To integrate the operation of the mechanisms described below, Eomes should be interpreted in three major RCC TME compartments. First, with respect to infiltrating leukocytes, divergent functions have been identified for Eomes in CD8⁺ T cells, NK cells, ILC1-like cells and type 1 Tregs (Tr1-like) cells. Secondly, in intrinsic RCC tumor cells, possible links with cell stemness, EMT, apoptosis resistance and proliferative signaling remain incompletely validated, and the links should therefore be interpreted with caution. Thirdly, in stromal and endothelial compartments, the majority of the Eomes-associated effects that have been proposed are probably indirect, mediated through immune cytokines, angiogenic signaling or tumor-stroma crosstalk. This compartment-based framework also explains the 'double-edged' character of Eomes: Restoring Eomes may support NK-cell cytotoxicity, whereas persistent Eomes in exhausted or regulatory lymphocyte populations may reinforce immune suppression. This evidence hierarchy, spanning direct RCC clinical/single-cell data, RCC-associated model evidence, and indirect or cross-model inferences, is summarized in Table I.

The TME of RCC harbors a diverse array of dysfunctional immune cells. Among them, CD8⁺ T-cell exhaustion is central to immune evasion (36,37). Eomes has been shown to modulate the efficacy of antitumor immune responses through alterations in CD8⁺ T-cell differentiation and functional status (6,38). In addition, previous studies have shown that, in advanced or metastatic RCC, tumor-infiltrating CD8⁺ T cells exhibit heterogeneous Eomes expression patterns. In particular, the population of CD8⁺ T cells of the Eomes⁺ T-bet^low subtype has been observed to be increased, which represents the dysfunctional phenotype with diminished secretion of key cytokines (including IFN-γ and TNF-α) and decreased cytotoxicity (namely, reduced expression of PRF1 and GZMB) (14,36,39). In terms of the underlying mechanism, Eomes engages the promoter locus of TIGIT, thereby promoting its expression. TIGIT is a key immune checkpoint receptor that mediates its function via binding to CD155, thereby inhibiting T-cell activity; this forms an Eomes-TIGIT regulatory axis that may exacerbate T-cell exhaustion (33).

The balance between the nuclear and cytoplasmic localization of Eomes is critical for CD8⁺ T-cell function (28). In chronic viral infection models, exhausted CD8⁺ T cells have been shown to exhibit high nuclear Eomes/T-bet ratios, leading to the transcriptional activation of inhibitory receptors, such as PD-1 (28,40). In patients with RCC, nuclear Eomes in tumor-infiltrating CD8⁺ T cells may competitively bind to T-box elements in the promoter of the PDCD1 gene (which encodes PD-1), thereby both weakening the transcriptional repression mediated by T-bet and sustaining high expression levels of PD-1 (14,28). Eomes has also been shown to downregulate the co-stimulatory molecule CD226, which further limits the activation and proliferation of CD8⁺ T cells. Bhat et al (35) demonstrated that CD226 expression is reduced in Eomes⁺ CD8⁺ T cells, where the loss of CD226 was found to be associated with resistance to anti-PD-1 therapy. However, since several of the mechanistic details have been determined from cases of chronic infection or non-RCC immune models, these findings should be interpreted as supportive evidence, rather than as definitive proof of RCC-specific causality.

