The cover image is based on the Research Article Neoadjuvant endocrine therapy expands stromal populations that predict poor prognosis in estrogen receptor-positive breast cancer by Heather M. Brechbuhl et al., https://doi.org/10.1002/mc.23377.
Abstract Cell-free DNA (cfDNA) contains a composite map of the epigenomes of its cells-of-origin. Tissue-specific transcription factor (TF) binding inferred from cfDNA could enable us to track disease states in humans in a minimally invasive manner. Here, by enriching for short cfDNA fragments, we directly map TF footprints at single binding sites from plasma. We show that the enrichment of TF footprints in plasma reflects the binding strength of the TF in cfDNA tissue-of-origin. Based on this principle, we were able to identify the subset of genome-wide binding sites for selected TFs that leave TF-specific footprints in plasma. These footprints enabled us to not only identify the tissue-of-origin of cfDNA but also map the chromatin structure around the factor-bound sites in their cells-of-origin. To ask if we can use these plasma TF footprints to map cancer states, we first defined pure tumor TF signatures in plasma in vivo using estrogen receptor-positive (ER+) breast cancer xenografts. We found that the tumor-specific cfDNA protections of ER-α could distinguish WT, ER-amplified, and ER-mutated xenografts. Further, tumor-specific cfDNA protections of ER-α and FOXA1 reflect TF-specific accessibility across human breast tumors, demonstrating our ability to capture tumor TF binding in plasma. We then scored TF binding in human plasma samples and identified specific binding sites whose plasma TF protections can identify the presence of cancer and specifically breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of cancer in humans.
Abstract The tumor microenvironment (TME) is an important modulator of response and resistance to endocrine therapy in estrogen receptor alpha (ER) positive breast cancer. Endocrine therapy is highly effective at reducing tumor burden and preventing recurrence in most estrogen receptor alpha (ER) positive breast cancers. Existing drugs work either directly by targeting tumor‐cell ER or indirectly by inhibiting estrogen production in stromal cells with aromatase inhibitors (AI). However, many stromal cells also express ER and the direct impact of endocrine therapies on ER + stromal cells remain unclear. In this study, we investigated how neoadjuvant endocrine therapy (NET) directly effects stromal cells by measuring changes in stomal components of the TME that favor tumor progression. We previously defined two major subsets of tumor‐associated stromal cells (TASCs): CD146 positive/CDCP1 negative (TASC CD146 ), CD146 negative/CDCP1 positive (TASC CDCP1 ), and generated a differentially expressed genes list associated with each type. Here, we applied the TASC gene list for classification and an algorithm that estimates immune cell abundance (TIMEx) to METABRIC transcriptomic data for ER + breast cancer patients coupled with multiplex imaging and analysis of paired tissue samples pre‐ and post‐ NET with the AI exemestane. TASC CDCP1 composition predicted for decreased patient survival in the METABRIC cohort. Exemestane treatment significantly increased expression of TASC CDCP1 and decreased expression of TASC CD146 . The posttreatment shift toward TASC CDCP1 composition correlated with increased macrophage infiltration and increased CD8+ T‐cell, B cell, and general stromal components. The effectiveness of NET is currently based solely on the reduction of ER+ breast cancer cells. Here, we show NET displays clear TME effects that promote the expansion of the less favorable TASC CDCP1 population which are correlated with TME remodeling and reshaping immune infiltration supportive of tumor progression. Our findings highlight the need to further understand the role of endocrine therapy on TME remodeling, tumor progression, and patient outcomes.
Abstract Our current understanding of solid tumors and their progression primarily relies on in vitro models, cell lines, patient-derived xenografts, and scarce data from invasive tissue biopsies from patients. The ability to monitor changes in chromatin structure and transcription factor binding in tumor cells using a minimally invasive approach in humans has the potential to revolutionize our understanding of disease progression and treatment resistance. In this study, we use the example of estrogen receptor (ER) positive breast cancer, the most common disease subtype, and define the ER axis from plasma cell-free DNA (cfDNA). While lymphoid/myeloid cell turnover represents the dominant source of cfDNA in the bloodstream, a detectable fraction of DNA from tumor tissue-of-origin can be found in patients with solid cancers. cfDNA is the product of the action of endogenous nucleases on chromatin; and retains the map of epigenomes from cells of origin. Our method therefore non-invasively captures TF-nucleosome dynamics in tumor tissue-of-origin using plasma cfDNA. First, we show that we can reliably identify the active binding of hematopoietic pioneer factor PU.1 and CTCF from cfDNA of healthy humans and cancer patients. Then to define cfDNA binding of disease specific TF ER, we used ER+ patient-derived xenograft (PDX) models allowing for a clear separation of tumor signal from hematopoietic background. This allowed us to establish the sensitivity and specificity of our approach. We also identified the subset of CUT&RUN-defined ER binding sites that feature the strongest binding in vivo from both lymphocyte background as well as cancer cells. Furthermore, we can define the active binding sites of pioneer factor FOXA1, which facilitates ER binding by opening the chromatin. Based on the TF protection levels from cfDNA we were able to define tumor as well as hematopoietic-specific TF binding sites that can serve as potential hotspots to monitor ER+ disease state at around 1% tumor fraction. These data demonstrate our ability to simultaneously monitor TF and nucleosome dynamics at disease sites just from plasma that can enable real-time monitoring of disease phenotype in a minimally invasive manner. Citation Format: Satyanarayan Rao, Amy Han, Alexis Zukowski, Etana Kopin, Peter Kabos, Srinivas Ramachandran. Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype [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 2611.
