Breast Tumor Gene Expression Research Articles

Association of early menarche with breast tumor molecular features and recurrence

BackgroundEarly menarche is an established risk factor for breast cancer but its molecular contribution to tumor biology and prognosis remains unclear.MethodsWe profiled transcriptome-wide gene expression in breast tumors (N = 846) and tumor-adjacent normal tissues (N = 666) from women in the Nurses’ Health Studies (NHS) to investigate whether early menarche (age < 12) is associated with tumor molecular and prognostic features in women with breast cancer. Multivariable linear regression and pathway analyses using competitive gene set enrichment analysis were conducted in both tumor and adjacent-normal tissue and externally validated in TCGA (N = 116). Subgroup analyses stratified on ER-status based on the tumor were also performed. PAM50 signatures were used for tumor molecular subtyping and to generate proliferation and risk of recurrence scores. We created a gene expression score using LASSO regression to capture early menarche based on 28 genes from FDR-significant pathways in breast tumor tissue in NHS and tested its association with 10-year disease-free survival in both NHS (N = 836) and METABRIC (N = 952).ResultsEarly menarche was significantly associated with 369 individual genes in adjacent-normal tissues implicated in extracellular matrix, cell adhesion, and invasion (FDR ≤ 0.1). Early menarche was associated with upregulation of cancer hallmark pathways (18 significant pathways in tumor, 23 in tumor-adjacent normal, FDR ≤ 0.1) related to proliferation (e.g. Myc, PI3K/AKT/mTOR, cell cycle), oxidative stress (e.g. oxidative phosphorylation, unfolded protein response), and inflammation (e.g. pro-inflammatory cytokines IFNα\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\alpha$$\\end{document} and IFNγ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\gamma$$\\end{document}). Replication in TCGA confirmed these trends. Early menarche was associated with significantly higher PAM50 proliferation scores (β = 0.082 [0.02–0.14]), odds of aggressive molecular tumor subtypes (basal-like, OR = 1.84 [1.18–2.85] and HER2-enriched, OR = 2.32 [1.46–3.69]), and PAM50 risk of recurrence score (β = 4.81 [1.71–7.92]). Our NHS-derived early menarche gene expression signature was significantly associated with worse 10-year disease-free survival in METABRIC (N = 952, HR = 1.58 [1.10–2.25]).ConclusionsEarly menarche is associated with more aggressive molecular tumor characteristics and its gene expression signature within tumors is associated with worse 10-year disease-free survival among women with breast cancer. As the age of onset of menarche continues to decline, understanding its relationship to breast tumor characteristics and prognosis may lead to novel secondary prevention strategies.

Heat shock protein 72 supports extracellular matrix production in metastatic mammary tumors.

This study identified tumorigenic processes most dependent on murine heat shock protein 72 (HSP72) in the mouse mammary tumor virus-PyMT mammary tumor model, which give rise to spontaneous mammary tumors that exhibit HSP72-dependent metastasis to the lung. RNA-seq expression profiling of Hspa1a/Hspa1b (Hsp72) WT and Hsp72-/- primary mammary tumors discovered significantly lower expression of genes encoding components of the extracellular matrix (ECM) in Hsp72 knockout mammary tumors compared to WT controls. In vitro studies found that genetic or chemical inhibition of HSP72 activity in cultured collagen-expressing human or murine cells also reduces mRNA and protein levels of COL1A1 and several other ECM-encoding genes. In search of a possible mechanistic basis for this relationship, we found HSP72 to support the activation of the tumor growth factor-β-suppressor of mothers against decapentaplegic-3 signaling pathway and evidence of suppressor of mothers against decapentaplegic-3 and HSP72 coprecipitation, suggesting potential complex formation. Human COL1A1 mRNA expression was found to have prognostic value for HER2+breast tumors over other breast cancer subtypes, suggesting a possible human disease context where targeting HSP72 may have a therapeutic rationale. Analysis of human HER2+breast tumor gene expression data using a gene set comprising ECM-related gene and protein folding-related geneas an input to the statistical learning algorithm, Galgo, found a subset of these genes that can collectively stratify patients by relapse-free survival, further suggesting a potential interplay between the ECM and protein-folding genes may contribute to tumor progression.

PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer

BackgroundAberrant epigenetic remodeling events contribute to progression and metastasis of breast cancer (Bca). The specific mechanims that epigenetic factors rely on to mediate tumor aggressiveness remain unclear. We aimed to elucidate the roles of epigenetic protein PHF6 in breast tumorigenesis.MethodsPublished datasets and tissue samples with PHF6 staining were used to investigate the clinical relevance of PHF6 in Bca. CCK-8, clony formation assays were used to assess cell growth capacity. Cell migration and invasion abilities were measured by Transwell assay. The gene mRNA and protein levels were measured by quantitative real-time PCR and western blot. Chromatin immunoprecipitation (ChIP)-qPCR assays were used to investigate transcriptional relationships among genes. The Co-immunoprecipitation (Co-IP) assay was used to validate interactions between proteins. The CRISPR/Cas9 editing technology was used to construct double HIF knockout (HIF-DKO) cells. The subcutaneous xenograft model and orthotopic implantation tumor model were used to asess in vivo tumor growth.ResultsIn this study, we utilized MTT assay to screen that PHF6 is required for Bca growth. PHF6 promotes Bca proliferation and migration. By analyzing The Cancer Genome Atlas breast cancer (TCGA-Bca) cohort, we found that PHF6 was significantly higher in tumor versus normal tissues. Mechanistically, PHF6 physically interacts with HIF-1α and HIF-2α to potentiate HIF-driven transcriptional events to initiate breast tumorigenesis. HIF-DKO abolished PHF6-mediated breast tumor growth, and PHF6 deficiency in turn impaired HIF transcriptional effects. Besides, hypoxia could also rely on YAP activation, but not HIF, to sustain PHF6 expressions in Bca cells. In addition, PHF6 recuits BPTF to mediate epigenetic remodeling to augment HIF transcriptional activity. Targeting PHF6 or BPTF inhibitor (AU1) is effective in mice models. Lastly, PHF6 correlated with HIF target gene expression in human breast tumors, which is an independent prognostic regulator.ConclusionsCollectively, this study identified PHF6 as a prognostic epigenetic regulator for Bca, functioning as a HIF coactivator. The fundamental mechanisms underlying YAP/PHF6/HIF axis in breast tumors endowed novel epigenegtic targets for Bca treatment.

