Lck kinase fine-tunes T cell activation by phosphorylating autophagy receptor p62

When a T cell senses a threat, its receptor fires off a cascade of signals that must be calibrated with remarkable precision. A new study published in EMBO Reports reveals an unexpected dial controlling this calibration: the kinase Lck, long known as a master switch of T cell receptor signaling, also restrains autophagy in the earliest moments of T cell activation by chemically modifying a key autophagy receptor called p62.

The research, led by Zhihui Xiao, Yun-Yi Li, Zhi-long Chen and colleagues under senior author Yingqiu Li, shows that within minutes of T cell receptor stimulation, Lck attaches a phosphate group to p62 at a specific tyrosine residue, position 433. This transient modification, which peaks at five minutes and fades by fifteen minutes, prevents p62 from carrying out its autophagic duties. In doing so, Lck protects Bcl10, a signaling protein essential for activating the transcription factor NF-κB, from being swallowed up and destroyed by the cell’s own degradation machinery. The result is stronger NF-κB activation and greater production of interleukin-2, a growth signal that fuels T cell proliferation.

Autophagy is the cellular recycling system in which cytoplasmic material is sequestered and delivered to the lysosome for degradation, with receptor proteins such as p62 recognizing polyubiquitinated substrates and delivering them to autophagic degradation via LC3. It is not merely a housekeeping process; in T cells it regulates survival, differentiation, metabolism and signaling itself. Previous work had shown that T cell receptor signaling ultimately boosts autophagic flux, yet autophagy is transiently suppressed during the initial stages of T cell activation. How the receptor signaling pathway imposed this early brake remained a puzzle the new study set out to solve.

The team began by asking whether Lck, a Src-family kinase that rides along with the CD4 and CD8 co-receptors, influences autophagy at all. Comparing normal Jurkat E6.1 T cells with Lck-deficient JCaM1.6 cells, they found that loss of Lck drove markedly higher levels of LC3-II, a standard marker of autophagic flux, both at rest and after stimulation. Transient knockdown of Lck in Jurkat cells produced the same effect, and treating human and mouse primary T cells with an Lck inhibitor likewise increased LC3-II accumulation. Confocal microscopy confirmed more LC3 puncta in the Lck-deficient cells. The Lck-deficient cells also showed reduced p62 protein levels without any change in p62 messenger RNA, a shortened p62 half-life, and greater accumulation of polyubiquitinated protein aggregates when lysosomal degradation was blocked with bafilomycin A1, all signs of accelerated autophagic turnover.

Crucially, the suppression depended on Lck’s kinase activity. When the researchers reconstituted Lck-deficient cells with wild-type Lck, LC3-II levels fell; reconstitution with a kinase-dead Lck-K273R mutant did nothing. Overexpression of Lck also dampened LC3-II accumulation in Jurkat TAg cells and in HEK293T cells, which lack endogenous Lck. Together these experiments established that Lck negatively regulates T cell receptor-induced autophagy in a kinase-dependent manner.

Why would a kinase best known for phosphorylating CD3 chain motifs reach into the autophagy machinery? The answer traces back to an old observation: p62, also called SQSTM1, was originally cloned in 1995 as a ligand of the Lck SH2 domain. The new work shows that this interaction is functionally meaningful. Upon T cell receptor engagement, Lck directly phosphorylates p62, as demonstrated by immunoprecipitation of endogenous p62 from stimulated cells, by experiments in human primary T cells where Lck inhibition diminished p62 phosphorylation, and by an in vitro kinase assay in which immunopurified Lck phosphorylated purified GST-p62. The related Src-family kinase Fyn showed negligible activity toward p62, and other autophagy receptors such as OPTN and NBR1 did not bind Lck or become phosphorylated after T cell receptor stimulation, pointing to a specific functional link between Lck and p62.