Small primary breast cancers can show surprisingly high potential for metastasis. Clinical decision-making for tumor aggressiveness, including molecular profiling, relies primarily on analysis of the cancer cells. Here we show that this analysis is insufficient — that the stromal microenvironment of the primary tumor plays a key role in tumor cell dissemination and implantation at distant sites. We previously described 2 cancer-associated fibroblasts (CAFs) that either express (CD146+) or lack (CD146–) CD146 (official symbol MCAM, alias MUC18). We now find that when mixed with human breast cancer cells, each fibroblast subtype determines the fate of cancer cells: CD146– fibroblasts promoted increased metastasis compared with CD146+ fibroblasts. Potentially novel quantitative and qualitative proteomic analyses showed that CD146+ CAFs produced an environment rich in basement membrane proteins, while CD146– CAFs exhibited increases in fibronectin 1, lysyl oxidase, and tenascin C, all overexpressed in aggressive disease. We also show clinically that CD146– CAFs predicted for likelihood of lymph node involvement even in small primary tumors (<5 cm). Clearly small tumors enriched for CD146– CAFs require aggressive treatments.
Abstract Transitional cell carcinoma (TCC) is the most common type of bladder cancer and can be categorized as either non-muscle invasive (Ta-T1) or muscle invasive (≥T2). Approximately 50% of bladder cancers are T1 at initial diagnosis; however, the recurrence rate for these tumors is high and they may progress into T2. In this study, we aimed to determine if there are specific gene expression differences between T1 vs. T2 bladder cancer that can help identify key regulators in bladder cancer progression and invasion. T1 and T2 bladder cancer tissues were subjected to RNA-Seq to evaluate for differences among these stages. Additionally, the Oncomine database was examined to further narrow down potential candidates that differentiate T1 from T2. These efforts led to the identification of an extracellular matrix glycoprotein, fibulin-3 (FBLN3), as being highly expressed in T2 compared to T1 tissues. To validate these findings, FBLN3 expression was measured using qRT-PCR from formalin fixed and paraffin embedded tissues from patient bladder samples ranging from stages Ta-T4. These studies confirmed that FBLN3 expression was elevated in muscle-invasive compared to non-muscle invasive bladder cancer. Consistent with these findings, FBLN3 expression level correlated with the invasive ability of several bladder cancer cell lines. Specifically, FBLN3 expression was determined using both qRT-PCR and western blotting amongst the T24, UMUC-13, UMUC-3, RT4, and 5637 bladder cancer cell lines. The most invasive cell lines, T24 and UMUC-13, demonstrated the highest FBLN3 expression. In contrast, the least invasive cells, RT4 and 5637, demonstrated the least FBLN3 expression. To determine a functional role for FBLN3 in bladder cancer invasion, we knocked down or increased FBLN3 expression in bladder cancer cell lines using lentiviral transduction. Knockdown of FBLN3 expression in the T24 and UMUC-13 cells inhibited the invasion and migration of these bladder cancer cells; whereas, FBLN3 overexpression in the 5637 cells promoted the invasiveness of the bladder cancer cells. Furthermore, cell viability and growth rates were not affected by manipulation of FBLN3 expression. Our results indicate that FBLN3 serves as a pro-invasive factor in bladder cancer. These findings suggest that FBLN3 could serve as (1) a biomarker to differentiate T1 from T2 bladder cancers and (2) a promising therapeutic target. Citation Format: Amy L. Han, Brendan Veeneman, Scott A. Tomlins, Evan T. Keller. Identifying genes that regulate bladder cancer progression and invasion. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 692.
