METABRIC Cohorts Research Articles

Elevated expression of Aurora-A/AURKA in breast cancer associates with younger age and aggressive features.

Aurora kinase A (AURKA) is reported to be overexpressed in breast cancer. In addition to its role in regulating cell cycle and mitosis, studies have reported AURKA involvements in oncogenic signaling in suppressing BRCA1 and BRCA2. We aimed to characterize AURKA protein and mRNA expression in a breast cancer cohort of the young, investigating its relation to clinico-pathologic features and survival, and exploring age-relatedAURKA-associated biological processes. Aurora kinase A immunohistochemical staining was performed on tissue microarrays of primary tumors from an in-house breast cancer cohort (n = 355) with information on clinico-pathologic data, molecular markers, and long and complete follow-up. A subset of the in-house cohort (n = 127) was studied by the NanoString Breast Cancer 360 expression panel for exploration of mRNA expression. METABRIC cohorts < 50 years at breast cancer diagnosis (n = 368) were investigated for differentially expressed genes and enriched gene sets in AURKA mRNA high tumors stratified by age. Differentially expressed genes and gene sets were investigated using network analyses and g:Profiler. High Aurora kinase A protein expression associated with aggressive clinico-pathologic features, a basal-like subtype, and high risk of recurrence score. These patterns were confirmed using mRNA data. High AURKA gene expression demonstrated independent prognostic value when adjusted for traditional clinico-pathologic features and molecular subtypes. Notably, high AURKA expression significantly associated with reduced disease-specific survival within patients below 50 years, also within the luminal A subtype. Tumors of high AURKA expression showed gene expression patterns reflecting increased DNA damage activation and higher BRCAness score. Our findings indicate higher AURKA expression in young breast cancer, and associations between high Aurora-A/AURKA and aggressive tumor features, including higher tumor cell proliferation, and shorter survival, in the young. Our findings point to AURKA as a marker for increased DNA damage and DNA repair deficiency and suggest AURKA as a biomarker of clinical relevance in young breast cancer.

CD133 expression is associated with less DNA repair, better response to chemotherapy and survival in ER-positive/HER2-negative breast cancer.

CD133, a cancer stem cells (CSC) marker, has been reported to be associated with treatment resistance and worse survival in triple-negative breast cancer (BC). However, the clinical relevance of CD133 expression in ER-positive/HER2-negative (ER + /HER2-) BC, the most abundant subtype, remains unknown. The BC cohorts from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1904) and The Cancer Genome Atlas (TCGA, n = 1065) were used to obtain biological variables and gene expression data. Epithelial cells were the exclusive source of CD133 gene expression in a bulk BC. CD133-high ER + /HER2- BC was associated with CD24, NOTCH1, DLL1, and ALDH1A1 gene expressions, as well as with WNT/β-Catenin, Hedgehog, and Notch signaling pathways, all characteristic for CSC. Consistent with a CSC phenotype, CD133-low BC was enriched with gene sets related to cell proliferation, such as G2M Checkpoint, MYC Targets V1, E2F Targets, and Ki67 gene expression. CD133-low BC was also linked with enrichment of genes related to DNA repair, such as BRCA1, E2F1, E2F4, CDK1/2. On the other hand, CD133-high tumors had proinflammatory microenvironment, higher activity of immune cells, and higher expression of genes related to inflammation and immune response. Finally, CD133-high tumors had better pathological complete response after neoadjuvant chemotherapy in GSE25066 cohort and better disease-free survival and overall survival in both TCGA and METABRIC cohorts. CD133-high ER + /HER2- BC was associated with CSC phenotype such as less cell proliferation and DNA repair, but also with enhanced inflammation, better response to neoadjuvant chemotherapy and better prognosis.

Infiltration of Common Myeloid Progenitor (CMP) Cells is Associated With Less Aggressive Tumor Biology, Lower Risk of Brain Metastasis, Better Response to Immunotherapy, and Higher Patient Survival in Breast Cancer.

To investigate the clinical relevance of common myeloid progenitor (CMP) cells in breast tumor microenvironment (TME). The role of rare cells in TME is less studied. In Silico transcriptomic analyses of real-world data enable us to detect and quantify rare cells, including CMP cells. A total of 5176 breast cancer (BC) patients from SCAN-B, METABRIC, and 5 single-cell sequence cohorts were analyzed using the xCell algorithm. The high group was defined as more than two-thirds of the CMP scores in each cohort. CMP cells consist of 0.07% to 0.25% of bulk breast tumor cells, more in estrogen receptor-positive (ER+) compared with triple-negative (TN) subtype (0.1% to 0.75%, 0.18% to 0.33% of immune cells, respectively). CMP cells did not correlate with any of the myeloid lineages or stem cells in TME. CMP infiltration was higher in smaller tumors, with lower Nottingham grade, and in ER+/HER2- than in TNBC consistently in both SCAN-B and METABRIC cohorts. High CMP was significantly associated with a lower risk of brain metastasis and with better survival, particularly in ER+/HER2-. High CMP enriched epithelial-to-mesenchymal transition and angiogenesis pathways, and less cell proliferation and DNA repair gene sets. High CMP ER+/HER2- was associated with less immune cell infiltration and cytolytic activity ( P <0.001). CMP infiltration correlated with neoadjuvant chemoimmunotherapy response for both ER+/HER2- and TNBC in the ISPY-2 cohort (AUC=0.69 and 0.74, respectively). CMP in BC is inversely associated with cell proliferation and brain metastasis, better response to immunotherapy, and survival. This is the first to report the clinical relevance of CMP infiltration in BC.

Abstract PO3-25-03: Can intratumoral microRNA-125a levels be a prognostic biomarker of a ER-positive breast cancer patients？