To pinpoint the phosphorylation site, the team used mass spectrometry and identified tyrosine 433 as the residue modified in cells expressing wild-type Lck but not the kinase-dead mutant. Mutating tyrosine 433 to phenylalanine nearly abolished p62 tyrosine phosphorylation, whereas mutations at two other candidate sites, Tyr98 and Tyr383, had little effect. An in vitro kinase assay confirmed that a truncated UBA-domain fragment of p62 carrying the Y433F mutation could no longer be phosphorylated by Lck. Strikingly, the researchers extended the analysis to amphioxus, a basal chordate occupying an evolutionary position between invertebrates and vertebrates. Amphioxus Lck bound and phosphorylated amphioxus p62 at a residue homologous to human Tyr433, and the corresponding mutant lost phosphorylation, suggesting that this regulatory mechanism is ancient and conserved.

What does phosphorylation at Tyr433 actually do to p62? The experiments indicate that it weakens p62’s grip on both its cargo and the autophagy initiation machinery. In p62-knockout Jurkat cells reconstituted with either wild-type or Y433F p62, the mutant bound substantially more polyubiquitinated proteins, more LC3B, and more of the ULK1 complex components ULK1 and FIP200 after T cell receptor stimulation. The Y433F mutant also showed increased colocalization with ubiquitin, accelerated autophagic degradation of p62 itself, and higher LC3-II levels, indicating enhanced autophagic flux. Notably, the mutation did not alter p62’s own ubiquitination or its oligomerization, suggesting the effect is specific to substrate association and recruitment of autophagosome-forming machinery rather than a general destabilization of the protein.

The functional consequences for T cell activation were clear. In reporter assays, reconstitution of p62-knockdown Jurkat cells with wild-type p62 restored T cell receptor-induced NF-κB activation, but reconstitution with the Y433F mutant did not. Similarly, p62-knockout cells expressing wild-type p62 produced elevated interleukin-2 upon stimulation, while cells expressing the phosphorylation-defective mutant produced markedly less. The mechanism lies in Bcl10: the Y433F mutant accelerated Bcl10 degradation and bound Bcl10 more strongly than wild-type p62, and further experiments using a Bcl10 mutant deficient in binding Malt1 and CARMA1 indicated that Tyr433 phosphorylation specifically regulates p62’s interaction with Bcl10 within the CBM signalosome complex rather than with free Bcl10. In this way, Lck-mediated phosphorylation acts as a molecular switch, converting p62 from an autophagy receptor that would destroy Bcl10 into a signaling scaffold that protects it, allowing NF-κB signaling to proceed.

The authors acknowledge an important limitation: the core findings were confirmed in cell lines and primary human and mouse T cells, but the study lacks in vivo animal data, and future work with animal models will be needed to establish the physiological relevance of the Lck-p62 signaling axis in living organisms. The phosphatase that removes the Tyr433 phosphate also remains unidentified, although the authors suggest SHP1 as a plausible candidate. They also note that Tyr433 has been implicated in forming a ubiquitin-binding surface and that EGFR-mediated phosphorylation of the same residue in lung cancer cells has been shown to inhibit autophagic flux, raising the possibility that dysregulated Lck, which is aberrantly expressed in some solid tumors, could contribute to malignancy through a similar route. Whether therapeutic strategies targeting the Lck-p62 interaction might one day modulate immune responses or tumor growth remains an open question that the authors flag for further exploration. For now, the study adds a striking piece to the picture of how T cells choreograph their own activation: the very kinase that ignites the signaling cascade also reaches into the recycling machinery, buying Bcl10 enough time to deliver its message.

Subject of Research: How Lck-mediated phosphorylation of p62 regulates autophagy and T cell activation

Article Title: Lck regulates T cell activation through phosphorylation of p62

Article References: Xiao, Z., Li, Y.-Y., Chen, Z.-L., Ye, W., Wang, L., Zhao, C.-S., & Li, Y. (2026). Lck regulates T cell activation through phosphorylation of p62. EMBO Reports. https://doi.org/10.1038/s44319-026-00902-5

Image Credits: AI Generated

DOI: 10.1038/s44319-026-00902-5

Keywords: Lck, p62, SQSTM1, autophagy, T cell receptor, T cell activation, NF-κB, Bcl10, phosphorylation, ULK1, LC3, interleukin-2