CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity

Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing cancer cell immunogenicity, apoptotic responses, and differentiation. Using cell-based and mouse models of breast cancer together with clinical specimens, we show that CDK4/6 inhibitors induce remodeling of cancer cell chromatin characterized by widespread enhancer activation, and that this explains many of these effects. The newly activated enhancers include classical super-enhancers that drive luminal differentiation and apoptotic evasion, as well as a set of enhancers overlying endogenous retroviral elements that is enriched for proximity to interferon-driven genes. Mechanistically, CDK4/6 inhibition increases the level of several Activator Protein-1 (AP-1) transcription factor proteins, which are in turn implicated in the activity of many of the new enhancers. Our findings offer insights into CDK4/6 pathway biology and should inform the future development of CDK4/6 inhibitors.

Interferon Signaling Is Diminished with Age and Is Associated with Immune Checkpoint Blockade Efficacy in Triple-Negative Breast Cancer

Immune checkpoint blockade (ICB) therapy, which targets T cell-inhibitory receptors, has revolutionized cancer treatment. Among the breast cancer subtypes, evaluation of ICB has been of greatest interest in triple-negative breast cancer (TNBC) due to its immunogenicity, as evidenced by the presence of tumor-infiltrating lymphocytes and elevated PD-L1 expression relative to other subtypes. TNBC incidence is equally distributed across the age spectrum, affecting 10% to 15% of women in all age groups. Here we report that increased immune dysfunction with age limits ICB efficacy in aged TNBC-bearing mice. The tumor microenvironment in both aged mice and patients with TNBC shows decreased IFN signaling and antigen presentation, suggesting failed innate immune activation with age. Triggering innate immune priming with a STING agonist restored response to ICB in aged mice. Our data implicate age-related immune dysfunction as a mechanism of ICB resistance in mice and suggest potential prognostic utility of assessing IFN-related genes in patients with TNBC receiving ICB therapy. SIGNIFICANCE: These data demonstrate for the first time that age determines the T cell-inflamed phenotype in TNBC and affects response to ICB in mice. Evaluating IFN-related genes from tumor genomic data may aid identification of patients for whom combination therapy including an IFN pathway activator with ICB may be required.This article is highlighted in the In This Issue feature, p. 1143.

CDK4/6 Inhibition in Cancer: Beyond Cell Cycle Arrest

Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) have recently entered the therapeutic armamentarium of clinical oncologists, and show promising activity in patients with breast and other cancers. Although their chief mechanism of action is inhibition of retinoblastoma (RB) protein phosphorylation and thus the induction of cell cycle arrest, CDK4/6 inhibitors alter cancer cell biology in other ways that can also be leveraged for therapeutic benefit. These include modulation of mitogenic kinase signaling, induction of a senescence-like phenotype, and enhancement of cancer cell immunogenicity. We describe here the less-appreciated effects of CDK4/6 inhibitors on cancer cells, and suggest ways by which they might be exploited to enhance the benefits of these agents for cancer patients.

IL-1β inflammatory response driven by primary breast cancer prevents metastasis-initiating cell colonization

Lack of insight into mechanisms governing breast cancer metastasis has precluded the development of curative therapies. Metastasis-initiating cancer cells (MICs) are uniquely equipped to establish metastases, causing recurrence and therapeutic resistance. Using various metastasis models, we discovered that certain primary tumours elicit a systemic inflammatory response involving interleukin-1β (IL-1β)-expressing innate immune cells that infiltrate distant MIC microenvironments. At the metastatic site, IL-1β maintains MICs in a ZEB1-positive differentiation state, preventing MICs from generating highly proliferative E-cadherin-positive progeny. Thus, when the inherent plasticity of MICs is impeded, overt metastases cannot be established. Ablation of the pro-inflammatory response or inhibition of the IL-1 receptor relieves the differentiation block and results in metastatic colonization. Among patients with lymph node-positive breast cancer, high primary tumour IL-1β expression is associated with better overall survival and distant metastasis-free survival. Our data reveal complex interactions that occur between primary tumours and disseminated MICs that could be exploited to improve patient survival.