Abstract Background: MicroRNA-125a (miR-125a) has been shown to function as tumor suppressive miRNA by pre-clinical in vitro studies. However, to the best of our knowledge, there has been no study that investigated the clinical relevance of miR-125a in breast cancer patients. We hypothesized that miR-125a expression in breast cancer associate with its aggressiveness and can be a prognostic biomarker. Material and Methods: Non-tumorigenic epithelial cell line, MCF-10A and breast cancer cell lines, MCF-7, T47D, and MDA-MB231, were used to analyze the expression levels of miR-125a as well as cell viability. The data of 2042 patients were extracted from publicly available databases, The Molecular Taxonomy of Breast Cancer International Consortium (METARBRIC), The Cancer Genome Atlas (TCGA), and GSE57897. These databases included clinicopathological and survival data as well as transcriptome data. The survival analysis, gene set enrichment analysis (GSEA) were conducted comparing miR-125a high expressing and low expressing tumors, divided by the median cutoff. The association between the miR-125a expression and tumor immune microenvironment was assessed by xCell. Results: The expression levels of miR-125a were suppressed in breast cancer cell lines, MCF-7, T47D, and MDA-MB231compared with MCF-10A. This was concordant with human samples. The expression levels of miR-125a were lower in tumors compared with normal breast tissues in both TCGA and GSE57897 cohorts. These results were in agreement with the notion that it is a tumor suppressive miRNA (p&amp;lt; 0.001 and p&amp;lt; 0.001, respectively). ER-positive/HER2-negative (ER+/HER2-) showed the highest miR-125a expression among the subtypes in TCGA (p&amp;lt; 0.001). MiR-125a expression was not associated with cancer staging in any of the subtypes in neither TCGA nor METABRIC cohorts. To our surprise, high miR-125a tumors demonstrated worse disease free survival (DFS), disease specific survival (DSS), and overall survival (OS) compared with low expressing in ER+/HER2- breast cancer patients (p=0.008, p=0.005, and p=0.037) which was not the case for the other subtypes in METABRIC cohort. Interestingly, miR-125a expression was associated with Nottingham histological grade only in ER+/HER2- among the subtypes (p&amp;lt; 0.001). Also, high miR-125a tumors significantly demonstrated higher expression of MKI67, one of the most commonly used parameters for cell proliferation, correlated with miR-125a expression in ER+/HER2- (p=0.02), but not in other subtypes. Furthermore, high miR-125a tumors enriched four out of five cell proliferation-related gene sets in Hallmark collection, such as E2F Targets, G2M Checkpoint, Mitotic Spindle, and MYC Targets V2 in ER+/HER2- subtype, but not in TNBC. This was also the case in immune-related gene sets; interferon-alpha response and interferon-gamma response that enriched to high miR-125a tumors in ER+/HER2-, but not in TNBC. Anti-tumor immune cells, CD8 cells, T-helper type 1 cells, and M1 macrophages, were all elevated in high miR-125a tumors in ER+/HER2- subtype (all p&amp;lt; 0.03), but none in TNBC. Also, pro-cancerous immune cell such as T-helper type 2 cells were similarly highly infiltrated with high miR-125a tumors only in ER+/HER2- subtype (p=0.026). Given its association with the survival outcome, we cannot help but speculate that miR-125a expression is parallel with highly proliferative ER+/HER2- breast cancer, but its tumor suppressive effect is not enough to improve survival outcome. Conclusion: High miR-125a levels in tumors were associated with aggressive biology and worse survival, thus it can be a candidate for a prognostic biomarker in ER+/HER2- patients. Citation Format: Yoshihisa Tokumaru, Masanori Oshi, Mai Okawa, Saki Ando, Yoshimi Niwa, Ryutaro Mori, Kazuaki Takabe, Manabu Futamura. Can intratumoral microRNA-125a levels be a prognostic biomarker of a ER-positive breast cancer patients？ [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-25-03.

Abstract PO3-09-05: Potential novel treatments for high-risk subsets of breast cancer in postpartum and African American women

Abstract Semaphorin 7a (SEMA7A) is a neuroimmune molecule first recognized for its roles in axonal guidance and inflammation. More recently, SEMA7A has emerged as a driver of tumor progression in multiple types of cancer including lung, glioblastoma and breast. Our studies have focused on the roles of SEMA7A in promoting tumor cell growth and survival as well as invasion and metastasis in mouse models including xenograft and syngeneic. Using patient samples and datamining we have shown that SEMA7A can predict for recurrence in women with postpartum breast cancer (PPBC), or breast cancers diagnosed within 10 years of recent childbirth, and SEMA7A mRNA expression in TCGA is highest in young and African American (AA) women with BC, who typically have poor prognosis. Additionally, our analysis of the Cancer Genome Atlas (TCGA) breast cancer (n=593) and METABRIC cohorts (n=2,136) revealed that SEMA7A is increased in invasive disease and in the top 9% and 27% of upregulated genes (p=1.09E-19&amp;p=0.009), respectively. Additionally, ~1.2 (TCGA) and ~1.1 (METABRIC) fold increases in SEMA7A mRNA conferred significantly decreased 5-year survival rates (p=0.009&amp;p=0.002) and SEMA7A was in the top 4% of mRNAs upregulated in patients who died within 5 years of diagnosis 20,24-26. Cumulatively, these results suggest that identifying therapeutic vulnerabilities of SEMA7A+BC, or direct targeting of SEMA7A, could improve prognosis for these high-risk populations. We have identified several targets in pre-clinical models of SEMA7A+BC that include clinically available, FDA approved drugs, as well as novel inhibitors that exhibit efficacy. In published studies, we have shown that venetoclax, a Bcl-2 inhibitor, reverses ER+SEMA7A+BC resistance to endocrine therapy in mouse models. In unpublished studies, we have extended our observations in ER+SEMA7A+BC to show that alpelisib and a novel PI3K kinase inhibitor, GCT-007, both inhibit growth of human and mouse mammary tumor cells. Furthermore, in models of ER-SEMA7A+BC where we have shown cells to be resistant to chemotherapy, we have utilized age matched cell lines from AA and CA women to dissect the downstream pro-survival signaling that is mediated by SEMA7A and we have shown that anti-PD-1 and anti-PD-L1 therapies are efficacious in reducing tumor growth in vivo. Finally, we have developed a novel monoclonal antibody-based therapy that directly targets SEMA7A signaling via pro-survival pathways and inhibits tumor growth in vivo and in vitro. Collectively our results suggest that SEMA7A+BC should be identified clinically, and alternative treatments advised for this high-risk subset of breast cancer. Citation Format: Traci Lyons, Lyndsey Crump, Rachel Steinmetz, Kelsey Kines, Heather Fairchild, Alan Elder. Potential novel treatments for high-risk subsets of breast cancer in postpartum and African American women [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-09-05.

Abstract PO2-15-12: Novel Transcriptomic Classification System Unveils HER2-Low Breast Tumors

Abstract Breast cancers (BCs) are segregable into subtypes based on their intrinsic molecular features. When evaluating HER2 status, clinicians often rely on IHC, which is plagued by reproducibility issues. The widely used PAM50 transcriptomic system also does not include the HER2-low subtype. Addressing these limitations is particularly important given the recent approval of targeted therapy for HER2-low BCs. Here, we developed a unique transcriptomic classification system that can identify HER2-low BCs. Accurate identification of HER2-low BCs can help physicians navigate treatment selection and, in turn, allow patients to benefit from the new targeted therapy. We analyzed 6,361 BC samples with clinical and pathological annotation, including FISH and IHC data, from three public datasets (TCGA BRCA and SCAN-B [total n = 4,457]; METABRIC [n = 1,904]) for gene expression, differential expression, gene enrichment, copy number alterations, and mutations. An algorithm was applied to categorize samples from TCGA and SCAN-B into subtypes by customizing a gene set, employing UMAP dimensionality reduction, and utilizing clustering with the HDBSCAN algorithm. Each resulting cluster that was associated with a specific gene set was named and excluded from the next analysis. After four iterations, five subtypes were sequentially identified: Basal, HER2-high, HER2-low, Luminal B (LumB), and Luminal A (LumA). The Light GBM-based hierarchical classifier model was trained on the TCGA and SCAN-B cohorts and validated on the METABRIC dataset. Samples with high ERBB2 expression and copy number amplification were classified as HER2-high, and samples with similar PAM50 expression profiles but lacking ERBB2 expression were considered HER2-low. Luminal samples were grouped into two subtypes: LumA, characterized by low proliferation rates, and LumB, characterized by high proliferation rates. HER2-high, Basal, LumA, and LumB subtypes exhibited expected mutational and gene expression profiles. We observed ERBB2 copy number amplification and high gene expression in HER2-high samples from the TCGA and METABRIC cohorts, as confirmed by FISH and IHC in 97% and 93% of samples, respectively. Conversely, we did not see high ERBB2 expression or copy number amplification in the HER2-low samples, which was concordant with an absence of HER2 3+ expression by IHC. HER2-low samples had high mutational frequencies in PTEN, KMT2C, and ERBB2 (12%, 14%, and 8% respectively, adj. p &amp;lt; 0.005, chi-square test). HER2-low samples also showed increased EGFR (logFC = 2.8, adj. p &amp;lt; 0.001) and CLDN8 (logFC = 3.4, adj. p &amp;lt; 0.001) expression levels. The novel classifier identified 55% of the HER2-low samples as the luminal androgen receptor (LAR) Burstein subtype, as a result of higher AR expression than in HER2-high samples (logFC = 2.9, p = 0.04). Classification of SCAN-B luminal samples into the LumA and LumB subtypes also better predicted Ki-67 positivity (≥ 20% of Ki-67+ malignant cells by IHC, F1-score = 0.77) than the previously reported PAM50 classification (F1-score = 0.62). Our refined classifier effectively defined five breast cancer subtypes, including the HER2-low subtype, based on their molecular profiles. By determining HER2 status with transcriptomic data, our classifier may help minimize IHC-related reproducibility issues and, in turn, facilitate more precise treatment decision-making. Given its concordance with copy number amplification, IHC, and FISH data, our classification system can distinguish between HER2-high and HER2-low BCs. Since HER2-low BCs may represent a unique group that requires different treatment approaches, further optimization of our classifier may assist in identifying effective therapies for patients with HER2-low BCs. Citation Format: Polina Turova, Vladimir Kushnarev, Oleg Baranov, Anna Butusova, Sofia Menshikova, Sheila Yong, Anna Love, Konstantin Chernyshov, Nikita Kotlov. Novel Transcriptomic Classification System Unveils HER2-Low Breast Tumors [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-15-12.

