Gastric adenocarcinoma (GAC) is a common malignant tumor, and patients with advanced GAC have a poor prognosis. At present, clinical trials of anti-PD-1 (programmed cell death protein-1)/PD-L1(Programmed Cell Death-Ligand 1) therapy for GAC have achieved good results. Microsatellite instability-high (MSI-H), high tumor mutational burden (TMB) or PD-L1 expression are the main indicators to predict its efficacy. However, the response to treatment remains highly variable, and some patients remain unresponsive to immunotherapy (1). It is therefore necessary to further study the related mechanisms of tumor immunity and to find specific and effective predictive biomarkers related to the tumor immune response.

Whole-exome sequencing revealed that genes encoding subunits of the SWItch/Sucrose Nonfermentable (SWI/SNF) complex are mutated in more than 20% of cancers, involving multiple cancer types (2). The SWI/SNF complex is a subfamily of adenosine triphosphate-dependent (ATP-dependent) chromatin remodeling proteins that regulate the access of transcription factors through control based on nucleosome topology remodeling and can recruit proteins to promote DNA repair through mechanisms such as nucleotide excision and double-strand break repair. Therefore, the loss or abnormality of its function may lead to genome instability and the occurrence and progression of tumors and can also enhance the antitumor immune response and affect the biological behavior of tumors (2). This complex includes the BRG1(BRM(Brahma)/SWI2 related gene 1)/BRM-associated factor complex (BRG1/BRM-associated factor, BAF) and polybromo-associated BAF complex (polybromo-associated BAF, PBAF). Polybromo 1(PBRM1) is an important accessory regulatory subunit of the latter. PBRM1 is localized to 3p21, and loss or inactivating mutations of PBRM1 can mediate the regulation of cell growth, migration, proliferation and differentiation in a variety of cancers and can be involved in tumor immune responses and related immune treatments (3). Therefore, we hypothesized that abnormal PBRM1 may play a role in the carcinogenesis and tumor immune activity of GAC.

This study sought to explore the relationship between PBRM1 gene abnormalities and the occurrence and development of GAC and tumor immune activity and to provide evidence for its potential use as a predictive marker for GAC immunotherapy. In this paper, cBioPortal, LinkedOmics and TISIDB datasets were used to analyze the abnormality of the PBRM1 gene in GAC and its relationship with prognosis, related molecular changes and tumor-infiltrating lymphocytes (TIL). GAC cases were collected to further verify and study the effect of PBRM1 loss/attenuation on clinicopathology and prognosis and analyze its relationship with microsatellite stability, PD-L1 expression and TILs in GAC.

Analysis of public databases and the data of GAC cases collected in our group showed that the PBRM1 gene was significantly abnormal in a small number of GACs (approximately 10%), including gene deletion/mutation, methylation and loss/attenuation of expression. According to the literature, PBRM1 inactivating mutation or expression loss exists in approximately 40% of clear cell renal carcinoma, 32% of cholangiocarcinoma and 83% of epithelioid sarcoma (12), which is an important tumor driver gene, suggesting that it may be an important driving carcinogenesis factor for a small portion of GAC. This study also showed that PBRM1 deletion/mutation or loss/attenuation of PBRM1 expression often coexists with other SWI/SNF subunit mutations, indicating that the functions of SWI/SNF subunits may have mutual compensatory effects, improving the dysfunction of the complex caused by the inactivation of a certain subunit function, and its dysfunction may be associated with simultaneous abnormalities of multiple subunits (13). At the same time, according to our sequencing and LinkedOmics data results, we also found that the loss or downregulation of PBRM1 expression may involve multiple mechanisms, including deletion/mutation and CpG island methylation in the gene promoter region.

Interestingly, prognostic analysis showed that abnormality of the PBRM1 gene was a favorable prognostic factor, and multivariate regression analysis showed that iTILs, which were closely positively related to PBRM1 expression loss/attenuation, were an independent prognostic factor. Comprehensive public databases and the data in our group found that the abnormal SWI/SNF subunit PBRM1 was closely related to tumor immune microenvironment-related factors, such as high expression of the immunosuppressive molecules PD-L1 and CTLA4, high sTIL, and iTIL. This indicates that there may be a balance between carcinogenesis and tumor suppressor immune activity of PBRM1 abnormalities (14), thereby affecting the overall biological behavior and prognosis of tumors. A study using a genome-wide CRISPR–Cas9 screen found that PBRM1 expression was inversely correlated with the expression of T-cell cytotoxicity genes in a variety of cancers. Low expression of PBRM1 was associated with higher cytotoxic activity and degree of infiltration of CD8 T cells. Loss of PBAF function increases tumor cell sensitivity to interferon-gamma, resulting in increased secretion of chemokines that recruit effector T cells, an increased percentage of dendritic cells and a higher ratio of tumor-inhibitory M1-like macrophages to tumor-promoting M2-like macrophages. Single-cell RNA-seq analysis of sorted CD45⁺ immune cells showed that gene expression signatures were associated with tumor immunity (IFN-γ response, IFN-α response, and tumor necrosis factor-α signaling through NF-κB) in myeloid cells (dendritic cells and M1-like macrophages) and lymphocytes (T cells and natural killer cells) in PBRM1-deficient individuals (15). Rhabdoid tumors (RTs) are malignant tumors driven by inactivation of the SWI/SNF subunit SMARCB1. A study found that RTs in the brain with low PBAF expression had a better overall prognosis. PBRM1 knockdown resulted in decreased immunosuppressive cytokines, and PBRM1 levels in tumor tissues were negatively correlated with CD8 cytotoxic T-cell (CTC) infiltration (16).