Abstract B04: CDK4/6 inhibition triggers an antitumor immune response

Introduction: Cyclin-dependent kinases 4 and 6 (CDK4/6) inhibitors have demonstrated significant efficacy in clinical trials in a number of solid tumors, including breast cancer. In some cases, tumor regression has been observed. CDK4/6 inhibition induces G1 cell cycle arrest and causes cytostasis, but does not directly induce breast cancer cell apoptosis. Consequently, the mechanisms by which these drugs cause tumor regression are not fully understood. We therefore hypothesized that tumor extrinsic factors may play a role in the response to CDK4/6 inhibition.

Results: Consistent with clinical experience, treatment with the CDK4/6 inhibitor, abemaciclib, resulted in significant regression of bulky tumors in mice with Her2+ mammary carcinoma (MMTV-rtTA/tetO-Her2 transgenic mice). To explore mechanisms underlying this response, we evaluated the effects of abemaciclib therapy on intratumoral immune cell populations by flow cytometry. Abemaciclib treatment resulted in increased CD3+ T cells in these tumors, while decreasing the proportion of immunosuppressive regulatory T cells (Tregs). Reductions in infiltrating Tregs were also observed in MMTV-PyMT mammary tumors and CT-26 colon tumors from mice treated with abemaciclib. Interestingly, Treg depletion was also seen in spleens and lymph nodes of tumor-free mice treated with abemaciclib and was the result of selective inhibition of Treg proliferation.

Transcriptomic analysis of bulk tumor tissues revealed increased expression of antigen processing and presentation-related genes. In vitro treatment of cancer cell lines confirmed that CDK4/6 inhibition directly causes increased antigen presentation by tumor cells via MHC Class I, and these tumor cells were capable of stimulating T cell proliferation and IFNγ and TNFα production.

Tumor regression was no longer observed in response to abemaciclib when we depleted CD8+ T cells with a neutralizing antibody in the MMTV-rtTA/tetO-HER2 mice, indicating that cytotoxic T cells play a necessary role in the response of these tumors to CDK4/6 inhibitors. Furthermore, addition of anti-PDL1 immune checkpoint blockade further enhanced the depth and duration of response to CDK4/6 inhibition in both the MMTV-rtTA/tetO-HER2 and CT-26 models.

To confirm the clinical applicability of our findings, we analyzed transcriptomic data from serial biopsies obtained as part of a clinical trial of a CDK4/6 inhibitor in breast cancer patients. In concordance with our data from the MMTV-rtTA/tetO-HER2 mice, top-ranked GSEA signatures after 12 weeks of CDK4/6 inhibitor treatment included allograft rejection, inflammatory response, and interferon gamma response.

Conclusions: Our study has revealed a new, unexpected effect of CDK4/6 inhibition: the promotion of an anti-tumor immune response. This occurs through two mechanisms: selective depletion of regulatory T cells and increased tumor immunogenicity. These findings provide strong rationale for further explorations into combining CDK4/6 inhibition with immunotherapy as a treatment strategy for patients with solid tumors. Such combinations are of particular interest in breast oncology, where the benefits of immunotherapy have been limited thus far.

Citation Format: Molly J. DeCristo, Shom Goel, April C. Watt, Haley BrinJones, Jaclyn Sceneay, Ben B. Li, Naveed Khan, Jessalyn M. Ubellacker, Shaozhen Xie, Otto Metzger-Filho, Jeremy Hoog, Matthew J. Ellis, Cynthia Ma, Susanne Ramm, Ian E. Krop, Eric P. Winer, Thomas M. Roberts, Hye-Jung Kim, Jean J. Zhao, Sandra S. McAllister. CDK4/6 inhibition triggers an antitumor immune response [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B04.

Abstract B13: Plasma G-CSF levels are predictive of lack of response to zoledronic acid treatment in reducing breast cancer recurrence

