FAT3 and LRP1B gene mutations are common in a variety of solid tumors, but there are still relatively few studies on these two tumor suppressor genes at present, especially FAT3, which is not currently routinely detected in clinical practice or even included in most large Panel gene sequencing products. FAT3 is cadherin superfamily members involved in tumor suppression and planar cell polarity (PCP)[35]. LRP1B encodes a low-density lipoprotein (LDL) family receptor with broad roles in normal cell function and development[36]. Here, in endometrial cancer, we provided a comprehensive discussion of the antitumor immune response and prognostic value of FAT3 and LRP1B genes in cancer patients based on a TCGA cohort of 502 samples. Both FAT3 and LRP1B mutations occurred in about one-fifth of EC patients, with an incidence of 19.52% and 19.32%, respectively. There was a co-occurrence relationship between FAT3 and LRP1B mutations, and the co-mutation frequency in EC was 11.16%, which is similar to that in NSCLC (10.87%)[26]. Based on the analysis of the relationships between molecular characteristics related to the efficacy of PD-1/PD-L1 blockades, we identified that the subgroup with FAT3 and LRP1B co-mutation had unique features in immunogenicity, SCNAs, T-effector signature and tumor immune microenvironment, and affected body functions and physiological processes by dysregulating the expression of a series of gene sets, thereby enhancing the antitumor immune response and improving the prognosis of patients with endometrial cancer.
A recent follow-up from the phase II clinical trial KEYNOTE-158 demonstrated that advanced endometrial cancer patients with MSI-H/dMMR could benefit from ICIs treatment, with an objective response rate (ORR) of 48%[5]. Correspondingly, our study indicated that ECs with FAT3 and LRP1B co-mutation had a significantly higher proportion of MSI-H. What was even more surprising was that TMB and PD-L1 expression, the other two classic biomarkers that predict the efficacy of immunotherapy, also exhibited significantly higher levels in the co-mutation subgroup than other samples. Further exploration showed that all ECs in the FAT3+/LRP1B+ subgroup were positive for at least one of these three predictors, and even 30.36% (17/56) of samples met TMB-H, MSI-H and high expression of PD-L1 at the same time, which was much higher than the marginal overlap (0.6%) reported in a previous study on multiple cancer types[37]. Also, tumor aneuploidy, an indicator associated with immune evasion and reduced response to immunotherapy, displayed strikingly lower level in samples with co-mutation. Furthermore, our findings revealed that FAT3 and LRP1B co-mutation were also accompanied by a higher proportion of PD-L1 and CD8A dual positivity, a signature that defines an adaptive immune resistance TME. This type of microenvironment is thought to be associated with TMB-H and PD-L1 amplification and may increase patient susceptibility to immunotherapy, which, to some extent, just supports the points we have made above. Specifically, POLE polymerase domain mutation, a highly predictive marker in EC, were also significantly enriched in the co-mutation subgroup, and most (2/3) of the ECs with FAT3 and LRP1B co-mutation also had POLE proofreading defects. In the aggregate, the prominence of all these features in FAT3 and LRP1B co-mutated ECs highlights that such patients have enhanced immune response and are likely to be excellent candidates for immune checkpoint inhibitors. Nevertheless, we also uncovered the fact that FAT3 and LRP1B co-mutation equally enhance the expression of some other non-PD-L1 immunosuppressive checkpoints, which may serve as a potential primary mechanism of resistance in co-mutated ECs treated with anti-PD-1/PD-L1 blockades.
Notably, we found that FAT3 and LRP1B co-mutation in endometrial cancer also significantly associated with prognosis. According to the results of relevant studies on EC molecular classification, POLE-mutant and MSI-H should be two subtypes with longer survival, and our findings confirmed that POLE mutation and MSI-H were significantly enriched in the FAT3+/LRP1B+ subset, which was completely composed of POLE-mutant and MSI-H subtypes. Besides, higher proportion of endometrioid adenocarcinoma also predicts better clinical outcome. On the other hand, the upregulation of several key cytotoxic T-cell markers and cytokine gene expression also represented a remarkable enhancement of T-cell effector and interferon-γ (IFN-γ) signatures, which are thought to be associated with activated T cells, immune cytolytic activity, and IFN-γ release[38]. More importantly, analysis of the relationship between mutation status and prognosis confirmed significantly prolonged PFS and OS in the subgroup of ECs with co-mutation of FAT3 and LRP1B compared to other samples. Although the association between co-mutation and immunotherapy efficacy has previously been thoroughly evaluated in NSCLC, this is the first time, to our knowledge, that the prognostic significance of co-mutation has been demonstrated, illustrating that FAT3 and LRP1B co-mutation in EC may be used not only for treatment selection but also for risk stratification.
The results of lymphocyte infiltration in the tumor microenvironment and pathway enrichment analysis further verified the predictive and prognostic significance of FAT3 and LRP1B co-mutation in EC. Cytotoxic CD8+ T cells are major killers of neoplastic cells and constitute the backbone of cancer immunotherapy, while CD4+ T cells play important roles in maintaining CD8+ response and preventing exhaustion[39]. T follicular helper cells provide B cells with essential help for potent antibody response, and their presence often correlates with better outcomes[40]. M1 macrophages can accelerate the activation of adaptive immune responses and promote inflammatory responses[41]. The increased abundance of these immune cells precisely implied a robust immune response against tumor cells in EC patients with FAT3 and LRP1B co-mutation. Meanwhile, GSEA analysis discovered multiple meaningful gene sets significantly enriched in the FAT3+/LRP1B+ subgroup. The prominent enrichment of signatures relating to DNA replication and DNA repair (including homologous recombination and nucleotide excision repair) potentially increased mutation probability, thereby enhancing genomic instability and immunogenicity and activating the immune system[42]. The immune response of helper T cells, which requires recognition of major histocompatibility complex (MHC) class II antigens for activation, is critical for the antitumor effect of CD8+ effector T cells[43], and T cell receptor (TCR) activates T cells by recognizing and binding antigens presented by MHC, which promotes the division and differentiation of T cells[44]. T cell chemotaxis and responses directed against tumor cells also represented enhanced in vivo surveillance and killing capabilities against cancer.
Although previous studies have identified the association of FAT3 and LRP1B mutations in multiple cancer types with features such as prognosis and TMB, we demonstrated that compared to samples with only one of these mutations, FAT3 and LRP1B co-mutation is more valuable for research in endometrial cancer, it can not only activate a more powerful antitumor immune response, but also can be used to improve prognostic typing. However, considering the retrospective nature and preliminary evidence of this study, a prospective study with a large sample size to validate our findings is warranted in the future. Nonetheless, through a systematic analysis of the endometrial cancer population, we have revealed that FAT3 and LRP1B co-mutation define a specific cluster correlated with activation of antitumor immunity and prognosis. Since FAT3 and LRP1B mutations have high incidence in a variety of solid tumor entities, we need to conduct more research on these two genes, especially co-mutation, to comprehensively evaluate their potential as pan-solid tumor biomarker.