Studies have shown that the mRNA and protein expression levels of the immune checkpoint molecules PD-L1 and CTLA4 are also closely related to high TILs, an active immune response, and a “hot” immune microenvironment, which is beneficial for the tumor-targeted immune response or immunotherapy (17, 18). iTILs can further enhance antitumor activity through direct contact with cancer cells. These include conventional CD4⁺ or CD8⁺ T cells (also known as inducible iTILs) as well as unconventional γδ T cells or CD4⁻CD8αβ-TCRαβ+ T cells (double negative T) (also known as native iTILs). Native iTILs possess autoreactive T-cell receptors (TCRs), granzymes A and B, and high cytotoxic activity (19). We preliminarily explored the specific types of TILs associated with abnormal PBRM1 genes in GAC through the TISIDB database, including activated CD4 and CD8 T cells, activated dendritic cells, monocytes, and NK cells. Therefore, an abnormal PBRM1 gene can lead to a more favorable tumor microenvironment and make tumor cells more sensitive to immune cell-mediated cytotoxicity, such as that driven by T cells.

There is a significant correlation between abnormal SWI/SNF subunit and MSI-H, and both are related to PD-L1 expression, high tumor genome mutation rate, and high TIL, resulting in high tumor immune activity. There are several hypotheses regarding the causal affiliation of the two: 1) SWI/SNF complex subunit gene mutations may be caused by MSI; 2) the two may be a reflection of genome-wide hypermethylation, that is, a CpG island methylation phenotype; and 3) SWI/SNF complex deficiency leads to impaired MMR, mutation or MLH1 promoter methylation and epigenetic alterations (20, 21). Studies have found that SWI/SNF subunit ARID1A deficiency attenuates mismatch repair (MMR) capacity, impairs mismatch repair in a variety of cancers, leads to genomic alterations in microsatellite instability (22, 23), increases TMB, increases neoantigen presentation, increases TILs, and makes tumors susceptible to immune checkpoint blockade. In low MSI/microsatellite stable subtype gastrointestinal cancer (excluding the influence of MSI-H), ARID1A mutant cases still had significantly higher tumor immune activity scores than ARID1A wild type tumors, including high TMB, PD-L1 expression and CTC infiltration (24, 25). Therefore, the effects of abnormal SWI/SNF subunits (including the PBRM1 gene) and MSI on tumor immune activity may be both synergistic and independent, and the former may be another important factor leading to increased tumor immunity in addition to MSI-H. In pancreatic cancer with SWI/SNF subunit loss, some cases that were not accompanied by MSI-H, high TMB and/or PD-L1 expression also responded to immune checkpoint inhibitors (26). Therefore, abnormal SWI/SNF subunits, including PBRM1, should be considered as other important markers in addition to MSI and PD-L1 expression in GAC immunotherapy.

In clinical practice, it is difficult to recover from the abnormal deletion of gene products, but abnormal SWI/SNF subunits often co-occur with abnormalities of other molecular signaling pathways. The use of specific synthetic lethal relationships is an effective approach to its treatment and has now become a hot field of precision therapy (27). This study showed that PBRM1 deletion/mutation is closely related to PIK3CA mutation and that KEGG signaling pathways enriched for PBRM1 expression loss include lysine degradation, antigen processing and presentation, the Notch signaling pathway and phagosome-related genes in GACs. In the future, it may be applied in the treatment of synthetic lethal mechanisms or as a predictive marker for anti-gene targeted therapy in GAC.

In conclusion, PBRM1 gene abnormalities may play an important carcinogenic role in some gastric cancer subgroups and may affect their tumor immune activity, thereby influencing the clinicopathological and overall prognosis of GAC. The detection of PBRM1 gene abnormalities may be an effective predictive marker in immunotherapy, and harnessing the synthetic lethal relationship associated with PBRM1 gene abnormalities may also be a potential novel therapeutic strategy in GAC.