STAT3 protects hematopoietic stem cells by preventing activation of a deleterious autocrine type-I interferon response

Hematopoietic stem and progenitor cells (HSPCs) maintain blood-forming and immune activity, yet intrinsic regulators of HSPCs remain elusive. STAT3 function in HSPCs has been difficult to dissect as Stat3-deficiency in the hematopoietic compartment induces systemic inflammation, which can impact HSPC activity. Here, we developed mixed bone marrow (BM) chimeric mice with inducible Stat3 deletion in 20% of the hematopoietic compartment to avoid systemic inflammation. Stat3-deficient HSPCs were significantly impaired in reconstitution ability following primary or secondary bone marrow transplantation, indicating hematopoietic stem cell (HSC) defects. Single-cell RNA sequencing of Lin-ckit+Sca1+ BM cells (LSKs) revealed aberrant activation of cell cycle, p53, and interferon (IFN) pathways in Stat3-deficient HSPCs. Stat3-deficient LSKs accumulated γH2AX and showed increased expression of DNA sensors and type-I IFN (IFN-I), while treatment with A151-ODN inhibited expression of IFN-I and IFN-responsive genes. Further, the blockade of IFN-I receptor signaling suppressed aberrant cell cycling, STAT1 activation, and nuclear p53 accumulation. Collectively, our results show that STAT3 inhibits a deleterious autocrine IFN response in HSCs to maintain long-term HSC function. These data signify the importance of ensuring therapeutic STAT3 inhibitors are targeted specifically to diseased cells to avoid off-target loss of healthy HSPCs.

Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis

Metastatic disease remains the leading cause of death due to cancer, yet the mechanism(s) of metastasis and its timely detection remain to be elucidated. Neutrophil elastase (NE), a serine protease secreted by neutrophils, is a crucial mediator of chronic inflammation and tumor progression. In this study, we used the PyMT model (NE+/+ and NE-/-) of breast cancer to interrogate the tumor-intrinsic and -extrinsic mechanisms by which NE can promote metastasis. Our results showed that genetic ablation of NE significantly reduced lung metastasis and improved metastasis-free survival. RNA-sequencing analysis of primary tumors indicated differential regulation of tumor-intrinsic actin cytoskeleton signaling pathways by NE. These NE-regulated pathways are critical for cell-to-cell contact and motility and consistent with the delay in metastasis in NE-/- mice. To evaluate whether pharmacologic inhibition of NE inhibited pulmonary metastasis and phenotypically mimicked PyMT NE-/- mice, we utilized AZD9668, a clinically available and specific NE inhibitor. We found AZD9668 treated PyMT-NE+/+ mice showed significantly reduced lung metastases, improved recurrence-free, metastasis-free and overall survival, and their tumors showed similar molecular alterations as those observed in PyMT-NE-/- tumors. Finally, we identified a NE-specific signature that predicts recurrence and metastasis in patients with breast cancer. Collectively, our studies suggest that genetic ablation and pharmacologic inhibition of NE reduces metastasis and extends survival of mouse models of breast cancer, providing rationale to examine NE inhibitors as a treatment strategy for the clinical management of patients with metastatic breast cancer.

Exploring Novel Frontiers: Leveraging STAT3 Signaling for Advanced Cancer Therapeutics

Signal Transducer and Activator of Transcription 3 (STAT3) plays a significant role in diverse physiologic processes, including cell proliferation, differentiation, angiogenesis, and survival. STAT3 activation via phosphorylation of tyrosine and serine residues is a complex and tightly regulated process initiated by upstream signaling pathways with ligand binding to receptor and non-receptor-linked kinases. Through downstream deregulation of target genes, aberrations in STAT3 activation are implicated in tumorigenesis, metastasis, and recurrence in multiple cancers. While there have been extensive efforts to develop direct and indirect STAT3 inhibitors using novel drugs as a therapeutic strategy, direct clinical application remains in evolution. In this review, we outline the mechanisms of STAT3 activation, the resulting downstream effects in physiologic and malignant settings, and therapeutic strategies for targeting STAT3. We also summarize the pre-clinical and clinical evidence of novel drug therapies targeting STAT3 and discuss the challenges of establishing their therapeutic efficacy in the current clinical landscape.

Cell cycle arrest induces lipid droplet formation and confers ferroptosis resistance

How cells coordinate cell cycling with cell survival and death remains incompletely understood. Here, we show that cell cycle arrest has a potent suppressive effect on ferroptosis, a form of regulated cell death induced by overwhelming lipid peroxidation at cellular membranes. Mechanistically, cell cycle arrest induces diacylglycerol acyltransferase (DGAT)-dependent lipid droplet formation to sequester excessive polyunsaturated fatty acids (PUFAs) that accumulate in arrested cells in triacylglycerols (TAGs), resulting in ferroptosis suppression. Consequently, DGAT inhibition orchestrates a reshuffling of PUFAs from TAGs to phospholipids and re-sensitizes arrested cells to ferroptosis. We show that some slow-cycling antimitotic drug-resistant cancer cells, such as 5-fluorouracil-resistant cells, have accumulation of lipid droplets and that combined treatment with ferroptosis inducers and DGAT inhibitors effectively suppresses the growth of 5-fluorouracil-resistant tumors by inducing ferroptosis. Together, these results reveal a role for cell cycle arrest in driving ferroptosis resistance and suggest a ferroptosis-inducing therapeutic strategy to target slow-cycling therapy-resistant cancers.

Adavosertib Enhances Antitumor Activity of Trastuzumab Deruxtecan in HER2-Expressing Cancers

PURPOSE

Cyclin E (CCNE1) has been proposed as a biomarker of sensitivity to adavosertib, a Wee1 kinase inhibitor, and a mechanism of resistance to HER2-targeted therapy.

EXPERIMENTAL DESIGN

Copy number and genomic sequencing data from The Cancer Genome Atlas and MD Anderson Cancer Center databases were analyzed to assess ERBB2 and CCNE1 expression. Molecular characteristics of tumors and patient-derived xenografts (PDX) were assessed by next-generation sequencing, whole-exome sequencing, fluorescent in situ hybridization, and IHC. In vitro, CCNE1 was overexpressed or knocked down in HER2+ cell lines to evaluate drug combination efficacy. In vivo, NSG mice bearing PDXs were subjected to combinatorial therapy with various treatment regimens, followed by tumor growth assessment. Pharmacodynamic markers in PDXs were characterized by IHC and reverse-phase protein array.

RESULTS

Among several ERBB2-amplified cancers, CCNE1 co-amplification was identified (gastric 37%, endometroid 43%, and ovarian serous adenocarcinoma 41%). We hypothesized that adavosertib may enhance activity of HER2 antibody-drug conjugate trastuzumab deruxtecan (T-DXd). In vitro, sensitivity to T-DXd was decreased by cyclin E overexpression and increased by knockdown, and adavosertib was synergistic with topoisomerase I inhibitor DXd. In vivo, the T-DXd + adavosertib combination significantly increased γH2AX and antitumor activity in HER2 low, cyclin E amplified gastroesophageal cancer PDX models and prolonged event-free survival (EFS) in a HER2-overexpressing gastroesophageal cancer model. T-DXd + adavosertib treatment also increased EFS in other HER2-expressing tumor types, including a T-DXd-treated colon cancer model.

CONCLUSIONS

We provide rationale for combining T-DXd with adavosertib in HER2-expressing cancers, especially with co-occuring CCNE1 amplifications. See related commentary by Rolfo et al., p. 4317.

Distinct Mechanisms of Resistance to CDK4/6 Inhibitors Require Specific Subsequent Treatment Strategies: One Size Does Not Fit All

Cyclin-dependent kinase (CDK) 4/6 inhibitors have transformed the treatment landscape of patients with hormone receptor-positive breast cancers. However, despite improvements in clinical outcomes, the approximately 70% of patients with tumors that are not intrinsically resistant to a CDK4/6 inhibitor still ultimately acquire resistance, which leads to a dilemma for clinicians when deciding which treatment to offer patients when they demonstrate disease progression on a CDK4/6 inhibitor. As such, many groups have sought to understand the mechanisms of resistance to CDK4/6 inhibitors, mostly focusing on genetic alterations associated with resistance. Though several recurrent mutations have been described, they are not consistent enough to guide clinical practice or generate novel rational treatment options. Two recent publications have used transcriptomic analysis to unravel distinct mechanisms driving resistance to individual CDK4/6 inhibitors and in doing so have identified biomarkers that could potentially help identify the next course of treatment for patients following disease progression.

Abemaciclib Is Effective in Palbociclib-Resistant Hormone Receptor-Positive Metastatic Breast Cancers

Cyclin-dependent kinases 4/6 inhibitor (CDK4/6i) plus endocrine therapy (ET) is standard of care for patients with hormone receptor (HR)-positive, HER2-negative metastatic breast cancer (MBC). However, resistance to CDK4/6is plus ET remains a clinical problem with limited therapeutic options following disease progression. Different CDK4/6is might have distinct mechanisms of resistance, and therefore using them sequentially or targeting their differentially altered pathways could delay disease progression. To understand pathways leading to resistance to the CDK4/6is palbociclib and abemaciclib, we generated multiple in vitro models of palbociclib-resistant (PR) and abemaciclib-resistant (AR) cell lines as well as in vivo patient-derived xenografts (PDX) and ex vivo PDX-derived organoids (PDxO) from patients who progressed on CDK4/6i. PR and AR breast cancer cells exhibited distinct transcriptomic and proteomic profiles that sensitized them to different classes of inhibitors; PR cells upregulated G2-M pathways and responded to abemaciclib, while AR cells upregulated mediators of the oxidative phosphorylation pathway (OXPHOS) and responded to OXPHOS inhibitors. PDX and organoid models derived from patients with PR breast cancer remained responsive to abemaciclib. Resistance to palbociclib while maintaining sensitivity to abemaciclib was associated with pathway-specific transcriptional activity but was not associated with any individual genetic alterations. Finally, data from a cohort of 52 patients indicated that patients with HR-positive/HER2-negative MBC who progressed on palbociclib-containing regimens can exhibit a meaningful overall clinical benefit from abemaciclib-based therapy when administered after palbociclib. These findings provide the rationale for clinical trials evaluating the benefit of abemaciclib treatment following progression on a prior CDK4/6i.

SIGNIFICANCE

Palbociclib-resistant breast cancers respond to abemaciclib and express pathway-specific signatures of sensitivity, providing a biomarker-driven therapeutic option for patients with metastatic breast cancer following disease progression on cyclin-dependent kinases 4/6 inhibitors.

Evaluation of Alisertib Alone or Combined With Fulvestrant in Patients With Endocrine-Resistant Advanced Breast Cancer: The Phase 2 TBCRC041 Randomized Clinical Trial

Importance

Aurora A kinase (AURKA) activation, related in part to AURKA amplification and variants, is associated with downregulation of estrogen receptor (ER) α expression, endocrine resistance, and implicated in cyclin-dependent kinase 4/6 inhibitor (CDK 4/6i) resistance. Alisertib, a selective AURKA inhibitor, upregulates ERα and restores endocrine sensitivity in preclinical metastatic breast cancer (MBC) models. The safety and preliminary efficacy of alisertib was demonstrated in early-phase trials; however, its activity in CDK 4/6i-resistant MBC is unknown.

Objective

To assess the effect of adding fulvestrant to alisertib on objective tumor response rates (ORRs) in endocrine-resistant MBC.

Design, Setting, and Participants

This phase 2 randomized clinical trial was conducted through the Translational Breast Cancer Research Consortium, which enrolled participants from July 2017 to November 2019. Postmenopausal women with endocrine-resistant, ERBB2 (formerly HER2)-negative MBC who were previously treated with fulvestrant were eligible. Stratification factors included prior treatment with CDK 4/6i, baseline metastatic tumor ERα level measurement (<10%, ≥10%), and primary or secondary endocrine resistance. Among 114 preregistered patients, 96 (84.2%) registered and 91 (79.8%) were evaluable for the primary end point. Data analysis began after January 10, 2022.

Interventions

Alisertib, 50 mg, oral, daily on days 1 to 3, 8 to 10, and 15 to 17 of a 28-day cycle (arm 1) or alisertib same dose/schedule with standard-dose fulvestrant (arm 2).

Main Outcomes and Measures

Improvement in ORR in arm 2 of at least 20% greater than arm 1 when the expected ORR for arm 1 was 20%.

Results

All 91 evaluable patients (mean [SD] age, 58.5 [11.3] years; 1 American Indian/Alaskan Native [1.1%], 2 Asian [2.2%], 6 Black/African American [6.6%], 5 Hispanic [5.5%], and 79 [86.8%] White individuals; arm 1, 46 [50.5%]; arm 2, 45 [49.5%]) had received prior treatment with CDK 4/6i. The ORR was 19.6%; (90% CI, 10.6%-31.7%) for arm 1 and 20.0% (90% CI, 10.9%-32.3%) for arm 2. In arm 1, the 24-week clinical benefit rate and median progression-free survival time were 41.3% (90% CI, 29.0%-54.5%) and 5.6 months (95% CI, 3.9-10.0), respectively, and in arm 2 they were 28.9% (90% CI, 18.0%-42.0%) and 5.4 months (95% CI, 3.9-7.8), respectively. The most common grade 3 or higher adverse events attributed to alisertib were neutropenia (41.8%) and anemia (13.2%). Reasons for discontinuing treatment were disease progression (arm 1, 38 [82.6%]; arm 2, 31 [68.9%]) and toxic effects or refusal (arm 1, 5 [10.9%]; arm 2, 12 [26.7%]).

Conclusions and Relevance

This randomized clinical trial found that adding fulvestrant to treatment with alisertib did not increase ORR or PFS; however, promising clinical activity was observed with alisertib monotherapy among patients with endocrine-resistant and CDK 4/6i-resistant MBC. The overall safety profile was tolerable.

Trial Registration

ClinicalTrials.gov Identifier: NCT02860000.

