Mutational Analysis of PBRM1 and Significance of PBRM1 Mutation in Anti-PD-1 Immunotherapy of Clear Cell Renal Cell Carcinoma

Abstract

Renal cell carcinoma is a common solid tumor. PBRM1 is one of the most mutation-prone genes in clear cell renal cell carcinoma (ccRCC) with the occurrence of mutation in 40% of ccRCC patients. Mutations in PBRM1 have been correlated with the efficacy of immunotherapy. However, the mutation types of PBRM1 are not well characterized. The effects of PBRM1 expression levels in the tumor microenvironment are not well studied. In addition, the mechanism and effect of anti-PD-1 immunotherapy in ccRCC tumor microenvironments are not well clarified. In this study, using bioinformatics methods we analyzed the alternation frequency and expression levels of PBRM1 in various tumors. Next, we experimentally validated their expression levels in ccRCC tissues from human and mouse models. We attempted to clarify the mechanisms of anti-PD-1 immunotherapy in ccRCC with various PBRM1 expression levels. Our results showed that deficiency of PBRM1 protein is correlated with CD4 T cell reduction in human and mouse ccRCC tissues. We also showed that anti-PD-1 Immunotherapy can increase the infiltration of T cells in both PBRM1 high and PBRM1 low tumors but to different degrees. Our study indicates that the reduction of CD4 cells in tumor tissues with low expression of PBRM1 may explain the compromised efficacy of anti-PD-1 immunotherapy in patients with PBRM1 mutated ccRCC. Our study sheds light on the potential of PBRM1 as a therapeutic target in ccRCC.

Keywords: CD4 T cell; PBRM1 expression; PBRM1 mutation; anti-PD-1 immunotherapy; clear cell renal cell carcinoma.

Figure 1

The expression level of PBRM1 varies in different tumors and tumor stages. (A) The expression status of the PBRM1 gene in diverse cancer types were analyzed through the TIMER dataset. *P < 0.05; **P < 0.01; ***P < 0.001. (B) Based on the CPTAC dataset, the expression level of PBRM1 total protein between normal tissues and primary tumor tissues of breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and kidney renal clear cell carcinoma (KIRC, ccRCC) were analyzed. (C) Based on the TCGA data, the expression levels of the PBRM1 gene were analyzed by the main pathological stages (stage I, stage II, stage III, and stage IV) of BRCA, COAD, LUAD, ccRCC. Log2 (TPM+1) was applied for log-scale. (D) PBRM1 protein expression levels in Stage I and Stage IV of our ccRCC samples. The expression levels were detected using immunohistochemistry and analyzed by unpaired t-test.

Figure 2

Mutation frequency of PBRM1 in tumors reproduced from the Cancer Genome Atlas (TCGA) database. (A) Alternation frequency of PBRM1 in various tumors are shown. (B) Mutation types of PBRM1 in ccRCC are shown. (C) 3D structure of PBRM1 and the mutation cite is shown. (D) Protein-protein interaction network of PBRM1 are shown. The top 10 experimentally determined genes ranked by degree are shown.

Figure 3

The mutation of PBRM1 affects the survival rates of patients. Overall survival (A) and disease-free survival (B) of PBRM1 high and PBRM1 low patients in different tumors. GEPIA2 tool was used to analyze the TCGA dataset. BRCA, breast invasive carcinoma; COAD, colon adenocarcinoma; LUAD, lung adenocarcinoma; KIRC, kidney renal clear cell carcinoma (ccRCC). (C) Overall survival of KIRC (ccRCC) patients based on the PBRM1 expression level and tumor grade. Kaplan-Meier curves with positive results are given.

Figure 4

Low expression of PBRM1 correlates with decreased CD4 cells in human ccRCC. (A) The correlation of PBRM1 expression with CD4, CD8 within tumors from 533 ccRCC patients were analyzed using the TIMER database. (B) Opal Multiplex Immunohistochemistry detection of PBRM1, CD4, CD8 in human ccRCC samples.180 ccRCC samples were tested and classified as High (>80%), Medium (50-60%), Low (<20%) according to the expression level of PBRM1 in the tumor tissues. (C) Represents the numbers of CD4, CD8 cells in (B). PBRM1 High, PBRM1 Low groups were calculated by unpaired t-test, **P < 0.01; ***P < 0.001. Data indicates Mean+SD.

Figure 5

Low expression of PBRM1 causes reduction of tumor-infiltrating CD4 cells in ccRCC mouse model. (A) PBRM1 protein expression level in PBRM1 high and PBRM1 low Renca cells were detected by western blot. PBRM1 low Renca cells were obtained using shRNA to PBRM1. β-actin was used as an internal control. (B) Growth curves of PBRM1 High and PBRM1 Low tumors in ccRCC mouse model. (C) Flow cytometry image of tumor-infiltrating T cells. TIL cells were isolated from tumors and gated CD45⁺ CD3⁺cells. Percentage (D) and absolute numbers (E) of CD4 and CD8 cells in tumors of PBRM1 High and PBRM1 Low mice model. CD4 andCD8 cells gated in CD45⁺ CD3⁺ cells. Data represents 3 independent experiments at least 6 mice per group. *P < 0.05; ns, no significance.

Figure 6

Anti-PD-1 immunotherapy increased CD4 T cell infiltration in ccRCC mouse model. (A) Treatment scheme of anti-PD-1 immunotherapy in ccRCC mouse model. Anti-PD-1 antibody and control antibody were administrated at day 6, day 9, and day 12 after tumor inoculation. (B) Growth curves of PBRM1 High and PBRM1 Low tumors treated with anti-PD-1 antibody or control isotype antibody in ccRCC mouse model. Test was stopped when mice died or tumors reached 1000mm³ in size. (C) Survival rates of mice in different groups. Data were analyzed with GraphPad Prism 8.0.2. Absolute cell numbers (D) and percentages (E) of CD4 and CD8 T cells in tumors of different groups were shown. All live mice were euthanized at day39 and tumor infiltrating T cells were detected by Flow Cytometry. Data are presented as mean ± SD with at least 6 mice for each group. *p < 0.05; ns, no significance.