Molecular Characterization of HER2-Low Invasive Breast Carcinoma by Quantitative RT-PCR Using Oncotype DX Assay.

BACKGROUND: HER2 immunohistochemistry (IHC) reproducibility is suboptimal for HER-low cases (IHC 1+ or 2+). METHODS: The Yale cohort included 214 stages I-II estrogen receptor positive breast cancers with IHC scores 0, 1+, and 2+ and routine Oncotype DX Recurrence Score (RS) results. The Exact Sciences (ES) cohort included 9 57 624 patients who had an Oncotype DX RS assay that assigns HER2-negative, equivocal, or positive status based on HER2 mRNA levels. RESULTS: HER2 mRNA levels varied across IHC categories but with increasing medians of 9.10 (n = 89), 9.20 (n = 71), and 9.45 (n = 54) in IHC 0, 1+, and 2+, respectively. 22.4% of HER2-low (1+/2+) cancer had RS > 25. Over 98% of HER-low cancers were HER2-negative by Oncotype DX assignment. CONCLUSIONS: Cancers with higher mRNA levels exist within IHC 0 and low categories, most of the HER2-low patients by IHC have low RS indicating no benefit from current adjuvant chemotherapies.

PD-L1 protein expression in relation to recurrence score values in early-stage ER + breast cancer.

PURPOSE: We assessed associations between PD-L1 protein expression, RS, tumor grade, and stromal tumor-infiltrating lymphocyte (TIL) count in early-stage ER + cancers. METHODS: FFPE tissue blocks of 213 patients with RS in 2012-2017 were identified. PD-L1 immunohistochemistry was performed with SP142 assay, cases with ≥ 1% tumor-infiltrating immune cell positivity in the tumor area were considered PD-L1 + . TIL scores were determined following the international TIL counting guidelines. PD-L1 expression positivity rates were compared across RS (< 11, 11-25, > 25) and TIL categories (< 10%, 10-29%, > 30%), and tumor grade using Wilcoxon and Chi-square tests. Multivariate analysis was performed using logistic regression. RESULTS: PD-L1 and TIL results were available for 201 and 203 patients. Overall, 53% of cases were PD-L1 +. PD-L1 expression was higher among cases with RS > 25, versus RS < 11 (p = 0.00019) and RS 11-25 (p = 0.0017). PD-L1 positivity also correlated with TIL score, tumor grade, and tumor size. Among cancers with TIL > 30%, 92% were PD-L1 + versus 44% PD-L1 + among TIL < 10% (p = 2.8 × 10-6). Grade 3 cancers had higher PD-L1 positivity (79% PD-L1 +) versus grade 2 (49% PD-L1 +) or 1 tumors (48% PD-L1 +) (p = 0.00047). T2 and T3 tumors had more frequent PD-L1 positivity (67% and 83%, respectively) versus T1 cancers (46%) (p = 0.008). In multivariate analysis, only TIL and RS remained as independent predictors of PD-L1 positivity. CONCLUSION: PD-L1 expression is significantly more frequent and higher in larger tumors (T2, T3), grade 3 cancers, and in cancers with RS > 25. PD-L1 expression also correlates with TIL score.

Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness.

Functional buffering that ensures biological robustness is critical for maintaining tissue homeostasis, organismal survival, and evolution of novelty. However, the mechanism underlying functional buffering, particularly in multicellular organisms, remains largely elusive. Here, we proposed that functional buffering can be mediated via expression of buffering genes in specific cells and tissues, by which we named Cell-specific Expression-BUffering (CEBU). We developed an inference index (C-score) for CEBU by computing C-scores across 684 human cell lines using genome-wide CRISPR screens and transcriptomic RNA-seq. We report that C-score-identified putative buffering gene pairs are enriched for members of the same duplicated gene family, pathway, and protein complex. Furthermore, CEBU is especially prevalent in tissues of low regenerative capacity (e.g., bone and neuronal tissues) and is weakest in highly regenerative blood cells, linking functional buffering to tissue regeneration. Clinically, the buffering capacity enabled by CEBU can help predict patient survival for multiple cancers. Our results suggest CEBU as a potential buffering mechanism contributing to tissue homeostasis and cancer robustness in humans.