Abstract PO2-24-01: Kif11 Inhibition Preferentially Kills TP53-mutant Breast Cancer Cells

Abstract Background Triple-Negative Breast Cancer (TNBC) makes up 15-20% of breast cancer diagnoses and is more common in younger women, those with BRCA mutations, and Black patients. Furthermore, TNBCs are defined by their lack of expression of the targetable receptors: estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), and progesterone receptor (PR), resulting in few targeted therapy options for TNBC patients. One potential therapeutic target in TNBC is mutant p53, since 85-90% of TNBCs harbor TP53 mutations. However, the mutant p53 protein is challenging to target directly. Therefore, we have sought to identify survival pathways critical to TP53 mutant cells. Through a combined in vitro and in silico drug screen, we identified that the Kif11 inhibitor SB-743921 differentially kills TP53 mutant breast cancer cells compared to TP53 wild-type cells. Hypothesis Based on this screening data, we hypothesized that Kif11 inhibition causes TP53 mutant cells to undergo mitotic catastrophe resulting in cell death due to failure of activation of p53-mediated cell cycle checkpoints. Methods Clinical data was obtained from cBioPortal from the TCGA and METABRIC cohorts. Expression data analysis and survival analyses were performed using GraphPad Prism. Cell growth assays were conducted by seeding cells in 96 well plates, treating under designated conditions, then staining with Hoechst 33342 for cell counting on the ImageXpress Pico. Cell death was determined by co-staining with Hoechst 33342 and DRAQ7 followed by imaging and analysis on the ImageXpress Pico and by Annexin V and Propidium Iodide Staining followed by flow cytometry analysis. Cell cycle analysis was conducted following synchronization with Lovastatin and Mevalonate release followed by collection of samples, fixation, PI staining, and flow cytometry analysis. Immunofluorescence imaging was conducted by staining with anti-alpha-tubulin-AlexaFluor488 and DAPI and imaging at 20x and 63x on the ImageXPress PICO. In vitro expression experiments were carried out through qPCR and western blotting. &amp;lt; Results In human breast cancers, KIF11 is more highly expressed in TP53 mutant, as compared to wild-type breast cancers, and in TNBCs, as compared to other breast cancer subtypes. Patients with tumors that had higher expression of Kif11 had poorer overall survival outcomes. Inhibition of Kif11 with the small molecule inhibitor SB-743921 induces greater death of TP53 mutant as compared to wild-type breast cancer cells. Kif11 inhibition leads to a cell cycle block in both TP53 mutant and wild-type cells, but TP53 mutant cells then die following this cell cycle block. Kif11 inhibition causes mitotic dysfunction, including monopolar spindle formation, in mutant and wild-type cells, but greater incidence of spindle abnormalities and multinucleated cells in TP53 mutants. Introduction of a TP53 mutation into TP53 wild-type cells also induces cell death following Kif11 inhibition. Conclusions The Kif11 mitotic kinesin is more highly expressed in TP53 mutant and triple-negative breast cancers than in TP53 wild-type breast cancers, and high expression is associated with poorer survival outcomes. In TP53 mutant cells, Kif11 inhibition results in mitotic dysfunction and cell death due to mitotic catastrophe. Acknowledgments Research reported in this publication was supported by the John Charles Cain Endowment and the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Numbers TL1TR003169 and UL1TR003167. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We would also like to thank the MDACC NORTH Campus Flow Cytometry and Cellular Imaging Core Facility for their assistance. Citation Format: Amanda Lanier, William Tahaney, Jing Qian, Cassandra Moyer, Yanxia Ma, Banu Arun, Abhijit Mazumdar, Powel Brown. Kif11 Inhibition Preferentially Kills TP53-mutant Breast Cancer Cells [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-24-01.

Abstract PO2-04-06: Investigation of the genomic evolution of HER2-positive breast cancer following progression on dual HER2-targetted therapy with Trastuzumab and Tucatinib

Abstract Background: Advanced HER2-positive breast cancer remains an incurable and highly morbid condition. One of the key challenges has been treatment of central nervous system (CNS) metastases, commonly seen in those with HER2-positive disease. Tucatinib is a recently approved treatment HER2-targetting tyrosine kinase inhibitor with proven CNS activity. There has been little analysis of potential genomic mechanisms of drug resistance. Method: We retrospectively identified patients that were treated with tucatinib, capecitabine and trastuzumab. We collated baseline clinical data and treatment history and all tumour and plasma samples available were obtained for testing. DNA was extracted from plasma samples using the QIAamp DNA Mini Kit (Qiagen) on 4ml plasma samples. Targeted next generation sequencing (NGS) of serial tumour and plasma samples was performed using a custom hybrid capture assay that covered 180 genes known to be recurrently mutated in breast cancer focusing on the known genomic landscape of metastatic disease as well as the inclusion of specific actionable targets. Survival analyses was performed using Cox regression models. Results: We identified 11 patients at our institution. Plasma samples were available for all 11 patients with a total of 107 serial samples across multiple time points, with a median of 8 (range 2-19) samples per patient. All 11 patients had baseline and End of Treatment (EOT) samples. In addition, 6/11 (54%) patients had tumour sequenced on the same NGS platform prior to commencement of therapy, with 12 individual tumour samples tested. The median PFS of our cohort was 9.6 months (4.0 - NR) with a median OS of 36.2 months (10.4-NR). 7/11 (64%) patients had CNS disease at baseline with their median PFS being 13.5 months (3.9-24.4) and median OS of 36.2months (10.4-NR). Overall, we observed an average of 18.4 (4-35) mutations per patient in tumour, 5.1 (1-15) in baseline plasma and 5.8 (2-14) in EOT plasma. The most frequent mutations seen in baseline tumour samples were ERBB2 (92%), KMT2C (67%) and NCOR1 (58%) compared with KMT2C (64%), NOTCH4 (36%) and PIK3CA (27%) in baseline plasma. Patients with a lower number of ctDNA mutations at baseline showed a trend towards improved survival (PFS 14 months vs 7.5 months). In this small cohort of patients we identified a higher than expected rates of KMT2C mutations. A KMT2C mutation was identified in 67% of samples which is higher than previously described rates of 7-15% in TCGA and METABRIC cohorts respectively. The presence of a concordant ctDNA KMT2C mutation in baseline and progression samples was a poor prognostic indicator (mPFS 7.5 months) when compared with no KMT2C mutation (mPFS 15.5 months) p =0.14 suggesting a possible mechanism of resistance to tucatinib. Conclusions: In this retrospective analysis of patients treated with Tucatinib, Trastuzumab and Capecitabine we established the genomic landscape of heavily pre-treated, advanced HER2-positive disease is complex. We observed there may be a correlation with KMT2C mutations and poorer clinical outcomes, however given the very small number of patients this data remains hypothesis generating, requiring validation with larger datasets. Citation Format: Elizabeth Blackley, Courtney van Geelen, Yi-An Ko, Stephen Wong, Miriam Yeung, Stephen Luen, Sarah-Jane Dawson, Sherene Loi. Investigation of the genomic evolution of HER2-positive breast cancer following progression on dual HER2-targetted therapy with Trastuzumab and Tucatinib [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-04-06.

