we hope that they will continue to do so going forward.

Q: Are there any new developments for you personally as well?

As a researcher, I’m also studying the so-called ‘immortal jellyfish’ (Turritopsis dohrnii).
This small jellyfish measuring about 5mm to 1cm lengthwise has a Japanese name, benikurage, derived from the reddish color of its stomach. When the lifespan of this jellyfish nears its end, its entire body condenses into a ball shape, and its cells change, growing new polyps, and is reborn as a young body. Among multicellular animals, this jellyfish is the only organism that has been proven to repeatedly undergo this rejuvenation process, and we’re studying the mechanism of its rejuvenation. We hope that our research will lead to the understanding of general cell regeneration and dedifferentiation through the elucidation of the immortal jellyfish rejuvenation mechanism, which will then be applied to research on human aging and the promotion of a healthy lifespan.

Q: What are your goals for the future and what would you like to achieve?

Although the price of instruments has skyrocketed and their operation has become more complicated, we, as a research institute and a research group, would like to maintain a contract-based genomic/genetic analysis service system based on the latest knowledge. To achieve this, the most important thing is to maintain high quality and earn trust through our “Kazusa Pride.” We will continue to be involved not only in contracted research, but also in collaborative joint research, and serve everyone as a public interest incorporated foundation. In the process, we would like to continue to conduct original research, such as our research on the immortal jellyfish.

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