Some breast cancer patients have no evidence of metastatic disease at the time of original diagnosis, yet ~30-40% of patients will experience recurrent breast cancer. Over 90% of breast cancer deaths occur due to distant spread of the disease, and bone is the most common site of breast cancer metastasis. Bisphosphonates, such as zoledronic acid (ZA), are used to treat patients with osteolytic disease, including metastatic breast cancer. ZA has been demonstrated to reduce disseminated tumor cells (DTCs) and breast cancer recurrence, but not all patients see this benefit and it is not yet clear what predicts benefit from adjuvant ZA treatment; the mechanism of action for this effect of ZA in reducing breast cancer remains undetermined. Here, we establish that ZA renders osteoclast progenitor cells (OCPs) tumor suppressive, primarily by directing their lineage potential. In instances where the OCP lineage potential was modulated via systemic or tumor-derived granulocyte-colony stimulating factor (G-CSF), OCPs did not differentiate into tumor-suppressive populations but instead into mature osteoclasts. High G-CSF was sufficient to abrogate the tumor-suppressive effect of ZA. Furthermore, we determined that in a subset of patient plasma samples from the AZURE clinical trial where stage II/III breast cancer patients were randomized to receive standard systemic treatment alone with adjuvant ZA treatment, patients who had baseline plasma G-CSF levels >23 pg/mL had reduced disease-free survival as assessed over a 10-year period post treatment initiation compared to patients with baseline plasma G-CSF levels <23 pg/mL (p=0.02). These findings indicate that patients with higher baseline plasma G-CSF levels will not likely observe reduction in breast cancer recurrence with adjuvant ZA treatment, and in fact may have worse prognosis with adjuvant ZA treatment as compared to control treatment. Our data are the first to demonstrate that ZA mediates its tumor-suppressive function via the OCP population and implicate capitalizing on the differentiation potential of the OCPs to maximize patient response to adjuvant ZA treatment in breast cancer risk of recurrence.

Citation Format: Jessalyn M. Ubellacker, Ninib Baryawno, Nicolas Severe, Molly J. DeCristo, Jaclyn Sceneay, Marie-Therese Haider, Catherine S. Rhee, Yuanbo Qin, Ingunn Holen, Walter M. Gregory, Janet E. Brown, Robert E. Coleman, David T. Scadden, Sandra S. McAllister. Plasma G-CSF levels are predictive of lack of response to zoledronic acid treatment in reducing breast cancer recurrence [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B13.

Modulating Bone Marrow Hematopoietic Lineage Potential to Prevent Bone Metastasis in Breast Cancer

The presence of disseminated tumor cells in breast cancer patient bone marrow aspirates predicts decreased recurrence-free survival. Although it is appreciated that physiologic, pathologic, and therapeutic conditions impact hematopoiesis, it remains unclear whether targeting hematopoiesis presents opportunities for limiting bone metastasis. Using preclinical breast cancer models, we discovered that marrow from mice treated with the bisphosphonate zoledronic acid (ZA) are metastasis-suppressive. Specifically, ZA modulated hematopoietic myeloid/osteoclast progenitor cell (M/OCP) lineage potential to activate metastasis-suppressive activity. Granulocyte-colony stimulating factor (G-CSF) promoted ZA resistance by redirecting M/OCP differentiation. We identified M/OCP and bone marrow transcriptional programs associated with metastasis suppression and ZA resistance. Analysis of patient blood samples taken at randomization revealed that women with high-plasma G-CSF experienced significantly worse outcome with adjuvant ZA than those with lower G-CSF levels. Our findings support discovery of therapeutic strategies to direct M/OCP lineage potential and biomarkers that stratify responses in patients at risk of recurrence.Significance: Bone marrow myeloid/osteoclast progenitor cell lineage potential has a profound impact on breast cancer bone metastasis and can be modulated by G-CSF and bone-targeting agents. Cancer Res; 78(18); 5300-14. ©2018 AACR.

Accounting for tumor heterogeneity when using CRISPR-Cas9 for cancer progression and drug sensitivity studies

Gene editing protocols often require the use of a subcloning step to isolate successfully edited cells, the behavior of which is then compared to the aggregate parental population and/or other non-edited subclones. Here we demonstrate that the inherent functional heterogeneity present in many cell lines can render these populations inappropriate controls, resulting in erroneous interpretations of experimental findings. We describe a novel CRISPR/Cas9 protocol that incorporates a single-cell cloning step prior to gene editing, allowing for the generation of appropriately matched, functionally equivalent control and edited cell lines. As a proof of concept, we generated matched control and osteopontin-knockout Her2+ and Estrogen receptor-negative murine mammary carcinoma cell lines and demonstrated that the osteopontin-knockout cell lines exhibit the expected biological phenotypes, including unaffected primary tumor growth kinetics and reduced metastatic outgrowth in female FVB mice. Using these matched cell lines, we discovered that osteopontin-knockout mammary tumors were more sensitive than control tumors to chemotherapy in vivo. Our results demonstrate that heterogeneity must be considered during experimental design when utilizing gene editing protocols and provide a solution to account for it.