Abstract 308: Low molecular weight cyclin E deregulates DNA replication and damage repair to promote genomic instability in breast cancer

Background: Low molecular weight cyclin E (LMW-E) are oncogenic forms of cyclin E that are post translationally generated from the full-length cyclin E1 (FL-cycE). LMW-E is detected in breast cancer cells and tumor tissues, but not in normal mammary epithelial cells or adjacent normal tissues. Unlike FL-cycE, LMW-E drives mammary epithelial cell transformation in human cells and spontaneous mammary tumor formation in transgenic mouse models, but the oncogenic mechanisms of LMW-E and its unique function(s) independent of FL-cycE are not fully understood. It is currently assumed that LMW-E drives the tumorigenic process by promoting G1/S cell cycle transition and accelerating mitotic exit. Biochemical features such as longer protein half-life, higher affinity to its kinase partner CDK2, and resistance to endogenous CDK inhibitors such as p21 and p27 all promote the tumorigenic ability of LMW-E. Clinical studies in breast cancer reveal that overexpression of LMW-E predicts recurrence and poor survival in breast cancer patients independent of molecular subtype, Ki67 status, nodal status, or tumor grade, suggesting LMW-E may drive breast cancer development independent of its role in cell proliferation. In the current study, we tested the hypothesis that LMW-E promotes genomic instability by deregulating DNA replication and damage repair.

Results: We generated immortalized pre-cancerous human mammary epithelial cells (hMECs) to express doxycycline inducible LMW-E or FL-cycE in CCNE1 knock-out background. We found that FL-cycE overexpression led to DNA replication stress and DNA damage accumulation, resulting in reduced cell viability. LMW-E overexpression, on the other hand, promoted cell survival under replication stress, resulting in persistent genomic instability. RNA-sequencing results showed LMW-E but not FL-cycE overexpression enhanced DNA replication and damage repair pathways. Molecularly, LMW-E interacted with and facilitated pre-replication complex assembly. LMW-E also mediated DNA repair by upregulating RAD51 and C17orf53, showing a dominant repairing effect over DNA damage induced by FL-cycE. Moreover, targeting the replication stress response pathway ATR-CHK1-RAD51 with small molecule inhibitors significantly decreased viability of LMW-E overexpressing hMECs and breast cancer cells. Lastly, we showed that positive LMW-E status was associated with genomic instability in tumors from a cohort of 725 patients diagnosed with early-stage breast cancer, further supporting our hypothesis that LMW-E promotes genomic instability to fuel breast cancer development.

Conclusions: Collectively, our findings delineated a novel role for LMW-E in breast tumorigenesis mediated by replication stress tolerance and genomic instability, providing novel therapeutic strategies for LMW-E overexpressing breast cancers.

Citation Format: Mi Li, Spiridon Tsavachidis, Fuchenchu Wang, Tuyen Bui, Tuyen D. Nguyen, Linjie Luo, Asha S. Multani, Melissa L. Bondy, Kelly K. Hunt, Khandan Keyomarsi. Low molecular weight cyclin E deregulates DNA replication and damage repair to promote genomic instability in breast cancer [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 308.

Abstract 950: Targeting PKMYT1 kinase is an effective treatment strategy in triple negative breast cancers with low molecular weight cyclin E (LMW-E) expression

Background: Cyclin E is post-translationally modified by neutrophil elastase mediated proteolytic cleavage to generate the low molecular weight isoforms of cyclin E (LMW-E) that are detected in various human cancers. We previously reported that 70% of triple negative breast cancers (TNBC) examined overexpress LMW-E, and these patients have a poor prognosis. Expression of LMW-E promotes genomic instability by causing DNA replication stress. PKMYT1 prevents premature mitotic entry by catalyzing CDK1 phosphorylation at T14, essential for preventing DNA damage and cell death when cyclin E, including LMW-E, is overexpressed. In this study, we tested the hypothesis that LMW-E positive status can be used as a biomarker of response in selecting TNBC patients who are likely to respond to RP-6306, a first in-class and selective inhibitor of PKMYT1 kinase.

Results: Assessment of pre-treatment breast biopsies from TNBC patients (n=40) enrolled in a neoadjuvant chemotherapy prospective study for LMW-E and CDK1-pT14 revealed significant positive correlation between these two proteins. Furthermore, positivity of both biomarkers was associated with lack of pathologic complete response (pCR) to neoadjuvant chemotherapy. We next examined the mechanism of response to RP-6306 in vitro and in vivo using TNBC cell lines, patient-derived xenograft (PDX) models and transgenic mouse mammary tumor virus (MMTV) models expressing human LMW-E (hLMW-E). In vitro results using 7 different TNBC cell lines, revealed that high LMW-E levels are significantly predictive of response to RP-6306 (R2=0.78, p= 0.008), while LMW-E knockdown resulted in a 7X increase in IC50 values of RP-6306 (p&lt;0.001). In high LMW-E cells, treatment with RP-6306 resulted in significant (i) downregulation of CDK1-pT14, PKMYT1, WEE1, cyclin B and pRb, (ii) accumulation of sub-G1 and polyploid cell population, (iii) apoptosis, (iv) accumulation of chromosomal breakage, (v) increased DNA damage (increase in γ-H2AX and 53BP1 foci/cell) and lack of DNA repair (downregulation of Rad51), and (vi) premature mitotic entry. Treatment of both breast cancer PDX models and hLMW-E transgenic tumors with RP-6306 revealed that only in animals with high LMW-E tumors, treatment results in significant decrease in tumor volume. However, RP-6306 was ineffective in reducing tumor volume in low cyclin E in vivo models. Immunohistochemical analysis revealed that in vivo efficacy of RP-6306 (in both PDX and transgenic models) was concomitant with increase in γ-H2AX and decrease in CDK1-pT14 and Ki67.

Conclusion: Collectively, our results show that overexpression of LMW-E and CDK1-pT14 in TNBC can be used to stratify patients whose tumors are likely to respond to RP-6306. Mechanistically, LMW-E overexpressing TNBC cells activate CDK1 (in vitro and in vivo) to accelerate premature mitotic entry, leading to DNA damage and apoptosis.

Citation Format: Amriti Lulla, Tuyen D. Nguyen, Mi Li, Sofia Mastoraki, Yan Wang, Tuyen Bui, Marc Pina, Spiridon Tsavachidis, Gary Marshall, Kelly K. Hunt, Khandan Keyomarsi. Targeting PKMYT1 kinase is an effective treatment strategy in triple negative breast cancers with low molecular weight cyclin E (LMW-E) expression [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 950.

Abstract 4346: TFF1 and TFF3 predict response to CDK4/6 inhibitors in breast cancer patients

Background: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) in combination with endocrine therapy (ET) have become the mainstay treatment for patients with hormone receptor (ER)-positive, HER2-negative metastatic breast cancer (BC). However, one-third of patients do not respond to the treatment (intrinsic resistance), leading to early tumor progression and treatment failure, and most patients eventually acquire resistance to therapy. The exact mechanisms of resistance to CDK4/6i are yet to be elucidated, and due to subsequent early (intrinsic) or late progression on CDK4/6i, long-term cures are not achieved.

Methods: Transcriptomic profiles of BC cell lines that were sensitive or resistant to approved CDK4/6i, independent of subtype, were downloaded from the Cancer Cell Line Encyclopedia database. Bioinformatics analysis was performed by integrated Differential Expression and Pathway (iDEP) workflow. In parallel, transcriptomic profiles of metastatic biopsies from pre-CDK4/6i-treated BC patients (n = 54) were generated using RNA-Access technology. Key common biomarkers identified from the BC cell lines and patient tumor samples were validated by immunohistochemistry in formalin-fixed paraffin-embedded (FFPE) metastatic specimens from 73 patients prior to CDK4/6i therapy.

Results: Transcriptomic profile comparisons of BC cell lines (n = 35) that were sensitive versus resistant to CDK4/6is identified Trefoil Factor 1 and 3 (TFF1 and TFF3) secretory proteins as top predictors of response. Correlation analysis showed a strong negative correlation between TFF1 and TFF3 levels to IC50 values of palbociclib and abemaciclib. Knockdown of TFF3 in CDK4/6i-sensitive BT20 cells with shRNA induced drug resistance in the cells. Transcriptomic data from 54 BC patients pre-treated with CDK4/6i showed the expression levels of TFF1 and TFF1/3 receptors (CCR4 and CCR7) were significantly increased in patients who developed late progression (&gt; 6 months) compared to early progressors (&lt; 3 months). In addition, IHC analysis of TFF1 and TFF3 expressions in 73 pre-treated BC patient samples showed significantly higher protein expression levels in late progressors than in early progressors.

Conclusions: Our results identified and validated the common biomarkers, TFF1 and TFF3, as predictors of CDK4/6i response efficacy in ER-positive, HER2-negative BC patients. These findings provide a predictive tool capable of selecting de novo metastatic BC patients who will have the greatest benefit from the combination of CDK4/6i with endocrine treatment. Furthermore, our discovery of biomarkers in early versus late progression on CDK4/6i therapy will enable new therapeutic avenues and provide the rationale for future large-scale clinical trials.

Citation Format: Linjie Luo, Yan Wang, Sophia Mastoraki, Akshara Singareeka Raghavendra, Juliana Navarro-Yepes, Nicole M. Kettner, Serena Kim, Debasish Tripathy, Kelly Hunt, Khandan Keyomarsi. TFF1 and TFF3 predict response to CDK4/6 inhibitors in breast cancer patients. [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 4346.

Multicenter Phase II Trial of the WEE1 Inhibitor Adavosertib in Refractory Solid Tumors Harboring CCNE1 Amplification

PURPOSE

Preclinical cancer models harboring CCNE1 amplification were more sensitive to adavosertib treatment, a WEE1 kinase inhibitor, than models without amplification. Thus, we conducted this phase II study to assess the antitumor activity of adavosertib in patients with CCNE1-amplified, advanced refractory solid tumors.

PATIENTS AND METHODS

Patients aged ≥ 18 years with measurable disease and refractory solid tumors harboring CCNE1 amplification, an Eastern Cooperative Oncology Group performance status of 0-1, and adequate organ function were studied. Patients received 300 mg of adavosertib once daily on days 1 through 5 and 8 through 12 of a 21-day cycle. The trial followed Bayesian optimal phase II design. The primary end point was objective response rate (ORR).

RESULTS

Thirty patients were enrolled. The median follow-up duration was 9.9 months. Eight patients had partial responses (PRs), and three had stable disease (SD) ≥ 6 months, with an ORR of 27% (95% CI, 12 to 46), a SD ≥ 6 months/PR rate of 37% (95% CI, 20 to 56), a median progression-free survival duration of 4.1 months (95% CI, 1.8 to 6.4), and a median overall survival duration of 9.9 months (95% CI, 4.8 to 15). Fourteen patients with epithelial ovarian cancer showed an ORR of 36% (95% CI, 13 to 65) and SD ≥ 6 months/PR of 57% (95% CI, 29 to 82), a median progression-free survival duration of 6.3 months (95% CI, 2.4 to 10.2), and a median overall survival duration of 14.9 months (95% CI, 8.9 to 20.9). Common treatment-related toxicities were GI, hematologic toxicities, and fatigue.

CONCLUSION

Adavosertib monotherapy demonstrates a manageable toxicity profile and promising clinical activity in refractory solid tumors harboring CCNE1 amplification, especially in epithelial ovarian cancer. Further study of adavosertib, alone or in combination with other therapeutic agents, in CCNE1-amplified epithelial ovarian cancer is warranted.

Sequential Targeting of Retinoblastoma and DNA Synthesis Pathways Is a Therapeutic Strategy for Sarcomas That Can Be Monitored in Real Time

Treatment strategies with a strong scientific rationale based on specific biomarkers are needed to improve outcomes in patients with advanced sarcomas. Suppression of cell-cycle progression through reactivation of the tumor suppressor retinoblastoma (Rb) using CDK4/6 inhibitors is a potential avenue for novel targeted therapies in sarcomas that harbor intact Rb signaling. Here, we evaluated combination treatment strategies (sequential and concomitant) with the CDK4/6 inhibitor abemacicib to identify optimal combination strategies. Expression of Rb was examined in 1,043 sarcoma tumor specimens, and 50% were found to be Rb-positive. Using in vitro and in vivo models, an effective two-step sequential combination strategy was developed. Abemaciclib was used first to prime Rb-positive sarcoma cells to reversibly arrest in G1 phase. Upon drug removal, cells synchronously traversed to S phase, where a second treatment with S-phase targeted agents (gemcitabine or Wee1 kinase inhibitor) mediated a synergistic response by inducing DNA damage. The response to treatment could be noninvasively monitored using real-time positron emission tomography imaging and serum thymidine kinase activity. Collectively, these results show that a novel, sequential treatment strategy with a CDK4/6 inhibitor followed by a DNA-damaging agent was effective, resulting in synergistic tumor cell killing. This approach can be readily translated into a clinical trial with noninvasive functional imaging and serum biomarkers as indicators of response and cell cycling.

SIGNIFICANCE

An innovative sequential therapeutic strategy targeting Rb, followed by treatment with agents that perturb DNA synthesis pathways, results in synergistic killing of Rb-positive sarcomas that can be noninvasively monitored.

CHD1 Promotes Sensitivity to Aurora Kinase Inhibitors by Suppressing Interaction of AURKA with Its Coactivator TPX2

Clinical studies have shown that subsets of patients with cancer achieve a significant benefit from Aurora kinase inhibitors, suggesting an urgent need to identify biomarkers for predicting drug response. Chromodomain helicase DNA binding protein 1 (CHD1) is involved in chromatin remodeling, DNA repair, and transcriptional plasticity. Prior studies have demonstrated that CHD1 has distinct expression patterns in cancers with different molecular features, but its impact on drug responsiveness remains understudied. Here, we show that CHD1 promotes the susceptibility of prostate cancer cells to inhibitors targeting Aurora kinases, while depletion of CHD1 impairs their efficacy in vitro and in vivo. Pan-cancer drug sensitivity analyses revealed that high expression of CHD1 was associated with increased sensitivity to Aurora kinase A (AURKA) inhibitors. Mechanistically, KPNA2 served as a direct target of CHD1 and suppressed the interaction of AURKA with the coactivator TPX2, thereby rendering cancer cells more vulnerable to AURKA inhibitors. Consistent with previous research reporting that loss of PTEN elevates CHD1 levels, studies in a genetically engineered mouse model, patient-derived organoids, and patient samples showed that PTEN defects are associated with a better response to AURKA inhibition in advanced prostate cancer. These observations demonstrate that CHD1 plays an important role in modulating Aurora kinases and drug sensitivities, providing new insights into biomarker-driven therapies targeting Aurora kinases for future clinical studies.

SIGNIFICANCE

CHD1 plays a critical role in controlling AURKA activation and promoting Aurora kinase inhibitor sensitivity, providing a potential clinical biomarker to guide cancer treatment.