NK cells perform a vital role in immune surveillance of RCC (41,42). Eomes is a critical transcription factor for NK cell maturation and functional maintenance. Its expression has been shown to be closely correlated with NK cell cytotoxicity and cytokine production (43) (Fig. 2). Although NK cells and ILC1 cells share a similar lineage and phenotypic markers, they differ significantly in terms of their function. High expression levels of Eomes support the maturation of NK cells with cytotoxicity and immune surveillance, whereas the loss or downregulation of Eomes induces a shift toward an 'ILC1-like' phenotype (43-45). Within the RCC TME, both activation of the TGF-β signaling pathway and other inhibitory signals may suppress Eomes expression, thereby contributing to NK cell dysfunction (12,46,47). Under physiological conditions, Eomes maintains NK cell cytotoxicity by transcriptionally activating effectors, such as PRF1, GZMB, IFN-γ and granulocyte-macrophage colony-stimulating factor (GM-CSF), and also by supporting activating receptors and chemokine receptors that are involved in tumor recognition and tissue homing (44,48-51). Hypoxia-inducible factor-1α (HIF-1α) in the hypoxic TME may inhibit Eomes expression in the NK-cell context, thereby promoting ILC1-like markers such as CD49a and C-X-C motif chemokine receptor 6 (CXCR6) (52-55). Therefore, selectively modulating the HIF-1α-Eomes axis in NK cells should be viewed as an experimental strategy, rather than as an established RCC therapy. In addition, decreased expression levels of gp96 in RCC have been documented to relieve its suppression of the ubiquitin ligase Trim28, thereby promoting Eomes ubiquitination and degradation, as well as contributing to NK cell dysfunction (21). Dysregulated cytokines, such as TGF-β and IL-15, have been shown to activate ILC1 differentiation-associated transcription factors, including homolog of Blimp-1 in T cells (Hobit) and runt-related transcription factor 3 (Runx3), thereby reprogramming Eomes-deficient NK cells into an ILC1-like state (7,56,57). This remodeling is characterized by the downregulation of cytotoxic factors and an increased expression both of inhibitory receptors, such as TIGIT and CD96, and of immune-regulating factors, such as IL-10 and TGF-β (58,59).

Accumulating evidence suggests that Eomes^low or Eomes-ILC1-like cells can be enriched in the RCC TME, where their heightened presence has been associated with tumor progression and resistance to immunotherapy (15,60).

In conclusion, Eomes has been demonstrated to act as a core controller of NK cell function, although the therapeutic implications are cell-type-specific. Restoring or stabilizing Eomes may be useful for mature NK cells when its loss drives the conversion of NK cells into the ILC1-like state, and cytotoxic failure. This does not imply that a global activation of Eomes would be beneficial, however, since other Eomes-positive lymphocyte states may contribute to exhaustion or immunosuppression.

Eomes reshapes the immune microenvironment of RCC. It can promote immune escape during tumor progression by modulating the recruitment, expansion and functional polarization of immunosuppressive populations (Fig. 3). These immunosuppressive cells include Tregs and Tr1-like cells (61,62). A single-cell transcriptomic study previously conducted by Bonnal et al (62) identified a subset of Eomes⁺ Tr1-like cells within the TME. These cells underwent clonal expansion, expressed high levels of IL-10 and granzyme K, and exhibited potent immunosuppressive functions. Unlike conventional Forkhead box (FOX)P3⁺ Tregs, however, Tr1-like cells primarily inhibited effector T-cell responses through cytokine secretion, instead of via direct cell-cell contact. In particular, their abundance was shown to be positively correlated with cancer progression (62). A study by Jian et al (63) revealed that tumor cells with high Eomes expression promoted the secretion of C-C motif chemokine ligand 20 (CCL20), also recruiting C-C chemokine receptor type 6 (CCR6)⁺ Tregs into the TME, thereby enhancing immunosuppression. Collectively, these studies suggested that Eomes may function as a vital regulator in remodeling the immune microenvironment of RCC by enhancing the function of Tregs and other immunosuppressive cells.

The accumulation of Eomes⁺ Tr1-like cells has also been associated with resistance to immunotherapy in RCC. An increase in their numbers was negatively correlated with progression-free survival in patients receiving anti-PD-1 therapy. This may be due to Eomes⁺ Tr1-like cells producing high levels of IL-10 and TGF-β, which has the effect of inhibiting both the infiltration and activation of effector T cells (62,64). In particular, Eomes⁺ Tr1-like cells do not produce the same specific effector cytokines as are produced by Th1 or Th2 cells, such as IFN-γ or IL-4 respectively (65-67). Furthermore, Eomes may sculpt the immune microenvironment through regulation of macrophage polarization. For example, in hepatocellular carcinoma, macrophage-derived itaconic acid was shown to upregulate the expression of Eomes via an epigenetic mechanism (namely, H3K4me3 modification) to promote CD8⁺ T-cell exhaustion (68). Given the abundance of M2 macrophages in the RCC microenvironment, a similar mechanism is plausible, although the evidence remains indirect and requires RCC-specific validation.

