The COVID-19 pandemic showed the challenges of protecting populations when a new respiratory virus emerges. Although vaccines were developed at unprecedented speed, there was still a period when vaccines were not yet available, and people remained vulnerable to infection. This raises an important question: Could the body's natural defenses be temporarily strengthened without knowing which virus will emerge?
One possible answer lies in innate immunity, the body's first line of defense. Unlike adaptive immunity, which learns to recognize specific targets, innate immunity can respond to threats without prior exposure. Some studies have shown that certain stimuli can leave innate immune cells more responsive through a phenomenon called trained immunity. However, questions remain about how long this protection can last and which cells are responsible for maintaining it in the respiratory tract.
To bridge these knowledge gaps, a research team led by Professor Ken Ishii from the Division of Vaccine Science, Department of Microbiology and Immunology at The Institute of Medical Science, The University of Tokyo, Japan, investigated how the vaccine adjuvant K3-SPG modulates innate immunity. The study was co-authored by PhD candidate Asuka Joy Tobuse of The University of Tokyo and Associate Project Scientist Kouji Kobiyama of the University of California San Diego, USA, formerly a member of Prof. Ishii’s laboratory at The University of Tokyo. Their study will be published in Science Advances on October 9, 2026.
K3-SPG is a nanosized adjuvant that combines a short piece of synthetic DNA called CpG oligodeoxynucleotide, which activates the immune sensor toll-like receptor 9 (TLR9), with a β-glucan called schizophyllan. The researchers first tested whether a single dose given through the nose could protect mice against influenza A virus. Treated mice lost less weight and had higher survival than control mice. Protection was still detectable 100 days after treatment, although it waned over time. The treatment also protected mice against SARS-CoV-2 in a susceptible mouse model.
The route of administration was important. Nasal treatment produced stronger protection than treatment given under the skin or into the bloodstream. Despite improving survival and reducing lung damage, however, K3-SPG did not substantially reduce the amount of virus in the lungs. The findings suggest that the treatment mainly helped the host to tolerate the infection and limit tissue damage rather than directly preventing viral replication.
The team then investigated how this protection developed. Using several analytical approaches, including single-cell RNA sequencing, they found evidence of a two-stage response. Macrophages were important during the early phase, while innate lymphoid cells became important later. Some of the innate lymphoid cells showed changes down to the chromatin level, which is the DNA–protein structure that helps regulate gene activity, suggesting longer-lasting changes in their function.
The team also found that the response depended on TLR9, an immune receptor activated by K3-SPG, as well as the inflammatory signaling molecule TNF-α. “Our research has identified unique mechanisms by which vaccine adjuvants can induce protective innate immunity against respiratory viral infections, suggesting that adjuvants may have potential applications beyond their traditional role in enhancing vaccine responses,” says Prof. Ishii.
The researchers caution that these findings were demonstrated primarily in mice and do not establish that K3-SPG can protect people from respiratory viral infections. Further studies are needed to assess its safety, effectiveness, and suitability for human use, including differences in TLR9 biology and respiratory delivery.
“Because an adjuvant-based preventive approach may not require prior knowledge of the specific pathogen, it could potentially provide an additional layer of protection while pathogen-specific vaccines are being developed and manufactured,” explains Prof. Ishii. Such an approach could potentially complement pandemic preparedness efforts such as the 100 Days Mission by providing temporary protection while targeted vaccines are being developed.
Reference
Authors: Asuka Joy Tobuse¹˒², Kouji Kobiyama¹˒³˒⁴, Jun Tsuchida¹, Masamitsu N. Asaka⁵˒⁶, Daichi Utsumi⁵, Mariana Silva Almeida³˒⁷˒⁸, Yaeko Nakajima-Takagi⁹, Motohiko Oshima⁹, Tomoya Hayashi¹˒³˒⁸, Burcu Temizoz¹˒³˒⁸, Etsushi Kuroda¹⁰, Cevayir Coban²˒³˒⁷˒⁸, Yasuhiro Yasutomi⁵˒¹¹, Atsushi Iwama²˒⁸˒⁹, and Ken J. Ishii¹˒²˒³˒⁸
Title of original paper: Long-term Immunoprophylaxis by TLR9 Ligand Mediates Macrophage-ILC Crosstalk Against Respiratory Viral Infection
Journal: Science Advances
DOI: 10.1126/sciadv.aeh6480
Affiliations:
About The Institute of Medical Science, The University of Tokyo
The Institute of Medical Science, The University of Tokyo (IMSUT), established in 1892 as the Institute of Infectious Diseases and renamed IMSUT in 1967, is a leading research institution with a rich history spanning over 130 years. It focuses on exploring biological phenomena and disease principles to develop innovative strategies for disease prevention and treatment. IMSUT fosters a collaborative, interdisciplinary research environment and is known for its work in genomic medicine, regenerative medicine, and advanced medical approaches like gene therapy and AI in healthcare. It operates core research departments and numerous specialized centers, including the Human Genome Center and the Advanced Clinical Research Center, and is recognized as Japan’s only International Joint Usage/Research Center in life sciences.
About Professor Ken Ishii from the Institute of Medical Science, The University of Tokyo
Professor Ken Ishii is a Professor at the Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo. He also directs the International Vaccine Design Center at IMSUT, Japan. He holds M.D. and Ph.D. degrees from Yokohama City University and has extensive experience in vaccine research, with publications dating back to 1994. He also spent 7 years as a Visiting Scientist and IND reviewer at the U.S. Food and Drug Administration. His research focuses on innate immune recognition of vaccine adjuvants and translating these findings into vaccine development and applications in Japan.
Funding information
This work was supported by the Japan Agency for Medical Research and Development (AMED) grant Nos. JP223fa727002, JP223fa727001, JP223fa627001, JP25m2110005, JP223fa627007, JP223fa627005, JP223fa727001, and 21ak0101162.
Science Advances
Experimental study
Animals
Long-term Immunoprophylaxis by TLR9 Ligand Mediates Macrophage-ILC Crosstalk Against Respiratory Viral Infection
9-Oct-2026
Kouji Kobiyama and Ken J. Ishii are inventors on patents related to K3-SPG filed by the National Institutes of Biomedical Innovation, Health and Nutrition and Daiichi Sankyo Co., Ltd. (JP6698069B2, Filed 18 March 2016, Published 27 May 2020; WO2015041318A1, Filed 19 September 2014, Published 26 March 2015). The authors declare no other competing interests.