Imagine a world where cancer isn't just battled with one-size-fits-all treatments, but with vaccines tailored uniquely to each patient's own genetic blueprint—potentially turning the tide on even the toughest cancers. Exciting news from the Japan Foundation for Cancer Research (JFCR) and NEC Corporation is bringing that vision closer to reality. But here's where it gets intriguing: their latest research harnesses the power of whole-genome data and cutting-edge AI to uncover hidden cancer fighters in areas of our DNA we barely understand. Stick around to learn how this could revolutionize immunotherapy and why it might spark debates on privacy and innovation in medicine.
Tokyo, November 7, 2025 – The Japan Foundation for Cancer Research (JFCR) and NEC Corporation (NEC; TSE: 6701) have announced groundbreaking research findings that pave the way for crafting bespoke neoantigen cancer vaccines customized to individual patients, drawing on comprehensive whole-genome data (1). By employing NEC's advanced AI tools, their analysis of samples from breast cancer and soft tissue sarcoma cases has revealed a wealth of cancer-specific markers, including cryptic antigens (2) from the so-called 'dark genome'—those mysterious stretches of DNA whose purposes are still mostly unknown. This goes beyond traditional neoantigens (*3), opening up exciting possibilities for treating cancers that have long resisted effective therapies.
These organizations plan to unveil these discoveries at the Society for Immunotherapy of Cancer (SITC) annual conference, taking place in National Harbor, Maryland, USA, from Wednesday, November 5 to Sunday, November 9, 2025.
This collaborative effort forms part of the Japan Agency for Medical Research and Development (AMED)’s initiative called the "Action Plan for Whole-Genome Analysis for Cancer and Rare/Intractable Diseases," specifically under the program focused on "Demonstrating the Clinical Value of Cancer Whole-Genome Analysis and Building Systems for Patient Benefits."
In the modern landscape of healthcare, personalized medicine is gaining traction—think of treatments designed precisely around a person's unique genetic makeup and how their genes express themselves. Among the frontrunners in this field is immunotherapy, which uses personalized cancer vaccines aimed at neoantigens unique to a patient's tumor cells. These approaches promise stronger results with fewer unwanted side effects. In Japan, momentum is building for research and new drug creation powered by whole-genome data, as seen in the Ministry of Health, Labour and Welfare's "Action Plan for Whole Genome Analysis 2022" (*4). Building on this trend, the Cancer Institute and NEC have teamed up since 2024 to innovate a new kind of personalized neoantigen vaccine leveraging whole-genome insights.
It's well-known that the number of neoantigens can differ depending on the type of cancer. In their investigation, the Cancer Institute and NEC scrutinized whole-genome information from breast cancer and soft tissue sarcoma—tumors often linked with fewer neoantigens—using NEC's proprietary AI. The goal was to show that by combining data from the entire genome, they could spot more immune-triggering targets, even for patients whose cancers traditionally produce limited standard antigens.
The partnership's research triumphantly identified a plethora of non-traditional antigens alongside the familiar ones. Crafting vaccines from these discoveries could usher in fresh strategies for tackling cancers previously seen as challenging for individualized neoantigen vaccines.
"We're thrilled to present the outcomes of our foundational research into advanced personalized cancer vaccines," shared Tetsuo Noda, M.D., Ph.D., Advisor, and Atsushi Ohtsu, M.D., Ph.D., Research Director at the Japanese Foundation for Cancer Research. "This project unfolded within an AMED initiative aligned with the Ministry of Health, Labour and Welfare's Action Plan for Whole-Genome Analysis 2022. Through blending whole-genome data with NEC’s unique AI capabilities, we've uncovered the likely existence of varied cancer-specific antigens—referred to as cryptic antigens—from the dark genome, even in cancers thought to express few neoantigens. Ahead, we'll assess the immune-stimulating potential of these antigens and push forward the creation of tailored cancer vaccines to usher in cutting-edge immunotherapy."
