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Immune restraint through the ages: PD-1 pathway traced to sharks

Immune restraint through the ages: PD-1 pathway traced to sharks
(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: 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. in Frontiers in Immunology, 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 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 Âé¶¹ÒùÔºiology 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. 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.

Since its in 1992, 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 by others very recently.

Immune restraint through the ages: PD-1 pathway traced to sharks
Conservation of PD-1 and PDL-1 interaction between fish and mammals. The figures show superimpositions of the (membrane-distant) IgSF domains of human PD-1 bound to human PD-L1 (PDB accession 4ZQK) and a MultiFOLD predicted interaction structure of the corresponding domains in tarpon PD-1 and PD-L1. Depictions are in cartoon format, except for the highlighted residues that are also in sticks format. The conserved intermolecular hydrogen bonds of PD-1 Y68 with PD-L1 D122 and of PD-1 K78 and PD-L1 F19 are indicated by dashed lines. Credit: Frontiers in Immunology (2025). DOI: 10.3389/fimmu.2025.1573492

Key findings of the new Japanese study, with Dr. Ryohei Kondo—a former student of Dr. Ishida—as first author, include:

  1. Residues forming hydrogen bonds between PD-1 and PD-L1 are well conserved throughout PD-1 and PD-L (including PD-L2) evolutionary history.
  2. PD-L2, which emerged only in tetrapods, is consistently different from PD-L1 by unique motifs in its IgC domain.
  3. (The ITIM and ITSM motif regions in the PD-1 cytoplasmic tail show conservation patterns that suggest a need for their redefinition.
  4. 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.
  5. 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. 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. 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."

More information: Ryohei Kondo et al, 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).

Journal information: Frontiers in Immunology

Citation: Immune restraint through the ages: PD-1 pathway traced to sharks (2025, May 30) retrieved 1 June 2025 from /news/2025-05-immune-restraint-ages-pd-pathway.html
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