Cancer stem cells (CSCs) perform a key role in progression, distant metastasis and treatment resistance in RCC. CSCs are characterized by self-renewal and multipotent differentiation potential (69-71). In solid tumors, including RCC, the presence of CSCs is closely associated with poor clinical outcomes. Previous studies have suggested that the concurrent expression of stemness markers (such as Oct4 and Nanog) in RCC tissues is associated with poor patient prognosis (72,73). In the embryonic hematopoietic system, Eomes operates upstream of runt-related transcription factor 1 (Runx1) in the hemogenic endothelium lineage, serving to regulate lineage differentiation and the self-renewal of hematopoietic stem cells (74). On the basis of this developmental role, Eomes may regulate genetic networks that are involved in CSC-like properties in RCC; however, this tumor-cell-intrinsic mechanism requires further experimental validation in RCC models.

The long non-coding RNA (lncRNA) HOX transcript antisense RNA has been shown to promote RCC stemness and angiogenesis both through formation of a feedback loop with the androgen receptor, and by synergistically activating the transcription of glioma-associated oncogene family zinc finger 2 (GLI2) (75). Similar regulatory mechanisms governing RCC stemness may also be observed in the Wnt/β-catenin cascade. In RCC, δ-catenin has been documented to induce the transcription and expression of downstream target genes, including those encoding c-Myc, cyclin D1, membrane type 1 matrix metalloproteinase (MT1-MMP) and Bcl-2, by enhancing the nuclear translocation of β-catenin and driving signaling pathways that are associated with stemness maintenance (76). Eomes may act as a transcriptional co-activator of β-catenin, although the direct contribution of this proposed Eomes-β-catenin mechanism to RCC CSC biology has yet to be validated (76).

Although Eomes is conventionally recognized for immune regulation, abnormal expression in tumor cells may influence malignant biological behavior. Research on human protein expression patterns has suggested that Eomes exhibits high expression levels in renal cancer tissues (77). A regulatory link between aberrant PI3K/Akt/mTOR signaling and Eomes expression in RCC is plausible, but direct tumor-cell causality remains incompletely established. Phosphorylation of Akt by mechanistic target of rapamycin complex 1 (mTORC1) inhibits FOXO1, and suppressed FOXO1 activity upregulates T-bet and inhibits Eomes expression. By contrast, activated FOXO1 can promote Eomes transcription, suggesting a potential Akt/FOXO1/T-bet/Eomes feedback axis. In parallel, Wong et al (15) found that deletion of Eomes impaired IL-15 receptor signaling and downstream PI3K/Akt activation in immune cells. Collectively, these findings suggested that Eomes may influence RCC progression directly in tumor cells, or indirectly through antitumor immune cells, although these two contexts should not be conflated. In another tumor model, Eomes promoted G₂/M phase cell cycle progression by promoting CCL20 and CCR6 expression; its relevance to RCC proliferation remains hypothesis-generating (63) (Fig. 4).

In terms of apoptosis regulation, Eomes may affect cell survival through pathways involving Bax, caspase-3 and Bcl-2 (16,78,79). In a study by Wagner et al (16), inducible knockout of Eomes led to rapid NK cell loss, accompanied by increased caspase-3 expression and upregulation of the Bax pathway. These findings support a survival role for Eomes in NK cells. Whether a similar mechanism operates in RCC cells remains uncertain. Concomitantly, Junction adhesion molecule 3 (JAM3) has been demonstrated to facilitate RCC cell migration, whilst inhibiting apoptosis by upregulating N-cadherin and MMP2. Considering that Eomes is a T-box transcription factor, Eomes may contribute to JAM3-associated RCC migration by transcriptional regulation, although direct promoter binding requires validation (80). In addition, Eomes has been linked to EMT-associated transcriptional programs in other contexts. Therefore, its proposed role in regulating E-cadherin, N-cadherin, vimentin and Twist in RCC should be regarded as an experimental hypothesis (61,81).