Subtype-specific expression of MELK is partly due to copy number alterations in breast cancer.

Maternal embryonic leucine-zipper kinase (MELK) regulates cell cycle progression and is highly expressed in many cancers. The molecular mechanism of MELK dysregulation has not been determined in aggressive forms of breast cancer, such as triple negative breast cancer (TNBC). To evaluate molecular markers of MELK aberrations in aggressive breast cancer, we assessed MELK gene amplification and expression in breast tumors. MELK mRNA expression is highly up-regulated in basal-like breast cancer (BLBC), the major molecular subtype of TNBC, compared to luminal or other subtypes of breast tumors. MELK copy number (CN) gains are significantly associated with BLBC, whereas no significant association of CpG site methylation or histone modifications with breast cancer subtypes was observed. Accordingly, the CN gains appear to contribute to an increase in MELK expression, with a significant correlation between mRNA expression and CN in breast tumors and cell lines. Furthermore, immunohistochemistry (IHC) assays revealed that both nuclear and cytoplasmic staining scores of MELK were significantly higher in invasive ductal carcinoma (IDC) tumors compared to ductal carcinoma in situ (DCIS) and normal breast tissues. Our data showed that upregulation of MELK in BLBC may be in part driven by CN gains, rather than epigenetic modifications, indicating a potential for overexpression and CN gains of MELK to be developed as a diagnostic and prognostic marker to identify patients who have more aggressive breast cancer.

Abstract 6165: DARC/ACKR1 expression is associated with immune landscape changes among triple negative breast tumors

Abstract Recent work defining the immune landscape across breast cancer (BC) subtypes have revealed that TNBC tumors have increased immunogenicity, and these increases in immune cell infiltration are associated with better prognosis and outcomes. Our recent work has proposed the Duffy Antigen Receptor for Chemokines (DARC), as a potential driver of immune regulation in breast tumors. DARC/ACKR1 is an atypical chemokine receptor that promiscuously binds both pro-inflammatory CC and pro-angiogenic CXC class chemokines and plays a role in chemokine gradient establishment both in circulation, and at sites of inflammation via chemokine transcytosis. In the BC context, we and others have reported DARC/ACKR1 protein expression on breast tumor epithelial cells by IHC and have also shown a range of gene expression in breast tumors from bulk RNAseq data in the TCGA cohort. Specifically, alongside CIBERSORT deconvolution of tumor associated immune cell populations, we have shown a strong positive correlation between DARC/ACKR1 gene expression and total tumor-associated leukocyte (TAL) abundance across all BC subtypes. To investigate the role of DARC/ACKR1 specifically in the TNBC tumor microenvironment (TME), we have analyzed (1) in silico bulk RNAseq data from two independent TNBC cohorts, (2) imaging mass cytometry data from TNBC patients and (3) murine model of DARC/ACKR1 BC progression in a basal-like BC transgenic mouse model. Our in silico data shows strong positive correlation of DARC/ACKR1 expression and TAL abundance, when DARC/ACKR1 expression is both dichotomized and analyzed as a continuous variable. Immune cell populations increasing with DARC/ACKR1 expression include B cell, T cell, monocyte and macrophage populations, which was consistent with our previous findings across all BC subtypes. IMC analysis of TNBC FFPE sections to determine protein expression of various immune and structural markers on the single-cell level between DARC/ACKR1 high or low expressing tumors show cells from DARC/ACKR1 high expressing tumors clustered distinctly from DARC/ACKR1 low expressing tumors. Image analysis also revealed increased infiltration among our DARC/ACKR1 high tumors. Finally, our murine model of DARC/ACKR1 in TNBC, shows that tumor development followed similar disease progression as human BC, following early through late-stage disease. DARC/ACKR1 deficient mice were found to have larger tumor volume and more palpable tumors, where DARC/ACKR1 expressing mice show co-localization of DARC and immune cell expression. This is the first work to describe the role of DARC/ACKR1 in the TNBC TME in bulk tumor transcriptomic data, spatial single-cell protein level data, and murine BC tumor model. Further investigation of factors that drive immune response in TNBC tumors, like DARC/ACKR1, may lead the way to novel therapeutic options or biomarkers for better outcomes for women with TNBC. Citation Format: Rachel Martini, Kiel Telesford, Brittany Lord, Hiranmayi Ravichandran, Olivier Elemento, Nancy Manley, Michele Monteil, Lisa Newman, Upender Manne, Clayton Yates, Melissa B. Davis. DARC/ACKR1 expression is associated with immune landscape changes among triple negative breast tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6165.