Zoledronic acid alters hematopoiesis and generates breast tumor-suppressive bone marrow cells

BACKGROUND

The bone-targeting agent zoledronic acid (ZOL) increases breast cancer survival in subsets of patients, but the underlying reasons for this protective effect are unknown. ZOL modulates the activity of osteoclasts and osteoblasts, which form hematopoietic stem cell niches, and therefore may affect hematopoietic cells that play a role in breast cancer progression.

METHOD

Immunocompetent and immunocompromised strains of mice commonly used for breast cancer research were injected with a single, clinically relevant dose of ZOL (100 μg/kg) or vehicle control. The effects of ZOL on the bone marrow microenvironment (bone volume, bone cell number/activity, extracellular matrix composition) were established at various time points following treatment, using micro-computed tomography (μCT) analysis, histomorphometry, ELISA and immunofluorescence. The effects on peripheral blood and bone marrow hematopoietic progenitor populations were assessed using a HEMAVET® hematology analyzer and multicolor flow cytometry, respectively. Tumor support function of bone marrow cells was determined using an in vivo functional assay developed in our laboratory.

RESULTS

Using multiple mouse strains, we observed transient changes in numbers of hematopoietic stem cells, myeloid-biased progenitor cells, and lymphoid-biased cells concurrent with changes to hematopoietic stem cell niches following ZOL administration. Importantly, bone marrow cells from mice treated with a single, clinically relevant dose of ZOL inhibited breast tumor outgrowth in vivo. The ZOL-induced tumor suppressive function of the bone marrow persisted beyond the time point at which numbers of hematopoietic progenitor cells had returned to baseline.

CONCLUSIONS

These findings provide novel evidence that alterations to the bone marrow play a role in the anti-tumor activity of ZOL and suggest possibilities for capitalizing on the beneficial effects of ZOL in reducing breast cancer development and progression.

Abstract A66: Systemic effects of AC-T chemotherapy in breast cancer

Cytotoxic chemotherapy is the only standard of care treatment currently available for patients with triple negative breast cancer (TNBC) because this breast cancer subtype lacks expression of therapeutic targets, namely, estrogen receptor, progesterone receptor, and amplification of Her2. Despite the efficacy of neoadjuvant chemotherapy for some TNBC patients, approximately 60-80% of TNBC patients will still present with local and distant disease after therapy, and these patients suffer poor prognosis. In addition to direct effects on tumor cells, systemic chemotherapy also has the potential to impact patient physiology. However, the implications of tumor-cell independent effects of chemotherapy for metastatic progression are not well understood. We are using mouse models of TNBC to study the effects of chemotherapy on host physiology and how these effects impact metastasis. Treatment of TNBC tumor-bearing mice with doxorubicin (A), cyclophosphamide (C), and paclitaxel (T) decreased overall bone marrow cell counts; although, the degree of decrease and subsequent recovery of individual bone marrow and circulating cell populations varied among populations. Notably, parallel experiments in tumor-free mice demonstrated that chemotherapy-dependent effects on the bone marrow and circulating cell populations dominate tumor-dependent effects. These findings highlight the potential implications of the physiological effects of chemotherapy on metastasis and response to therapy.

Citation Format: Molly J. DeCristo, Sandra S. McAllister. Systemic effects of AC-T chemotherapy in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr A66.

