Laboratories

Medical Genomics

Prof. Kato Assoc.Prof. Kukita
Professor
Kikuya KATO
Associate Professor
Yoji KUKITA

Outline of Research and Education

Our current research focus is circulating tumor DNA (ctDNA), which is cell-free DNA released from dying cancer cells (Fig.1). Because ctDNA enables detection of cancer cell DNA of various lesions using only a small amount of blood (~1ml), there are huge expectation for clinical applications including early detection. We use next-generation sequencing (NGS) to detect ctDNA. We offer students the opportunity to study experimental basics and bioinformatics of NGS.

Major Research Topics

Noninvasive genotyping of EGFR for lung cancer therapy

Gefitinib (Iressa) is a molecular target agent for lung cancer to inhibit tyrosine kinase activity of EGFR. It is effective only for lung cancer with activating EGFR mutations, and patients are selected through a genetic test. Gefitinib is a good example of “personalized medicine” (Fig.2), a new concept of medicine, i.e., choosing therapy based on genetic information of each patient. An important concern in clinical practice is that tumor samples are often difficult to obtain by biopsy. In particular, biopsy for advanced or resistant cases and repeated sampling is extremely difficult.

We developed a noninvasive detection system for EGFR mutation in ctDNA based on NGS (Kukita et al., 2013). The mutations are sought in more than 100,000 reads of the EGFR fragments. We conducted a multi-institute prospective study to evaluate the performance of the detection system, and demonstrated that the system was sufficient for practical use (Uchida et al., 2015). This study was done in collaboration with the Department of Thoracic Oncology, Osaka International Cancer Institute.

Development of methodologies for cancer detection

The accuracy of current sequencing technologies has limitations when detecting rare mutations in multiple loci. To overcome this problem, we developed a new sequencing method named NOIR-SeqS (non-overlapping integrated read sequencing system) (Fig.3) (Kukita et al, 2015). The system employs the barcode technology, and achieved 60-100 fold increase of accuracy from that of the standard NGS. We applied NOIR-SeqS to ctDNA, demonstrating its feasibility for practical use.

References

  1. Kukita Y. et al., PloS One, 13, e0192611, 2018
  2. Segawa H. et al., BMC Genomics, 18, 914, 2017
  3. Kato K. et al., Sci Rep., 6, 38639, 2016
  4. Kukita Y. et al., Cold Spring Harb Mol Case Stud., 2, a001032, 2016
  5. Nakanishi K. et al., Cancer Med., 5, 2513-2521, 2016
  6. Kato K. et al., Sci Rep., 6, 29093, 2016
  7. Imamura F. et al., Lung Cancer, 94, 68-73, 2016
  8. Uchida J. et al., Cancer Sci., 107, 353-358, 2016
  9. Uchida J. et al., Clin. Chem., 61, 1191-1196, 2015
  10. Kukita Y. et al., DNA Res., 22, 269-277, 2015
  11. Kukita Y. et al., PLoS One, 8, e81468, 2013
  12. Taniguchi K. et al., Clin. Cancer Res., 17, 7808-7815, 2011
Fig.1 Circulating tumor DNA.
Fig.1 Circulating tumor DNA.
Fig.2 Personalized medicine.
Fig.2 Personalized medicine.
Fig.3 Detection of a mutation in <i>TP53</i>. Top, NOIR-SeqS; bottom, conventional next-generation sequencing.
Fig.3 Detection of a mutation in TP53. Top, NOIR-SeqS; bottom, conventional next-generation sequencing.
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