Abstract 2569: VEGFA gene expression is associated with cell proliferation, less immune cell infiltration, and worse survival, but better response to chemotherapy and immunotherapy

Abstract Introduction: Vascular endothelial growth factor-A (VEGFA) is a well-known factor that induces angiogenesis, one of the hallmarks of cancer, which generates new blood vessels in the tumor microenvironment (TME) and provides conduit for cancer to metastasize. Interestingly, an anti-VEGFA drug (Avastin) failed to show benefit in clinical trials for breast cancer (BC). In this study we investigated the clinical relevance of VEGFA gene expression in BC. Methods: A total of 7336 BC patients from eight independent cohorts, TCGA (n= 1073), METABRIC (n= 1903), SCAN-B (GSE96058, n= 3069), GSE20194 (n=278), GSE34138 (n=178), GSE163882 (n=222), GSE25066 (n=508), and ISPY2 (GSE173839, n= 105) were analyzed. These cohorts were divided into high and low VEGFA gene expression groups using the median. Results: High VEGFA expression in BC was associated with worse overall survival in SCAN-B cohort which was validated in METABRIC cohort with overall, disease-specific, and disease-free survival (all p&amp;lt;0.02). VEGFA expression was higher in Triple Negative BC (TNBC) but was lower in BC with lymph node metastasis. High VEGFA BC was associated with significantly high intratumoral heterogeneity, homologous recombination defect, silent and non-silent mutations, and SNV neoantigens in TCGA, and was also associated with higher cell proliferation, evidenced by higher Nottingham histological grade, higher Ki67 gene expression, and enrichment of all the Hallmark cell proliferation-related gene sets: Mitotic spindle, G2M Checkpoint, E2F Targets, MYC Targets v1 and v2, and mTorC1 signaling, consistently, in SCAN-B, METABRIC, and TCGA cohorts. Reflecting its enhanced growth, high VEGFA expression was associated with less infiltration of fibroblasts and adipocytes (all p&amp;lt;0.05). Surprisingly, VEGFA expression did not enrich angiogenesis gene set in any of the cohorts, nor was related with infiltrations of blood or lymphatic vascular endothelial cells, besides pericytes. But high VEGFA BC was associated with significantly less infiltrations of anti-cancer immune cells; CD8, CD4, and dendritic cells were all significantly less, and T helper type 1 cells and regulatory T cells were significantly higher consistently in SCAN-B, METABRIC, and TCGA cohorts. VEGFA expression was significantly higher in BC that achieved pathological complete response after Anthracycline and Taxane based neoadjuvant therapy in both ER+/HER2- and TNBC subtypes in the GSE25066 cohort, and after immunotherapy in ER+/HER2- subtype, but not TNBC, in the ISPY2 clinical trial cohort. This was not validated in GSE20194, GSE34138, GSE163882 cohorts. Conclusion: Our research indicates that high VEGFA BC is associated with high cell proliferation, less immune cell infiltration, and worse survival, but better response to Anthracycline and Taxane based chemotherapy, and immunotherapy. Citation Format: Pia Sharma, Kohei Chida, Kenichi Hakamada, Kazuaki Takabe. VEGFA gene expression is associated with cell proliferation, less immune cell infiltration, and worse survival, but better response to chemotherapy and immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2569.

Abstract 2520: CD133 expression is associated with less DNA repair, better response to chemotherapy, and survival in ER-positive/ER-negative breast cancer

Abstract Introduction: Cancer stem cells (CSC) constitute only 0.1-1% of all the cells in a bulk tumor, yet they play a crucial role in treatment resistance and relapses. Its role in breast cancer (BC) has been studied but a consensus remains elusive. We focused on gene expression of a CSC marker CD133 and studied its clinical significance in ER-positive/HER2-negative (ER+/HER2-) BC, the most prevalent subtype. We utilized multiple independent large patient cohorts of gene expression and clinical variables for transcriptome analysis. Methods: A total of 2969 patients from The Cancer Genome Atlas (TCGA, n=1065) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n=1904) BC cohorts, as well as BC patients who underwent neoadjuvant chemotherapy (NAC; GSE25066, GSE20194, GSE32646 cohorts) were analyzed. Results: By analyzing SCP1039 and SCP1106 single-cell sequencing cohorts, we found that epithelial cells were the predominant source of CD133 gene expression in the tumor microenvironment. High expression of CD133 in ER+/HER2- BC correlated with elevated gene expressions of the other CSC markers; CD24, NOTCH1, DLL1, and ALDH1A1 (all p&amp;lt;0.001), and significantly enriched WNT/β-Catenin, Hedgehog, and Notch signaling (all FDR&amp;lt;0.25), which are all known pathways related with CSC in TCGA and validated in METABRIC cohort. Consistent with CSC phenotype, CD133-high BC was negatively enriched with Hallmark cell proliferation-related gene sets, such as E2F Targets, G2M Checkpoint, MYC Targets V1, Ki67 gene expression and proliferation score (FDR&amp;lt;0.25 and p&amp;lt;0.001, respectively) in both cohorts. CD133-high BC was negatively associated with DNA repair genes, such as BRCA1, E2F7 in both cohorts (all p&amp;lt;0.001). In agreement, CD133-high BC was associated with less homologous recombination deficiency, lower silent and non-silent mutation rates. Surprisingly, CD133-high BC exhibited a proinflammatory microenvironment, as represented by higher cytolytic activity in the METABRIC and higher lymphocyte infiltrations, TGF-beta response, and TCR richness in TCGA (both p&amp;lt;0.001), but less Th1 cells, M1 macrophages and dendritic cell infiltrations consistently in both cohorts. It also enriched signaling pathways related to inflammation and immune responses such as inflammatory response, allograft rejection, TNF-alpha, IL-6, TGF-beta signaling, and complement signaling (all FDR&amp;lt;0.25). CD133-high tumors had better pathological complete response after NAC in GSE25066 cohort and improved Disease-Free Survival and Overall Survival in both TCGA and METABRIC cohorts (all p&amp;lt;0.05). Conclusion: CD133-high ER+/HER2- BC is associated with CSC phenotype, reduced cell proliferation, and impaired DNA repair, but enhanced inflammation, potentially explaining the better response to NAC and favorable patient prognosis. Citation Format: Takumi Sato, Masanori Oshi, Jing Lee, Arya M. Roy, Kohei Chida, Itaru Endo, Masato Obayashi, Kazuaki Takabe. CD133 expression is associated with less DNA repair, better response to chemotherapy, and survival in ER-positive/ER-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2520.