Abstract 2045: Spatial organization of the immune microenvironment after neoadjuvant treatment of breast cancer

Abstract Using the immune system to fight cancer has garnered tangible success, but some treatments, like neoadjuvant chemotherapy (NAC), modulate the immune microenvironment. Recent studies show that the spatial organization of tumor infiltrating lymphocytes (TIL) have greater predictive value than TIL density. The effect of NAC on immune composition and spatial distribution is not fully understood but new insight could help to guide its use in combination with immune therapy and identify patients with potential to derive benefit. We spatially profiled 84 RNA targets (GeoMx®) in a cohort of 12 NAC-treated breast cancer patients (4 Luminal, 4 HER2+ and 4 triple negative), none of whom achieved a pathological complete response. Matched pre- and post-treatment tissue samples were analyzed together with regions of interest (tumor center, invasive margin and TIL aggregates) identified using CD3, CD20, Syto83 and pan-cytokeratin for stromal/tumor segmentation. NAC decreases overall gene expression in breast tumors with the biggest declines seen in tumor promoting (CCND1, AKT1, CTNNB1, EPCAM, VEGFA, KRT and MKI67) and some inflammatory (CXCL10, STAT1 and STAT2) genes (p-value &amp;lt;0.05; other immune related transcripts showed little variation). Expression was compared between patients with a good response (&amp;lt;20% tumor cellularity) and those with a poor response (&amp;gt;50% cellularity). Poor responders expressed higher levels of tumor promoting genes pre-NAC, which remained high after treatment (KRT p=0.023, CTNNB1 p=0.031). No differences were detected in immune genes in the stroma based on patient responsiveness; however, higher antigen presentation and inflammatory gene transcripts were found at the tumor margins of good responders. Post-NAC differences between the margin and center decrease in good responders paralleled by a shift towards higher or equal expression of some inflammatory markers at the tumor center. Poor responders maintain high expression of all immune markers at the margin. A higher number of aggregates (mean n=5 vs n=1.3) were detected in good compared to poor responders together with more tertiary lymphoid structures (mean n=2.4 vs n=0.3) and distinguished by higher immune gene expression (CD8 p=0.046, CCL5 p=0.054, NKG7 p=0.022). NAC induces changes in other cells in the tumor microenvironment while targeting tumor cells. Our data show that spatial analysis of gene expression comparing good and poor responders (without a pathological complete response) reveal that tumor cells in the latter retain expression of tumor promoting genes while the immune compartment remains excluded. Good responders are characterized by a decrease in tumor promoting genes in parallel with lymphoid aggregates, including TLS, of active immune cells in the stroma and at the tumor center. These findings suggest that tailoring adjuvant treatment between good and poor responding patients might be warranted. Citation Format: Noémie Thomas, Soizic Garaud, Mireille Langouo, Ioannis Zerdes, Doïna Sofronii, Anaïs Boisson, Theodoros Foukakis, Alexandre De Wind, Roberto Salgado, Ahmad Awada, Karen Willard-Gallo. Spatial organization of the immune microenvironment after neoadjuvant treatment of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2045.

Abstract PO-150: Comparison of RUNX1, RUNX2, RUNX3 and CBFβ gene expression in breast tumors Indicate ethnic differences and similarities by receptor status

Abstract The RUNX family of transcription factors RUNX1, RUNX2 and RUNX3 encode nuclear proteins with a Runt DNA-binding domain that functions in a complex with their obligate partner core-binding factor CBFβ to regulate gene expression. RUNX genes are known for paradoxical roles, with oncogenic as well as tumor suppressor functions, dependent on context. Interestingly, RUNX2 has been shown to play a potentially important functional role in Triple-Negative Breast Cancer (TNBC), and RUNX1 expression associates with poor prognosis in TNBC in a cohort of women of European descent. Women of African descent experience more aggressive TNBC with higher mortality rates than their women of European ancestry counterparts. TNBC is the most difficult breast cancer subtype to treat globally and has a poor prognosis and low survival which remains an important clinical challenge. There is a paucity of genomics studies interrogating TNBC of diverse populations. Hence, RNAseq datasets of 782 breast cancer patients were leveraged from a web-based platform -CbioPortal and published literature. 685 patients were queried for the RUNX1, RUNX2, RUNX3, and CBFβ genes, and an additional 97 patient data were harnessed from research publications. The cohort includes 595 (70%) patients of European ancestry (EA), 90 (11%) of African descent (AD), both from The Cancer Genome Atlas (TCGA), and 97 (13%) patients indigenous African from Nigeria (IAN). The queried genes were compared for race/ethnic disparity by estrogen receptor status (er). Mutual exclusivity was analyzed and P-values were determined by Fisher's extract test with the null hypothesis that a pair of genes alteration frequency of occurrence is proportional to uncorrelated occurrence in each gene. The queried genes enrichment in TP53, PIK3CA, CDH1, MAP3K1, and GATA3 between patients of European ancestry and African descent were analyzed and the Kaplan-Meier plots with P-value from the Long rank test were determined. The queried genes were altered in 69 patients (12%) of EA and 9 patients of AD due to unavailability of data on RUNX2 and RUNX 3 in IAN only RUNX1 and CBfβ was altered in 4 (4%) patients of 97 patients. Ethnic disparities and similarities were indicated in the queried altered genes in RUNX1 and RUNX 2 and showed similar expression in ER-negative correlating with the TNBC poor prognosis however RUNX3 genes were silenced in that of AD and was expressed in EA. They were differences in mutual exclusivity and co-occurrence but were not statistically significant, this may be due to the small data size. Interestingly, there was statistically significant equal gene enrichment of RUNX1 and CBfβ in CDH1mutations of both EA and AD. Larger cohorts in particular the AD cohort is needed, to further elucidate some of these borderline findings. In conclusion, our findings are insightful towards deciphering the characteristic aggressive nature of TNBC in ethnic disparity. Citation Format: Uzoamaka A. Okoli. Comparison of RUNX1, RUNX2, RUNX3 and CBFβ gene expression in breast tumors Indicate ethnic differences and similarities by receptor status [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-150.

