Abstract 2383: Fluorescence lifetime imaging microscopy to assess drug response in patient-derived colorectal cancer organoids

Patient-derived tumor organoids (PDTOs) have been shown to be predictors of clinical response. While evidence suggests PDTOs are a more physiologically relevant cell model to use for drug discovery, challenges still exist to fully characterize their response to chemotherapies. Assays which attempt to quantify drug response in preclinical models are often end-point and cannot separate responses of heterogeneous cultures or capture dynamic information. Image based technologies attempt to counteract these shortcomings but often require fluorescent protein expression or cell staining to observe changes long-term. We utilized a label-free approach, fluorescence lifetime imaging microscopy (FLIM) and phasor analysis, to determine the metabolic state of individual PDTOs and correlate our findings to traditional cell viability assays (e.g., ATP measurements, phototoxic dyes) in response to drug perturbations.

By measuring the fluorescence lifetime of NADH, an autofluorescent metabolite, we were able to quantify the metabolic signature of KRAS mutant (KRASMUT) colorectal cancer (CRC) PDTOs. The emission decay at each pixel was Fourier transformed and represented on a phasor plot. Pixels that had a shorter lifetime of NADH were indicative of glycolysis (GLY) while longer lifetimes indicated regions of oxidative phosphorylation (OXPHOS). PDTOs were treated with clinically-relevant drugs, SN-38 (an active metabolite of irinotecan), 5-FU, and cetuximab (CTX). FLIM images were taken after 6 and 72 hours of treatment. KRASMUT tumors do not respond to CTX, thus this was used as a negative control. Staurosporine (ST) was used as a positive control for cell death. A shift in metabolic signature towards OXPHOS in a dose-dependent manner was seen in PDTOs treated with ST or SN-38. These shifts correlated with cell death measured using the CellTiter Glo cell viability assay and confocal fluorescence images of PDTOs stained with a vital dye, DRAQ7. Changes in metabolism were seen within hours while DRAQ7 signal was detected after a few days. No changes in metabolic signature, cell viability, or DRAQ7 levels were seen in CTX treated PDTOs as expected. 5-FU was found to be an ineffective drug for the specific PDTO tested in our assay as shown by the lack of metabolic shifts compared to untreated PDTOs and no decrease in cell viability. Metabolic heterogeneity was also seen with FLIM, including distinguishing different cell types in co-cultures of PDTOs and cancer-associated fibroblasts (CAFs). We were able to separate the metabolic signatures of each cell type and determine that CAFs have a more GLY signature. Taken together, FLIM supported label-free imaging of multicellular 3D organoid models for the purposes of determining dynamic tumor drug response. We are adapting this workflow to a high-throughput multimodal imaging platform for drug screening to make more informed decisions on patient care.

Citation Format: Emma Jane Fong, Mathias Bigger, Seungil Kim, Michael Doche, Scott Valena, Pratiksha Kshetri, Shannon Mumenthaler. Fluorescence lifetime imaging microscopy to assess drug response in patient-derived colorectal cancer organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2383.