Abstract 522: TP53mutations promote death of breast cancer cells following Kif11 inhibition

Abstract Background: Triple-Negative Breast Cancer (TNBC) comprises 15-20% of breast cancer diagnoses. These aggressive breast cancers are characterized by their lack of expression of the estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), and progesterone receptor (PR), resulting in few targeted therapy options for TNBC patients. While 85-90% of TNBCs contain mutations in TP53, mutant p53 is challenging to target directly. Instead, we aim to identify other survival pathways critical for the growth and survival of TP53 mutant cells. Through a combined in vitro and in silico drug screen, we identified the Kif11 inhibitor SB-743921 as more effective in TP53 mutant compared to wild-type breast cancer cells. Hypothesis: We hypothesized that Kif11 inhibition causes TP53 mutant cells to undergo cell death due to failure of activation of p53-mediated cell cycle checkpoints. Methods: Clinical data from the TCGA and METABRIC cohorts was obtained from cBioPortal. Expression and survival analyses were performed using GraphPad Prism. Cell growth assays were conducted by seeding cells, treating under designated conditions, then staining with Hoechst 33342 for cell counting on the ImageXpress Pico. Cell death was determined by staining with Annexin V and PI or DAPI Staining followed by flow cytometry analysis. Cell cycle analysis was conducted following synchronization with Lovastatin and Mevalonate release followed by imaging analysis of cell lines expressing the Fast FUCCI reporter or PI staining and flow cytometry analysis. Immunofluorescence imaging was conducted by staining with anti-alpha-tubulin-AlexaFluor488 and DAPI and imaging on the Nikon TI2 or ImageXPress PICO. In vitro expression experiments were carried out through qPCR and western blotting. Results: KIF11 is most highly expressed in TP53 mutant and triple-negative tumors and high expression of KIF11 is associated with poorer overall survival. In breast cancer cell lines, Kif11 inhibition leads to a cell cycle block in both TP53 mutant and wild-type cells, but TP53 mutant cells then die following this cell cycle block. Furthermore, Kif11 inhibition causes mitotic dysfunction, including monopolar spindle formation and multinucleated cells in TP53 mutants. Introduction of a TP53 mutation into TP53 wild-type cells also induces cell death following Kif11 inhibition. Conclusions: KIF11 is highly expressed in aggressive breast cancers and is associated with poorer prognosis. Using the small molecule inhibitor SB-74321 that has been tested in phase I/II clinical trials with favorable tolerability, we found that Kif11 inhibition results in mitotic dysfunction and death of TP53 mutant breast cancer cells due to mitotic catastrophe. These results suggest that Kif11 is a promising target for the treatment of TP53 mutant TNBCs. Citation Format: Amanda L. Lanier, William Tahaney, Jing Qian, Cassandra Moyer, Yanxia Ma, Banu Arun, Abhijit Mazumdar, Powel H. Brown. TP53mutations promote death of breast cancer cells following Kif11 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 522.

Ferroptosis Inducers Upregulate PD-L1 in Recurrent Triple-Negative Breast Cancer.

(1) Background: Triple-negative breast cancer (TNBC) is a distinct subgroup of breast cancer presenting a high level of recurrence, and neo-adjuvant chemotherapy is beneficial in its therapy management. Anti-PD-L1 immunotherapy improves the effect of neo-adjuvant therapy in TNBC. (2) Methods: Immune-modulation and ferroptosis-related R-packages were developed for integrative omics analyses under ferroptosis-inducer treatments: TNBC cells stimulated with ferroptosis inducers (GSE173905, GSE154425), single cell data (GSE191246) and mass spectrometry on breast cancer stem cells. Clinical association analyses were carried out with breast tumors (TCGA and METABRIC cohorts). Protein-level validation was investigated through protein atlas proteome experiments. (3) Results: Erastin/RSL3 ferroptosis inducers upregulate CD274 in TNBC cells (MDA-MB-231 and HCC38). In breast cancer, CD274 expression is associated with overall survival. Breast tumors presenting high expression of CD274 upregulated some ferroptosis drivers associated with prognosis: IDO1, IFNG and TNFAIP3. At the protein level, the induction of Cd274 and Tnfaip3 was confirmed in breast cancer stem cells under salinomycin treatment. In a 4T1 tumor treated with cyclophosphamide, the single cell expression of Cd274 was found to increase both in myeloid- and lymphoid-infiltrated cells, independently of its receptor Pdcd1. The CD274 ferroptosis-driver score computed on a breast tumor transcriptome stratified patients on their prognosis: low score was observed in the basal subgroup, with a higher level of recurrent risk scores (oncotypeDx, ggi and gene70 scores). In the METABRIC cohort, CD274, IDO1, IFNG and TNFAIP3 were found to be overexpressed in the TNBC subgroup. The CD274 ferroptosis-driver score was found to be associated with overall survival, independently of TNM classification and age diagnosis. The tumor expression of CD274, TNFAIP3, IFNG and IDO1, in a biopsy of breast ductal carcinoma, was confirmed at the protein level (4) Conclusions: Ferroptosis inducers upregulate PD-L1 in TNBC cells, known to be an effective target of immunotherapy in high-risk early TNBC patients who received neo-adjuvant therapy. Basal and TNBC tumors highly expressed CD274 and ferroptosis drivers: IFNG, TNFAIP3 and IDO1. The CD274 ferroptosis-driver score is associated with prognosis and to the risk of recurrence in breast cancer. A potential synergy of ferroptosis inducers with anti-PD-L1 immunotherapy is suggested for recurrent TNBC.

Quantification of subtype purity in Luminal A breast cancer predicts clinical characteristics and survival

PurposePAM50 profiling assigns each breast cancer to a single intrinsic subtype based on a bulk tissue sample. However, individual cancers may show evidence of admixture with an alternate subtype that could affect prognosis and treatment response. We developed a method to model subtype admixture using whole transcriptome data and associated it with tumor, molecular, and survival characteristics for Luminal A (LumA) samples.MethodsWe combined TCGA and METABRIC cohorts and obtained transcriptome, molecular, and clinical data, which yielded 11,379 gene transcripts in common and 1,178 cases assigned to LumA. We used semi-supervised non-negative matrix factorization (ssNMF) to compute the subtype admixture proportions of the four major subtypes—pLumA, pLumB, pHER2, and pBasal—for each case and measured associations with tumor characteristics, molecular features, and survival.ResultsLuminal A cases in the lowest versus highest quartile for pLumA transcriptomic proportion had a 27% higher prevalence of stage > 1, nearly a threefold higher prevalence of TP53 mutation, and a hazard ratio of 2.08 for overall mortality. We found positive associations between pHER2 and HER2 positivity by IHC or FISH; between pLumB and PR negativity; and between pBasal and younger age, node positivity, TP53 mutation, and EGFR expression. Predominant basal admixture, in contrast to predominant LumB or HER2 admixture, was not associated with shorter survival.ConclusionBulk sampling for genomic analyses provides an opportunity to expose intratumor heterogeneity, as reflected by subtype admixture. Our results elucidate the striking extent of diversity among LumA cancers and suggest that determining the extent and type of admixture holds promise for refining individualized therapy. LumA cancers with a high degree of basal admixture appear to have distinct biological characteristics that warrant further study.