Abstract 3107: Identifying therapeutic vulnerabilities in HR-positive, HER2-negative advanced breast cancer patient-derived xenograft models refractory to CDK4/6 inhibition

Background: Clinically, the addition of CDK4/6 inhibitors (e.g. palbociclib) to endocrine therapy (ET) significantly delays progression of advanced hormone receptor-positive (HR+), HER2-negative (HER2-) breast cancer patients. However, most patients develop resistance and progress following long-term treatment. Thus, an ongoing clinical challenge has been the identification of biomarkers that predict response to CDK4/6 inhibitors. There is also an unmet need to identify actionable targets for patients who have progressed. Currently, there are no clinically useful biomarkers to predict response and/or resistance to anti-CDK4/6 therapy. Hence, the goal of our study was to identify the therapeutic vulnerabilities of CDK4/6 inhibitor resistant patient derived xenograft (PDX) models and identify key markers that longitudinally correlate with development of resistance and inform new treatment directions.

Methods: We obtained 4 different PDX models, two from patients who progressed after 2-4 months on treatment with palbociclib plus ET (i.e. intrinsic resistance) and the other two who developed resistance over time (i.e. acquired resistance) with disease progression between 12-18 months while on palbociclib plus ET. To elucidate mechanisms of resistance, we performed genome-wide expression analysis via RNA-sequencing.

Results: The molecular assessment of the PDX models revealed different transcriptomic signatures for intrinsic resistance compared to acquired resistance. We identified 3,386 upregulated and 2,829 downregulated significant differentially expressed genes (DEGs) in the acquired compared to intrinsic resistant PDX models. Further, gene set enrichment analysis (GSEA) revealed enrichment of distinct driver pathways in the acquired-compared to the intrinsic resistant models.

Conclusions: Collectively, these results have identified potential unique targets for intrinsic and acquired resistance to guide treatment strategies. Thus, our ongoing studies are geared towards identifying and targeting distinct therapeutic vulnerabilities of intrinsic and acquired resistance to palbociclib.

Citation Format: Nicole M. Kettner, Juliana Navarro-Yepes, Tuyen N. Bui, Xiayu Rao, Jing Wang, Funda Meric-Bernstam, Kelly K. Hunt, Debu Tripathy, Khandan Keyomarsi. Identifying therapeutic vulnerabilities in HR-positive, HER2-negative advanced breast cancer patient-derived xenograft models refractory to CDK4/6 inhibition [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 3107.

Abstract 327: Antitumor efficacy of trastuzumab deruxtecan in combination with adavosertib in HER2-expressing Cyclin E amplified gastroesophageal cancers

Purpose: Trastuzumab deruxtecan (T-DXd) is a HER2-directed antibody-drug conjugate approved for patients with HER2-positive gastric/gastroesophageal junction (GEJ) cancers. Amplification of CCNE1, which encodes cyclin E, has been proposed as a mechanism of resistance to HER2-targeted therapies. The Wee1 kinase inhibitor adavosertib (AZD1775) has demonstrated enhanced antitumor activity in the setting of cyclin E overexpression. We investigated the efficacy of T-DXd in combination with adavosertib in HER2-expressing cancers with and without co-amplification of CCNE1.

Methods: Frequency of CCNE1 amplification was determined among patients with ERBB2 amplification in a clinical genomic database at the MD Anderson Cancer Center (MDACC) and within The Cancer Genome Atlas (TCGA). Sulforhodamine B assay, western blotting, and Annexin V staining were used to determine the effects of T-DXd and DXd in combination with adavosertib in vitro. Four HER2-expressing gastric/GEJ patient-derived xenograft (PDX) models with or without co-amplification of CCNE1 were tested with T-DXd in combination with adavosertib in vivo. Tumor volume and body weights were measured twice weekly and treatment responses were assessed by the relative treatment-to-control ratio, waterfall plots, and event-free survival (event defined as the day which tumors doubled in size from baseline).

Results: Of 515 patients identified at MDACC with ERBB2 amplification, 60 (11.6%) had co-amplification of CCNE1. Of the 405 patients identified within the TCGA with ERBB2 amplification, 43 (10.6%) had co-amplification of CCNE1. Tumor types with the highest frequency of ERBB2/CCNE1 co-amplification were gastric/GEJ (38.1% MDACC, 31.0% TCGA), endometrial (25.0% MDACC, 29.6% TCGA), and ovarian (15.4% MDACC, 15.4% TCGA). Adavosertib was synergistic in combination with DXd in four cell lines with ERBB2 amplification, CCNE1 amplification, or ERBB2/CCNE1 co-amplification. Both DXd and T-DXd upregulated cyclin E and γH2AX protein expression at 24 and 96 hours, and the combination of DXd or T-DXd with adavosertib enhanced apoptosis. T-DXd induced durable tumor regression in two HER2 amplified and HER2 overexpressing gastroesophageal PDX cancer models with HER2 amplification/3+ overexpression and concomitant cyclin E amplification/expression. Adavosertib enhanced the antitumor activity of T-DXd in two HER2 low, cyclin E amplified gastroesophageal cancer PDX models (one with an ERBB2 G778A mutation).

Conclusions: ERBB2 and CCNE1 are frequently co-amplified. Our findings provide supporting rationale for combining T-DXd with adavosertib in HER2-expressing cancers with CCNE1 co-amplification. Further study is needed to determine if therapeutic induction of cyclin E with DXd may sensitize to Wee1 kinase inhibition in patients without cyclin E amplification as well.

Citation Format: Timothy P. DiPeri, Kurt W. Evans, Gabriela Raso, Yasmeen Q. Rizvi, Xiaofeng Zheng, Bryce Kirby, Kathleen Kong, Khandan Keyomarsi, Jaffer A. Ajani, Timothy A. Yap, Funda Meric-Bernstam. Antitumor efficacy of trastuzumab deruxtecan in combination with adavosertib in HER2-expressing Cyclin E amplified gastroesophageal cancers [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 327.

Abstract 264: Neutrophil elastase (NE) inhibition enhances metastasis free survival by altering regulation of tumor intrinsic cytoskeletal and cellular adhesion pathways in murine breast cancer models

Background: Neutrophil elastase (NE), a serine protease exclusively secreted in neutrophils, is a crucial mediator of chronic inflammation and tumor progression. Studies from our group reveal that NE may be a prognostic marker of metastasis. In a cohort of 192 breast cancer patients (58% ER/PR+ve, 20%-HER-2 +ve and 22% TNBC), our results show that higher infiltration of NE-positive Tumor Associated Neutrophils (TANs), is associated with a decrease in recurrence free survival (hazard ratio=3.4, 95% CI, 1.1-5.5), regardless of breast cancer subtype Further, we observe that the genetic deletion of Elane (encoding NE) inhibits lung metastasis in in vivo models of breast cancer. Yet the precise mechanism(s) by which NE promotes tumorigenesis and metastasis of breast cancer remains to be elucidated. To address this gap in knowledge, we have identified the tumor-intrinsic and -extrinsic mechanisms by which NE promotes metastasis.

Methods: The role of NE in breast cancer metastasis was assessed using Elane+/+ and Elane-/- mice in FVB/NJ genetic background, bearing PyMT tumors (orthotopic and spontaneous) respectively. These mice develop lung metastasis in 80-90% of the tumor-bearing mice within 1-3 months of primary tumor initiation. To assess metastasis-free survival (MFS), mice received orthotopic engraftment of PyMT tumors, followed by resection and subsequent monitoring for metastasis. The efficacy of the NE inhibitor AZD9668 was assessed in Elane+/+ mouse models by treating the mice with 100mg/kg B.I.D treatments.

Preliminary results: Genetic ablation of NE (Elane-/-) in the PyMT models, reduced lung metastasis by ~90% (Lung metastatic index =21.8 vs. 2.7, respectively; p=0.0044). Survival studies in FVB Elane-/- showed a MFS benefit of 345 days compared to controls, which succumbed to metastasis-related death in 46 days post primary tumor resection. RNA-sequencing analysis of PyMT- Elane+/+ and Elane-/- tumors showed differential regulation of tumor intrinsic actin cytoskeleton and integrin signaling pathways between the two genetic backgrounds. These NE-regulated pathways are critical for cell-to-cell contact and tissue integrity, explaining the delay in metastasis in the Elane-/- mice. 100mg/kg daily treatment of AZD9668 reduced lung metastasis in PyMT mice by 94% compared to vehicle-treated mice (0.49+/- 0.21% vs. 0.03+/-0.01%; p=0.05) and significantly reduced instances of primary tumor recurrence.

Conclusions: Collectively, our studies suggest that genetic and pharmacological ablation of NE reduces metastasis and extends MFS in in vivo models of breast cancer. Our preclinical studies presented here are likely to provide the much-needed rationale for the use of this class of NE inhibitors as a viable treatment strategy for the metastatic breast cancer.

Citation Format: Amriti R. Lulla, Said Akli, Lucas D. Warma, Natalie W. Fowlkes, Kelly K. Hunt, Xiayu Rao, Jing Wang, Stephanie S. Watowich, Khandan Keyomarsi. Neutrophil elastase (NE) inhibition enhances metastasis free survival by altering regulation of tumor intrinsic cytoskeletal and cellular adhesion pathways in murine breast cancer models [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 264.

Abstract 515: Single-cell transcriptomic analysis of HR+/HER2- breast cancer identifies gene signatures that predict outcomes of luminal A and B subtypes

Introduction: Patients with luminal A and B early-stage ER+/HER2- breast cancer (BrCa) are uniformly treated with adjuvant endocrine therapy (ET) (±chemotherapy). A better understanding of drivers of ET resistance is required as subsequent lethal metastatic disease remains a major clinical problem. Therefore, there is an unmet clinical need to identify biomarkers that select low- and high-risk patients who may benefit from de-escalation of current treatments or alternative therapeutic interventions. In the present study, we hypothesized that while luminal A and B tumors both arise from normal hormone-responsive cells, they are transcriptionally distinct, hence allowing the identification of unique gene signatures that can predict outcomes in each subtype.

Methods: Tumors from 10 early-stage ER+/HER2- BrCa patients were subjected to single-cell RNA-sequencing (scRNA-seq) analysis (10X Genomics); 6/10 tumors were classified as luminal A and 4/10 as luminal B based on combined PAM50 and immunohistochemical classification (Ki67 cut-off=20%). We performed a direct transcriptional comparison between luminal A and B tumors, using well-established signatures and unbiased differential gene expression analysis. To identify unique luminal A and B tumor-specific genes, we compared the gene expression profile of each luminal subtype with 10 non-neoplastic breast tissues. A predictive model (LASSO) was applied to select genes with the highest frequency using a training dataset. This resulted in 5- and 4-gene signatures for luminal A and B, respectively, which were used to calculate risk scores that divided each subtype into low- and high-risk groups. The prognostic value of the above signatures was validated in an independent dataset.

Results: The integrated scRNA-seq analysis of luminal A and B tumors revealed transcriptionally distinct tumor cell clusters while tumor microenvironment (TME) clusters were well intermixed. Luminal B tumors had higher cell cycle and BrCa-specific scores, low ER pathway-gene expression scores, and increased 8q amplifications. IFNγ, OXPHOS, p53, hypoxia and MYC targets were the most upregulated pathways in the luminal B subtype. The TME of luminal B tumors was comprised of lower CD4+ and CD8+ T cell but higher Treg levels. Comparison with normal breast tissues revealed that early-stage ER+ BrCa arises from hormone-responsive epithelial cells and provided a number of tumor-specific genes that were used to generate prognostic signatures. These signatures were capable of differentiating high- from low-risk patients within each subtype and predicting survival outcomes in two large-scale training and validation cohorts.

Conclusions: We developed a novel prognostic tool that can be used to determine duration of adjuvant ET and/or new therapeutic strategies for high-risk luminal A and B patients in the early-stage ER+/HER2- setting.

Citation Format: Sofia Mastoraki, Jerome Lin, Xiayu Rao, Sophie R. Liu, Harsh Batra, Maria G. Raso, Edwin R. Parra Cuentas, Akshara S. Raghavendra, Komal S. Rasaputra, Min Yi, Jing Wang, Aysegul Sahin, Debasish Tripathy, Kelly K. Hunt, Nicholas E. Navin, Khandan Keyomarsi. Single-cell transcriptomic analysis of HR+/HER2- breast cancer identifies gene signatures that predict outcomes of luminal A and B subtypes [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 515.

Abstract 1798: Mechanisms of acquired resistance to palbociclib reveals pathways of response to abemaciclib

Background: CDK4/6 inhibitors (CDK4/6i) plus endocrine therapy (ET) delay progression and improve survival in patients with hormone receptor positive (HR+), HER2 negative metastatic breast cancer (MBC). However, most patients develop resistance to CDK4/6i leading to disease progression, thus new therapies to overcome resistance are needed. CDK4/6i [palbociclib (palbo), ribociclib (ribo), and abemaciclib (abema)] have the same nominal targets but vary in their target specificity and are pharmacologically distinct. Clinical benefit was observed in patients treated with abema after progression on a prior CDK4/6i suggesting that palbo/ribo refractory tumors retain abema sensitivity. We hypothesize that mechanisms driving acquired resistance to palbo and abema are distinct, and palbo-resistant models may be responsive to abema.

Models: 1) MCF-7 and T47D palbo and abema resistant cells, 2) patient derived xenografts (PDX) established from patients who progressed on ET alone (ET-resistant) or palbo + ET (palbo-resistant), 3) organoids derived from the palbo-resistant PDX, and 4) a HR+/HER2- MBC patient cohort who received abema after progression on palbo therapy.

Results: RNA-sequencing and proteomic analysis revealed that palbo and abema resistant cells exhibit more than 30 differentially altered pathways. EMT, IL6/STAT3, and CSC pathways were upregulated only in palbo-resistant cells, but not in abema-resistant cells. Palbo-resistant cells also showed upregulation of G2M/Mitotic spindle and downregulation of ER pathways, whereas abema-resistant cells displayed downregulation of G2M/Mitotic spindle and upregulation of ER pathways. Mechanistic analysis revealed that palbo-resistant cells are responsive to abema with a delay in doubling time and a reduction of the proliferation marker pHH3. Further, cells accumulated in the G2M-phase with concomitant high phospho-(Y15)-CDK1 and cyclin B levels. Organoid cultures generated from palbo-resistant PDX were sensitive to abema. Likewise, abema significantly delayed the tumor growth of palbo-resistant PDX, correlating in vivo with ex vivo treatments. Moreover, we assessed response to abema after progression on palbo in the ET-resistant PDX model (CDK4/6 sensitive) demonstrating a continued survival benefit from abema treatment compared to palbo. Clinical outcome analyses of a MBC patient cohort treated with abema following prior CDK4/6i showed a median progression free survival (PFS) of 6.3 months in those treated sequentially vs a PFS of 4.0 months in non-sequential treated patients.