Stem gene expression in breast tumors during chemotherapy: Connection with the main clinical and morphological factors and the disease outcome.

In this research, we studied how the expression of 14 stem genes (TERT; OCT3; SMO; MYC; SNAI2; MOB3B; KLF4; BMI1; VIM; FLT3; LAT; SMAD2; LMNB2; KLF1), as well as the TGF-β1 cytokine gene and its TGFBR1 receptor in breast tumors before and after NAC is associated with clinical and morphological parameters and the disease outcome. The study included 82 patients with the morphologically verified diagnosis of T1-4N0-3M0 breast cancer (stages IIA - IIIB). The material was paired biopsy samples of tumor and surgical material for each patient. The stem genes expression was analyzed via qPCR. As a result, we found that increased level of stem genes expression in breast tumors is associated with lymphogenic metastasis, young age, small tumor size, expression of estrogen and progesterone receptors, and the luminal B molecular subtype. NAC stimulates the expression of 7 out of 16 stem genes. Patients who further developed hematogenic metastases have twice as many hyperexpressed stem genes in their tumors before the treatment and after NAC than patients with no hematogenic metastases. The expression level of three genes - OCT3, LAT, and LMNB2 - in a residual tumor allows us to predict metastasis-free survival of patients with breast cancer of various molecular subtypes with a 79% accuracy. Thus, stem genes hyperexpression is associated with tumor progression.

Lineage-specific silencing of PSAT1 induces serine auxotrophy and sensitivity to dietary serine starvation in luminal breast tumors.

SUMMARYA major challenge of targeting metabolism for cancer therapy is pathway redundancy, in which multiple sources of critical nutrients can limit the effectiveness of some metabolism-targeted therapies. Here, we analyze lineage-dependent gene expression in human breast tumors to identify differences in metabolic gene expression that may limit pathway redundancy and create therapeutic vulnerabilities. We find that the serine synthesis pathway gene PSAT1 is the most depleted metabolic gene in luminal breast tumors relative to basal tumors. Low PSAT1 prevents de novo serine biosynthesis and sensitizes luminal breast cancer cells to serine and glycine starvation in vitro and in vivo. This PSAT1 expression disparity preexists in the putative cells of origin of basal and luminal tumors and is due to luminal-specific hypermethylation of the PSAT1 gene. Our data demonstrate that luminal breast tumors are auxotrophic for serine and may be uniquely sensitive to therapies targeting serine availability.

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.

Abstract 869: Breast tumor gene expression in the mTOR pathway and clinicopathological characteristics in Black women and White women

Abstract Background: Aberrant activation of the mammalian Target of Rapamycin (mTOR) pathway is implicated in breast carcinogenesis and outcomes. Based on protein expression data, the activation could be heterogeneous by race, body fatness, and tumor clinicopathological characteristics. To understand potential impacts of mTOR pathway signaling in breast cancer, we evaluated the association of race and clinicopathological characteristics with gene expression of select mTOR pathway genes in breast tumors. Methods: Study participants were from the Women's Circle of Health Study (WCHS), complemented with samples from the Roswell Park Pathology Network Shared Resource (PNSR). Tumor tissue blocks were collected from 367 newly-diagnosed breast cancer cases (190 Black and 177 White women). Gene expressions of AKT1, EIF4EBP1, MTOR, RPS6KB2, TSC1 were quantitated using NanoString assays. Generalized linear models were performed to relate gene expression levels with demographic and clinicopathological variables. The regression coefficient (β) was converted to percentage difference. Additionally, we conducted an external validation of mTOR gene expression using data from The Cancer Genome Atlas (TCGA; N=332). Results: Study participants were mostly within the ages of 51 to 65 years old. Black women had lower expression levels of AKT1, MTOR, RPS6KB2 and TSC1 compared to White women. Black race vs White race was significantly associated with lower gene expression of AKT1 (-21.34%, 95% CI = -31.61%, -8.61%) and RPS6KB2 (-12.19%, 95% CI = -19.75%, -3.92%). The racial differences in expression levels of these two genes were consistent across luminal A, luminal B, HER2-enriched, and triple-negative subtypes. Higher tumor grade was associated with higher expression levels of EIF4EBP1 and RPS6KB2, but with lower expression of TSC1. In comparison to luminal A tumors, luminal B tumors had higher expression of RPS6KB2 (17.35%, 95% CI = 4.08%, 32.31%); whereas HER2-enriched (-23.66%, 95% CI= -41.73%, -1.00%) and triple-negative (-22.89%, 95% CI= -40.55%, -1.00%) had lower expression of TSC1. All these associations were unchanged after additionally adjusting for body mass index in a subset. Similarly, results from the TCGA data showed that in comparison to luminal A tumors, luminal B tumors had higher expression of RPS6KB2 (53.73%, 95% CI = 27.12%, 87.76%) whereas HER2-enriched had a lower expression of TSC1 (-26.66%, 95% CI = -43.45%, -4.88%) and triple-negative subtype had a lower expression of TSC1 (-17.30%, 95% CI = -50.68%, -3.05%). Conclusions: Variables such as race and breast cancer subtypes should be considered in studying the mTOR pathway genes in breast cancer tumors. Citation Format: Mmadili N. Ilozumba, Song Yao, Adana A. Llanos, Angela Omilian, Weizhou Zhang, Susmita Datta, Chi-Chen Hong, Warren Davis, Thaer Khoury, Christine B. Ambrosone, Ting-Yuan D. Cheng. Breast tumor gene expression in the mTOR pathway and clinicopathological characteristics in Black women and White women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 869.