Abstract P4-08-06: Clock Genes in Breast Cancer

Background: Disruption of circadian processes has been linked to cancer initiation, progression, metastasis, resistance, and mortality. Clock proteins are an emerging target for therapy in breast cancer. Circadian rhythms are controlled by a network of transcription/translation feedback loops primarily driven by BMAL and CLOCK and the transcriptional repressors period (PER1-3) and cryptochrome (CRY1-2). We investigated the molecular and clinical associations of clock genes in breast cancer. Methods: A total of 9563 breast tumors underwent molecular profiling (Caris Life Sciences). Analyses included next-generation sequencing of DNA (592 genes-NextSeq, WES-NovaSeq) and RNA (NovaSeq). Clock gene Score (CS) was determined using expression of clock pathway gene Z scores (positives of BMAL, CLOCK and negatives of PER1/2 and CRY1/2) and then stratified into quartiles. xCell was used to quantify immune cell infiltration in the tumor microenvironment (TME). ER/PR was tested by IHC and HER2 was tested by either IHC or CISH. Significance was determined as P values adjusted for multiple comparison (Q) of < 0.05. Real-world survival information was obtained from insurance claims data and was calculated from either tissue collection to last contact or time on treatment (TOT); comparison was done by Kaplan-Meier test. Results: TNBC had the highest median CS score, while HR+/HER2- had the lowest CS (0.96 vs 0.26 q<.001). In TNBC, PDL1 was significantly associated with higher CS (56% Q4 vs 28% Q1, q<.05). TP53 mutation was associated with higher CS (88% Q4 vs 75% Q1), while CDH1 and STK11 mutations were associated with lower CS (3.4% Q4 vs 8.7% Q1 and 0.1% Q4 vs 2.2% Q1). For the TME (xCell) in TNBC, CD8+ T cells, B cells, monocytes and NK cells were positively associated with CS, whereas CD4+ central and effector memory T cells, eosinophils, and endothelial cells were associated with lower CS (Q1 vs Q4 all q<.05). In HR+/HER2- tumors, PDL1 was also associated with higher CS (24% Q4 vs 14% Q1, q<.05). TP53 mutations (39% Q4 vs 23% Q1), HMGA2 (2% Q4 vs 0.4% Q1) and LGR5 amplifications (3% Q4 vs 0.4% Q1), and LOH (WES) (35% Q4 vs 21% Q1) were associated with higher CS. CDH1(12% Q4 vs 23% Q1), KMT2C (6% Q4 vs 10% Q1) and PIK3CA mutations (37% Q4 vs 45% Q1) were associated with lower CS (all q<.05). In HR+/HER2- tumors there was a decrease in CD4+ central memory cells, common myeloid progenitor cells, endothelial cells, and eosinophils in high CS tumors. Activated myeloid dendritic cells, B cells, CD4+ memory T cells, CD8+ naïve T cells, M1 macrophages, and Tregs all had higher abundance in high CS tumors. In HR+/HER2+ tumors, PDL1 trended positively with CS but did not reach significance likely due to sample size. For all tumors, PDL1 expression positively correlated with CS (17% Q1 vs 37% Q4) while ER (75% Q1 vs 55% Q4) and PR (49% Q1 vs 38% Q4, all q<.05) were negatively associated; no association was seen with HER2. Expression of TIMELESS (HR:0.7, CI: 0.65-0.77) and CLOCK (HR: 0.8, CI: 0.72-0.86) below median were associated with longer OS, while expression of CRY2 (HR: 1.4, CI: 1.3-1.6); PER2/3 (HR: 1.1, CI:1.0-1.2; HR:1.3, CI:1.2-1.4) above median was associated with longer OS. In TNBC, TOT IO therapy was prolonged with higher expression of CLOCK (HR: 0.5, CI: 0.41-0.72), TIMELESS (HR: 0.7 CI: 0.53-0.91), ARNTL (HR: 0.7 CI:0.54-0.92) and CRY1/2 (HR: 0.6, CI: 0.46-0.80; HR: 0.75 CI: 0.57-0.98). Conclusions: Dysregulation of clock genes is strongly associated with breast cancer subtype and survival. Higher CS is associated with TNBC and PDL1 expression and supports the use of checkpoint inhibitors. Prognosis is better with low expression of TIMELESS and CLOCK and high expression of CRY2 and PER2/3, suggesting a role in tumor development and maintenance. HR+/HER2- tumors have lowest CS, fitting with less aggressive phenotype and better prognosis. Clock genes are novel predictive and prognostic molecular markers and emerging targets for the development of new treatments in breast cancer.

Citation Format: Priya Jayachandran, Yasmine Baca, Joanne Xiu, Yuanzhong Pan, Phil Walker, Francesca Battaglin, Hiroyuki Arai, Moh’d Khushman, Janice Lu, Darcy Spicer, Shannon Mumenthaler, Richard Goldberg, Benjamin Weinberg, Emil Lou, Michael Hall, Arielle L. Heeke, W. Michael Korn, Steve A. Kay, Heinz-Josef Lenz, Evanthia T. Roussos Torres. Clock Genes in Breast Cancer [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 P4-08-06.

