Abstract PS2-08-02: Comprehensive Characterization of PTEN loss by IHC and PTEN alteration by NGS in Metastatic HR-Positive, HER2-Negative Breast Cancer-- An Exploratory Analysis of Biomarker Concordance and Co-Occurrence

Abstract Introduction: PTEN, a key negative regulator of the PI3K/AKT signaling pathway, can get inactivated in hormone receptor positive (HR+), HER2-negative (HER2−) metastatic breast cancer (mBC). While genomic alterations can inactivate PTEN, a subset of tumors lose PTEN protein expression without any PTEN genomic alterations, resulting in a discordance between genomic and protein-based test results. The CAPItello-291 trial (NCT04305496) led to the approval of capivasertib (AKT inhibitor) in combination with fulvestrant in patients with HR+/HER2- mBC with alterations in PIK3CA, AKT1, and/or PTEN. Here, we report a prespecified exploratory analysis evaluating the concordance between PTEN loss of expression by IHC and its genomic alteration by NGS, as well as the respective co-occurrences with PIK3CA and AKT1 mutations. Methods: 2,716 breast tumors underwent comprehensive tumor profiling at Caris Life Sciences (Phoenix, AZ) between August 2024 to June 25, 2025. All tumors were identified as HR positive and HER2 negative by a combination of IHC and CISH based on ASCO/CAP guidelines. Gene mutations were determined by Whole Exome Sequencing. PTEN IHC was performed using 6H2.1 antibody and scored by board-certified pathologists; PTEN loss was defined as complete absence of staining (0+, 0%). Results: Among the 2,716 tumors, 196 (7.21%) demonstrated PTEN loss by IHC. The overall concordance between PTEN IHC loss and PTEN NGS genomic alterations was 92.9%. In the absence of a definitive reference standard, the positive percent agreement was 52%; negative percent agreement was 96%. Among the discordant cases, two distinct patterns were observed. In tumors with PTEN loss by IHC but wild-type (wt) by NGS (N=112), PIK3CA and AKT1 mutation rates were 36.6% (41/112) and 0.89% (1/112), respectively. Conversely, in tumors with intact PTEN by IHC but PTEN alterations (alt) by NGS (N=77), PIK3CA and AKT1 mutation rates were 49.4% (38/77) and 1.3% (1/77), respectively. Notably, 5.41% (70/1293) of tumors that were wild-type for PTEN, PIK3CA and AKT1 by NGS demonstrated PTEN loss by IHC suggesting PI3K pathway activation that would have been missed without IHC testing. Conclusion: To our knowledge, this is the largest study highlighting a substantial discordance between PTEN expression by IHC and genomic alterations by NGS in HR+/HER2− mBC. Our results underscore the necessity for a multimodal approach to patient selection for markers of treatment resistance and suggest that PTEN IHC may identify additional patients with PI3K/AKT pathway activation. Citation Format: R. L. Mahtani, S. C. Smith, S. M. Swain, S. Wu, J. R. Klemp, M. Benrashid, S. Puri, T. Nicolaides, J. Xiu, M. Oberley, M. Chaki, G. Sledge. Comprehensive Characterization of PTEN loss by IHC and PTEN alteration by NGS in Metastatic HR-Positive, HER2-Negative Breast Cancer-- An Exploratory Analysis of Biomarker Concordance and Co-Occurrence abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-08-02.