"We're excited to discuss our findings on cryptic antigens, achieved through our partnership with JFCR," stated Motoo Nishihara, Executive Officer, Corporate EVP and CTO at NEC. "This endeavor, which taps into whole-genome data and NEC's specialized AI, will be featured at the SITC Annual Meeting under AMED's support. Looking ahead, the NEC Group is dedicated to pioneering AI-driven healthcare innovations that improve lives globally."
Presentation Details
- Abstract Number: 162
- Title: A Whole-Genome-Informed Pipeline for Neoantigen Discovery in Solid Tumors: Integrating SNV, Splice Variant, and Exon-Transposon Junction Analysis to Enable Personalized Cancer Vaccines
- Presenters: Jun Masuda
- Authors: Jun Masuda1, Kazuma Kiyotani2, Kazuhide Onoguchi3, Per Brattås4, Hugues Fontenelle4, Angelina Sverchkova4, Sumana Kalyanasundaram4, Pierre Machart5, Yuki Tanaka3, Daiki Miura3, Noboru Nagata3, Koji Yoshino1, Mingyon Mun1, Yasuji Miyakita1, Hiroki Mitani1, Souya Nunobe1, Yu Takahashi1, Hiroyuki Kanao1, Takashi Akiyoshi1, Keisuke Ae1, Kengo Takeuchi1, Junji Yonese1, Masayuki Watanabe1, Seiichi Mori6, Seiya Imoto7, Ippei Fukada1, Shunji Takahashi1, Takayuki Ueno1, Noboru Yamamoto8, Kaïdre Bendjama4, and Shigehisa Kitano1
- Affiliation: 1) The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan. 2) National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan. 3) NEC Corporation, Tokyo, Japan. 4) NEC OncoImmunity AS, Oslo, Norway. 5) NEC Laboratories Europe GmbH, Heidelberg, Germany. 6) Japanese Foundation for Cancer Research, Tokyo, Japan. 7) The Institute of Medical Science, the University of Tokyo, Tokyo, Japan. 8) National Cancer Center Hospital, Tokyo, Japan.
- Release Date: November 8, 2025
Note:
- (*1)
Genome analysis can focus on just the coding regions of DNA—parts that directly instruct cells to build proteins—or include non-coding areas too. In this research, they used whole-genome data (the second approach) from samples donated by cancer patients.
- (*2)
This is a specific kind of neoantigen, coming from non-coding parts of the genome that don't produce proteins.
- (*3)
These are unique markers on cancer cells created by genetic changes. Healthy cells don't have them, so the body's immune system spots them as invaders and can attack the cancer.
- (*4)
This is a national strategy mainly to boost genome studies in medicine, aiming to create new ways to diagnose and treat cancers, rare diseases, and hard-to-manage conditions, while making personalized care more accessible.
About Japanese Foundation for Cancer Research
The Japanese Foundation for Cancer Research (JFCR), established in 1908, stands as Japan's pioneering group dedicated to cancer study and management. JFCR has been at the forefront of cancer research and care for over a century. They operate three research hubs and a hospital: the Cancer Institute for fundamental studies, the Cancer Chemotherapy Center for developing new drugs, the Cancer Precision Medicine Center (CPM Center) for innovative treatments, and the Cancer Institute Hospital of JFCR for patient care. Together, these entities collaborate to conquer cancer.
About NEC
The NEC Group harnesses innovation to foster positive societal impact and build a greener, more equitable world where individuals can fulfill their potential. Founded in 1899, NEC Corporation's team of roughly 110,000 professionals today deploys leading AI, security, and networking technologies to address critical challenges for clients and communities alike. For further details, visit https://www.nec.com, and connect with us on Instagram, Facebook, and LinkedIn.
NEC is a registered trademark of NEC Corporation. All Rights Reserved. Other product or service marks mentioned herein are the trademarks of their respective owners. © NEC Corporation.
And this is the part most people miss: While this research promises breakthroughs in targeted cancer vaccines, it also raises eyebrows over data privacy in whole-genome sequencing. Could widespread use of personal genetic information lead to misuse, or is the potential for saving lives worth the risk? What do you think—should we embrace AI-driven medicine fully, or tread more cautiously? Share your thoughts in the comments below; I'd love to hear if you agree this is a game-changer or if it sparks concerns about ethics and accessibility!