Abstract 4521: Long term hypoxia induces stable overexpression of JUNB and the TGFβ pathway in colon cancer

Introduction: Metastasis is responsible for over 90% of cancer related mortality, however mutations unique to the metastatic phenotype have yet to be identified. This raises the possibility that the metastatic phenotype is the result of a transcriptional profile adopted by cells of the primary tumor enabling them to spread to distal regions of the body. The tumor microenvironment (TME) is capable of influencing gene expression and cellular behavior. Hypoxia, low oxygen tension, is a component of the TME that arises due to improper tissue architecture and correlates with poor survival outcome. Stabilization of the transcription factor HIF-1α during hypoxia induces the expression of genes involved in metastasis through direct activation and through the alteration of the epigenome. However, upon re-oxygenation HIF-1α is degraded and can no longer induce expression of hypoxic responsive genes. During the metastatic process, cells that have adopted hypoxia induced metastatic behavior such as increased motility and invasiveness must transit through regions of normoxia on their way to metastatic colonization.

Hypothesis: As hypoxic cell migrate away from regions of low oxygen towards oxygen rich environments, such venous blood, genes induced by hypoxia would be expected to return to basal levels of expression. Those genes whose expression does not return to levels associated with normoxia, but instead remain elevated following re-oxygenation, may be crucial for maintaining the hypoxia induced metastatic phenotype.

Experimental Design: To study the stability of hypoxia induced gene expression alterations following re-oxygenation, colon cancer cell lines were grown under hypoxic conditions (1% O2) for up to 3 weeks and then transitioned to normoxic conditions (21% O2). RNA sequencing was used to assess changes in gene expression during hypoxia adaptation and for 3 more weeks following re-oxygenation.

Results: While the majority of genes whose expression was induced by hypoxia returned to basal levels following re-oxygenation, a subset of genes clustered in the TGF-β pathway remained at elevated levels. In particular the expression of JunB, a component of the AP-1 transcription factor, was induced by hypoxia and continued to remain overexpressed after return to normoxic growth conditions. Conclusion: Long term culturing of colon cancer cells in hypoxic conditions induces changes in gene expression that remain stable following return to normoxic growth conditions. We hypothesis that genes whose expression follows this pattern may be involved in the hypoxia induced metastatic phenotype. RNA-seq profiling of cells grown in hypoxic conditions for three weeks and then returned to normoxic growth conditions for an additional three weeks identified genes involved in the TGF-β pathway and in particular JunB that were induced by hypoxia and remained stable following return to normoxia.

Citation Format: Colin Flinders, Norah Alwash, Shannon Mumenthaler. Long term hypoxia induces stable overexpression of JUNB and the TGFβ pathway in colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4521. doi:10.1158/1538-7445.AM2017-4521

Abstract 5786: Histopathology of patient derived organoids for the quantitative analysis of response to microenvironmental perturbations

Patient derived organoids are becoming a popular 3D in vitro model that more accurately recapitulate in vivo conditions compared to standard 2D culture systems. Organoids consist of epithelial cells and lack stroma and mesenchyme, allowing cells of interest to be studied as an isolated system. However, the tunability of the organoid model also permits the re-addition of microenvironmental factors, i.e. cancer associated fibroblasts (CAFs), resulting in a wide range of experimental capabilities. Organoids are easily scalable, making them more efficient and cost-effective than traditional animal models. Despite the popularity of animal models for pre-clinical drug testing, there still remain issues with translating results from animal testing to patient outcomes; even patient-derived xenograph models experience non-physiological mouse-human interactions. Therefore, studying the impact of microenvironmental perturbations, such as the presence of CAFs, or nutrient and drug gradients, on organoids may reduce translational error. Using our biorepository of patient derived colon cancer (primary and liver metastases) organoids, we can observe changes in tumor architecture and cell growth or death, allowing us to more accurately assess the efficacy of drug therapies and observe how interpatient heterogeneity impacts their efficacy. Here we focus on the histopathology of different patient derived organoids to quantitatively study cell growth or death under drug treatments (+/- CAFs) which could ultimately become a standard procedure for drug screening.