Eomes expression is tightly controlled by various epigenetic mechanisms. HDAC inhibitors, such as trichostatin A, have been reported to reduce Eomes expression and to suppress the production of PRF1 and GZMB in γ-δ T cells (35,88,89). This suggests that HDAC activity can affect Eomes-associated cytotoxic programs in immune cells. Additionally, nLSD1p has been shown to interact with Eomes, regulating its nuclear localization and transcriptional activity and thereby influencing CD8⁺ T-cell function (18). In patients with immune-resistant melanoma, nLSD1p was found to be overexpressed in PD-1⁺CD8⁺ T cells, and it co-localized with Eomes in the nucleus. Collectively, these findings have provided a useful immune-oncology model, although direct validation in RCC remains necessary (18,90).

DNA methylation is a key epigenetic regulatory mechanism. In RCC, the tumor suppressor gene serine protease inhibitor Kazal-type 5 (SPINK5) is silenced by H3K9me2 methylation at its promoter. Euchromatic histone-lysine N-methyltransferase 2 (EHMT2; also commonly known as G9a) is the main enzyme that catalyzes H3K9me2 methylation, and its high expression has been associated with RCC progression (91,92). If H3K9me2 modifications occur at the Eomes promoter, G9a may inhibit EOMES transcription by increasing chromatin compaction, although this specific axis has not yet been fully established in RCC. Additionally, Eomes expression is regulated by lncRNAs and miRNAs. In CD4⁺ T cell-based competing endogenous RNA (ceRNA) networks, Eomes has been shown to be modulated by the small, non-coding miRNA has-miR-23b-3p, which is, in turn, modulated by the lncRNA AC104820.2. By contrast, in the CD8⁺ T-cell ceRNA network, Eomes is regulated by the small, non-coding miRNA has-miR-23a-3p, which is itself regulated by the lncRNA AC000476.1. At the present time, these axes should be regarded as candidate regulatory mechanisms, pending RCC-specific functional verification (93,94).

Aberrant activation of the PI3K/Akt/mTOR signaling pathway is a hallmark of RCC, which causes enhanced tumor cell proliferation and survival, and metabolic reprogramming (95). In RCC, the Ras-related protein RAP2a has been shown to promote metastasis by upregulating phosphorylated Akt (96). A bidirectional regulatory association between Eomes and this signaling pathway is plausible; however, the direction may differ between immune cells and tumor cells. In immune cells, Eomes may be associated with IL-15 receptor signaling and Akt activation, whereas in tumor cells, Eomes may either be downstream of, or interact with, PI3K/Akt/mTOR-associated transcriptional programs. However, the direct binding of Eomes to PI3K/Akt target gene promoters in RCC has yet to be firmly established, and additional evidence is required.

In NK cells, a positive feedback loop involving IL-15, phosphoinositide-dependent kinase 1 (PDK1), mTOR, nuclear factor IL-3-regulated protein, Eomes and CD122 serves a vital role in primary stages of NK cell development. Within this loop, Eomes enhances the responsiveness of NK cells to IL-15 by upregulating CD122, thereby promoting its own expression in a self-reinforcing circuit (96,97). Furthermore, Zeng et al (98) suggested that in RCC, the lncRNA distal-less homeo box 6-antisense 1 (DLX6-AS1) sequesters miR-26a (functioning as a ceRNA) to upregulate the tumor suppressor gene PTEN, a negative regulator of the PI3K/Akt pathway, thereby limiting tumor progression; this study did not examine Eomes. Whether Eomes intersects with this DLX6-AS1/miR-26a/PTEN axis in RCC has not been directly investigated and remains an open question for future study. Given that Eomes is a key regulator of Akt activation, and PTEN is a critical negative modulator of the PI3K/Akt pathway, Eomes may indirectly regulate PTEN expression and downstream Akt activation by interacting with DLX6-AS1 or miR-26a; for example, by transcriptionally regulating DLX6-AS1 expression or modulating miR-26a maturation (98,99).

The regulation of mTORC1 signaling has also been known to intersect with metabolic reprogramming. In NK cells, inhibiting mTORC1 activity may suppress ubiquitin-mediated Eomes degradation, thereby enhancing the antitumor function of NK cells (100). In RCC, the Warburg effect has been demonstrated to activate mTORC1 signaling, and may alter Eomes-associated transcriptional programs; however, supporting evidence for a direct mTORC1-Eomes oncogenic axis in RCC remains scarce (101,102). Therefore, targeting the mTORC1-Eomes axis should currently be viewed as a preclinical hypothesis, rather than as a validated treatment strategy.