Abstract PS7-69: Molecular profiles and clinical-pathological features of Asian early-stage breast cancer patients

Abstract Background/Objective: Breast cancer incidence in Asian populations has increased in recent years, and variation in prognosis and tumor subtypes indicates that further study is warranted to characterize these differences and identify actionable targets. Patients of Asian ancestry are underrepresented in US registries, and few studies have characterized molecular profiles for these patients. In the current analysis, we assess clinical, pathological, and molecular profiles from self-reported Asian breast cancer patients (AS), in comparison with age-matched Caucasian (CA) and African American patients (AA), to evaluate the influence of Asian ancestry on differential gene expression in breast tumors. Methods: This meta-analysis included cohorts of self-reported AS, CA, and AA with early-stage, invasive breast cancer (EBC) prospectively enrolled in the US from 2011 to 2020 in FLEX (NCT03053193), MINT (NCT01501487), or IMPACt (NCT02670577) trials. AS were significantly younger (mean, 55 years) than CA (mean, 61 years, p&amp;lt;0.001) or AA (mean, 59 years, p=0.005); thus, an age-matched subset was selected for analyses. 70-gene signature (MammaPrint, MP), 80-gene signature (BluePrint, BP), and clinical-pathological features were compared among age-matched AS (n=103), CA (n=103), and AA (n=100). Whole-genome expression data were quantile normalized using R limma package, and differentially expressed genes (DEGs) were compared among AS (n=90), CA (n=102), and AA (n=96). DEGs with adjusted p-value &amp;lt;0.05 and log2 fold change &amp;gt; ± 0.5 were considered significant. Results: AS tumors were classified as 59% MP HR, compared with 44% HR in age-matched CA (p=0.08) and 64% HR in age-matched AA (p=0.17). AS had a significantly lower rate of obesity (16%, body mass index ≥30) compared with CA (41%) and AA (67%) (p&amp;lt;0.001). Tumors of AS were predominantly ductal carcinoma (84%), T1 (59%), grade 1 or 2 (70%), lymph-node negative (69%), ER+ (95%), and HER2-negative (89%). Distribution of ER, PR, and HER2 pathology and BP subtypes for AS were similar to CA but significantly different from AA (Table). Histologic tumor type, tumor grade, tumor stage, nodal stage, menopausal status, and frequency of Type 2 diabetes mellitus were not significantly different between AS and CA or AA. Whole-genome expression comparisons revealed 19 significant DEGs between AS and CA, and 45 significant DEGs between AS and AA. Immune-related genes, primarily those involved with B cell responses and signaling, were more highly expressed in AS compared with CA. Expression of genes related to cell-cycle pathways was greater in AS compared with AA. Conclusions: AS were significantly younger and more often pre/peri-menopausal at diagnosis compared with CA and AA, consistent with the literature. Most clinical-pathological factors were similar between age-matched groups, except for the obesity rate, which was significantly lower in AS than in CA or AA. Although not significant, AS had EBC that was more often MP HR than CA and less often HR than AA; studies with larger patient groups will help confirm these trends. The current analysis revealed different underlying gene expression pathways in AS compared with other ethnic groups, which may result in differential clinical outcomes. As genomic profiling data are not widely available for Asian American EBC patients, further analyses are warranted to elucidate these outcomes and identify appropriate therapeutic strategies. Pathology and Genomic Results(unknowns excluded)Asian (n=103)Caucasian (n=103)African American (n=100)p-valueAS vs. CAp-value AS vs. AAER status (IHC)ER Positive69 (94.5%)89 (98.9%)73 (80.2%)0.1250.010ER Negative4 (5.5%)1 (1.1%)18 (19.8%)PR status (IHC)PR Positive64 (87.7%)81 (90%)63 (69.2%)0.4110.006PR Negative9 (12.3%)9 (10%)28 (30.8%)HER2 (IHC/FISH)HER2 Positive3 (4.2%)3 (3.4%)13 (14.3%)0.1720.017HER2 Negative64 (88.9%)85 (95.5%)77 (84.6%)Equivocal5 (6.9%)1 (1.1%)1 (1.1%)MP/BP resultsLuminal A39 (40.6%)51 (53.7%)28 (30.4%)0.2320.043Luminal B45 (46.9%)38 (40.0%)42 (45.7%)HER2 (MP HR)7 (7.3%)4 (4.2%)5 (5.4%)Basal (MP HR)5 (5.2%)2 (2.1%)17 (18.5%) Citation Format: Margaret Chen, Ava Kwong, Carolyn Hendricks, Nina D'Abreo, Laura Lee, Hatem H. Soliman, Charles Cox, Heather M. Kling, Rajith Bhaskaran, Shiyu Wang, Andrea Menicucci, Sarah Untch, William Audeh, FLEX Investigators Group. Molecular profiles and clinical-pathological features of Asian early-stage breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS7-69.

