image: (A) Presence of PD-1, its ligands PD-L1 and PD-L2, and the phosphatases SHP-1, SHP-2, and SHP-2-like (SHP-2L) in representative jawed vertebrates, including sharks, ray-finned fish, amphibians, and mammals. In fish, the ancestral version of PD-L1/PD-L2 is referred to as “PD-L1.”
(B) Conserved molecular interactions between PD-1 and PD-L1 (PDB accession 4ZQK): Human PD-1 residues Y68 and K78 form hydrogen bonds with PD-L1 residues F19 and D122, interactions that are conserved across species and also apply to PD-L2.
(C) Unique residues in the PD-L2 IgC domain (carbon atoms in yellow) distinguish it from PD-L1 (PDB accession 3BP5). Notably, residues N189 and S191 form an N-glycosylation site, and residue L150, together with aromatic residues at positions 166 and 174, forms a unique surface structure with currently unknown function.
Credit: Image credit: J.M. Dijkstra. Silhouette figures are from PhyloPic.org and used in accordance with their individual licensing terms.
In 1992, graduate student Yasumasa Ishida discovered PD-1, marking the beginning of a journey that would make this molecule a major target in cancer immunotherapy. Now, Dr. Ishida and colleagues provide a comprehensive overview of the evolution of PD-1 and its interacting molecules. This new work underscores the essential nature of the PD-1 system across jawed vertebrates and offers interesting new molecular insights that may guide future immunotherapies.
PD-1 (programmed cell death 1; CD279) is a key immune checkpoint molecule and an effective target in cancer immunotherapy. This was discovered by Professor Tasuku Honjo at Kyoto University, and these findings earned him a share of the 2018 Nobel Prize in Physiology or Medicine, alongside Professor James Allison, for their “discovery of cancer therapy by inhibition of negative immune regulation.” The PD-1 research in Professor Honjo’s lab began in the early 1990s, when Dr. Yasumasa Ishida, then a graduate student, identified the PD-1 gene. Dr. Ishida—currently a group leader at the Nara Institute of Science and Technology—has always continued to study PD-1, and now, together with other Japanese researchers, reports a detailed analysis of the distribution and sequences of PD-1 and its ligands throughout jawed vertebrate species [1].
Since its discovery in 1992 [2], PD-1 was long believed to be exclusive to tetrapods (animals with four limbs). However, the consortium of Japanese researchers presents evidence that PD-1, along with its ligands PD-L1 and the phosphatases SHP-1 and SHP-2, and their critical interaction motifs, are conserved throughout jawed vertebrates, from sharks to humans. These findings were made possible through the growing number of available whole-genome sequences. Notably, the presence of PD-1 in fish was independently reported by others very recently [3].
Key findings of the new Japanese study, with Dr. Ryohei Kondo—a former student of Dr. Ishida—as first author, include:
(i) Residues forming hydrogen bonds between PD-1 and PD-L1 (Figure 1B) are well conserved throughout PD-1 and PD-L (including PD-L2) evolutionary history.
(ii) PD-L2, which emerged only in tetrapods, is consistently different from PD-L1 by unique motifs in its IgC domain (Figure 1C).
(iii) The ITIM and ITSM motif regions in the PD-1 cytoplasmic tail show conservation patterns that suggest a need for their redefinition.
(iv) Also in fish, PD-1 gene expression is predominantly associated with T cells, especially those with regulatory properties. This suggests a conserved role for PD-1 as an immune checkpoint.
(v) A previously unrecognized ancient molecule, SHP-2-like (SHP-2L), is conserved across most jawed vertebrates but lost independently in rodents and higher primates.
Immune systems balance activation and inhibition, with activating pathways often discovered first. The PD-1 system was one of the last major components of the immune system without a known fish counterpart. Its discovery in sharks and bony fishes indicates that immune restraint via PD-1 is a deeply conserved feature across jawed vertebrates.
Dr. Ryohei Kondo, of the National Center for Geriatrics and Gerontology, notes, "It’s incredible to realize that immune checkpoint molecules like PD-1 are conserved across jawed vertebrates. It highlights the necessity of immune downregulation ability."
Dr. Yasumasa Ishida reflects, "It’s deeply moving to see how a molecule I helped discover connects across 450 million years of evolution. In many ways, the circle has now come full."
Dr. Johannes (Hans) M. Dijkstra, a molecular evolution expert at Fujita Health University, adds, "Conservation reveals what is important, and the novel findings of conserved motifs in PD-1’s ITIM and ITSM regions, as well as in PD-L2’s IgC domain, may ultimately lead to novel therapeutic approaches targeting the PD-1 system."
References
[1] Kondo R, Kondo K, Nabeshima K, Nishikimi A, Ishida Y, Shigeoka T, DijkstraJM. PD-1 is conserved from sharks to humans: new insights into PD-1, PD-L1, PD-L2, and SHP-2 evolution. Frontiers in Immunology (2025) https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1573492/full
[2] Ishida Y, Agata Y, Shibahara K, Honjo T. Induced expression of PD-1, a novel member of the immunoglobulin gene superfamily, upon programmed cell death. EMBO Journal (1992) 11(11):3887-95. https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1992.tb05481.x
[3] Quiniou SMA, Clark T, Bengtén E, Rast JP, Ohta Y, Flajnik M et al. Extraordinary diversity of the CD28/CTLA4 family across jawed vertebrates. Frontiers in Immunology (2024) 15:1501934. https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1501934/full
About the authors
This research was conducted by a collaborative team from several Japanese institutions:
Ryohei Kondo and Akihiko Nishikimi, National Center for Geriatrics and Gerontology, Obu
Kohei Kondo, National Institute of Infectious Diseases, Tokyo
Kei Nabeshima, National Institute for Environmental Studies, Tsukuba
Yasumasa Ishida and Toshiaki Shigeoka, Nara Institute of Science and Technology, Nara
Johannes M. Dijkstra, Fujita Health University, Toyoake
About Fujita Health University
Fujita Health University is a private university situated in Toyoake, Aichi, Japan. It was founded in 1964 and houses one of the largest teaching university hospitals in Japan in terms of the number of beds. With over 900 faculty members, the university is committed to providing various academic opportunities to students internationally. Fujita Health University has been ranked eighth among all universities and second among all private universities in Japan in the 2020 Times Higher Education (THE) World University Rankings. THE University Impact Rankings 2019 visualized university initiatives for sustainable development goals (SDGs). For the “good health and well-being” SDG, Fujita Health University was ranked second among all universities and number one among private universities in Japan. The university became the first Japanese university to host the "THE Asia Universities Summit" in June 2021. The university’s founding philosophy is “Our creativity for the people (DOKUSOU-ICHIRI),” which reflects the belief that, as with the university’s alumni and alumnae, current students also unlock their future by leveraging their creativity.
Website: https://www.fujita-hu.ac.jp/en/index.html
Journal
Frontiers in Immunology
Method of Research
Data/statistical analysis
Article Title
PD-1 is conserved from sharks to humans: new insights into PD-1, PD-L1, PD-L2, and SHP-2 evolution
Article Publication Date
28-May-2025