Here we investigate the effects of CAF co-culture in patient derived organoids in response to standard chemotherapies such as Irinotecan and Oxaliplatin. Following treatment, the organoids are paraffin fixed to retain their structural integrity, then sectioned. The samples are stained with H&E to show the tumor architecture, and immunofluorescent antibodies (IF) to identify cells that are proliferating (Ki67) or apoptotic (TUNEL). As a result, we are able to investigate how tumor microenvironmental factors affect the tumor architecture of an individual patient tumor. We also examine the cytotoxic or cytostatic effects of standard chemotherapies by quantitating the number of proliferative and apoptotic cells, as well as their location within the tumor, in response to the presence of both CAFs and therapy.

Ultimately, we envision the method outlined here will further personalize medicine by allowing physicians to more rapidly assess an individual patient’s response to therapy and adjust treatment accordingly. Additionally, this method could prove to be a more inexpensive and faster means of screening new drug compounds. By creating a system that more closely recapitulates patient outcomes, we hope to move therapies towards faster approval while still retaining results representative of in vivo outcomes.

Citation Format: Sarah J. Choung, Erin Spiller, Roy Lau, Shannon Mumenthaler. Histopathology of patient derived organoids for the quantitative analysis of response to microenvironmental perturbations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5786. doi:10.1158/1538-7445.AM2017-5786

Abstract C08: Stability of hypoxia induced expression of colon cancer metastasis-associated genes

Introduction: Metastasis is responsible for over 90% of cancer related mortality; however, somatic mutations unique to the metastatic phenotype have yet to be identified. This raises the possibility that the metastatic phenotype is the result of a transcriptional profile adopted by cells of the primary tumor enabling them to spread to distal regions of the body. The tumor microenvironment (TME) is capable of influencing gene expression and cellular behavior. Hypoxia is a component of the TME that arises due to improper vascular architecture, which leads to reduced oxygen delivery to tissues and correlates with poor survival outcome. Stabilization of the transcription factor HIF-1α during hypoxia induces the expression of genes involved in metastasis through direct activation or through the alteration of the epigenome. However, upon re-oxygenation, HIF-1α is degraded and can no longer induce expression of hypoxic responsive genes. During metastasis, cells that have adopted hypoxia induced metastatic behavior such as increased motility and invasiveness must transit through regions of normoxia on their way to metastatic colonization.

Hypothesis: As hypoxic cells migrate away from regions of low oxygen toward oxygen rich environments (e.g. venous blood) genes induced by hypoxia would be expected to return to basal levels of expression. Those genes whose expression does not return to levels associated with normoxia, but instead remain elevated following re-oxygenation may be crucial for maintaining the hypoxia induced metastatic phenotype.

Experimental Design: To study the stability of hypoxia induced gene expression alterations following re-oxygenation, colon cancer cell lines were grown under hypoxic conditions (1% O2) for up to 3 weeks and then transitioned back to normoxic conditions. Gene expression changes were assessed during hypoxia adaptation and for 3 additional weeks following re-oxygenation.

Results: The continued expression of hypoxia induced genes following re-oxygenation varied greatly among those tested. Gene transcription associated with epithelial-to-mesenchymal transition (EMT) such as VIM and ZEB1 were induced by 3 weeks of hypoxic conditioning and remained elevated following their return to normoxic culturing conditions. However, in contrast, hypoxia induced genes involved in the Warburg effect such as PDK1 were induced during hypoxia, yet quickly returned to at or below basal levels following re-oxygenation.

Conclusion: Continued expression of hypoxia induced genes following re-oxygenation varies from gene to gene and from pathway to pathway. There appears to be some consistency in expression of genes following re-oxygenation that are involved in migration and invasion such as ZEB1. These results suggest that certain pathways such as EMT may be vital for the maintenance of the hypoxia induced metastatic phenotype as these cells transit from regions of low oxygen to regions of higher or normal oxygen levels.

Citation Format: Colin Flinders, Sonya Liu, Shannon Mumenthaler. Stability of hypoxia induced expression of colon cancer metastasis-associated genes. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr C08.