Conclusion: Differential mechanism underlying palbo and abema acquired resistance can be exploited to overcome CDK4/6i resistance. These results provide rationale for clinical trials evaluating the benefit of abema treatment following progression on a prior CDK4/6i.

Citation Format: Juliana Navarro-Yepes, Nicole M. Kettner, Tuyen Bui, Akshara S. Raghavendra, Xiayu Rao, Jing Wang, Aysegul Sahin, Senthil Damodaran, Debasish Tripathy, Kelly K. Hunt, Khandan Keyomarsi. Mechanisms of acquired resistance to palbociclib reveals pathways of response to abemaciclib [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 1798.

Abstract 1268: Early proliferative response via [18]FLT-PET/CT and serum TK1 activity are predictive biomarkers for synergistic effect of sequential cell cycle targeted therapy in sarcoma

Introduction: Sarcomas are rare, aggressive tumors that make up a higher percentage of overall cancer mortality in children and young adults. Primary management of sarcoma patients includes surgical resection with adjuvant or neoadjuvant radiation/chemotherapy. Even with aggressive multimodal treatment regimens, patients with high-grade sarcomas experience suboptimal prognosis and advanced disease is almost universally fatal. Innovative biomarker driven targeted therapies are in urgent need to improve survival in these patients. Discoveries in molecular and genetic basis of sarcoma have revealed new targets that deserve consideration. Inactivation of retinoblastoma (Rb) pathway, which causes unabated cell proliferation, through overexpression of cyclin D1 and/or CDK4/6 has been detected in the majority of sarcomas even when wild-type Rb protein is expressed. Hence, inhibition of cell cycle progression through reactivation of the tumor suppressor function of Rb by inhibiting CDK4/6 activity poses a potential avenue for new therapeutic options.

Methods: A panel of 4 sarcoma cell lines and 4 patient derived xenograft (PDX) models were used: 2 with an intact Rb pathway (Rb+ve, p16-ve) and 2 with an altered Rb pathway (Rb low/-ve, p16+ve). CDK4/6 inhibitor, abemaciclib, was used to reactivate the Rb pathway followed by treatment with gemcitabine or WEE1-kinase-inhibitor, to target the enriched S and G2/M phase cells post-abemaciclib removal. 18F-FLT PET imaging and serum thymidine kinase 1 (TK1) were used to monitor changes in cell proliferation and treatment response in both in vitro and in vivo. Changes in cell cycle biomarkers in response to treatment were also interrogated.

Results: Rb+ve sarcoma cell lines were sensitive to the anti-proliferative activity of abemaciclib leading to their reversible G1 arrest, while Rb null cells did not arrest in any phase of cell cycle in response to CDK4/6 inhibition. Following abemciclib removal, Rb+ve models (but not Rb-ve) showed significant increase in 18F-FLT biotracer uptake concomitant with elevated serum TK1 and enrichment of cells in S phase. The enrichment of cells in S phase maximized therapeutic efficacy of S-phase or G2/M targeting agents leading to synergistic cell killing in Rb+ve cell lines and PDX models.

Conclusion: Our study presents an innovative treatment strategy inhibiting the Rb pathway followed by S or G2/M pathway sequentially resulting in synergistic cell killing in those cells/tumors with wild-type Rb. We also incorporate real-time PET imaging and serum TK1 as non-invasive indicators of response to the treatment strategy. The study with PDX models also identified biomarkers of cell proliferation to be used in conjunction with PET imaging to provide the pre-clinical rationale to translate our findings into clinical trials for this aggressive disease.

Citation Format: Tuyen Duong Nguyen, Marc A. Pina, Yan Wang, Cansu Karakas, Tuyen N. Bui, Osama Mawlawi, Alexander J. Lazar, Davis R. Ingram, Peter J. Hougton, Kelly K. Hunt, Khandan Keyomarsi. Early proliferative response via [18]FLT-PET/CT and serum TK1 activity are predictive biomarkers for synergistic effect of sequential cell cycle targeted therapy in sarcoma [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 1268.

Abstract 1348: LMW-E induction and crosstalk with immune cells potentiates local immune responses leading to an immunosuppressive microenvironment at the early stages of breast tumorigenesis in mouse models

Introduction: Cyclin E is an independent predictor of poor outcomes and response to treatment in breast cancer (BrCa). Expression of low-molecular-weight cyclin E (LMW-E) is associated with more aggressive disease in all BrCa subtypes. While tumor infiltrating lymphocytes (TILs) are more abundant in LMW-E+ tumors, high-TIL/LMW-E+ tumors have lower probability of pathological complete response (pCR) to neoadjuvant chemotherapy. We hypothesized that LMW-E induces immune changes that create a permissive microenvironment in the mammary gland for promoting tumor initiation and subsequent growth. We aimed to evaluate the role of mammary epithelial expression of LMW-E in the temporal induction of systemic and local immune responses that ultimately prime the mammary gland for tumor development.

Methods: We generated a tri-transgenic mouse model capable of conditionally expressing human LMW-E under the control of the MMTV promoter in a p53 heterozygous background (MPT) upon doxycycline (Dox) administration. Female MPT mice were treated with Dox for 3, 6 and 9 months and age-matched untreated controls were sacrificed at each time point. An independent group of non-transgenic mice in a p53 heterozygous background were maintained +/- Dox as positive and negative controls. Mammary glands and peripheral organs (spleen, lung, bone marrow) were harvested for immune profiling by flow cytometry and multiplex immunofluorescence microscopy (mIF). Serum was also collected for cytokine/chemokine assessment. Immune profiling via flow cytometry was performed using two multi-color panels to assess basic immune and more specialized T-cell subsets. For the mIF experiments, two 5-marker panels were applied to mammary tissue.

Results: Histological examination of MPT mammary glands over time showed a temporal increase in acinar proliferation and mitotic figures, which was further confirmed by the co-localization of panCK+ and Ki-67+ markers. We report that although immune cell frequencies changed with age, these specific changes were dependent on LMW-E induction as compared to the non-transgenic cohort of mice. LMW-E+ mammary glands showed a temporal enrichment in B cells, macrophages, T cells (CD4+, PD1+, CD4+Ki67+, and Tregs), cDCs, and panCK+, panCK+vimentin+ populations over time. By contrast, pDCs increased from 3 to 6 months but decreased in the pre-tumorigenic mammary gland of the 9-month old LMW-E+ mice.

Conclusions: LMW-E induction mediates an increase in epithelial cell proliferation and epithelial-to-mesenchymal transition events that result in local immune alterations, specifically affecting T-cell subsets. Our findings suggest that the immunological changes driven by LMW-E lead to an immunosuppressive microenvironment that may promote tumor formation at the early stages of breast tumorigenesis.

Citation Format: Sofia Mastoraki, Amriti R. Lulla, Sarah Schneider, Karen Clise-Dwyer, Morgan M. Green, Natalie W. Fowlkes, Kelly K. Hunt, Stephanie S. Watowich, Khandan Keyomarsi. LMW-E induction and crosstalk with immune cells potentiates local immune responses leading to an immunosuppressive microenvironment at the early stages of breast tumorigenesis in mouse models [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 1348.

Abstract 1774: Circulating IL-6, an early biomarker in HR-positive, HER2-negative metastatic breast cancer patients progressing on CDK4/6 inhibitors

Background: CDK4/6 inhibitors (CDK4/6i, e.g. palbociclib) in combination with endocrine therapy (ET) have proven successful in delaying progression in hormone receptor-positive (HR+), HER2-negative (HER2-) metastatic breast cancer patients; however, 60-70% will progress within 1-2 years of treatment. Thus, understanding the mechanisms of resistance and identifying novel treatment strategies are needed to improve survival. Our previously published data shows that palbociclib resistance is marked by significant upregulation of the IL6-STAT3 signaling pathway in HR+, HER2- breast cancer cells and treatment with TTI-101, a small-molecule STAT3 inhibitor completing Phase I studies in solid tumor patients, significantly decreased cell viability. Additionally, matched biopsies from advanced HR+, HER2- breast cancer patients who progressed on palbociclib plus ET had an upregulation in activated STAT3 (STAT3 phosphorylated on Y705, pY-STAT3) as compared to their pre-treatment biopsy. Collectively, these data suggest that targeting the IL-6/STAT3 pathway is a viable therapeutic strategy. Our ongoing studies are directed at delineating the role of IL-6 and pY-STAT3 as predictive biomarkers to provide preclinical rationale for targeting STAT3 in patients who develop CDK4/6i resistance.

Methods: We downregulated IL-6 using shRNA in MCF7 and T47D palbociclib sensitive and resistant cells. We tested the efficacy of TTI-101 in patient-derived xenograft (PDX) models from patients with metastatic HR+, HER2- breast cancer who progressed on treatment with palbociclib + ET. We also collected plasma samples from patients with metastatic HR+, HER2- breast cancer just prior to CDK4/6i treatment and at disease progression.

Results: Downregulation of IL-6 in palbociclib resistant cells reduced pY-STAT3 levels and re-sensitized cells to ET and palbociclib. Induction of IL-6 is an early event by treating sensitive cells with 1uM palbociclib for 21 days during which the cells adapted and eventually developed resistance. Suppression of IL-6 in sensitive cells revealed that it is needed for cells to overcome growth inhibition by palbociclib. Targeting STAT3 in palbociclib resistant PDX mouse models using TTI-101 (50mg/kg twice daily by oral gavage), resulted in significantly reduced tumor volume; a synergistic effect was observed when TTI-101 was combined with palbociclib. Lastly, IL-6 levels in plasma samples from metastatic HR+, HER2- breast cancer patients were significantly higher at disease progression compared to pre-treatment with CDK4/6i.

Conclusion: Collectively, these studies suggest that IL-6 signaling through STAT3 is a key mediator of resistance to palbociclib. We provide the rationale for using circulating IL-6 as a biomarker of disease progression and tumor pY-STAT3 as a selection criterion for treatment with TTI-101 to prevent or reverse resistance.

Citation Format: Nicole M. Kettner, Tuyen N. Bui, Juliana Navarro-Yepes, T Kris Eckols, Akshara S. Raghavendra, David J. Tweardy, Kelly K. Hunt, Debu Tripathy, Khandan Keyomarsi. Circulating IL-6, an early biomarker in HR-positive, HER2-negative metastatic breast cancer patients progressing on CDK4/6 inhibitors [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 1774.

PARP inhibitors as single agents and in combination therapy: the most promising treatment strategies in clinical trials for BRCA-mutant ovarian and triple-negative breast cancers

INTRODUCTION

Poly (ADP-ribose) polymerase inhibitors (PARPis) are an exciting class of agents that have shown efficacy, particularly for BRCA-mutant triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC). However, most patients who receive PARPi as their standard of care therapy inevitably develop resistance and this underscores the need to identify additional targets that can circumvent such resistance. Combination treatment strategies have been developed in preclinical and clinical studies to address the challenges of efficacy and resistance.

AREAS COVERED

This review examines completed or ongoing clinical trials of PARPi mono- and combination therapies. PARPi monotherapy in HER2 negative breast (HR+ and TNBC subtypes) and ovarian cancer is a focal point. The authors propose potential strategies that might overcome resistance to PARPi and discuss key questions and future directions.

EXPERT OPINION

While the advent of PARPis has significantly improved the treatment of tumors with defects in DNA damage and repair pathways, careful patient selection will be essential to enhance these treatments. The identification of molecular biomarkers to predict disease response and progression is an endeavor.

Abstract P1-19-01: Palbociclib plus endocrine therapy significantly enhances overall survival of HR+/HER2- metastatic breast cancer patients compared to endocrine therapy alone - A large institutional study

PURPOSE: Cyclin-dependent kinase 4/6 inhibitor (CDKi) therapy combined with endocrinetherapy is considered standard of care for patients with advanced hormone receptor (HR)-positive, HER2-negative breast cancer (BC). The Breast Medical Oncology Database at MDAnderson Cancer Center (MDACC) was analyzed to assess effectiveness of CDKi+palbociclib. PATIENTS AND METHODS: From a total of 5402 advanced HR+ HER2- BC patients referred toMDACC between 1997 and 2020, we identified eligible patients who received palbociclib incombination with first- (n=778) and second-line (n=410) endocrine therapy. We furtheridentified “control” patients who received endocrine therapy alone in the first- (n=2452) andsecond-line (n=1183) setting. We conducted a propensity score matching analysis to balancethe baseline demographic and clinical characteristics between the palbociclib treated andcontrol cohorts to assess the effect of palbociclib treatment on progression-free survival (PFS)and overall survival (OS). Stratified log-rank test was used to assess the effect of palbociclib inthe matched cohorts. RESULTS: For the propensity-matched cohort in the first-line setting (n=708), the palbociclibgroup had significantly longer median PFS (17.4 vs. 11.1 months; p&lt;0.0001) compared tocontrols. Median OS (44.3 vs. 40.2 months; p =1) did not show any survival benefit in the firstline setting. However, in the second-line setting, with 380 propensity-matched cohort, thepalbociclib group had significantly longer PFS (10 vs 5 months, p&lt;0.0001) as well as OS (33 vs 24months; p &lt; 0.022), compared to controls.2. CONCLUSION: In this single center analysis, of a large cohort of metastatic HR+ HER2- BCpatients, palbociclib in combination with endocrine therapy was associated with improved PFSin both first- and second-line settings and OS in the second-line setting compared withendocrine therapy alone cohort.3

Citation Format: Akshara Singareeka Raghavendra, Min Jin Ha, Nicole M. Kettner, Senthil Damodaran, Rachel Layman, Kelly K Hunt, Yu Shen, Debu Tripathy, Khandan Keyomarsi. Palbociclib plus endocrine therapy significantly enhances overall survival of HR+/HER2- metastatic breast cancer patients compared to endocrine therapy alone - A large institutional study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-19-01.