Abstract Introduction: ErbB3 serves as a critical co-receptor of erbB2 and plays a vital role in the development of erbB2-overexpressing (erbB2+) breast cancer. It is thought to be an important compensatory target for combinatorial strategy to improve the treatments for erbB2+ breast cancer patients. MiRNAs regulate gene expression by the sequence-specific targeting of mRNAs, leading to translational repression or mRNA degradation. ErbB3 is a direct target of both miR-125a and miR-205. Here, we study the potential activity of miRNA based erbB3-targeted therapy in erbB2+ breast cancer cells. Methods: Cell growth assays were used to determine cell viability. Western blot analyses were performed to assess the expression and activation of proteins. Flow cytometry analysis was carried out to examine cell cycle progression. Lentiviral vector containing one or two miRNAs was used to ectopically express miR-125a and/or miR-205. Results: Co-expression of miR-125a and miR-205 showed a potent activity to downregulate erbB3 while single miRNA had no or little effect on erbB3 when miR-125a or miR-205 was only increased below 10-fold in BT474 cells. Combination of the two miRNAs not only resulted in a dramatic reduction of phosphorylated erbB3 (P-erbB3) and the downstream signaling kinases Akt (P-Akt) and Src (P-Scr), it also inhibited cell proliferation and increased the cells at G1 phase. More importantly, concomitant expression of the two miRNAs significantly enhanced trastuzumab-mediated growth inhibition and cell cycle G1 arrest in BT474 cells. Interestingly, the expression levels of miR-125a, but not miR-205 in the trastuzumab-resistant BT474-HR20 cells were much lower than that in the parental BT474 cells. Ectopic expression of miR-125a alone profoundly inhibited proliferation of BT474-HR20 cells. These data suggested that reduced miR-125a might be a novel mechanism leading to trastuzumab resistance; and upregulation of miR-125a could be a useful tool to abrogate the resistance. Conclusions: Co-expression of miR-125a and miR-205 is a new approach to inhibit erbB3. Specific targeting of erbB3 via the functional cooperative miRNAs enhances efficacy of trastuzumab against erbB2+ breast cancer cells. Our data support further exploration of the possible role of miR-125a in the development of trastuzumab resistance. Keywords: ErbB3, ErbB2, miRNA, Trastuzumab, Breast Cancer Citation Format: Hui Lyu, Jingcao Huang, Bolun Wang, Amy Han, Bolin Liu. Targeting of ErbB3 with functional cooperative miRNAs enhances efficacy of trastuzumab in ErbB2-overexpressing breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 477.
ABSTRACT Purpose The development of endocrine resistance remains a significant challenge in the clinical management of estrogen receptor-positive ( ER+ ) breast cancer. Metabolic reprogramming is a prominent component of endocrine resistance and a potential therapeutic intervention point. However, a limited understanding of which metabolic changes are conserved across the heterogeneous landscape of ER+ breast cancer or how metabolic changes factor into ER DNA binding patterns hinder our ability to target metabolic adaptation as a treatment strategy. This study uses dimethyl fumarate ( DMF ) to restore tamoxifen ( Tam ) and fulvestrant ( Fulv ) sensitivity in endocrine-resistant cell lines and investigates how metabolic changes influence ER DNA-binding patterns. Experimental Design To address the challenge of metabolic adaptation in anti-endocrine resistance, we generated Tam and Fulv resistance in six ER+ breast cancer ( BC ) cell lines, representing ductal (MCF7, T47D, ZR75-1, and UCD12), lobular (MDA-MB-134--VI), and HER2 amplified (BT474) BC molecular phenotypes. Metabolomic profiling, RNA sequencing, proteomics, and CUT&RUN assays were completed to characterize metabolic shifts, transcriptional and protein changes, and ER DNA-binding patterns in resistant cells. Dimethyl fumarate was assessed for its ability to reverse Tam and Fulv resistance, restore tricarboxylic acid cycle ( TCA ) cycle function, and restore parental cell (endocrine sensitive) ER DNA binding patterns. Results Tamoxifen-resistant (TamR) and fulvestrant-resistant (FulvR) cells exhibited disrupted TCA cycle activity, reduced glutathione levels, and altered nucleotide and amino acid metabolism. DMF treatment replenished TCA cycle intermediates and reversed resistance in both TamR and FulvR cells. DMF also increased mevalonate pathway enzyme expression in both TamR and FulvR cells, with TamR cells upregulating enzymes in the cholesterol synthesis phase and FulvR enhancing enzymes in the early part of the pathway. DMF restored ER DNA-binding patterns in TamR cells to resemble parental cells, re-sensitizing them to Tam. In FulvR cells, DMF reversed resistance by modulating ER-cofactor interactions but did not restore parental ER DNA-binding signatures. Conclusions Our findings provide new insights into how metabolic reprogramming affects ER DNA-binding activity in endocrine-resistant breast cancer. We demonstrate how altering metabolism can reprogram ER signaling and influence resistance mechanisms by targeting metabolic vulnerabilities, such as TCA cycle disruptions. Additionally, our data provide a comprehensive metabolomic, RNA-seq, and CUT&RUN data set relevant to tumor metabolic adaptation leading to acquired endocrine resistance in highly utilized ER+ breast cancer cell lines. This study improves our understanding of how metabolic states alter ER function in endocrine-resistant breast cancer.
