Background: Mutations (mut) in ESR1 and PIK3CA are key drivers of endocrine resistance in HR+ MBC, with ESR1 mut typically acquired after aromatase inhibitor therapy and PIK3CA mut often present early and clonally. The co-occurrence of these muts and their effects on the tumor immune microenvironment (iTME) and transcriptome are not well understood. Here, we compare gene expression and immune cell infiltration in patients (pts) with PIK3CA– and/or ESR1-mut versus wild-type (WT) HR+/HER2- MBC.
Methods: We used Tempus Lens (Tempus AI, Inc., Chicago, IL) to identify pts with a primary diagnosis of MBC who had Tempus xT/xF and xR testing from the Tempus multi-modal database. Pts with tumor purity of at least 30% were assessed and all pathogenic or likely pathogenic somatic SNVs/indels for PIK3CA and ESR1 were extracted. Pts were stratified into groups based on the presence of PIK3CA-mut and/or ESR1-mut. RNA-seq data were normalized to correct for assay/batch effects, quantified as transcripts per million (TPM) for all protein-coding transcripts, and reported as log2(TPM + 1). Immune infiltration was quantified using quantiseq. Differential gene expression (DGE) analyses were performed using Wilcoxon rank-sum tests; p values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate method.
Results: The study cohort included N=4,583 pts where 48% were WT, 36% PIK3CA-mut, 10% ESR1-mut, and 6% co-mut. Median age at diagnosis was 57 years and, among those with available race data, 77% were White, 12% were Black, 4% were Asian. DGE analyses revealed differences in genes known to promote cancer development and tumor growth. Specifically, compared to WT, both ESR1-mut pts and co-mut pts had higher expression of TFF1, FGA, FGB, ALB, and SCGB2A2 (p<0.001). Lower SFRP2 expression was specific to ESR1-mut tumors (p<0.001); PIK3CA-mutated pts also had higher expression of SCGB2A2 (mammaglobin) (p<0.001). iTME analysis revealed that PIK3CA-mut and co-mut tumors exhibited significantly higher levels of immunosuppressive cells, specifically M2 macrophages and regulatory T cells (Tregs)( p<0.001). This immunosuppressive profile was most pronounced in PIK3CA-mut pts, whereas ESR1-only pts showed the lowest numerical enrichment.
Conclusions: PIK3CA-mutant and co-mutant HR+/HER2- MBCs share a distinct immunosuppressive microenvironment, primarily driven by PIK3CA mutation status, and exhibit unique transcriptional profiles. SFRP2 downregulation is specific to ESR1-mutant tumors, while robust SCGB2A2 upregulation in PIK3CA-mutant and co-mutant tumors highlights its potential as a diagnostic and therapeutic target. These findings underscore the importance of further research to clarify the clinical significance of these molecular programs and to inform the development of new treatment strategies.
Table 1
|
No-mut (N=2,203) |
PIK3CA-only (N=1,668) |
ESR1-only (N=436) |
Co-mut (N=276) |
P-value |
| FF1 Expression |
6.7 (3.2, 9.3) |
7.9 (5.5, 9.7) |
8.3 (6.0, 10.1) |
9.3 (7.2, 10.8) |
<0.001 |
| FGA Expression |
0.5 (0.4, 2.3) |
0.5 (0.4, 1.6) |
7.2 (0.5, 10.9) |
3.5 (0.5, 10.3) |
<0.001 |
| FGB Expression |
0.9 (0.5, 4.4) |
0.9 (0.5, 3.3) |
8.3 (1.0, 11.7) |
5.1 (0.8, 11.0) |
<0.001 |
| ALB Expression |
2.9 (1.8, 6.4) |
2.9 (1.8, 5.3) |
10.9 (2.9, 14.5) |
6.9 (2.3, 14.1) |
<0.001 |
| SCGB2A2 Expression |
4.0 (0.7, 8.5) |
7.7 (3.0, 10.4) |
5.0 (0.9, 9.1) |
8.2 (4.1, 10.8) |
<0.001 |
| SFRP2 Expression |
6.1 (2.6, 8.2) |
6.9 (3.7, 8.7) |
2.3 (0.4, 5.7) |
3.5 (0.8, 6.8) |
<0.001 |
| % of M2 macrophages |
5.3 (3.9, 6.9) |
5.8 (4.53, 7.31) |
5.1 (3.53, 6.53) |
5.1 (4.0, 6.9) |
<0.001 |
| % of M1 macrophages |
3.2 (2.1, 4.5) |
3.4 (2.4, 4.6) |
2.8 (2.0, 3.0) |
3.3 (2.4, 4.4) |
<0.001 |
| % of Tregs |
2.6 (2.0, 3.8) |
2.8 (2.1, 3.8) |
2.2 (1.6, 3.0) |
2.3 (1.7, 3.1) |
<0.001 |
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