CHD4 Promotes Breast Cancer Progression as a Coactivator of Hypoxia-Inducible Factors.

Recruitment of RNA polymerase II to hypoxia-inducible factor (HIF) target genes under normoxia is a prerequisite for HIF-mediated transactivation. However, the underlying mechanism of this recruitment remains unknown. Here we report that chromodomain helicase DNA-binding protein 4 (CHD4) physically interacts with α and β subunits of HIF1 and HIF2 and enhances HIF-driven transcriptional programs to promote breast cancer progression. Loss of HIF1/2α abolished CHD4-mediated breast tumor growth in mice. In breast cancer cells under normoxia, CHD4 enrichment at HIF target gene promoters increased RNA polymerase II loading through p300. Hypoxia further promoted CHD4 binding to the chromatin via HIF1/2α, where CHD4 in turn enhanced recruitment of HIF1α, leading to HIF target gene transcription. CHD4 was upregulated and correlated with HIF target gene expression in human breast tumors; upregulation of CHD4 and other known HIF coactivators in human breast tumors was mutually exclusive. Furthermore, CHD4 was associated with poor overall survival of patients with breast cancer. Collectively, these findings reveal a new fundamental mechanism of HIF regulation in breast cancer, which has clinical relevance. SIGNIFICANCE: This study identifies CHD4 as a HIF coactivator and elucidates the fundamental mechanism underlying CHD4-mediated HIF transactivation in breast tumors.

Low dose environmental radon exposure and breast tumor gene expression

BackgroundThe International Agency for Research on Cancer classified radon and its decay-products as Group-1-human-carcinogens, and with the current knowledge they are linked specifically to lung cancer. Biokinetic models predict that radon could deliver a carcinogenic dose to breast tissue. Our previous work suggested that low-dose radon was associated with estrogen-receptor (ER)-negative breast cancer risk. However, there is limited research to examine the role of radon in breast cancer biology at the tissue level. We aim to understand molecular pathways linking radon exposure with breast cancer biology using transcriptome-wide-gene-expression from breast tumor and normal-adjacent tissues.MethodsOur study included 943 women diagnosed with breast cancer from the Nurses’ Health Study (NHS) and NHSII. We estimated cumulative radon concentration for each participant up-to the year of breast cancer diagnosis by linking residential addresses with a radon exposure model. Transcriptome-wide-gene-expression was measured with the Affymetrix-Glue-Human-Transcriptome-Array-3.0 and Human-Transcriptome-Array-2.0. We performed covariate-adjusted linear-regression for individual genes and further employed pathway-analysis. All analyses were conducted separately for tumor and normal-adjacent samples and by ER-status.ResultsNo individual gene was associated with cumulative radon exposure in ER-positive tumor, ER-negative tumor, or ER-negative normal-adjacent tissues at FDR < 5%. In ER-positive normal-adjacent samples, PLCH2—reached transcriptome-wide-significance (FDR < 5%). Gene-set-enrichment-analyses identified 2-upregulated pathways (MAPK signaling and phosphocholine biosynthesis) enriched at FDR < 25% in ER-negative tumors and normal-adjacent tissues, and both pathways have been previously reported to play key roles in ionizing radiation induced tumorigenesis in experimental settings.ConclusionOur findings provide insights into the molecular pathways of radon exposure that may influence breast cancer etiology.

AMPK Activation by Metformin Promotes Survival of Dormant ER+ Breast Cancer Cells.

Despite adjuvant endocrine therapy for patients with estrogen receptor alpha (ER)-positive breast cancer, dormant residual disease can persist for years and eventually cause tumor recurrence. We sought to deduce mechanisms underlying the persistence of dormant cancer cells to identify therapeutic strategies. Mimicking the aromatase inhibitor-induced depletion of estrogen levels used to treat patients, we developed preclinical models of dormancy in ER+ breast cancer induced by estrogen withdrawal in mice. We analyzed tumor xenografts and cultured cancer cells for molecular and cellular responses to estrogen withdrawal and drug treatments. Publicly available clinical breast tumor gene expression datasets were analyzed for responses to neoadjuvant endocrine therapy. Dormant breast cancer cells exhibited upregulated 5' adenosine monophosphate-activated protein kinase (AMPK) levels and activity, and upregulated fatty acid oxidation. While the antidiabetes AMPK-activating drug metformin slowed the estrogen-driven growth of cells and tumors, metformin promoted the persistence of estrogen-deprived cells and tumors through increased mitochondrial respiration driven by fatty acid oxidation. Pharmacologic or genetic inhibition of AMPK or fatty acid oxidation promoted clearance of dormant residual disease, while dietary fat increased tumor cell survival. AMPK has context-dependent effects in cancer, cautioning against the widespread use of an AMPK activator across disease settings. The development of therapeutics targeting fat metabolism is warranted in ER+ breast cancer.

