In the TCGA cohort, we observed that SMARCA4-Mut tended to occur between the ages of 60 and 75, with a median age of 67 years. The median age of the Mut group in the clinical sample was 63 years, and more men were involved. In TCGA samples, smoking was evident, with 35% in the Mut group and 22.5% in the WT group being smokers. Although no statistical difference was found between groups, a tendency to smoke was still present. Previous studies have indicated that thoracic SMARCA4-deficient undifferentiated tumors are most likely to occur in adults, with a median age of 48 years (ranging from 27 to 90 years), and are significantly more common in males, particularly heavy smokers(Nambirajan and Jain 2021). SMARCA4-dNSCLC, a smoking-related undifferentiated or differentiated invasive lung cancer, is predominantly observed in young men with a median age of 63 years and a high incidence of pleural and vascular infiltration(Tsuboi 2019). The age distribution in our clinical data aligns with previous studies, while the diversity in the TCGA cohort is attributed to its broader range of pathological types.
Tumors with SMARCA4 mutations have been shown to increase lymphocytes, macrophages, and multinucleated giant cells, corresponding to an increase in inflammatory cells in the surrounding tumor stroma. The SWI/SNF complex, to which SMARCA4 belongs, has been identified as a modulator of the immune system. Studies have demonstrated that SMARCA4 plays a pivotal role as a core gene in tumorigenesis by regulating the tumor microenvironment (TME) through both cell autonomy and TME interactions(Tian, Xu et al. 2023). Despite SMARCA4-Mut patients having a poor prognosis, especially those with truncated mutations, fusion, and homozygous deletion mutations, it has been found that SMARCA4-Mut-carrying lung cancer may be more sensitive to immunotherapy, with the latter showing the best response(Schoenfeld, Bandlamudi et al. 2020). The main direct downstream transcriptional targets of SMARCA4 include the epidermal growth factor receptor and TNS4. SMARCA4 interacts with PRMT1, activating the transcription of TNS4 and the epidermal growth factor receptor, promoting the proliferation of colorectal cancer cells(Yao, Gui et al. 2021). Several successful cases of immune checkpoint inhibitors (ICIs) in treating advanced SMARCA4-dNSCLC and SMARCA4-deficient malignant rhabdomyoma-like tumors have been reported(Takada K 2019, A, A et al. 2021).
We identified that SMARCA4-Mut patients carried three genes (PAPPA2, SETBP1, SPEN) more frequently than SMARCA4-WT patients (P < 0.05), and these three genes were involved in immunotherapy to varying degrees. The first is the PAPPA2 mutation, most common in skin melanoma (SKCM) and non-small cell lung cancer (NSCLC)(Dong, Zhao et al. 2022). Patients with PAPPA2-mutated lung adenocarcinoma (LUAD) have been found to have a longer survival time(Suzuki, Mimaki et al. 2013). In this study, the PAPPA2 mutation was identified as a potential predictive biomarker for immune checkpoint inhibitors (ICIs)(Dong, Zhao et al. 2022). Compared with other published ICIs-related gene mutations (EPHA family, MUC16, LRP1B), PAPPA2 showed outstanding predictive ability(Mariathasan, Turley et al. 2018, Bai, Duan et al. 2020, Brown, Tucker et al. 2021). It complements programmed cell death ligand 1 (PD-L1) and tumor mutational burden (TMB), improving patients' survival rates. Its mechanism is related to enhanced anti-tumor immunity, including a higher activated CD4 memory T cell level, lower regulatory T cell (Treg) level, and upregulated DNA damage repair pathway(Kamada, Togashi et al. 2019, Zuazo, Arasanz et al. 2020). The favorable prediction demonstrated by PAPPA2 is closely related to immunotherapy.
The SETBP1 gene, present in approximately 13% of patients with LUAD, has been identified as one of the signature mutations of LUAD, alongside KEAP1 and STK11, and may be a new marker for poor prognosis in NSCLC. Low-level expression of SETBP1 induces epithelial-mesenchymal transition (EMT) through the ERK1/2 signaling pathway, promoting proliferation, migration, and invasion of NSCLC cells. SETBP1 expression is significantly correlated with the regulation of tumor-infiltrating immune cells, especially M1 macrophages(Li, Gao et al. 2020). M1 macrophages are associated with a poor prognosis for lung cancer(Herbst, Morgensztern et al. 2018). This study also found that CD1 + T cells, CD, and monocytes were negatively correlated with SETBP1 expression levels. In another study, SETDB1 deletion was found to make tumors sensitive to immune checkpoint inhibitors (ICBs), acting as an epigenetic checkpoint to suppress the intrinsic immunogenicity of tumors and serving as a candidate target for immunotherapy(Griffin, Wu et al. 2021). The mechanism involves SETDB1 inhibiting a wide range of domains enriched with transposition elements (TEs) and immune clusters associated with segmenting repeat events(Dennis and Eichler 2016). SETDB1 deletion inhibits TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retrovirus antigens latent in these regions, triggering in vivo TE-specific cytotoxic T-cell responses(Griffin, Wu et al. 2021).