Abstract P2-05-02: Low molecular weight cyclin E facilitate replication stress tolerance in breast cancer development

Low Molecular Weight Cyclin E (LMW-E) are the tumor specific, oncogenic forms of cyclin E that are post translationally generated by neutrophil elastase (NE) mediated cleavage of the 50 KDa full-length cyclin E1 (FL-cycE, encoded by CCNE1 gene). While FL-cycE localizes mainly to the cell nucleus, LMW-E lack the N-terminus nuclear localization signal and are detected in both the nucleus and cytoplasm. Compared to FL-cycE, LMW-E exhibit longer half-life and higher affinity to their kinase partner CDK2 and are resistant to natural CDK inhibitors such as p21 and p27. It is currently assumed that LMW-E drive the tumorigenic process by promoting G1/S cell cycle transition and accelerating mitotic exit. Here we report that LMW-E overexpression also promotes genomic instability by deregulating DNA replication in a CDC6 dependent manner. To this end, we developed an immunohistochemistry (IHC) assay with a cyclin E antibody that can identify LMW-E expressing tumors and examined the association of genetic instability of each tumor with LMW-E status in 2 different cohorts of breast cancer patients. Cohort 1 is a retrospective cohort of 725 patients with stage I-II breast cancer treated at MD Anderson (Houston, TX) between 1985 and 1999. Cohort 2 is a prospective cohort of 85 patients with stage I-II breast cancer who enrolled in our study at MD Anderson between January 2000 and June 2010. Our results show that positive LMW-E status in stage 1 or 2 breast cancer patients correlates with increasing copy number variations, as identified by Molecular Inversion Probe (MIP) in cohort 1 and somatic mutations, as identified by Whole Exome Sequencing (WES) in cohort 2. Second, using immortalized human mammary epithelial cells (hMECs) engineered to express doxycycline inducible LMW-E or FL-cycE in CCNE1 knock-out background, we found that FL-cycE over-expression leads to DNA damage, cell cycle arrest and cell death. LMW-E overexpression, on the other hand, facilitates cell proliferation with damaged DNA, resulting in multi-nuclei and micro-nuclei formation in daughter cells. Third, overexpression of FL-cycE reduces chromatin bound MCM complex, while LMW-E overexpression promotes the chromatin loading of pre-replication complex including MCMs. Lastly, we show that LMW-E but not FL-cycE is the major form of cyclin E that binds to the chromatin. Specifically, in both LMW-Einducible hMECs and LMW-Ehighbreast tumor cell lines, CDC6 is required for the nuclear translocation and chromatin loading of LMW-E. Our findings have revealed the unique oncogenic function of LMW-E in deregulating replication licensing, promoting replication stress tolerance and genomic instability that fuels tumor development. These findings also provide potential novel therapeutic strategies for treating LMW-Ehigh breast tumors, who do not respond to the current standard of care therapies.

Citation Format: Mi Li, Kwang Huei Low, Tuyen Bui, Kelly K Hunt, Khandan Keyomarsi. Low molecular weight cyclin E facilitate replication stress tolerance in breast cancer development [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-05-02.

Palbociclib plus endocrine therapy significantly enhances overall survival of HR+/HER2- metastatic breast cancer patients compared to endocrine therapy alone in the second-line setting-a large institutional study

Cyclin-dependent-kinase-4/6 inhibitor (CDKi) plus endocrine therapy (ET) is standard of care for patients with advanced hormone receptor (HR)-positive, HER2-negative breast cancer (BC). The Breast Medical Oncology database at MD Anderson Cancer Center (MDACC) was analyzed to assess effectiveness of the CDKi palbociclib plus ET compared to ET alone. From a total of 5402 advanced HR+ HER2- BC patients referred to MDACC between 1997 and 2020, we identified eligible patients who received palbociclib in combination with first- (n=778) and second-line (n=410) ET. We further identified "control" patients who received ET alone in the first- (n=2452) and second-line (n=1183) settings. Propensity score matching analysis was conducted to balance baseline demographic and clinical characteristics between palbociclib and control cohorts to assess the effect of palbociclib treatment on progression-free survival (PFS) and overall survival (OS). For propensity-matched-cohort in the first-line setting (n=708), palbociclib group had significantly longer median PFS (17.4 vs. 11.1 months; p<0.0001) compared to controls. Median OS (44.3 vs. 40.2 months) did not show a statistically significant benefit in the first line setting. However, in the second-line setting, with 380 propensity-matched-cohort, the palbociclib group had significantly longer PFS (10 vs 5 months, p<0.0001) as well as OS (33 vs 24 months; p < 0.022), compared to controls. We conclude that in this single center analysis of a large cohort of metastatic HR+ HER2- BC patients, palbociclib in combination with ET was associated with improved PFS in both first- and second-line settings and OS in the second-line setting compared with ET alone cohort.

Cytoplasmic Cyclin E Expression Predicts for Response to Neoadjuvant Chemotherapy in Breast Cancer

BACKGROUND

Pathologic complete response (pCR) has been shown to be associated with favorable outcomes in breast cancer. Predictors of pCR could be useful in guiding treatment decisions regarding neoadjuvant therapy. The objective of this study was to evaluate cyclin E as a predictor of response to neoadjuvant chemotherapy in breast cancer.

METHODS

Patients (n = 285) with stage II-III breast cancer were enrolled in a prospective study and received neoadjuvant chemotherapy with anthracyclines, taxanes, or combination of the two. Pretreatment biopsies from 190 patients and surgical specimens following chemotherapy from 192 patients were available for immunohistochemical analysis. Clinical and pathologic responses were recorded and associated with presence of tumor infiltrating lymphocytes, cyclin E, adipophilin, programmed cell death-ligand 1, and elastase staining and other patient, tumor and treatment characteristics.

RESULTS

The pCR rate was significantly lower in patients with cytoplasmic cyclin E staining compared with those who had no cyclin E expression (16.1% vs 38.9%, P = 0.0005). In multivariable logistic regression analysis, the odds of pCR for patients who had cytoplasmic negative tumors was 9.35 times (P value < 0.0001) that compared with patients with cytoplasmic positive tumors after adjusting for ER, PR, and HER2 status. Cytoplasmic cyclin E expression also predicts long-term outcome and is associated with reduced disease free, recurrence free, and overall survival rates, independent of increased pretreatment tumor infiltrating lymphocytes.

CONCLUSIONS

Cyclin E independently predicted response to neoadjuvant chemotherapy. Hence, its routine immunohistochemical analysis could be used clinically to identify those breast cancer patients expected to have a poor response to anthracycline/taxane-based chemotherapy.

Phase I safety and efficacy study of autophagy inhibition with hydroxychloroquine to augment the antiproliferative and biological effects of preoperative palbociclib plus letrozole for estrogen receptor-positive, HER2-negative metastatic breast cancer (MBC)

1067

Background: Endocrine therapy with a CDK4/6 inhibitor is standard of care for patients (pts) with estrogen-receptor-positive (ER+), HER2-negative MBC, yet resistance ultimately develops. We have shown that low doses of palbociclib activates autophagy, which reverses initial G1 cell cycle arrest. High concentrations of palbociclib induce senescence, but these are off target effects of the drug. The autophagy inhibitor hydroxychloroquine (HCQ) induces senescence at a lower (i.e. on-target) continuous dosing of palbociclib, in in vitro and in vivo models. This strategy is being tested in a phase I/II trial (NCT03774472). Results from the phase I portion are reported here. Methods: The phase I part of this study uses a dose escalation 3+3 design testing HCQ, 400, 600 and 800 mg daily (6 pts at 800 mg) with continuously dosed palbociclib at 75 mg and letrozole 2.5 mg daily. Dose limiting toxicity (DLT) includes any study drug-related grade ≥ 3 nonhematological (lab) toxicity. Responding pts may continue on therapy beyond 8 weeks for up to 52 weeks. Primary objective is to determine safety, tolerability and the recommended phase 2 dose (RP2D) of HCQ. Secondary objectives are overall tumor response and time to progression. Eligible pts are ≥18 years of age, postmenopausal (ovarian suppression allowed) with ER+/HER2-negative MBC, ECOG performance status score of ≤1 and with adequate renal, hepatic, and hematologic function. Response is assessed per RECIST v1.1. Results: Between 9/24/18 and 12/15/20, 14 pts were evaluable for safety. Median age was 41 with Asian (1, 7.1%), Black (2, 14.3%) White (11, 78.6%) patients enrolled. No DLTs were observed. One pt progressed during the DLT period and 2 withdrew consent (one during the DLT period); two pts were replaced for DLT assessment. Reasons for coming off study were grade 3 skin toxicity (1), per protocol at 8 weeks (non-measurable or pt/physician preference, 9), and (2) full duration treatment at 50 and 52 weeks. Adverse events (AEs) of grade ≥3 were hematologic (29), metabolism/nutrition (2), musculoskeletal/ connective tissue (1), and skin/subcutaneous tissue (3), with no serious AEs reported. The percent of palbociclib doses held per pt due to neutrophil level ranged from 0-37.5% with no apparent relation to HCQ dose. Best response was partial (2) stable (11); and progression (1). For measurable disease, tumor decreases of 11%, 12%, 21%, 26%, 30%, 55% and increase in 1 pt by 55% were seen. Conclusions: This phase I study showed acceptable safety and no HCQ dose-toxicity relationship. The RP2D of HCQ is 800 mg/day with continuous dosing palbociclib at 75 mg/day and letrozole at 2.5 mg/day. The phase 2 trial will proceed in the neoadjuvant setting, with Ki67 proliferative index response as the primary endpoint. Clinical trial information: NCT03774472 .

LMW cyclin E and its novel catalytic partner CDK5 are therapeutic targets and prognostic biomarkers in salivary gland cancers

Salivary gland cancers (SGCs) are rare yet aggressive malignancies with significant histological heterogeneity, which has made prediction of prognosis and development of targeted therapies challenging. In majority of patients, local recurrence and/or distant metastasis are common and systemic treatments have minimal impact on survival. Therefore, identification of novel targets for treatment that can also be used as predictors of recurrence for multiple histological subtypes of SGCs is an area of unmet need. In this study, we developed a novel transgenic mouse model of SGC, efficiently recapitulating the major histological subtype (adenocarcinomas of the parotid gland) of human SGC. CDK2 knock out (KO) mice crossed with MMTV-low molecular weight forms of cyclin E (LMW-E) mice generated the transgenic mouse models of SGC, which arise in the parotid region of the salivary gland, similar to the common site of origin seen in human SGCs. To identify the CDK2 independent catalytic partner(s) of LMW-E, we used LMW-E expressing cell lines in mass spectrometric analysis and subsequent biochemical validation in pull down assays. These studies revealed that in the absence of CDK2, LMW-E preferentially binds to CDK5. Molecular targeting of CDK5, using siRNA, resulted in inhibition of cell proliferation of human SGCs overexpressing LMW-E. We also provide clinical evidence of significant association of LMW-E/CDK5 co-expression and decreased recurrence free survival in human SGC. Immunohistochemical analysis of LMW-E and CDK5 in 424 patients representing each of the four major histological subtypes of human salivary cancers (Aci, AdCC, MEC, and SDC) revealed that LMW-E and CDK5 are concordantly (positive/positive or negative/negative) expressed in 70% of these patients. The co-expression of LMW-E/CDK5 (both positive) robustly predicts the likelihood of recurrence, regardless of the histological classification of these tumors. Collectively, our results suggest that CDK5 is a novel and targetable biomarker for the treatment of patients with SGC presenting with LMW-E overexpressing tumors.

Targeting Replicative Stress and DNA Repair by Combining PARP and Wee1 Kinase Inhibitors Is Synergistic in Triple Negative Breast Cancers with Cyclin E or BRCA1 Alteration

Simple Summary

Triple-negative breast cancer (TNBC) is a subtype of invasive breast cancer with an aggressive phenotype that has decreased survival compared with other types of breast cancers, due in part to the lack of biomarker driven targeted therapies. Here, we show that breast cancer patients whose tumors show high levels of cyclin E expression have a higher prevalence of BRCA1/2 alterations and have the worst clinical outcomes. In vitro and in vivo studies revealed that combination therapies with poly (ADP-ribose) polymerase (PARP) and Wee1 kinase inhibitors in TNBC cells with either BRCA1 mutations or high levels of cyclin E results in synergistic cell death due to induction of replicative stress and downregulation of DNA repair. These studies suggest that by preselecting patients whose tumors have high cyclin E levels or harbor mutations in BRCA1, only those cases with the highest replicative stress properties will be subjected to combination treatment and likely result in synergistic activity of the two agents.

Abstract

The identification of biomarker-driven targeted therapies for patients with triple negative breast cancer (TNBC) remains a major clinical challenge, due to a lack of specific targets. Here, we show that cyclin E, a major regulator of G1 to S transition, is deregulated in TNBC and is associated with mutations in DNA repair genes (e.g., BRCA1/2). Breast cancers with high levels of cyclin E not only have a higher prevalence of BRCA1/2 mutations, but also are associated with the worst outcomes. Using several in vitro and in vivo model systems, we show that TNBCs that harbor either mutations in BRCA1/2 or overexpression of cyclin E are very sensitive to the growth inhibitory effects of AZD-1775 (Wee 1 kinase inhibitor) when used in combination with MK-4837 (PARP inhibitor). Combination treatment of TNBC cell lines with these two agents results in synergistic cell killing due to induction of replicative stress, downregulation of DNA repair and cytokinesis failure that results in increased apoptosis. These findings highlight the potential clinical application of using cyclin E and BRCA mutations as biomarkers to select only those patients with the highest replicative stress properties that may benefit from combination treatment with Wee 1 kinase and PARP inhibitors.

