Liver Macrophages Carrying Apolipoprotein E Act as a Molecular Brake That Drives T Cell Exhaustion and Preserves Transplant Tolerance

Liver transplantation remains the definitive treatment for end-stage liver failure, yet the immune battle that follows the operation continues to shape patient outcomes for decades. Even with modern immunosuppressive drugs, the genetic mismatch between donor and recipient forces lifelong medication, exposing patients to opportunistic infections, cancers, cardiovascular disease, and kidney failure. A new study published in iScience now reveals how a specialized population of liver-resident macrophages may hold the key to persuading the immune system to accept a transplanted organ without systemic drug toxicity. The research identifies a distinct subpopulation of Kupffer cells, the liver’s abundant tissue macrophages, that carries the lipid-handling protein apolipoprotein E, or APOE, and shows that these cells actively restrain the destructive immune response by driving attacking T cells into an exhausted state.

Kupffer cells have long been viewed primarily as scavengers, clearing debris and worn-out blood cells from the hepatic circulation. The new work, led by Zhuoyu Jia, Xinqiang Li, and Jinzhen Cai of Qingdao University and collaborators, demonstrates that they are far more sophisticated. Using single-cell RNA sequencing of liver graft biopsies and peripheral blood from transplant patients, the team mapped the full diversity of myeloid cells within the graft and isolated a cluster defined by exceptionally high APOE expression alongside canonical Kupffer cell markers such as CD5L, VSIG4, and MARCO. Functional enrichment analysis showed that this APOE-positive subset was strongly enriched in pathways governing receptor-mediated endocytosis, antigen processing and presentation, and efferocytosis, the engulfment of dying cells, pointing to a cell primed for both scavenging and immune regulation.

Computational modeling of intercellular communication using the CellChat algorithm revealed that these APOE-positive Kupffer cells behave as major signal senders within the graft, engaging T cells through a battery of co-stimulatory and co-inhibitory ligand-receptor pairs. Among the most prominent were CD86 engaging CTLA4 and CD28, LGALS9 binding the inhibitory receptor TIM-3, and NECTIN2 pairing with TIGIT. The strength and pattern of these interactions differed dramatically between patients whose grafts were tolerated and those experiencing rejection, suggesting that the APOE-positive macrophages help determine whether the local immune response escalates or winds down. Multiplex immunohistochemistry of patient biopsies confirmed that the proportions of these cells shift measurably as rejection develops.

To establish causality rather than mere correlation, the researchers built a technically demanding murine model of orthotopic liver transplantation, transplanting livers from C57BL/6 donors into C3H/He recipients and tracking the immune environment across four post-operative weeks. Histology and Banff rejection scoring documented the expected trajectory: severe acute rejection at one week, followed by spontaneous resolution and immune tolerance by week four. Flow cytometry with rigorous fluorescence-minus-one controls then revealed a striking biphasic dynamic. During acute rejection, the proportion of APOE-expressing Kupffer cells in the graft plummeted, likely reflecting ischemia-reperfusion injury and cellular death, while macrophages surged systemically across the spleen, blood, lymph nodes, and bone marrow.

As tolerance took hold, the picture reversed. Systemic myeloid expansion contracted, but the fraction of APOE-positive Kupffer cells within the graft climbed steadily, peaking at four weeks. These accumulating cells increasingly co-expressed CD206, a hallmark of alternatively activated, inflammation-resolving macrophages, and multiplex imaging showed extensive in-situ co-localization of F4/80, CD206, and APOE exclusively in tolerated grafts. A parallel enrichment of APOE-positive macrophages appeared in the spleen, lymph nodes, and bone marrow, hinting at a coordinated systemic regulatory program rather than a purely local phenomenon.