Abstract A23: Characterization of diverging molecular and phenotypic responses under changing extracellular matrix stiffness in MCF10A cells

Tissue stiffness has emerged as an important regulator in the maintenance of normal cellular processes. In general, solid tumors are known to be much stiffer than normal tissue, with increased extracellular matrix (ECM) density being indicative of a higher risk for many cancers, including those of the breast. Over the course of breast cancer progression, the ECM becomes increasingly stiffer, a phenomenon which is known to be a driver of malignancy. In a 3D culture system using self-assembling peptide (SAP) gels, we grew MCF10A acini under a dynamic range of stiffness environments (140-5800 Pa). Under normal breast tissue elasticity, mammary epithelial cells form rounded, polarized acini with cleared lumens. However, in tumor-like stiffnesses, the same cells form non-polarized, collapsed structures that invade into the gel. To investigate the specific genes and pathways affected by stiffness, we have conducted tandem mass spectrometry to identify protein expression changes in MCF10A cells grown on SAP gels of increasing stiffness. Interestingly, the resulting analysis showed that cells grown on higher stiffnesses exhibit greater variation in protein expression. These divergent force-regulated molecular pathways are involved in a variety of cellular functions, including cell adhesion and migration, metabolism, and the immune response, among others. This study underscores the significance of mechanical forces exerted by the ECM, and signifies the first large-scale proteomic screen carried out to analyze heterogeneous cellular responses to changing stiffness environments.

Citation Format: Sonya Liu, Russell Bainer, Yoshihiro Yui, Colin Flinders, Parag Mallick, Valerie Weaver, Shannon Mumenthaler. Characterization of diverging molecular and phenotypic responses under changing extracellular matrix stiffness in MCF10A cells. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr A23.

Abstract PR09: Extracellular stiffness cues drive spatial reorganization of the genome to globally constrain RNA abundance

The stiffness of the extracellular matrix (ECM) drives mechanosignaling that regulates tissue development and malignancy. We previously showed that a stiff ECM disrupts tissue organization and enhances malignant progression by inducing cell invasion and migration. However, the specific transcriptional and molecular events in which mechanotransduction directs these phenotypes are not well understood. To clarify this process, we used a combination of genome-scale approaches to monitor changes in gene expression and protein abundance as a function of acinar morphogenesis and tissue homeostasis in three dimensional extracellular matrix hydrogels with tunable stiffness. Elevated ECM stiffness perturbed tissue homeostasis and reverted the transcriptional phenotype of differentiated mammary acini to resemble that observed in rapidly proliferating nonpolarized mammary cell aggregates. These findings suggest that tissue tension induces cellular changes that directly reflect higher-order tissue organizational states. We found that these changes involve the spatial rearrangement of peripheral chromatin, and that the expression levels of multiple histone deacetylases increase in organized tissues concurrently with elevated nuclear heterochromatin content, an effect that is abrogated in rigid ECM conditions. We support these observations by mapping mechanoresponsive peripheral heterochromatin elements via ChIPseq, enabling us to directly identify dynamic regions containing genes whose transcriptional activity is responsive to mechanical cues. Finally, using a combination of genomic, imaging, and molecular biology techniques we demonstrated that ECM compliance and tissue organization significantly influences global RNA abundance. Notably, this model presents formidable conceptual and practical challenges for the interpretation of genomic data. Collectively, this work indicates that tissue organization is critically dependent on the cellular mechanical environment, which qualitatively and quantitatively shapes the epigenetic and transcriptional landscape by mechanisms that have not yet been elucidated.

Note: This abstract was not presented at the conference.

Citation Format: Russell Bainer, Yoshihiro Yui, Shannon Mumenthaler, Parag Mallick, Lin Liu, Hua-Jun Wu, Ondrej Podlaha, Franziska Michor, Jan Liphardt, Jonathan Licht, Valerie Weaver. Extracellular stiffness cues drive spatial reorganization of the genome to globally constrain RNA abundance. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR09.