Redox regulation of Rac1 by thiol oxidation

The Rac1 GTPase is an essential and ubiquitous protein that signals through numerous pathways to control critical cellular processes, including cell growth, morphology, and motility. Rac1 deletion is embryonic lethal, and its dysregulation or mutation can promote cancer, arthritis, cardiovascular disease, and neurological disorders. Rac1 activity is highly regulated by modulatory proteins and posttranslational modifications. Whereas much attention has been devoted to guanine nucleotide exchange factors that act on Rac1 to promote GTP loading and Rac1 activation, cellular oxidants may also regulate Rac1 activation by promoting guanine nucleotide exchange. Herein, we show that Rac1 contains a redox-sensitive cysteine (Cys(18)) that can be selectively oxidized at physiological pH because of its lowered pKa. Consistent with these observations, we show that Rac1 is glutathiolated in primary chondrocytes. Oxidation of Cys(18) by glutathione greatly perturbs Rac1 guanine nucleotide binding and promotes nucleotide exchange. As aspartate substitutions have been previously used to mimic cysteine oxidation, we characterized the biochemical properties of Rac1(C18D). We also evaluated Rac1(C18S) as a redox-insensitive variant and found that it retains structural and biochemical properties similar to those of Rac1(WT) but is resistant to thiol oxidation. In addition, Rac1(C18D), but not Rac1(C18S), shows greatly enhanced nucleotide exchange, similar to that observed for Rac1 oxidation by glutathione. We employed Rac1(C18D) in cell-based studies to assess whether this fast-cycling variant, which mimics Rac1 oxidation by glutathione, affects Rac1 activity and function. Expression of Rac1(C18D) in Swiss 3T3 cells showed greatly enhanced GTP-bound Rac1 relative to Rac1(WT) and the redox-insensitive Rac1(C18S) variant. Moreover, expression of Rac1(C18D) in HEK-293T cells greatly promoted lamellipodia formation. Our results suggest that Rac1 oxidation at Cys(18) is a novel posttranslational modification that upregulates Rac1 activity.

Effector recruitment method to study spatially regulated activation of Ras and Rho GTPases

Ras and Rho family GTPases control a wide variety of cellular processes, and the signaling downstream of these GTPases is influenced by their subcellular localization when activated. Since only a minority of total cellular GTPases is active, observation of the total subcellular distribution of GTPases does not reveal where active GTPases are localized. In this chapter, we describe the use of effector recruitment assays to monitor the subcellular localization of active Ras and Rho family GTPases. The recruitment assay relies on preferential binding of downstream effectors to active GTPases versus inactive GTPases. Tagging the GTPase-binding-domain (GBD) of a downstream effector with a fluorescent protein produces a probe that is recruited to compartments where GTPases are active. We describe an example of a recruitment assay using the GBD of PAK1 to monitor Rac1 activity and explain how the assay can be expanded to determine the subcellular localization of activation of other GTPases.

Abstract LB-30: A functional analysis of the nuclear RhoGEF Ect2 in ovarian cancer

Ect2 is a guanine nucleotide exchange factor (GEF) and activator of Rho family small GTPases. Ect2 regulates RhoA, Rac1, and Cdc42, thereby playing an important role in the control of cell proliferation, survival, and migration. Originally identified as an oncogene in vitro, the role of Ect2 in regulating migration makes it of particular interest in ovarian cancer, in which local invasion and ascites are prevalent. Notably, ECT2 is located on 3q26.1-3q26.2, the most frequent amplicon in ovarian cancer, and it has been found to be overexpressed at the mRNA level in ovarian tumors. We first explored the role of Ect2 in ovarian cancer by knocking it down using shRNA and assessing anchorage-independent growth and both random and directed migration in a panel of ovarian cancer cell lines. Our findings reveal that Ect2 expression is required for each of these functions. Interestingly, we found that Ect2 utilization of specific Rho GTPase substrates is highly context-dependent. In addition, to investigate the potential clinical importance of Ect2, we studied its expression and localization in primary epithelial ovarian cancers, using over 300 histological tumor and cyst samples incorporated into a tissue microarray (TMA). Ect2 is unusual among the RhoGEFs because of its localization. A critical regulator of cytokinesis, it is sequestered to the nucleus in interphase cells. It has been hypothesized that the overexpression and mislocalization of Ect2 into the cytoplasm leads to aberrant Rho activation and oncogenesis. Unexpectedly, our recently completed TMA data analysis suggests that malignant serous ovarian cancer is instead associated with nuclear Ect2, while benign disease is associated with mislocalized, cytosolic Ect2. We are currently exploring a possible nuclear mechanism to explain these findings. Although standard immunohistochemical analyses typically report only total protein levels, our new data reveal that unrestricted subcellular localization of Ect2 is likely to be more important than total protein levels for ovarian pathology.

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 LB-30. doi:1538-7445.AM2012-LB-30