SPEN is a tumor suppressor gene, and patients with SPEN mutations experience a significant decrease in OS in small cell lung cancer (SCLC), serving as a prognostic biomarker (Jiao, Zhang et al. 2022). Studies have found that SPEN mutation is significantly correlated with elevated TMB in various cancers, and its mutational characteristics are correlated with a good response to immunotherapy. Additionally, this study demonstrated that the TMBPS score (TMBPS=- (mutation × (ROS0) + b× mutation (SPEN) + c× mutation (PTPRT)) could predict cancer survival prognosis in immunotherapy settings(Li, Gao et al. 2023). In another study, mutations in the SPEN gene were found to result in better OS in a pan-cancer cohort treated with ICBs(Samstein, Lee et al. 2019). Based on the mechanisms of action of these three genes, we speculated that the susceptibility of SMARCA4-Mut lung cancer to immunotherapy may be related to the common mutation of these three genes.
Moreover, in this study, we also found that NapsinA-positive expression could indicate a longer survival in SMARCA4-Mut patients. Aspartic peptidase A (NapsinA), belonging to the peptidase A1 family, is a single-chain protein composed of 420 amino acids encoded by the NSPSA gene on chromosomal body 19q13.3.45, with a molecular weight of about 45 kDa. It is mainly expressed in the lungs and kidneys. In the lung, NapsinA is primarily expressed in alveolar type II epithelial cells and also exists in alveolar macrophages. NapsinA is an important biological indicator in the typing diagnosis of advanced NSCLC and a more sensitive marker of lung adenocarcinoma.
Studies have confirmed that the loss of SMARCA4 leads to both negative and positive effects on tumorigenesis(Walter, Venancio et al. 2017, Deribe, Sun et al. 2018). Recent studies have found that SMARCA4 plays a paradoxical role in tumor development, with SMARCA4-Mut inhibiting tumor progression in early tumors and accelerating it at highly advanced stages. The reason is that most transformed cells carrying SMARCA4-Mut are alveolar type II (ATII) cells, which gradually transform into Club cells at the later stage of tumor development and are sensitive to malignant transformation and tumor progression in a cell type-dependent manner, resulting in an increased incidence of highly advanced dedifferentiated tumors and metastases(Concepcion, Ma et al. 2022). We hypothesized that the effect of NapsinA may be related to the transformation of ATII cells in the occurrence and development of tumors. High expression of NapsinA predicted a higher proportion of SMARCA4-Mut ATII cells, during which the tumor progressed slowly, indicating a longer prognosis for survival. However, after the highly advanced stage, ATII cells were gradually transformed into Club cells, and NapsinA expression was low during this period, demonstrating the high malignancy of the tumor and a shorter prognosis for survival.
Currently, there have been no reports analyzing the prognostic survival of NapsinA in lung cancer with different gene mutation types. Our results, from this perspective, found that positive expression of NapsinA in SMARCA4-Mut correlated with a better prognosis, while there was no statistical difference in the WT group. This may also be related to the pathological type. NapsinA is mainly expressed in lung adenocarcinoma, while SMARCA4-Mut lung cancer exhibits a more complex pathological type. Positive expression indicates good typing, leading to slower tumor progression. The occurrence and development of SMARCA4-Mut lung cancer are influenced by various factors, including but not limited to the progressive transformation of advanced alveolar type II cells into Club cells. Studies have found that SMARCA4 deficiency leads to decreased expression of IP3R3, resulting in impaired calcium 2 + transfer from the endoplasmic reticulum to the mitochondria required for apoptosis induction. This results in a reduced response to chemotherapy(Xue, Morris et al. 2023). Simultaneously, the immunotherapy benefits associated with different gene mutations, as discussed earlier, and the expression of key cell groups and metabolic components in the tumor microenvironment also impact the results.
Our findings provide new insights for NSCLC-SMARCA4-Mut patients and warrant attention. However, the deeper role and mechanism of NSCLC-SMARCA4-Mut patients cannot be further analyzed due to the lack of clinical samples, requiring confirmation through further prospective studies.