Abstract PR16: Spatio-temporal heterogeneity in the tumor microenvironment influences the evolutionary dynamics of drug resistance

Tumor growth is a complex evolutionary process driven by dynamic feedback between a heterogeneous cell population and selection pressures from the tumor microenvironment. Spatio-temporal heterogeneity in the microenvironment can create physical niches that facilitate cellular adaptation as seen in regions of hypoxia and acidosis where cells may up-regulate glycolysis and become resistant to acid-meditated toxicity in order to survive. In recent studies, using clinically prevalent subtypes of EGFR-related non-small cell lung cancer (NSCLC), we observe that nutrient and drug gradients resulting from a cells' proximity to vasculature, can produce selective pressures driving tumor evolution. We provide a detailed examination of the microenvironmental impact (i.e. oxygen, glucose, and drug) on growth rates of NSCLC cell lines that are either sensitive or resistant to the EGFR TKI, erlotinib. Often we consider drug resistance to be associated with a fitness cost to the cell in the absence of drug. However, here we demonstrate that the situation is more complex, with the local tumor microenvironment influencing the magnitude and the directionality of the selective effect. In fact, the resistant cells actually gain a selective advantage in nutrient-stressed environments compared to the sensitive cells. The resulting growth dynamics were used to inform a stochastic compartment-based tumor model of pre-existing drug resistance where each compartment represents a specific tumor environmental niche. This integrative modeling framework was then used to predict rebound growth kinetics and tumor composition (i.e. % resistance) and in particular, provide insight into the magnitude by which the microenvironment influences these results. These investigations strongly suggest that ignoring the microenvironment or using laboratory environmental conditions to inform tumor dynamics can lead to inaccurate conclusions. Therefore, knowledge of the selective advantage/disadvantage of different cell populations within different regions of the tumor will better guide model predictions, influence overall tumor dynamics, and impact treatment strategies.

This abstract is also presented as Poster A80.

Citation Format: Shannon Mumenthaler, Jasmine Foo, Nathan Choi, William Pao, David Agus, Franziska Michor, Parag Mallick. Spatio-temporal heterogeneity in the tumor microenvironment influences the evolutionary dynamics of drug resistance. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr PR16. doi:10.1158/1538-7445.CHTME14-PR16

Abstract 2344: 3D extracellular stiffness cues drive localized changes in gene expression

The stiffness of the extracellular matrix (ECM) stimulates mechanotransduction pathways that regulate tissue development and tumor progression. We previously showed that a stiff ECM potentiates cell growth and survival, enhances cell migration to drive tumor cell invasion, and drives malignant progression of the mammary gland in culture and in vivo, but the specific transcriptional and molecular events that occur as cells acquire these phenotypic changes are not well understood. To clarify this process, we used expression microarrays, tandem mass spectrometry, and RNA sequencing to identify changes in gene expression levels, isoform usage, and protein abundance that occur as intact ascini respond to distinct stiffness environments. We found that in stiffer ECM conditions ascini acquire consistent changes in gene expression related to cell adhesion and mRNA splicing, and specifically induce the expression of a set of genes involved in epithelial cell differentiation that includes multiple SPRR and S100 proteins. Remarkably, these genes map to an apparent stiffness-mediated transcriptional hotspot on chromosome 1q21, a region containing elevated transcription in many cancers but whose activity has not been related to mechanotransduction. We then used a heuristic approach to identify additional candidate force-mediated transcriptional hotspots throughout the genome that contain multiple genes that are coordinately activated or silenced in response to elevated ECM stiffness. Provocatively, we find that genes whose expression levels are responsive to ECM stiffness cues are disproportionately located within chromosomal regions that associate with the nuclear lamina, suggesting that these transcriptional changes may be due in part to force-dependent alteration of genomic contacts with the nuclear envelope. These studies provide biological insight into the divergent cellular responses to distinct stiffness environments and suggest that genome regulatory responses to the force environment may specifically target distinct chromosomal regions via a mechanism that remains to be elucidated.