Abstract P4-02-28: EMP1 low expressing tumor is associated with cell proliferation and poor overall survival of ER-positive breast cancer patients

Abstract Background: Epithelial membrane protein 1 (EMP1) belongs to PMP22 gene family and is reported to be expressed low in numerous gastrointestinal cancers. However, little is known about its role in breast cancer. EMP1 functions to promote cell proliferation. In this study, we hypothesized that low EMP1 expressing breast cancer is associated with high proliferative characteristics and poor survival. Material and Methods: The clinicopathological data and transcriptome data of breast cancer patients from two independent large publicly available databases, The Cancer Genome Atlas (TCGA, n = 1090) and The Molecular Taxonomy of Breast Cancer International Consortium (METARBRIC, n = 1904), were utilized in the current study. Survival analyses; Overall survival (OS), Disease-specific survival (DSS) and Disease-free survival (DFS) were performed by comparing the high and low expression groups. CYT score, xCell, and other immunological factors were used to evaluate intratumoral immune cell composition. Also, gene set enrichment analysis (GSEA) was performed between EMP1 high and low expression groups. Results: We divided each cohort into EMP1 expression high and low groups by utilizing median cutoff. The expression levels of EMP1 were not associated with clinical stage in any subtypes. However, interestingly lower expression of EMP1 was significantly associated with more advanced grades in ER positive/HER2 negative (ER+/HER2) subtype in both TCGA and METABRIC cohorts (p&amp;lt; 0.001 and p&amp;lt; 0.001, respectively). Also, low EMP1 expressing tumors demonstrated higher MKI67 expression levels in ER+/HER2- subtype consistently in both TCGA (p&amp;lt; 0.001) and METABRIC cohorts (p&amp;lt; 0.001). Furthermore, GSEA demonstrated that low EMP1 expressing tumors enriched the gene sets associated with cell proliferation such as MYC Targets, E2F signaling, and G2M Checkpoint signaling, compared with low EMP1 expressing tumors in ER+/HER2- of both TCGA and METABRIC cohorts. On the contrary, high EMP1 expressing tumors enriched the immune related gene sets such as Coagulation, Inflammatory_Response, Complement, and IL-6_JAK_STAT3 Signaling in ER+/HER2- of both TCGA and METABRIC cohorts. To this end, we further hypothesized that high EMP1 tumors were associated with favorable tumor immune microenvironment (TIME) and analyzed TIME utilizing xCell. However, to our surprise high EMP1 expressing tumors were not associated with favorable TIME. Low EMP1 expressing tumors demonstrated worse DFS, DSS, and OS compared with high EMP1 expressing tumors in ER+/HER2- breast cancer patients (p=0.013, p=0.003, and p=0.006) which was not the case in the other subtypes in METABRIC cohort. Conclusion: Low EMP1 expressing tumors were associated with improved OS, DSS, DFS in ER-positive breast cancer patients. Also, low EMP1 expressing tumors were found to associate with advanced grades and enriched gene sets related to cell proliferation and cell cycle, which may explain the poor survival of patients with low EMP1 expressing ER+/HER2- breast cancer. Citation Format: Junko Ukai, Yoshihisa Tokumaru, Masanori Oshi, Yoshimi Niwa, Ryutaro Mori, Kazuaki Takabe, Manabu Futamura. EMP1 low expressing tumor is associated with cell proliferation and poor overall survival of ER-positive breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-28.

Abstract PD9-09: Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancers

Abstract Background: The RxPONDER and TAILORx trials demonstrated benefit from adjuvant chemotherapy in patients &amp;lt; 50 years with node-positive breast cancer and Recurrence Score (RS) 0-25, and with node-negative disease and RS 16-25, respectively. Neither trial showed benefit in older women with RS &amp;lt; 26. It is unclear what explains the interaction between age and adjuvant chemotherapy benefit. Methods: We analyzed transcriptomic and genomic data from n=4,507 ER+/HER2- breast cancers to compare differences in estrogen receptor (ER), proliferation, and immune-related gene expressions, and somatic mutation patterns and mutation burden between younger (&amp;lt; 50 years of age) and older (&amp;gt;55 years) patients. We restricted our analysis to patients in the lower 80% range of in silico RS distribution to mimic the RxPONDER and TAILORx populations. Results: Five data sets were analyzed independently to assess consistency of results (TCGA n=530; microarray cohort A n=865; Cohort B n=609, METABRIC n=867, SCAN-B n=1636). Older patients had significantly higher somatic mutation burden and more frequent copy number gain in ESR1, LATS1, ARID1B, SGK1, and MYB genes (odds ratio [OR] &amp;gt; 8.5, FDR&amp;lt; 0.05), but lower frequency of GATA3 mutations (12% versus 26%, P&amp;lt; 0.0001). Younger patients had higher rate of ESR1 copy number loss (OR: 0.45, FDR: 0.03). There was no difference in proliferation-related gene expression. ESR1 mRNA expression was significantly lower in younger women in all cohorts (P &amp;lt; 0.001). A regression model of ESR1 mRNA expression using age and ER IHC positivity indicated that lower ER expression in younger patients is primarily driven by lower ESR1 mRNA per cancer cell and not by fewer ER positive cells. We also assessed four gene signatures associated with endocrine therapy sensitivity including a 4-gene ERS, a 7-gene ERS-Lum, a 106-gene ERS-Pos signature, and a 59-gene ERS-Neg signature associated with endocrine resistance. In the TCGA and METABRIC cohorts, the ERS, ERS-Lum, and ERS-Pos signatures were all lower (FDR&amp;lt; 0.03) while the ERS-Neg signature was higher (FDR&amp;lt; 0.001) in younger patients. Similarly, in both microarray cohorts, and in the SCAN-B-cohort, the ERS-Pos signature was lower and the ERS-Neg signature was higher in younger patients (FDR&amp;lt; 0.002). Next, we assessed 4 different immune cell signatures that have been associated with response to chemotherapy. In the TCGA, B-cell, T-cell, Mast-cell, and TIS signatures were significantly higher (FDR&amp;lt;.05). In the microarray Cohort-A, B cells and mast cells were significantly higher, and the T cell and TIS signatures showed a trend for higher expression. In Cohort-B, T cells, B cells, TIS, and dendritic cells signatures were significantly higher in younger patients. Significantly higher expression of immune gene signatures in younger patients were also seen in the METABRIC and SCAN-B data sets. The ER-related and immune-related gene signatures showed negative correlation and joint analysis defined three subpopulations in younger women: (i) immune-high/ER-low, (ii) immune-intermediate/ER-intermediate and (iii) immune-low/ER-intermediate, whereas in older women the dominant pattern was immune-low/ER-high. Conclusion: ESR1 mRNA and ER-associated gene expression is lower in ER positive cancers of younger compared to older patients, while immune infiltration is higher. The cytotoxic and endocrine effects of adjuvant chemotherapy could both contribute to the survival benefit seen in younger patients, but the relative contributions of these effects may vary by ER and immune phenotype. We hypothesize that in immune-high/ER-low cancers, the cytotoxic effect of chemotherapy may drive the benefit, whereas in immune-low/ER-intermediate cancers chemotherapy induced ovarian suppression may play a more important role. Citation Format: Tao Qing, Thomas Karn, Mariya Rozenblit, Julia Foldi, Michal Marczyk, Naing Lin Shan, Kim Blenman, uwe Holtrich, Kevin Kalinsky, Funda Meric-Bernstam, Lajos Pusztai. Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD9-09.