The target of this regulatory activity emerged as a specific population of tissue-resident memory CD8-positive T cells. These cells, marked by CD69 but lacking CD103, reside permanently within the graft and act as rapid-response effectors of localized rejection. The team showed that during acute rejection, this CD69-positive CD103-negative subset expanded robustly, depressing the CD4-to-CD8 ratio within the graft. As tolerance developed, however, the pool contracted and progressively upregulated the inhibitory checkpoints PD-1 and TIGIT, the classic signature of T cell exhaustion, a hyporesponsive state that limits immune-mediated tissue damage without requiring systemic T cell depletion.

Genetic proof came from transgenic experiments. When the researchers transplanted livers from APOE-knockout donors into allogeneic recipients, rejection exploded in severity. Grafts showed dense inflammatory infiltrates and structural destruction with markedly elevated Banff scores, and serum alanine and aspartate aminotransferase levels surged, reflecting profound liver injury. Flow cytometry revealed unchecked expansion of the CD69-positive CD103-negative CD8-positive tissue-resident memory population, and, crucially, the exhausted PD-1-positive and TIGIT-positive phenotype failed to appear. Without APOE, the molecular brake on alloreactivity was effectively dismantled.

In vitro co-culture experiments reinforced the causal chain. Kupffer cells harvested from wild-type mice upregulated APOE when stimulated with allogeneic T cells over 72 hours, while cells from APOE-knockout mice could not mount this response and cells engineered to overexpress APOE amplified it. When these macrophages were paired with responder splenic T cells, APOE deficiency accelerated CD8-positive T cell proliferation, whereas forced APOE overexpression blunted expansion to near baseline levels. Notably, Transwell experiments that physically separated the two cell populations showed that the suppressive effect persisted without direct contact, implying that APOE acts as a secreted immunomodulator bathing neighboring T cells in co-inhibitory signals, potentially through lipid receptors such as LRP1 or other LDL receptor family members on the T cell surface.

The study also delivered a clinically actionable finding. Analyzing preoperative serum from 31 liver transplant donors, the researchers found that higher donor APOE levels correlated negatively with recipient MELD scores and with post-operative monocyte counts, and tracked consistently with lower bilirubin and ALT levels during the first five days after surgery. Donor APOE, the authors propose, may reflect an intrinsic tolerogenic reserve of the graft, a liver inherently predisposed to a smoother immunological recovery. This positions a simple blood measurement as a potential tool for stratifying donor organs, guiding the use of marginal grafts, or identifying recipients in whom immunosuppression might be safely tapered earlier.

The work is the first to systematically assign a tolerogenic role to the APOE-positive Kupffer cell subset in transplantation, and it reframes a protein best known for cholesterol transport and Alzheimer’s disease risk as a central player in graft acceptance. The authors acknowledge limitations: mRNA abundance does not always mirror protein levels, which they addressed by anchoring key conclusions in flow cytometry and multiplex imaging, and the precise receptor that binds Kupffer-cell-derived APOE on T cells remains to be identified. Even so, the mechanistic axis they describe, in which APOE-positive macrophages recruit and exhaust pathogenic CD8-positive tissue-resident memory cells through chemokine-guided proximity and checkpoint signaling, offers a blueprint for therapies that could coax the liver’s own immune circuitry toward tolerance, potentially freeing transplant recipients from a lifetime of systemic immunosuppression.

Subject of Research: The role of APOE-positive Kupffer cells in inducing CD8-positive T cell exhaustion and immune tolerance after liver transplantation

Article Title: ApolipoproteinE + Kupffer cells maintain immune homeostasis following liver transplantation by inducing CD8 + T cell exhaustion

Article References: ApolipoproteinE + Kupffer cells maintain immune homeostasis following liver transplantation by inducing CD8 + T cell exhaustion. (n.d.). https://doi.org/10.1016/j.isci.2026.117501

Image Credits: AI Generated

DOI: 10.1016/j.isci.2026.117501

Keywords: liver transplantation, Kupffer cells, apolipoprotein E, immune tolerance, T cell exhaustion, tissue-resident memory T cells, single-cell RNA sequencing, PD-1, TIGIT, macrophages, allograft rejection, transplant immunology