Citation Format: Russell Bainer, Yoshihiro Yui, Shannon Mumenthaler, Parag Mallick, Ondrej Podlaha, Franziska Michor, Jan Liphardt, Jonathan Licht, Valerie Weaver. 3D extracellular stiffness cues drive localized changes in gene expression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2344. doi:10.1158/1538-7445.AM2014-2344

Abstract 5124: Genomic and proteomic characterization of tamoxifen sensitive and resistant MCF7 cells

Among the most common and challenging aspect to the management of breast cancer is the development of tumor resistance to virtually all therapies. Our major research focus is to investigate genes and pathways that contribute to this process. We have previously derived a series of cultured breast cancer cell lines that were either highly sensitive or naturally resistant to tamoxifen to study the factors that lead to drug resistance. By comparing tamoxifen sensitive and resistant sub-clones we identified 227 genes that responded to tamoxifen in sensitive but not in resistant cells. From these, a signature of 67 genes demonstrated that women whose tumors matched the resistance pattern had a significantly greater likelihood of early relapse while on tamoxifen. Using automated high-throughput cell-based assays; we identified 31 kinases that repeatedly conferred resistance to tamoxifen when ectopically expressed. To further expand our understanding of the development of tamoxifen resistance to a genome level, we employed 6 of our tamoxifen-sensitive and -resistant sister cell lines. We previously showed that all 6 of these cell lines, which were all sub-cloned from the same parent without any drug selection, were identical for a set of 24 single nucleotide polymorphism (SNPs), confirming that they all derived from the same parent MCF7 line. We reasoned that they should be nearly identical genetically, thus allowing us to find genetic differences that account for the profound difference in drug response. For the genotyping, genomic DNA from an early passage of three independent sensitive and three resistant sub-clones were analyzed for copy number variation (CNV) and SNP by Illumina BeadArray and HiSeq200 next-generation sequencing. Preliminary analysis showed segregation between the genomic profiles of sensitive and resistant sub-clones in general. Chromosomes that showed more variation between sensitive and resistant sub-clones included chromosome number 2, 7, 10, 15 and 20. Visual examination of the data identified several regions of sub-clone specific chromosomal gain or loss across all chromosomes, where overlap regions across both sub-clones and regions that are either copy number gain in one cell but loss in the other one. Furthermore, by comparative analysis with cDNA microarray data, we also found that mRNA expression levels of several genes in these chromosomal regions were indeed correlated with their chromosomal status. In addition to a gene-level analysis, we are performing quantitative mass spectrometry analysis (SILAC) to identify the differences in proteomes of sensitive and resistant cells, which may account for molecular mechanisms underlying drug resistance.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5124. doi:1538-7445.AM2012-5124

17beta-estradiol prevents early-stage atherosclerosis in estrogen receptor-alpha deficient female mice

Estrogen is atheroprotective and a high-affinity ligand for both known estrogen receptors, ERα and ERβ. However, the role of the ERα in early-stage atherosclerosis has not been directly investigated and is incompletely understood. ERα-deficient (ERα−/−) and wild-type (ERα+/+) female mice consuming an atherogenic diet were studied concurrent with estrogen replacement to distinguish the actions of 17β-estradiol (E₂) from those of ERα on the development of early atherosclerotic lesions. Mice were ovariectomized and implanted with subcutaneous slow-release pellets designed to deliver 6 or 8 μg/day of exogenous 17β-estradiol (E₂) for a period of up to 4 months. Ovariectomized mice (OVX) with placebo pellets (E₂-deficient controls) were compared to mice with endogenous E₂ (intact ovaries) and exogenous E₂. Aortas were analyzed for lesion area, number, and distribution. Lipid and hormone levels were also determined. Compared to OVX, early lesion development was significantly (p < 0.001) attenuated by E₂ with 55–64% reduction in lesion area by endogenous E₂ and >90% reduction by exogenous E₂. Compared to OVX, a decline in lesion number (2- to 4-fold) and lesser predilection (~4-fold) of lesion formation in the proximal aorta also occurred with E₂. Lesion size, development, number, and distribution inversely correlated with circulating plasma E₂ levels. However, atheroprotection was independent of ERα status, and E₂ athero-protection in both genotypes was not explained by changes in plasma lipid levels (total cholesterol, triglyceride, and high-density lipoprotein cholesterol). The ERα is not essential for endogenous/exogenous E₂-mediated protection against early-stage atherosclerosis. These observations have potentially significant implications for understanding the molecular and cellular mechanisms and timing of estrogen action in different estrogen receptor (ER) deletion murine models of atherosclerosis, as well as implications to human studies of ER polymorphisms and lipid metabolism. Our findings may contribute to future improved clinical decision-making concerning the use of hormone therapy.