Prediagnostic 25-Hydroxyvitamin D Concentrations in Relation to Tumor Molecular Alterations and Risk of Breast Cancer Recurrence.

Although vitamin D inhibits breast tumor growth in experimental settings, the findings from population-based studies remain inconclusive. Our goals were to investigate the association between prediagnostic plasma 25-hydroxyvitamin D [25(OH)D] concentration and breast cancer recurrence in prospective epidemiologic studies and to explore the molecular underpinnings linking 25(OH)D to slower progression of breast cancer in the Nurses' Health Studies (NHS, N = 659). Plasma 25(OH)D was measured with a high-affinity protein-binding assay and a radioimmunoassay. We profiled transcriptome-wide gene expression in breast tumors using microarrays. Hazard ratios (HR) of breast cancer recurrence were estimated from covariate-adjusted Cox regressions. We examined differential gene expression in association with 25(OH)D and employed pathway analysis. We derived a gene expression score for 25(OH)D, and assessed associations between the score and cancer recurrence. Although 25(OH)D was not associated with breast cancer recurrence overall [HR = 0.97; 95% confidence interval (CI), 0.88-1.08], the association varied by estrogen-receptor (ER) status (P interaction = 0.005). Importantly, among ER-positive stage I to III cancers, every 5 ng/mL increase in 25(OH)D was associated with a 13% lower risk of recurrence (HR = 0.87; 95% CI, 0.76-0.99). A null association was observed for ER-negative cancers (HR = 1.07; 95% CI, 0.91-1.27). Pathway analysis identified multiple gene sets that were significantly (FDR < 5%) downregulated in ER-positive tumors of women with high 25(OH)D (≥30 ng/mL), compared with those with low levels (<30 ng/mL). These gene sets are primarily involved in tumor proliferation, migration, and inflammation. 25(OH)D score derived from these gene sets was marginally associated with reduced risk of recurrence in ER-positive diseases (HR = 0.77; 95% CI, 0.59-1.01) in the NHS studies; however no association was noted in METABRIC, suggesting that further refinement is need to improve the generalizability of the score. Our findings support an intriguing line of research for studies to better understand the mechanisms underlying the role of vitamin D in breast tumor progression, particularly for the ER-positive subtype. Vitamin D may present a personal-level secondary-prevention strategy for ER-positive breast cancer.

Abstract A85: Prediagnostic 25-hydroxyvitamin D concentrations in relation to tumor molecular alterations and risk of breast cancer recurrence

Abstract Although vitamin D inhibits breast tumor growth and development in experimental settings, the findings from population-based studies remain inconclusive. Our goals were to investigate the association between prediagnostic plasma 25-hydroxyvitamin D [25(OH)D] concentration and breast cancer recurrence in prospective epidemiologic studies and to explore the molecular underpinnings linking 25(OH)D to slower progression of breast cancer. Our study included 659 women with invasive breast cancer from the Nurses’ Health Studies (NHS) diagnosed from 1989 to 2010. Plasma 25(OH)D was measured with a high-affinity protein binding assay or a radioimmunoassay. We profiled transcriptome-wide gene expression in breast tumors using microarrays. Hazard ratios (HRs) of breast cancer recurrence were estimated from covariate-adjusted Cox proportional hazards models. We examined differential gene expression regulation in association with 25(OH)D with covariate-adjusted linear regression and employed pathway analysis. We derived a gene expression score for 25(OH)D, and further assessed associations between the standardized score and breast cancer recurrence. Although 25(OH)D was not associated with breast cancer recurrence overall (hazard ratio (HR)=0.96; 95% confidence interval (CI): 0.86, 1.08) (median follow-up=12.8 years), the association varied by estrogen receptor (ER) status (p for interaction=0.005). Importantly, among ER-positive stage I to III cancers, every 5 ng/ml increase in prediagnostic plasma 25(OH)D was associated with a 13% lowered risk of recurrence (HR=0.87; 95% CI: 0.76; 0.99). No association was observed in women with stage I to III ER-negative cancers (HR=1.07; 95% CI: 0.91; 1.27). Pathway analysis identified multiple gene sets that were significantly (FDR&amp;lt;5%) downregulated in ER-positive breast tumors of women with high prediagnostic 25(OH)D (≥30 ng/ml), compared to those with low levels (&amp;lt;30 ng/ml). These gene sets are primarily involved in tumor proliferation, apoptosis, migration and invasion, inflammation, and cancer cell metabolism. The standardized score of 25(OH)D signatures derived from these gene sets was marginally significantly associated with reduced risk of recurrence in ER-positive diseases (HR=0.77; 95% CI: 0.59, 1.01). Using TIMER, a mathematical algorithm to deconvolute tumor cellular heterogeneity, we found more infiltrated CD8+ T cells in ER-negative tumors as compared to ER-positive tumors, and this higher immune infiltration in ER-negative tumors may contribute to the observed heterogeneous response. Our findings support an intriguing line of research for future studies to better understand the biologic mechanisms underlying the role of vitamin D in breast tumor progression, particularly for the ER-positive subtype. Citation Format: Yujing Heng, Donghao Lu, Natalie DuPre, Kimberly Glass, Peter Kraft, David Feldman, Susan Hankinson, Kathryn Rexrode, Heather Eliassen, Rulla Tamimi, Cheng Peng. Prediagnostic 25-hydroxyvitamin D concentrations in relation to tumor molecular alterations and risk of breast cancer recurrence [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A85.