Abstract PD2-05: Randomized phaseII trial to evaluate alisertib alone or combined with fulvestrant for advanced, endocrine-resistant breast cancer (TBCRC 041)

Background: In ER+ breast cancer (BC) models, Aurora A kinase (AURKA) activation is associated with expansion of CD44+/CD24low/- tumor initiating cells, down-regulation of ERα, and endocrine therapy resistance. Alisertib, a selective AURKA inhibitor, can restore ERα expression and endocrine sensitivity. Early phase studies evaluating alisertib alone or with fulvestrant for ER+ metastatic BC (MBC) demonstrated a favorable safety profile and promising antitumor activity [Haddad, Breast Cancer Res Treat. 2018]. A phase II trial was conducted to determine if the addition of fulvestrant to alisertib improved objective response rate (ORR) and to assess clinical activity of alisertib alone or with fulvestrant in patients (pts) with prior fulvestrant and CDK 4/6 inhibitor (CDK 4/6i). Methods: Pts were randomized 1:1 to Arm A, alisertib (50 mg PO BID Days 1-3, 8-10, 15-17 q 28 days) or Arm B, alisertib with fulvestrant (500 mg IM Day 1, 15 for Cycle 1 and q 28 days thereafter). Eligibility included postmenopausal women, history of ER+ BC, prior fulvestrant, ≤ 2 prior chemotherapy lines, and measurable disease. Stratification factors included prior CDK4/6i, ER level (&lt;10%, ≥10%), and primary/secondary endocrine resistance. Pts on Arm A could cross over to Arm B at progression. With 45 pts per arm, a one sided alpha=0.15 sequential binomial test would have an 85% chance of detecting an increase of ≥ 20% in the ORR of ArmB when the true ORR for Arm A is ≤ 20%. ORR was defined as a partial response (PR) + complete response (CR) by RECIST v.1.1 criteria. Secondary endpoints include progression free survival (PFS), 24-week clinical benefit rate (CBR = CR + PR + absence of progression for&gt; 6 cycles), overall survival, duration of response (DoR), and safety. Blood and tumor specimens were collected at baseline, end of Cycle 1, and progression. Results: Pts enrolled July 2017 - November 2019 with 118 pre-registered, 96 registered, and 90 evaluable for the primary endpoint (Arm A: 45, Arm B: 45). Median age was 60 (range 33, 85). Nearly all received prior fulvestrant (n=89, 98.9%), aromatase inhibitor (n=83, 92.2%), and CDK4/6i (n=88, 97.8%). Most had secondary endocrine resistance (n=71, 78.9%). Pre-registration biopsy for ER was positive in 84 pts (86.7%) and negative in 6 pts (13.3%). More pts on Arm B had prior everolimus (A: 35.6%, B: 57.8%) and prior chemotherapy (A: 44.4%, B: 55.6%) for MBC. The ORR for alisertib and fulvestrant was 20.0% (90% CI: 10.9-32.3%), not significantly greater than alisertib alone 17.8% (90% CI: 9.2-29.8%). The 24-week CBR for Arm A was 42.2% (90% CI: 29.7-55.6%; n=19, including 7 PR) and Arm B was 31.1% (90% CI: 19.9-44.3%; n=14, including 8 PR). As of July 1, 2020, the median DoR was not reached in either arm. The median PFS time was 5.6 months (95% CI: 3.9 - 9.3) for Arm A and 5.1 months (95%CI: 3.8 - 7.6) for Arm B. Seventeen pts (18.9%) remain on treatment (A: 12, B: 5) having received at least 11 cycles (range up to 32+ cycles). At least one dose reduction was required for pts (A: 19, B: 18), most commonly due to neutropenia. The most common severe (grade ≥3) adverse events included neutropenia (n=19, 42.2% in each arm), anemia (A: 15.6%, B: 8.8%), and fatigue (n=5, 11.1% Arm B only). Pts discontinued therapy due to disease progression equally in each arm (n=28, 62.2%), however more pts on Arm B (n=12) than Arm A (n=5) discontinued therapy due to toxicity, refusal or other reasons. Conclusion: While the addition of fulvestrant to alisertib did not improve ORR, promising clinical activity with alisertib monotherapy was observed overall and notably for pts with endocrine and CDK 4/6i-resistant MBC. More severe toxicities and treatment discontinuation were observed in pts receiving combination therapy. Correlative blood (CTC/cfDNA) and tissue (AURKA, ERα, and stemness biomarkers) studies are underway.

Citation Format: Tufia Haddad, Antonino D'Assoro, Vera Suman, Jodi Carter, Brendan McMenomy, Erica Mayer, Meghan Karuturi, Aki Morikawa, Paul Marcom, Claudine Isaacs, Sun Young Oh, Amy Clark, Ingrid Mayer, Khandan Keyomarsi, Roberto Leon-Ferre, Karthik Giridhar, Ciara O'Sullivan, Prema Peethambaram, Timothy Hobday, Minetta Liu, James Ingle, Matthew Goetz. Randomized phaseII trial to evaluate alisertib alone or combined with fulvestrant for advanced, endocrine-resistant breast cancer (TBCRC 041) [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 PD2-05.

Selective CDK4/6 Inhibitors: Biologic Outcomes, Determinants of Sensitivity, Mechanisms of Resistance, Combinatorial Approaches, and Pharmacodynamic Biomarkers

CDK4/6 inhibitors are now part of the standard armamentarium for hormone receptor-positive breast cancer. In this article, we review the biologic outcomes imposed by these drugs on cancer cells, determinants of response, mechanisms of intrinsic and acquired resistance, as well as combinatorial approaches emanating from mechanistic studies that may allow use of these agents to extend beyond breast cancer. In addition, we will address tumor-, imaging-, and blood-based pharmacodynamic biomarkers that can inform rationally designed trials as clinical development continues.

Abstract P2-05-04: Low molecular weight cyclin E facilitates replication stress tolerance in breast cancer development

Purpose: Low Molecular Weight Cyclin E (LMW-E) are the oncogenic forms of cyclin E and were originally discovered in breast cancer (BC). LMW-E are generated from N-terminal cleavage of the 50 KDa, full-length cyclin E1 (FL-cycE). Our laboratory has established that LMW-E expression (i) correlates with poorer survival in BC patients; (ii) increases in frequency as BC progress from ductal carcinoma in situ to invasive ductal carcinoma; (iii) drives spontaneous and metastatic BC in murine transgenic models; (iii) causes human mammary epithelial cells (hMECs) to transform in vitro and form tumors in vivo. Elucidating the critical oncogenic functions and essential downstream factors of LMW-E is a current void in the field and may have important therapeutic implications.

Experimental Design: Immunohistochemistry (IHC) analysis were performed using tumor specimens (n=725) from breast cancer patients diagnosed with Stage 1 or 2 disease to determine the level of LMW-E. Micro-dissected tumor DNA from these tissues were analyzed for copy number variations (CNVs) using Molecular Inversion Probe (MIP) based arrays. CCNE1(encoding Cyclin E1) knock-out 76NE6 and 76NF2V hMEC lines were generated by CRISPR, followed by transfection of lentivirus vector expressing doxycycline inducible EGFP fused LMW-E or FL-cycE. Time-lapse live cell imaging was performed to monitor the cell growth and phenotypes after induced expression of LWM-E or FL-cycE. DNA replication and replication stress were examined by BrdU labeling and immunofluorescent (IF) assays using antibodies against BrdU and Replication Protein A (RPA). IF for gamma-H2AX and western blotting for phosphor-RPA32, ATR-CHK1 and ATM-CHK2 pathways were performed to determine the DNA damage and responses.

Results: Analysis of CNVs for the 725 tumors stratified by the cyclin E phenotypes reveal that the frequency of the CNVs (gains & losses) were the most significant in patients whose tumors expressed LMW-E and were predictive of poor prognosis independent of BC subtypes. DNA damage signals including gamma-H2AX foci and phosphor-CHK1 were similarly enhanced in hMECs induced for FL-cycE or LMW-E over-expression. Different effects of FL-cycE and LMW-E on DNA replication and replication stress were observed. Induced FL-cycE overexpression attenuated increased RPA foci and RPA phosphorylation, inhibits DNA replication and cell growth, and ultimately lead to cell death. LMW-E overexpression facilitated DNA replication and cell proliferation with damaged DNA, resulting in multi-nuclei and micro-nuclei formation in daughter cells.

Conclusion: LMW-E expression positively correlates with genomic instability in BC samples. LMW-E facilitates hMECs to by-pass replication stress induced tumor barrier and survive with damaged DNA, resulting in abnormal nuclei formation, an oncogenic phenotype.

Citation Format: Mi Li, Kwang Huei Low, Tuyen Bui, Kelly K Hunt, Khandan Keyomarsi. Low molecular weight cyclin E facilitates replication stress tolerance in breast cancer development [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-05-04.

Abstract PD2-05: Differential mechanisms of acquired resistance to abemaciclib versus palbociclib reveal novel therapeutic strategies for CDK4/6 therapy-resistant breast cancers

Background: Hormone receptor positive (HR+)/human epidermal growth factor receptor 2 negative (Her2-) is the most prevalent subtype of breast cancer, representing 70% of the cases with metastatic disease. Endocrine therapy plus FDA-approved cyclin-dependent kinases (CDK) 4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have improved the treatment of HR+/Her2- advanced breast cancer patients. However, patients develop clinical resistance (acquired) during the long-term treatment, and in some cases, they do not respond within the first 3 months of treatment (intrinsic resistance), leading to disease progression. Although these inhibitors have the same nominal targets, CDK4/6, abemaciclib can inhibit other kinases that are not inhibited by palbociclib/ribociclib, such as CDK9/7/2/1, GSK3α/β and CAMK2γ/δ. As such, abemaciclib has been shown to inhibit cell growth in Rb deficient cells, in which palbociclib/ribociclib are ineffective. Therefore, we hypothesized that 1) mechanisms driving palbociclib acquired resistance are distinct than those mediating abemaciclib resistance, 2) palbociclib resistant models may be responsive to abemaciclib, and 3) pathways underlying these mechanistic differences can be exploited as alternative therapies to overcome resistance.

Methods: We generated several models to examine mechanisms of resistance to different CDK4/6 inhibitors: 1) MCF7 and T47D (ER+) palbociclib resistant breast cancer cells with increasing concentrations of palbociclib, starting at 1.2 µM (initial IC 50) up to 5 µM (plasma concentrations in patients) in a stepwise manner over a 6 month period, 2) MCF7 abemaciclib resistant cells (0.5, 1 and 1.5 µM), and 3) organoids derived from patient derived xenografts (PDXs) with a similar molecular profile to palbociclib acquired resistance models. Cell cycle changes were evaluated by western blot analysis and flow cytometry.

Results: Western blot analysis revealed a dose dependent downregulation of ERα, Rb, p-Rb and p27, while levels of cyclin E and p-CDK2 increased in a stepwise fashion in palbociclib resistant cells, which were only partially cross resistant to abemaciclib and sensitive to CDK9 inhibitors LDC067 and SNS032. FACS analysis of abemaciclib resistant cells showed an increase in G2/M accompanied by a drastic reduction of p-Rb and a gradual decrease of Rb. ERα levels were slightly decreased in abemaciclib resistant cells compared to the complete loss in palbociclib resistant cells. As in the palbociclib resistant cells, a dose dependent increase in cyclin E and p-CDK2 were also observed. However, Rad51, a key mediator of DNA repair, was downregulated in a stepwise manner only in abemaciclib resistant cells, but not in palbociclib resistant cells. Therefore, we evaluated if a combination therapy targeting DNA repair pathways plus abemaciclib could render palbociclib resistant models more responsive to targets other than cell cycle inhibitors. To this end, we examined the combination of abemaciclib and niraparib in organoid cultures generated from PDX models that are transcriptomic surrogates of palbociclib resistance cells and found a significant reduction of viability, number and density of these organoids. In vivo, using the same PDX models, the combined treatment reduced the tumor growth rate and increased overall survival.

Conclusion: Our results suggest that mechanisms underlaying palbociclib and abemaciclib acquired resistance exhibit differentially altered pathways, such as DNA damage/repair pathways, which can be exploited to overcome CDK4/6 inhibitors therapy resistance in breast cancer patients.

Citation Format: Juliana Navarro-Yepes, Xian Chen, Tuyen Bui, Nicole M Kettner, Kelly K Hunt, Khandan Keyomarsi. Differential mechanisms of acquired resistance to abemaciclib versus palbociclib reveal novel therapeutic strategies for CDK4/6 therapy-resistant breast cancers [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD2-05.

Abstract P6-04-12: STAT3 as a therapeutic target in estrogen receptor positive breast cancer patients refractory to CDK4/6 inhibition

Background: CDK4/6 inhibitors (i.e. palbociclib) in combination with endocrine therapy (ET) are currently standard of care for estrogen receptor (ER) positive breast cancer patients with advanced/metastatic disease. While this combination has proven successful in delaying progression, no improvement in long-term survival has been observed to date in the post-menopausal setting. Further, resistance is inevitable as 50-60% of patients’ metastatic lesions progress on CDK4/6 inhibitor therapy within 2-years of treatment. For patients experiencing resistance to CDK4/6 inhibitors, novel treatment strategies are needed to delay progression or to improve survival. Our recently published data shows that palbociclib-resistance is marked by significant upregulation of the IL6- STAT3 signaling pathway in ER-positive breast cancer cells. Knockdown of STAT3 in resistance cancer cells restored sensitivity to palbociclib. Additionally, matched biopsies from advanced ER-positive breast cancer patients who progressed on palbociclib showed upregulation in p-STAT3 as compared to their pre-treatment biopsy samples (14 out of 25 patients; p=0.042). Collectively, these data suggest that STAT3 is viable therapeutic target to overcome palbociclib resistance. Hence, the goal of this study is to translate these findings in vivo and provide pre-clinical rational to the efficacy of TTI-101 (an orally bioavailable STAT3 inhibitor) in PDX models of palbociclib resistance.

Methods: To identify PDX models that recapitulate palbociclib resistance observed in cell line models, we correlated two published RNA-seq data sets of a panel of 64 PDX models from breast cancer patients to our multi-omics analysis of palbociclib resistant cell lines. Four PDXs that recapitulated the resistant-transcriptome expression pattern based on Spearman’s correlation, were narrowed down for future studies. In addition, we have also established PDX models (1st-4th passage) from two sets of patients (1) those who are intrinsically resistant to palbociclib (the patients progressed at 2-3 months while on palbociclib + ET) and (2) those who have developed resistance over time (i.e. acquired resistance-patients progress at 12-18 months while on palbociclib + ET).

Results: We chose PDX model BCX94 for our preliminary studies as it showed baseline induction of p-STAT3 by immunoblot analysis. Using BCX94, we show that TTI-101 at 50mg/kg twice a day potently reduced tumor volume and improved survival of these mice. We also observed a significant reduction in tumor-derived IL-6 in circulation; as assayed by hIL-6 levels in the serum. Further, complete blood count analysis of whole blood collected at endpoint (i.e. 28 days on treatment) showed no drug toxicities. Treatment of intrinsic palbociclib resistant PDX models with TTI-101, on the other hand, showed only a brief delay in tumor progression, but no overall benefit. Conclusions: Collectively, these results indicate that TT1-101 is safely tolerated and efficacious at the dose examined in PDX models and that TTI-101 may be a suitable target for those tumors that are resistant to palbociclib. The differences in response to TTI-101 in the BCX94 versus our intrinsic PDX models, suggest that acquired vs. intrinsic resistance signatures of palbociclib may be mutually exclusive and that the IL-6-STAT3 signaling axis may be a driver in acquired palbociclib resistance, but not the intrinsic setting. Our ongoing studies are therefore geared towards testing the efficacy of IL-6-STAT3 inhibition in both settings (i.e. acquired and intrinsic) and identifying distinct therapeutic vulnerabilities of intrinsic palbociclib resistance that may be unresponsive to STAT3 inhibition.

