Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer

The functional role of progesterone receptor (PR) and its impact on estrogen signaling in breast cancer remain controversial. In primary ER+ (estrogen receptor-positive)/PR+ human tumors, we report that PR reprograms estrogen signaling as a genomic agonist and a phenotypic antagonist. In isolation, estrogen and progestin act as genomic agonists by regulating the expression of common target genes in similar directions, but at different levels. Similarly, in isolation, progestin is also a weak phenotypic agonist of estrogen action. However, in the presence of both hormones, progestin behaves as a phenotypic estrogen antagonist. PR remodels nucleosomes to noncompetitively redirect ER genomic binding to distal enhancers enriched for BRCA1 binding motifs and sites that link PR and ER/PR complexes. When both hormones are present, progestin modulates estrogen action, such that responsive transcriptomes, cellular processes, and ER/PR recruitment to genomic sites correlate with those observedwith PR alone, but not ER alone. Despite this overall correlation, the transcriptome patterns modulated by dual treatment are sufficiently different from individual treatments, such that antagonism of oncogenic processes is both predicted and observed. Combination therapies using the selective PRmodulator/antagonist (SPRM) CDB4124 in combination with tamoxifen elicited 70% cytotoxic tumor regression of T47D tumor xenografts, whereas individual therapies inhibited tumor growth without net regression. Our findings demonstrate that PR redirects ER chromatin binding to antagonize estrogen signaling and that SPRMs can potentiate responses to antiestrogens, suggesting that cotargeting of ER and PR in ER+/PR+ breast cancers should be explored

The impact of RB deficiency on hepatocyte biology and tumorigenesis

The integrity of the RB tumor suppressor pathway is critical for inhibition of inappropriate proliferation and suppression of tumor development in a wide variety of human tissues. RB has been shown to play a number of distinct roles in contributing to tumor suppression; studies have implicated the RB pathway in DNA damage response, genome instability, establishment of senescence, and promotion of differentiation, among other processes. Despite intensive research, however, the specific functions of RB as they relate to individual disease contexts and distinct facets of cellular stress response remain unclear. Herein, research is directed at first unmasking the immediate underlying impact of RB deletion in vivo, and then subsequently probing the specific disease-relevant functions of RB deficiency during DNA damage response and subsequent liver tumorigenesis. Tissue specific deletion of RB revealed a profound induction of E2F-mediated DNA replication that was characterized by hyper-physiological formation of pre-replication complexes. These phenotypes were not accompanied by productive mitoses. Uniquely, RB-deficient hepatocytes accumulated aberrant ploidy and significant levels of DNA damage. Furthermore, in vitro and in vivo analyses demonstrate the LXCXE-binding function of RB, while dispensable for E2F-promoter association, is required for mediating appropriate transcriptional control during DNA damage response in the liver. Such aberrant responses were mediated preferentially through E2F3. Long-term studies demonstrated that disruption of LXCXE-binding accelerated DNA damage mediated tumorigenesis in vivo and gene expression profiling revealed that the transcriptional program mediated by this function of RB was associated with progression to HCC in humans. Surprisingly, gene expression profiling also revealed an unexpected role for RB in modulation of immune response gene transcription. Together, these studies demonstrate and establish highly tissue-specific and context-dependent roles for RB in transcriptional control and tumor suppression

Examining the Pathogenesis of Breast Cancer Using a Novel Agent-Based Model of Mammary Ductal Epithelium Dynamics

The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to augment the traditional investigatory workflow for future hypothesis generation and testing of the mechanisms of breast cancer oncogenesis.</p

Examining the Pathogenesis of Breast Cancer Using a Novel Agent-Based Model of Mammary Ductal Epithelium Dynamics

<div><p>The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the <u>D</u>uctal <u>E</u>pithelium <u>A</u>gent-<u>B</u>ased <u>M</u>odel (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely <i>TP53</i> and <i>Myc</i>, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to <i>BRCA1</i>-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor <i>RUNX3</i>. These data suggest that the DEABM can serve as a potentially valuable framework to augment the traditional investigatory workflow for future hypothesis generation and testing of the mechanisms of breast cancer oncogenesis.</p></div

Overall schematic of cell-types and their interactions involved in duct epithelial cell life cycle.

<p>This figure depicts the minimally sufficient set of cell types and their interactions necessary to represent the growth and maintenance of the breast duct epithelial cell population. In particular note that given this representation ER+ cells do not have proliferative potential, a state that is maintained through the suppression of cMet by RUNX3.</p

Set of included representative “genes” and their relationship to cellular behaviors and general functions within the DEABM.

<p>As the representational focus of the DEABM is on characterizing the functional dynamics associated with oncogenesis, potentially detrimental “genes” have been included on their known influences on those functions that are plausibly involved and altered in the process of tumorigenesis. Additionally, the arrows are intended to represent known direct regulatory effects; it is expected that there are many second and third order effects that might lead a named gene to affect other downstream behaviors. *Note that the labeling of these “genes” is not intended to be a comprehensive description of all the known effects of the named genes, but rather to label certain putative cellular behaviors possibly involved in malignant transformation.</p

Reproduction of ER tumor status in both wild-type/sporadic and BRCA1 mutated populations of breast cancer.

<p>These data demonstrate the similarity between DEABM simulation runs and data extracted from the literature concerning the percentage of ER+ tumors generated in both wild-type/sporadic and BRCA1-mutated populations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Easton1" target="_blank">[46]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Tung1" target="_blank">[57]</a>. Panel A depicts the ER+ percentage among wild-type/sporadic populations from both the literature, ∼68% (range 60–77%) of premenopausal breast tumors <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Atchley1" target="_blank">[51]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Haffty1" target="_blank">[54]</a>, and in simulated populations (n-individuals = 500, N-groups = 3) of ∼65% (range 59–71%) of the simulated breast cancers. Panel B demonstrates the same comparison of ER+ tumors in the <i>BRCA1</i> mutant population, where the DEABM shows that only ∼38% (range 29–44%) of tumors generated were ER+ as compared to published incidences of ER+ <i>BRCA1</i> mutant tumors of ∼36% (range 19–52%) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Atchley1" target="_blank">[51]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Lee1" target="_blank">[55]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064091#pone.0064091-Tung1" target="_blank">[57]</a>. For both Panel A and B published cancer population data is denoted by the name of the study’s first author, whereas the DEABM runs are labeled with their N-group number. These findings indicate that the DEABM incorporates plausible mechanisms for ER+ tumorigenesis, suggesting a role of <i>RUNX3</i> expression (or other genes performing a similar function) in the selectivity of ER+ breast cancer previously unknown.</p

Post-calibration behavior of the DEABM reproducing baseline, normal breast epithelial dynamics.

<p>These graphs demonstrate the ability of the DEABM to generate recognizable fluctuations in luminal cell mass during normal menses (Letter A), demonstrating the first stage of the face validity of the DEABM in being able to reproduce self-sustaining cellular population without evidence of unconstrained growth. Furthermore, the DEABM was also able to reproduce expected alterations in luminal cell population dynamics associated with pregnancy, initiation depicted by red arrow (Letter B). These data.</p

Schematic of control logic concerning DNA damage, repair and functional consequences of unrepaired DNA damage within the DEABM.

<p>A baseline premise of the DEABM is that DNA damage can occur during a luminal epithelial cell’s life-time, and that damage that remains unrepaired by the time the cell is to divide can be passed on as a mutation, a certain subset of which may affect a critical cellular function that may influence tumorigenesis. The DEABM incorporates abstract representations of DNA damage, damage repair, senescence, apoptosis and passage of mutations to subsequent cellular generations.</p