The pathogenesis and progression of RCC are also impacted by the Wnt/β-catenin signaling pathway (Fig. 6). As discussed above, RCC-specific evidence supports a role for δ-catenin- and β-catenin-associated signaling in cell proliferation and apoptosis resistance (76). However, direct Eomes-β-catenin co-activation is supported mainly by developmental models, and requires further validation in RCC. Therefore, the Eomes-Wnt/β-catenin signaling axis is best interpreted as a hypothesis-generating bridge between developmental transcriptional programs and RCC stemness, rather than as a proven RCC driver (29,76,103). Beyond a direct protein-protein interaction with β-catenin, Eomes also cooperates with chromatin remodelers to amplify Wnt-dependent transcription, and the BAF complex (a large ATP-dependent protein group that moves and changes nucleosomes to control gene activity) represents a critical epigenetic cofactor in this process. During embryonic development, Eomes interacts with the BAF chromatin remodeling complex, which serves to maintain chromatin accessibility in the trophoblast ectoderm (TE) and to regulate TE-specific gene expression (104). Given that Eomes often functions as a transcriptional activator, and the BAF complex facilitates chromatin accessibility for target gene binding, it is plausible that the Eomes-BAF complex may target and activate c-Myc expression in RCC cells, a process that would further enhance RCC cell proliferation, given that c-Myc is a well-established driver of RCC cell proliferation. However, this regulatory axis (Eomes-BAF→c-Myc) requires further validation via chromatin immunoprecipitation sequencing, co-immunoprecipitation analysis and functional assays in RCC models.

Single-cell transcriptomic data from a previous study showed that CD8⁺ T cells within RCC tissues express Eomes at high levels, and the clonal expansion of Eomes⁺ Tr1-like cells is associated with RCC disease progression (61,62). These findings suggest that either the expression level of Eomes or the proportion of Eomes-positive immune-cell subsets could be explored as prognostic biomarkers. However, Eomes should not currently be considered as a standalone diagnostic marker without independent validation in large RCC cohorts and in matched protein-level assays.

The expression levels of Eomes may vary among different RCC subtypes; however, the present evidence is insufficient to conclude that Eomes is able to reliably distinguish ccRCC from papillary RCC, or from other RCC subtypes. ccRCC is characterized by activation of the HIF pathway, whereas HIF-1α may suppress Eomes in the context of NK cells. This apparent tension can be reconciled by considering the cell types separately: In tumor-infiltrating NK cells, hypoxic HIF-1α signaling may suppress Eomes and promote NK dysfunction, whereas in intrinsic tumor cells, HIF-associated metabolic and epigenetic programs may be correlated with different Eomes expression patterns. Therefore, any subtype-differentiation claim requires direct analysis of TCGA, CPTAC, Human Protein Atlas and RCC single-cell datasets before any sort of clinical use can be proposed (12,54,55).

ICIs represent a significant therapeutic approach for RCC, although their efficacy is influenced by immune-cell functional status in the TME. As a key regulator of immune cell function, Eomes may be explored as a target for improving ICI responses; however, any intervention would require cell-type-specific modulation experiments to be performed. Enhancing the activity of Eomes may be beneficial in mature NK cells or selected memory CD8⁺ T-cell states, whereas reducing persistent Eomes activity may be considered in exhausted or Tr1-like immunosuppressive populations. HDAC inhibitors, PD-1 inhibitors and CD226-associated strategies should therefore be discussed as experimental combinations, rather than as established Eomes-directed RCC therapies (11,35).

Chimeric antigen receptor T-cell (CAR-T) therapy has shown promising results in hematological malignancies, although its efficacy in solid tumors is limited by T-cell exhaustion. Eomes expression has been shown to promote both the proliferation and survival of engineered T cells, and their IL-2 responsiveness, in certain contexts. However, Eomes-engineered CAR-T cells have not been validated as an RCC therapy, and the overexpression of Eomes may also carry exhaustion-associated risks, depending on the T-cell state. Therefore, Eomes modulation in CAR-T cells should be presented as a preclinical hypothesis that requires further RCC-specific testing (105,106).