Citation Format: Nicole M Kettner, Tuyen Bui, Min Jin Ha, T Kris Eckols, David J Tweardy, Funda Meric-Bernstam, Kelly K Hunt, Debu Tripathy, Khandan Keyomarsi. STAT3 as a therapeutic target in estrogen receptor positive breast cancer patients refractory to CDK4/6 inhibition [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-04-12.

Abstract P3-10-02: Neutrophil elastase as a therapeutic target to inhibit metastasis in breast cancer

Background: Chronic inflammation, a hallmark of cancer, is associated with poor prognosis in human various malignancies. Predominantly, tumor associated neutrophils (TANs) and myeloid-derived suppressor cells (MDSCs) are immune cells well characterized to promote inflammation, support tumor growth and metastasis, by secreting chemokines, serine proteases and reactive oxygen species. Increased TANs and MDSCs are predictive markers of both tumor progression and metastasis, suggesting that their inhibition may provide viable anti-tumor strategies. Neutrophil elastase (NE), a serine protease exclusively secreted by TANs and MDSCs, is a crucial mediator of inflammation and tumor progression. Recent preliminary studies from our group suggests that genetic deletion of Elane (encoding NE) inhibits lung metastasis in in vivo models of breast cancer. Yet the precise mechanism(s) by which NE promotes tumorigenesis and metastasis of breast cancer remains to be elucidated. To address this gap in knowledge, the current focus of our work is to identify the tumor-intrinsic and -extrinsic mechanisms by which NE promotes metastasis.

Methods: To determine the prognostic significance of NE, we analyzed 192 breast cancer patients (58% ER/PR+ve, 20%-HER-2 +ve and 22% TNBC) for infiltration of TANs. To examine the role of NE in breast cancer metastasis, we have generated Elane+/+ and Elane-/- mice in BALB/c and FVB/N genetic backgrounds, bearing 4T1 and PyMT tumors (orthotopic and spontaneous) respectively. Each of these mouse models develop lung metastasis in 80-90% in tumor-bearing mice within 1-3 months of primary tumor initiation.

Results: Immunohistochemical staining of NE, a marker of TANs shows that higher infiltration of NE-positive TANs is associated with recurrence free survival with a hazard ratio of 3.4 (95% CI, 1.1-5.5). Genetic ablation of NE (Elane −/−) in the PyMT and 4T1 models strongly inhibits lung metastasis. Specifically, the number of lung foci was reduced by ~90% in PyMT Elane−/− mice compared to controls (21.8 vs. 2.7, respectively; p=0.0044). Similarly, ~50% decrease in the number of lung foci was observed in the 4T1 Elane−/− mice compared to control (7.8 vs. 3.4, respectively; p=0.0281). Comparison of inflammatory factors in the tumor microenvironment revealed that Csf3 (G-CSF), Cxcr2 (CXCR2) and Cxcl1 (CXCL1/KC) were significantly elevated in tumors from PyMT/4T1 Elane+/+ mice vs. PyMT/4T1 Elane-/- animals. Mechanistically, our result implies NE-dependent recruitment of immunosuppressive subsets (CXCL1 and related chemokines), thus sustaining inflammation at the primary tumor site. NE- dependent secretion of CXCL1 can further enrich for cancer stem-like cells (CSCs) via CXCR2 signaling, thus aiding metastasis. Lastly, we interrogated the efficacy reversible NE inhibitor AZD9668 in Elane+/+ mouse models. 100mg/kg daily treatment of AZD9668 reduced lung metastasis in PyMT mice by 94% compared to vehicle-treated mice (0.49+/- 0.21% vs. 0.03+/-0.01%; p=0.05).

Conclusions: Collectively, our studies suggest that genetic and pharmacological ablation of NE reduces metastasis in in vivo models of breast cancer. NE inhibitors thus far have only been clinically tested in COPD patients and their efficacy in breast cancer remains to be evaluated. Our preclinical studies presented here are likely to provide the much needed rationale for the use of this class of NE inhibitors as a viable treatment strategy for the metastatic breast cancer.

Citation Format: Amriti Rajender Lulla, Said Akli, Taylor T Chrisikos, Marc A. Pina, Yifan Zhou, Haiyan Li, Stephanie S Watowich, Khandan Keyomarsi. Neutrophil elastase as a therapeutic target to inhibit metastasis in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-10-02.

Abstract P4-06-03: Assessment of intratumoral heterogeneity in early stage estrogen receptor (ER) positive breast cancer

Introduction: Tumor heterogeneity is a hallmark of cancer and its underlying clinical relevance has been well established across different tumor types. In the context of ER-positive breast cancer, variation in ER expression among different tumors or distinct cell populations within a single tumor are predicted to account for differences in clinical behavior, treatment response, and disease recurrence. However, a clear understanding of the molecular and cellular mechanisms of tumor heterogeneity that are relevant to the prognosis and therapy of early stage ER-positive breast cancer has not been established. Previous results from bulk RNA-sequencing (RNA-seq) of ER-positive biopsies represent an average of gene expression patterns; this might obscure biologically relevant differences between cells. Single-cell RNA-sequencing (scRNA-seq) is an approach to overcome this problem, allowing assessment of intratumoral cell populations and biological systems at unprecedented resolution. In this study, our aim is to compare gene expression profiles of bulk RNA-seq and scRNA-seq from tumor biopsies of early stage ER-positive patients. Methods: Tumor and normal biopsies obtained from ER-positive patients were divided into 3 parts; two being dissociated by enzymatic disaggregation and one by direct total RNA isolation. Tumor tissues were subjected to both scRNA-seq and bulk RNA-seq analyses while single-cell suspension of the normal matched tissue was used for bulk RNA-seq alone. Furthermore, patient-derived organoids were generated from both normal and tumor samples. Single-cell isolation and barcoding were assessed using the 10x Genomics technology followed by RNA sequencing with the Illumina NovaSeq6000 system (50PE), whereas bulk RNA-seq was performed using an Illumina PE150 strategy. Results: Our preliminary data represents an assessment of tumor and normal adjacent tissues collected after mastectomy from an 80-year old ER-positive, PR-positive, HER2-negative patient diagnosed with early stage infiltrating ductal carcinoma in situ (stage IB). scRNA-seq of tumor tissue from this patient identified 10 distinct clusters of cells, consisting of both immune and non-immune stromal populations (epithelial, endothelial, fibroblasts, and immune cells). 95% of single cells were luminal. However, there was a minor group (2%) of cells showing a basal-like signature, which can lead to disease recurrence. Interestingly, although the patient was clinically characterized as HER2-negative by IHC and FISH, HER2 overexpression is observed in the vast majority (95%) of single cells isolated. Furthermore, organoid cultures recapitulated the features of patients' tumors and presented similar transcriptomic profiles. We have adapted similar sequencing and downstream analyses for an additional number of patient biopsies. Our ongoing study is geared towards comparing bulk and single cell transcriptome profiles from these ER-positive cases and identifying overlapping populations that can predict recurrence or novel therapeutic vulnerabilities. Conclusions: Bulk RNA-seq approaches lack the resolution to visualize the true extent of stromal heterogeneity and may mask rare populations or cellular phenotypes that could be critical for tumor survival. ScRNA-seq highlights the dynamic and adaptive nature of all cellular populations within an evolving tumor microenvironment and reveal potential crosstalk between these two compartments. Lastly, establishment of organoid cultures presents the opportunity of high-throughput drug screening studies and the identification of new, patient-tailored therapeutic strategies.

Citation Format: Sofia Mastoraki, Juliana Navarro-Yepes, Tuan Tran, Aysegul Sahin, Kelly Hunt, Nicholas Navin, Khandan Keyomarsi. Assessment of intratumoral heterogeneity in early stage estrogen receptor (ER) positive breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-03.

Abstract P6-03-09: Role of IL-6 in promoting endocrine therapy and palbociclib resistance estrogen receptor positive breast cancer cells

Background: CDK4/6 inhibitors combined with endocrine therapy (ET) are mainstay to treat metastatic estrogen receptor (ER) positive patients. Yet, almost 60% develop resistance to CDK4/6 inhibition within 2 years of initial treatment. An ongoing clinical challenge has thus been identifying biomarkers of response to predict patients that will either respond or not respond to palbociclib. Further, there is an unmet need to identify actionable targets for patients that have progressed on CDK4/6 blockade regimens. Currently, the only biomarker being used to identify patients for anti-CDK4/6 therapy is estrogen receptor (ER) by IHC. The goal of our study was thus to identify the therapeutic vulnerabilities of CDK4/6 inhibitor resistance cells and identify key markers that can longitudinally correlate with development of resistance.

Methods: We have developed MCF7 and T47D resistant cells by treating them with increasing doses (1.2, 2.4, 3.6, and 4.8μΜ) of palbociclib over a 6-month period. At each dose, resistant cells were harvested to observe dose dependent changes that occur as the cells acquire resistance to palbociclib. At endpoint i.e. 4.8μM, multi-omics approach was used to compare sensitive vs. resistant cells.

Results: Our multi-omics data indicates that palbociclib resistant cells show i) Upregulation of the STAT3-IL6 pathway ii) Loss of ERα and iii) Loss RB protein levels. Primarily, resistant cells adapt to palbociclib treatment by a dose dependent upregulation of IL6. Further, we observe that induction of IL-6 is an early event which also correlates with senescence-associated secretory phenotype (SASP) signature in resistant cells, predicted to be induced with CDK4/6 inhibition. Importantly, time-course studies using 1μM palbociclib indicates that IL-6 is needed in overcome SASP and promote proliferation in cells adapting and eventually developing resistance to CDK4/6 inhibition. Lastly, we subjected MCF7 and T47D parental cells, which are sensitive to endocrine therapy and palbociclib, with exogenous IL-6 and IL-6 receptor (IL-6R). Treatment with IL-6/IL-6R lead to the downregulation of ER and RB protein levels. IL-6 treated parental cells are 5-fold more resistant to tamoxifen and 7-fold more resistant to fulvestrant compared to parental cells not treated with IL-6. Additionally, dose response studies with palbociclib showed parental cells treated with IL-6 are 5-fold more resistant to palbociclib treatment compared to the cells cultured in the absence of IL-6.

Conclusions: Collectively, our data suggests that resistance to palbociclib results in a cascade of events initiating with induction of senescence, leading to sustained upregulation of IL-6 which leads to the promotion of an aggressive tumor growth, accompanied by resistance to endocrine therapy. Our ongoing studies are geared towards delineating the role of each step of CDK4/6 resistance and determining if IL-6 is required to maintain CDK4/6 inhibition resistance. Our long-term goal is to correlate provide the pre-clinical rationale for using IL-6 as a predictive biomarker in patients receiving CDK4/6 inhibitor based therapies.

Citation Format: Nicole M Kettner, Tuyen Bui, Xian Chen, Kelly K Hunt, Debu Tripathy, Khandan Keyomarsi. Role of IL-6 in promoting endocrine therapy and palbociclib resistance estrogen receptor positive breast cancer cells [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-03-09.

Abstract 323: Combined inhibition of STAT-3 & DNA repair in palbociclib resistant breast cancer

The CDK4/6 inhibitor palbociclib is currently being used in combination with endocrine therapy to treat advanced ER positive breast cancer patients. While this treatment has shown great promise in the clinic, about 25-35% of the patients do not respond initially, and almost all patients eventually acquire resistance. Hence, understanding the mechanisms of acquired resistance to CDK4/6 inhibition is crucial to devise alternate treatment strategies.

To identify mechanisms of resistance to CDK4/6 inhibition we developed MCF-7 and T47D palbociclib resistant cells in a step-wise manner by gradually increasing concentrations of palbociclib. These cells are not only resistant to palbociclib, but exhibited resistance to the other approved CDK4/6 inhibitors; ribociclib and abemaciclib. Additionally, we assessed if these resistant cells have an altered response to endocrine therapy and observed that these cells are also resistant to treatment with tamoxifen or fulvestrant by about 16-fold. Multi-omics analyses revealed enrichment of pathways known to regulate EMT and promote stem-like properties, as well as, downregulation of estrogen response and DNA repair pathways.

Palbociclib resistant cells exhibited mammosphere formation and CD44high/CD24low population indicating the presence of increased breast cancer stem cell-like cells (B-CSC-L). Given the recently elucidated role of IL-6/STAT-3 mediated B-CSC-L phenotypes in drug resistance, we examined IL-6 mRNA levels, which increased by &gt;12-fold in the resistant cells. Treatment with STAT-3 inhibitors, napabucasin and C188-9, significantly decreased the B-CSC-L population and mammosphere formation, indicating a crucial role for the IL-6/STAT-3 pathway in driving B-CSC-L phenotype and palbociclib resistance.

Since DNA repair pathways were collectively downregulated in the palbociclib resistant cells, we examined their sensitivity to DNA damaging agents. Results showed that resistant cells were more sensitive to olaparib (PARP inhibition), with no effect on B-CSC-L population. Next, we examined if combined treatment with agents targeting STAT-3 and PARP would be synergistic in palbociclib resistant cells. Results show that combined treatment with olaparib and napabucasin or C-1889 significantly decreased B-CSC-L population, colony formation and increased cell death via apoptosis, when compared to no-treatment or single treatment controls of the palbociclib resistant cells.

Lastly, we interrogated matched tumor samples from breast cancer patients who progressed on palbociclib for deregulation of estrogen receptor, DNA repair, and IL-6/STAT3 signaling and found that these pathways are altered as compared to the pre-treatment samples.

Taken together, the results show that targeting IL-6/STAT-3 mediated cancer stem cells and DNA repair deficiency by PARP inhibitors in combination can effectively treat acquired resistance to palbociclib.