APPLICATIONS OF TRANSCRIPTOMICS METHODS IN BREAST CANCER

Gene expression studies using cDNA microarrays have revolutionized the breast cancer subclassification. The application of RNA sequencing technologies has revealed additional complexity of breast cancer. The integrated genomic/transcriptomic analysis of breast tumors (METABRIC) and the Cancer Genome Atlas (TCGA) with clinical follow-up data shaped the molecular landscape of breast cancer the last decade. High-throughput RNA sequencing technologies have shown that large proportions of mammalian transcriptome include regulatory non-protein-coding RNAs (ncRNAs) besides protein-coding RNAs. Role of ncRNAs have been well documented in breast cancer. Using RNA sequencing and probe-based transcriptome analyses, several studies, including ours, have emphasized the role alternative splicing events in breast cancer progression. We have demonstrated that Epithelial Splicing Regulatory Protein 1 (ESRP1), a splicing factor, is associated with poor prognosis and endocrine resistance in human ER-positive (ER+) breast tumors. These studies have further implicated that aberrant regulation of alternative splicing plays an important role in all hallmarks of cancer and provide novel strategies for the therapeutics in breast cancer. In addition to bulk sequencing, deconvolution methods such as CIBERSORT was useful to understand the role of individual cells in cancer progression. Using TCGA and METABRIC cohorts, we identified immune-subtypes with better outcomes in triple negative breast cancer (TNBCs). Recently, single cell RNA-seq (sc-RNAseq) and spatial RNA-seq technologies have enabled analysis of single tumor cell phenotypes and intratumor heterogeneity. The application of these technologies to formalin-fixed paraffin-embedded (FFPE) tumor samples with clinical outcomes will present a valuable resource for understanding the inter and intra-tumor heterogeneity in breast cancer.

Intratumoral PDGFB gene predominantly expressed in endothelial cells is associated with angiogenesis and lymphangiogenesis, but not with metastasis in breast cancer.

Platelet-derived growth factor B (PDGFB) is known to play essential roles in angiogenesis and lymphangiogenesis during development, and tumor growth and vessel stabilization in experimental models. However, whether these findings could be translated to breast cancer patients remains unclear. We hypothesized that PDGFB gene expression is associated with angiogenesis, cell proliferation, and clinical outcomes in breast cancer patients. A total of 7635 primary breast cancer patients with full transcriptome and clinical data available from 13 independent cohorts were analyzed using in silico approach. The median value was used to divide each cohort into high and low PDGFB expression groups. High PDGFB gene expression was associated with increased expression of angiogenesis-related genes, higher amount of vascular cell infiltrations, and with enrichment of angiogenesis gene set, lymphangiogenesis-related gene expressions, lymphangiogenesis-related cell infiltrations, and enrichmentof lymphangiogenesis gene set in GSE96058 and validated by TCGA cohorts; however, not with lymphatic metastasis. PDGFB expression was neither associated with cell proliferation as assessed by Ki67 expression nor with Nottingham histological grade, or response to neoadjuvant chemotherapy. We found that PDGFB was most extensively expressed by endothelial and perivascular-like cells in the tumor microenvironment, and minimally by cancer cells consistently in two single-cell sequence cohorts. High PDGFB expression enriched TGFβ, epithelial-mesenchymal transition, hypoxia, and cancer stem cell-associated pathways. However, no association with distant metastasis was observed. Disease-specific and disease-free survival were worse in the high PDGFB expression group consistently in TCGA and METABRIC cohorts. PDGFB is predominantly expressed in endothelial cells and is associated with angiogenesis and lymphangiogenesis, but not with cellular proliferation or metastasis in breast cancer.

HER2 expression, copy number variation and survival outcomes in HER2-low non-metastatic breast cancer: an international multicentre cohort study and TCGA-METABRIC analysis

BackgroundHER2-low breast cancer (BC) is currently an area of active interest. This study evaluated the impact of low expression of HER2 on survival outcomes in HER2-negative non-metastatic breast cancer (BC).MethodsPatients with HER2-negative non-metastatic BC from 6 centres within the Asian Breast Cancer Cooperative Group (ABCCG) (n = 28,280) were analysed. HER2-low was defined as immunohistochemistry (IHC) 1+ or 2+ and in situ hybridization non-amplified (ISH−) and HER2-zero as IHC 0. Relapse-free survival (RFS) and overall survival (OS) by hormone receptor status and HER2 IHC 0, 1+ and 2+ ISH− status were the main outcomes. A combined TCGA-BRCA and METABRIC cohort (n = 1967) was also analysed to explore the association between HER2 expression, ERBB2 copy number variation (CNV) status and RFS.ResultsABCCG cohort median follow-up was 6.6 years; there were 12,260 (43.4%) HER2-low BC and 16,020 (56.6%) HER2-zero BC. The outcomes were better in HER2-low BC than in HER2-zero BC (RFS: centre-adjusted hazard ratio (HR) 0.88, 95% CI 0.82–0.93, P < 0.001; OS: centre-adjusted HR 0.82, 95% CI 0.76–0.89, P < 0.001). On multivariable analysis, HER2-low status was prognostic (RFS: HR 0.90, 95% CI 0.85–0.96, P = 0.002; OS: HR 0.86, 95% CI 0.79–0.93, P < 0.001). These differences remained significant in hormone receptor-positive tumours and for OS in hormone receptor-negative tumours. Superior outcomes were observed for HER2 IHC1+ BC versus HER2-zero BC (RFS: HR 0.89, 95% CI 0.83–0.96, P = 0.001; OS: HR 0.85, 95% CI 0.78–0.93, P = 0.001). No significant differences were seen between HER2 IHC2+ ISH− and HER2-zero BCs. In the TCGA-BRCA and METABRIC cohorts, ERBB2 CNV status was an independent RFS prognostic factor (neutral versus non-neutral HR 0.71, 95% CI 0.59–0.86, P < 0.001); no differences in RFS by ERBB2 mRNA expression levels were found.ConclusionsHER2-low BC had a superior prognosis compared to HER2-zero BC in the non-metastatic setting, though absolute differences were modest and driven by HER2 IHC 1+ BC. ERBB2 CNV merits further investigation in HER2-negative BC.