Impact of a Pre-Operative Exercise Intervention on Breast Cancer Proliferation and Gene Expression: Results from the Pre-Operative Health and Body (PreHAB) Study.

Exercise after breast cancer diagnosis is associated with lower cancer-specific mortality, but the biological mechanisms through which exercise impacts breast cancer are not fully understood. The Pre-Operative Health and Body (PreHAB) Study was a randomized window-of-opportunity trial designed to test the impact of exercise on Ki-67, gene expression, and other biomarkers in women with breast cancer. Inactive women with newly diagnosed breast cancer were randomized to an exercise intervention or mind-body control group, and participated in the study between enrollment and surgery (mean 29.3 days). Tumor and serum were collected at baseline and surgery. Forty-nine women were randomized (27 exercise, 22 control). At baseline, mean age was 52.6, body mass index was 30.2 kg/m2, and exercise was 49 minutes/week. Exercise participants significantly increased exercise versus controls (203 vs. 23 minutes/week, P < 0.0001). There were no differences in changes of expression of Ki-67, insulin receptor, and cleaved caspase-3 in exercise participants versus controls. KEGG pathway analysis demonstrated significant upregulation of 18 unique pathways between the baseline biopsy and surgical excision in exercise participants and none in control participants (q < 0.1). Top-ranked pathways included several implicated in immunity and inflammation. Exploratory analysis of tumor immune infiltrates demonstrated a trend toward a decrease in FOXP3+ cells in exercise versus control participants over the intervention period (P = 0.08). A window-of-opportunity exercise intervention did not impact proliferation but led to alterations in gene expression in breast tumors, suggesting that exercise may have a direct effect on breast cancer.See related commentary by Koelwyn and Jones, p. 5179.

Epithelial to mesenchymal transition (EMT) is associated with attenuation of succinate dehydrogenase (SDH) in breast cancer through reduced expression of SDHC

BackgroundEpithelial to mesenchymal transition (EMT) is a well-characterized process of cell plasticity that may involve metabolic rewiring. In cancer, EMT is associated with malignant progression, tumor heterogeneity, and therapy resistance. In this study, we investigated the role of succinate dehydrogenase (SDH) as a potential key regulator of EMT.MethodsAssociations between SDH subunits and EMT were explored in gene expression data from breast cancer patient cohorts, followed by in-depth studies of SDH suppression as a potential mediator of EMT in cultured cells.ResultsWe found an overall inverse association between EMT and the SDH subunit C (SDHC) when analyzing gene expression in breast tumors. This was particularly evident in carcinomas of basal-like molecular subtype compared to non-basal-like tumors, and a low SDHC expression level tended to have a prognostic impact in those patients. Studies in cultured cells revealed that EMT was induced by SDH inhibition through SDHC CRISPR/Cas9 knockdown or by the enzymatic inhibitor malonate. Conversely, overexpression of EMT-promoting transcription factors TWIST and SNAI2 caused decreased levels of SDHB and C and reduced rates of SDH-linked mitochondrial respiration. Cells overexpressing TWIST had reduced mitochondrial mass, and the organelles were thinner and more fragmented compared to controls.ConclusionsOur findings suggest that downregulation of SDHC promotes EMT and that this is accompanied by structural remodeling of the mitochondrial organelles. This may confer survival benefits upon exposure to hostile microenvironment including oxidative stress and hypoxia during cancer progression.

Study the effect of indomethacin administration on breast tumor growth and iNOS gene expression in tumor-bearing mice

Breast cancer is a public health concern among the women. iNOS is stated by the effect of various inflammatory factors and is thus called inducible NOS. Investigating iNOS expression is a potent tool for understanding effective molecular parameters in tissue and cellular responses to external factors. In this research study, iNOS expression in mice with breast cancer was investigated and the effects of various doses of indomethacin on the iNOS gene expression in breast tumors was evaluated.4T1 cells were grown in RPMI 1640 Medium. 200 µl of cell suspension (107 cells)were injected into the mice right flank, subcutaneously. 35 Balb/C albino mice divided into five groups each group consist of 7 mice. First group was healthy control group, second group was tumor control, and the 3rd, 4th and 5th groups were treated by 25μg, 50μg and 100μg of indomethacin, respectively. The rate of breast tumor growth was measured in treated groups for two months. The levels of iNOS gene expression was determined using real time RT-PCR technique.Our results demonstrated, iNOS expression in tumor tissue increased with the growth of breast cancer cells. Furthermore, Administration of 25μg and 100μg indomethacin neither had significant effect on breast tumor growth nor effect on iNOS gene expression. While 50μg indomethacin decreased the tumor growth (P>0.05) and decreased iNOS gene expression. Further studies such as evaluating the effects of indomethacin on the other anti-tumor immunosuppressing factor and additional tests western blot, flow cytometry and immunohistochemistry recommended in order to obtain more practical findings.