Citation Format: Nicole M. Kettner, Smruthi Vijayaraghavan, Merih Guray Durak, Tuyen Bui, Mehrnoosh Kohansal, Min Jin Ha, Bin Liu, Xiayu Rao, Jing Yang, Min Yi, Jason P. Carey, Xian Chen, T. Kris Eckols, Akshara S. Raghavendra, Nuhad K. Ibrahim, Meghan Karuturi, Stephanie S. Watowich, Aysegul A. Sahin, David J. Tweardy, Kelly K. Hunt, Debu Tripathy, Khandan Keyomarsi. Combined inhibition of STAT-3 & DNA repair in palbociclib resistant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 323.

Combined Inhibition of STAT3 and DNA Repair in Palbociclib-Resistant ER-Positive Breast Cancer

PURPOSE

Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors are currently used in combination with endocrine therapy to treat advanced hormone receptor-positive, HER2-negative breast cancer. Although this treatment doubles time to progression compared with endocrine therapy alone, about 25%-35% of patients do not respond, and almost all patients eventually acquire resistance. Discerning the mechanisms of resistance to CDK4/6 inhibition is crucial in devising alternative treatment strategies.

EXPERIMENTAL DESIGN

Palbociclib-resistant cells (MCF-7 and T47D) were generated in a step-wise dose-escalading fashion. Whole-exome sequencing, genome-wide expression analysis, and proteomic analysis were performed in both resistant and parental (sensitive) cells. Pathway alteration was assessed mechanistically and pharmacologically. Biomarkers of altered pathways were examined in tumor samples from patients with palbociclib-treated breast cancer whose disease progressed while on treatment.

RESULTS

Palbociclib-resistant cells are cross-resistant to other CDK4/6 inhibitors and are also resistant to endocrine therapy (estrogen receptor downregulation). IL6/STAT3 pathway is induced, whereas DNA repair and estrogen receptor pathways are downregulated in the resistant cells. Combined inhibition of STAT3 and PARP significantly increased cell death in the resistant cells. Matched tumor samples from patients with breast cancer who progressed on palbociclib were examined for deregulation of estrogen receptor, DNA repair, and IL6/STAT3 signaling, and results revealed that these pathways are all altered as compared with the pretreatment tumor samples.

CONCLUSIONS

Palbociclib resistance induces endocrine resistance, estrogen receptor downregulation, and alteration of IL6/STAT3 and DNA damage response pathways in cell lines and patient samples. Targeting IL6/STAT3 activity and DNA repair deficiency using a specific STAT3 inhibitor combined with a PARP inhibitor could effectively treat acquired resistance to palbociclib.

Cytoplasmic cyclin E independently predicts recurrence in older patients with primary breast cancer

3128

Background: Primary breast cancer in the older ( > 70 years) population has distinct biological characteristics associated with favourable outcome, such as higher rate of estrogen receptor (ER) positivity. Due to comorbidities, older patients with primary breast cancer are more likely to die of non-breast cancer-related causes compared to their younger counterparts. Biomarkers that may influence treatment strategy therefore require interpretation in the specific biological and clinical context of older women. Cyclin E regulates cell cycle transition from G1 to S phase, and its deregulation is implicated in breast cancer pathogenesis. Tumour-specific isoforms of cyclin E localise to the cytoplasm. Expression of cytoplasmic cyclin E (c-cyclin E) is linked with poor clinical outcome. We now present multivariate analysis of breast cancer-specific survival (BCSS) by c-cyclin E and clinical markers of disease biology from a cohort of older women. The primary outcome, BCSS, excludes deaths from competing causes and is used as a surrogate for tumour biology. Methods: Between 1973 and 2010, 813 older women underwent initial surgery for early breast cancer and were followed up in a dedicated clinic in Nottingham. Excised tumours from 517 of these patients were successfully incorporated into a tissue microarray (TMA). Expression of c-cyclin E was assessed by IHC using an assay developed at MDACC, along with a panel of 24 biomarkers. Of these, ER, progesterone receptor (PR), human epidermal growth factor 2 (HER2) and Ki67 are in current clinical use and are analysed alongside c-cyclin E. Grade was assessed from the primary tumour. Multivariate analysis of BCSS was performed by Cox proportional hazard test. Results: In multivariate analysis alongside markers of disease biology currently used in the clinic (ER, PR, HER2, Ki67 and grade), c-cyclin E is the only factor that independently predicts BCSS in this cohort of older women (HR 5.0, 95% CI 2.1 – 12.0; p< 0.001). Conclusions: In the older population with primary breast cancer, c-cyclin E expression is the only independent biological marker of BCSS. Patients with low c-cyclin E expression are unlikely to die of breast cancer. These data have potential to influence treatment strategy in older patients. For example, patients with ER+, c-cyclin E negative disease plus multiple co-morbidities may be suitable for primary endocrine therapy. This hypothesis warrants prospective clinical evaluation.

Abstract PD7-11: Therapeutic strategy for ESR1 mutation driven-endocrine resistance in ER-positive breast cancers

Background: Endocrine therapy is used in estrogen receptor (ER)-positive breast cancers, however, 25% of these patients are at risk of distant relapse and the development of acquired endocrine resistance. Recently mutations in the ER gene (ESR1) have been validated to be acquired during the development of endocrine resistance. The most frequent ESR1 mutation, Y537S, promotes ligand-independent ER activity and emerges subclonally during aromatase inhibitor treatment. In this study, we examined the effects of the Y537S ESR1 mutation on cell cycle signaling and therapeutic response to a novel checkpoint inhibitor.

Material and Methods: MCF-7 cells expressing the Y537S ESR1 mutation were generated by CRISPR-Cas9 knock-in techniques. Cells were incubated in steroid deprived conditions. Cell cycle analysis and apoptosis were examined by flow cytometry annnexin-V assays. Proliferation was analyzed by BrdU incorporation. Cell cycle checkpoint kinases were examined by western blot analysis. Cell growth was analyzed using soft agar and MTT assays. Replication stress was identified by RPA32 and gamma-H2AX foci formation assay. For in vivo studies, MCF-7 ESR1 Y537S mutant cells were injected into female athymic nude mice with 17β-estradiol (E2) supplemented water. When tumors reached 350 mm3, tamoxifen (20 mg/kg; s.c.; three times a week), fulvestrant (200 mg/kg; s.c; once a week) and/or PF477736 Chk1 inhibitor (7.5 mg/kg; i.p.; twice a day and twice a week) was treated without E2.

Results: ESR1 Y537S mutant cells accumulated approximately 5 fold in S phase and 1.7 fold in G2/M phase compared to control cells in estrogen-deprived (ED) conditions. BrdU incorporation also increased about 2.5-fold, however, apoptosis was decreased about 60 % compared with wild-type ER parental cells. ESR1 Y537S mutant cells induced significant replication stress, showing increased RPA32 foci together with increased gamma H2AX foci, a marker of DNA double-stranded breaks. ChIP-seq analysis revealed binding sites on ATR and CHEK1 genomic locations. ATR/Chk1-mediated checkpoint signaling was activated in ESR1 Y537S mutant cells, and was repressed with fulvestrant, tamoxifen, or ESR1 siRNA treatment. The Chk1 inhibitor, PF477736, sensitized MCF-7 expressing the ESR1 Y537S mutation to endocrine treatments such as fulvestrant, tamoxifen, and the ER degrader AZD9496 in cell proliferation assays. In MCF-7 ESR1 Y537S mutant xenograft and patient derived mouse models, tamoxifen treatment combined with the Chk1 inhibitor PF477736 repressed primary xenograft tumor doubling times (P=0.038, Wilcoxon test). Treatment of mutant tumors with PF477736 together with fulvestrant significantly inhibited the frequency of distant lung metastases by 80% (P=0.0031, t-test), suggesting that these combinations may be useful in second line treatment of metastatic breast cancer patients resistant to endocrine therapies.

Conclusion: These preclinical results suggest that ESR1 mutant tumors have a therapeutic vulnerability to combination endocrine therapy with cell cycle checkpoint kinase inhibitors. These data demonstrate that this new therapeutic approach may be useful to restore endocrine sensitivity in metastatic breast cancer patients with ESR1 mutation driven-endocrine resistance.

Citation Format: Kim J-A, Dustin D, Gu G, Corona-Rodriguez A, Edwards D, Coarfa C, Keyomarsi K, Fuqua SA. Therapeutic strategy for ESR1 mutation driven-endocrine resistance in ER-positive breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD7-11.

Low-Molecular-Weight Cyclin E in Human Cancer: Cellular Consequences and Opportunities for Targeted Therapies

Cyclin E, a regulatory subunit of cyclin-dependent kinase 2 (CDK2), is central to the initiation of DNA replication at the G1/S checkpoint. Tight temporal control of cyclin E is essential to the coordination of cell-cycle processes and the maintenance of genome integrity. Overexpression of cyclin E in human tumors was first observed in the 1990s and led to the identification of oncogenic roles for deregulated cyclin E in experimental models. A decade later, low-molecular-weight cyclin E (LMW-E) isoforms were observed in aggressive tumor subtypes. Compared with full-length cyclin E, LMW-E hyperactivates CDK2 through increased complex stability and resistance to the endogenous inhibitors p21CIP1 and p27KIP1 LMW-E is predominantly generated by neutrophil elastase-mediated proteolytic cleavage, which eliminates the N-terminal cyclin E nuclear localization signal and promotes cyclin E's accumulation in the cytoplasm. Compared with full-length cyclin E, the aberrant localization and unique stereochemistry of LMW-E dramatically alters the substrate specificity and selectivity of CDK2, increasing tumorigenicity in experimental models. Cytoplasmic LMW-E, which can be assessed by IHC, is prognostic of poor survival and predicts resistance to standard therapies in patients with cancer. These patients may benefit from therapeutic modalities targeting the altered biochemistry of LMW-E or its associated vulnerabilities. Cancer Res; 78(19); 5481-91. ©2018 AACR.

Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition

PURPOSE

Poor prognosis in triple-negative breast cancer (TNBC) is due to an aggressive phenotype and lack of biomarker-driven targeted therapies. Overexpression of cyclin E and phosphorylated-CDK2 are correlated with poor survival in patients with TNBC, and the absence of CDK2 desensitizes cells to inhibition of Wee1 kinase, a key cell-cycle regulator. We hypothesize that cyclin E expression can predict response to therapies, which include the Wee1 kinase inhibitor, AZD1775.

EXPERIMENTAL DESIGN

Mono- and combination therapies with AZD1775 were evaluated in TNBC cell lines and multiple patient-derived xenograft (PDX) models with different cyclin E expression profiles. The mechanism(s) of cyclin E-mediated replicative stress were investigated following cyclin E induction or CRISPR/Cas9 knockout by a number of assays in multiple cell lines.

RESULTS

Cyclin E overexpression (i) is enriched in TNBCs with high recurrence rates, (ii) sensitizes TNBC cell lines and PDX models to AZD1775, (iii) leads to CDK2-dependent activation of DNA replication stress pathways, and (iv) increases Wee1 kinase activity. Moreover, treatment of cells with either CDK2 inhibitors or carboplatin leads to transient transcriptional induction of cyclin E (in cyclin E-low tumors) and result in DNA replicative stress. Such drug-mediated cyclin E induction in TNBC cells and PDX models sensitizes them to AZD1775 in a sequential treatment combination strategy.Conclusions: Cyclin E is a potential biomarker of response (i) for AZD1775 as monotherapy in cyclin E-high TNBC tumors and (ii) for sequential combination therapy with CDK2 inhibitor or carboplatin followed by AZD1775 in cyclin E-low TNBC tumors.

Abstract 1843: Combination therapy targeting Rb/Wee1 kinase pathways for rhabdomyosarcoma treatment

Introduction

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. New therapeutic strategies are needed particularly for high-risk patients where the survival rate is 20-40%. The FDA approved CDK4/6 inhibitor palbociclib (PD), and the WEE1 kinase inhibitor MK-1775 have anticancer effects when used as single agents. PD causes cell arrest at G1 phase (requiring intact Rb), while MK-1775 promotes cell death by abrogating DNA damage during the G2/M checkpoint phase by forcing premature mitosis entry. As the two drugs target tumor cells at different phases of the cell cycle, cells that are not in the targeted phase may escape single therapy. We hypothesized that sequential combination therapy will increase therapeutic efficacy. The use of PD first, will induce the cells to go under G1 arrest. Upon recovery, more cells will synchronize in the S/G2 phase, increasing their susceptibility to MK1775, resulting in synergistic cell killing.

Methods

Rb+ RMS (Rh-30) and Rb- osteosarcoma (OS) cell lines (CCH-D, LM7, and SASO2) were treated with increasing doses of PD for 6 days, then stained with propidium iodide (PI) and analyzed for cell cycle status to determine whether PD induced G1 arrest. To determine the optimal recovery time for Rb+ cells to be synchronized in S/G2 phase, cells were treated with PD (IC50-IC75) for 6 days and then were harvested either immediately or after 3-24 h recovery in drug free medium. Cells were stained with PI for cell cycle analysis. A 12-day long combination therapy assay was performed with or without recovery time between the two treatments. Combination index (CI) was calculated by using the statistical program calcusyn to determine whether the combinatorial drug treatment had acted in an antagonistic, additive or synergistic manner.

Results

Six days of treatment with PD resulted in reversible G1 arrest only in Rb+ cell lines, confirming that Rb, the downstream target of CDK4, must be intact to induce G1 arrest by palbociclib. Six days of treatment with PD followed by 9-12 h recovery in fresh medium (the optimal recovery time prior to treatment with MK-1775), led to re-entry of the Rb+ Rh-30 cells into the cell cycle and successful synchronization at S/G2 phase. By contrast, Rb- cells failed to arrest in G1 phase following treatment with PD and were not synchronized at S/G2 phase. Since cells synchronized in S/G2 phase are more vulnerable to MK1775, combination therapy resulted in a synergistic effect in the Rb+ cells but an antagonistic effect in the Rb- cells.

Conclusion:

Our results suggest that the combination therapy strategy of PD preceding MK1775 may be a novel therapeutic approach for patients with Rb+ RMS. This strategy will be investigated in xenograft and PDX RMS model.

Citation Format: Simin Kiany, Gangxiong Huang, Melanie Justice, Khandan Keyomarsi, Eugenie Kleinerman. Combination therapy targeting Rb/Wee1 kinase pathways for rhabdomyosarcoma treatment [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 1843.

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Background

Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

Results

To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells.

Discussion

Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway.

Conclusions

Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4533-0) contains supplementary material, which is available to authorized users.

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized (“normal”) human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.