Abstract P3-10-04: microRNA-125a high expressing tumors enrich cell proliferation associated gene sets and associated with poor prognosis in estrogen receptor positive breast cancer patients

Abstract Background: MicroRNA-125a (miR-125a) has been shown to function as tumor suppressive miRNA by pre-clinical in vitro studies. However, to the best of our knowledge, there is no study that investigated the clinical relevance of miR-125a in breast cancer patients. We hypothesized that miR-125a high expressing breast cancer associate with less aggressive cancer characteristics and with favorable survival outcome. Material and Methods: The clinicopathological and survival information associated with comprehensive transcriptomic data was analyzed in 2042 breast cancer patients from large publicly available databases, The Molecular Taxonomy of Breast Cancer International Consortium (METARBRIC) The Cancer Genome Atlas (TCGA), and GSE57897. The survival analysis, gene set enrichment analysis (GSEA) were conducted comparing miR-125a high expressing and low expressing tumors, divided by the median cutoff. The association between the miR-125a expression and tumor immune microenvironment was assessed by utilizing xCell. Results: The expression levels of miR-125a were lower in tumors compared with normal breast tissues in both TCGA and GSE57897 cohorts, which is in agreement with the notion that it is a tumor suppressive miRNA (p&amp;lt;0.001 and p&amp;lt;0.001, respectively). ER-positive/HER2-negative (ER+/HER2-) showed the highest miR-125a expression among the subtypes in TCGA (p&amp;lt;0.001). MiR-125a expression was not associated with cancer staging in any of the subtypes in neither TCGA nor METABRIC cohorts. Surprisingly, miR-125a high expressing tumors demonstrated worse disease free (DFS), disease specific (DSS), and overall survival (OS) compared with low expressing in ER+/HER2- breast cancer patients (p=0.008, p=0.005, and p=0.037) which was not the case for the other subtypes in METABRIC cohort. Interestingly, we found that miR-125a expression significantly correlated with Nottingham histological grade only in ER+/HER2- among the subtypes (p&amp;lt;0.001). miR-125a high tumors significantly demonstrated higher expression of MKI67, one of the most commonly used parameters for cell proliferation, correlated with miR-125a expression in ER+/HER2- and Her2-positive patients (both &amp;lt; p=0.02), but not in triple negative breast cancer (TNBC). Furthermore, miR-125a high expressing tumors enriched four out of five cell proliferation related gene sets in Hallmark collection, such as E2F Targets, G2M Checkpoint, Mitotic Spindle, and MYC Targets V2 in ER+/HER2- subtype, but not in TNBC. This was also the case in immune-related gene sets; interferon-alpha response and interferon-gamma response that enriched to miR-125a high tumors in ER+/HER2-, but not in TNBC. Infiltration of CD8 cells, T-helper type 1 cells, T-helper type 2 cells and M1 macrophages were all elevated in MiR-125a high ER+/HER2- subtype (all p&amp;lt;0.03), but none in TNBC. We found that tumor suppressive miR-125a was highly expressed in ER+/HER2- subtype, where its expression was associated with multiple clinical and molecular biological parameters of cell proliferation, as well as with both favorable and unfavorable immune response. Given its association with the survival outcome, we cannot help but speculate that miR-125a expression parallels with highly proliferative ER+/HER2- breast cancer, but its tumor suppressive effect is not enough to improve survival outcome. This study is hypothesis generating, and our results need mechanistic analyses by experimental investigations. Conclusion: MiR-125a high tumors were associated with aggressive characteristics in ER+/HER2- patients which may contribute to the worse survival outcomes. The current result support the importance of analyses of large patient cohorts to clarify the role of a miRNAs in patients. Citation Format: Yoshihisa Tokumaru, Manabu Futamura, Kohei Taniguchi, Masanori Oshi, Junichi Mase, Yoshimi Asano, Ryutaro Mori, Kazuaki Takabe, Kazuhiro Yoshida. microRNA-125a high expressing tumors enrich cell proliferation associated gene sets and associated with poor prognosis in estrogen receptor positive breast cancer patients [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-10-04.

Abstract P4-07-29: Reactive Oxygen Species (ROS) pathway is associated with aggressive cancer biology, elevated immune response, and with worse survival in ER-positive/HER2-negative breast cancer

Abstract Background: Reactive oxygen species (ROS) in tumor microenvironment are known to promote many aspects of cancer progression. On the other hand, excessive accumulation of ROS can induce cancer cell apoptosis. To our knowledge, clinical relevance of ROS response signaling in breast cancer has never been studied in multiple large patient cohorts. Here, we hypothesized that the high ROS pathway score reflect tumor aggressiveness, thus, it predicts worse survival in breast cancer patients. Methods: A total of 6245 breast cancer patients from three independent cohorts (GSE96058, METABRIC, and TCGA) were analyzed. We defined the ROS pathway score by the degree of enrichment by Gene Set Variant Analysis (GSVA) and median was used to divide high vs low score groups in each cohort. Results: The ROS score was significantly associated with aggressive clinical factors, such as triple-negative breast cancer (TNBC) subtype, Nottingham histological grade, American Joint Committee on Cancer (AJCC) Stage and lymph node metastasis consistently in both GSE96058 and METABRIC (all p &amp;lt; 0.001). High ROS score was significantly associated with worse overall survival (OS) in the GSE96058 (hazard ratio (HR) = 3.59, 95% confidence interval (CI); 2.47-5.20, p &amp;lt; 0.001), as well as OS (HR = 1.55, 95%CI; 1.16-2.07, p = 0.002), disease-free survival (HR = 1.63, 95%CI; 1.10-2.43, p = 0.016), and disease-specific survival (HR = 2.57, 95%CI; 1.75-3.77, p &amp;lt; 0.001) in the METABRIC cohort. Subgroup analysis revealed that a high ROS score was significantly associated with worse OS in ER-positive/HER2-negative breast cancer in both cohorts. High ROS ER-positive/HER2-negative breast cancer was significantly associated with high level of intratumor heterogeneity (p = 0.013), homologous recombination deficient (HRD) (p &amp;lt; 0.001), and mutation-related score (silent and non-silent mutation rate (p = 0.003 and 0.011, respectively), fraction altered (p = 0.038), and single-nucleotide variant (SNV) neoantigens (p = 0.006)) in the TCGA cohort. In agreement, high ROS ER-positive/HER2-negative breast cancer significantly enriched cell proliferation-related gene sets; E2F targets, G2M checkpoint, and MYC targets v1 and v2 consistently in both GSE96058 and METABRIC cohorts (all false discovery rate (FDR) &amp;lt; 0.25). On the other hand, high ROS ER-positive/HER2-negative tumors were associated with elevated infiltration of multiple immune cells, including anti-cancer immune cells (CD8+ T cell, CD4+ memory T cell, M1 macrophage, dendritic cell, gamma-delta T cell), as well as pro-cancer immune cells (regulatory T cell, T helper type2 cell, and M2 macrophage) and with high level of cytolytic activity (CYT) consistently in both cohorts (all p &amp;lt; 0.001). Those tumors also enriched immune-related pathway (Interferon (IFN)-α response, IFN-γ response, allograft rejection, complement, IL6/JAK/STAT3 signaling, and inflammatory response) consistently in both cohorts (all FDR &amp;lt; 0.25). Finally, high ROS ER-positive/HER2-negative breast cancer was significantly associated with high expression of immune checkpoint molecules including PD-1, PD-L1 and PD-L2, CTLA4, IDO1, LAG3, BTLA, HLA-A, and TIGIT, in (all p &amp;lt; 0.005). Conclusion ROS pathway is associated with cancer aggressiveness, elevated immune response, and with worse survival in ER-positive/HER2-negative breast cancer. Citation Format: Masanori Oshi, Rongrong Wu, Akimitsu Yamada, Li Yan, Takashi Ishikawa, Itaru Endo, Kazuaki Takabe. Reactive Oxygen Species (ROS) pathway is associated with aggressive cancer biology, elevated immune response, and with worse survival in ER-positive/HER2-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-07-29.