Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer

The MYC oncogene is frequently amplified in triple-negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set expression and tumor-infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING1 enhancer region, resulting in downregulation of the T-cell chemokines CCL5, CXCL10, and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small-molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC expression, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.

Abstract PD3-07: Combined inhibition of CDK4/6 and AKT is effective in Rb-intact triple-negative breast cancer of the luminal androgen receptor (LAR) subtype

Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease group with variable clinico-pathologic features. Based on gene expression profiles, TNBCs are grouped into 6 major subtypes. The Luminal androgen receptor (LAR) subtype is enriched for potentially targetable biomarkers, including high androgen receptor (AR) expression, high rates of PIK3CA mutations, and intact Rb. The purpose of this study was to investigate the most effective combinations of CDK4/6, AR, and PI3K-AKT inhibitors in pre-clinical models of LAR TNBC for future clinical trial design. Methods: MDA-MB-453 and MFM-223 (both Rb-intact/PTEN-intact/PIK3CA-mutant) and CAL-148 (Rb-null/PTEN-null/PIK3CA-mutant) LAR TNBC cell lines were treated with the CDK4/6 inhibitor palbociclib, the PI3Kα inhibitor alpelisib, the AKT inhibitor capivasertib, and the AR antagonist enzalutamide, each alone or in different combinations. Drug sensitivity was determined by coulter counter cell counts in 2D, colony formation, and the CellTiterGlo cell viability assay. The combination index (CI) which defines synergism (CI < 1), additive effect (CI = 1) and antagonism (CI > 1), calculated by the CompuSyn method, was used to evaluate the synergistic effects of drug combinations. Expression of cell cycle and PI3K-AKT downstream signaling molecules was measured by western blot analysis. An androgen response element (ARE) luciferase-based reporter assay was used to evaluate AR transcriptional activity. Results: Rb-intact LAR TNBC cell lines were sensitive to single-agent palbociclib, alpelisib or capivasertib (IC50, ~500 nM). Enzalutamide had minimal growth inhibitory activity (IC50, 15-25 μM). Palbociclib combined with either alpelisib or capivasertib synergistically inhibited proliferation of LAR TNBC cells (CI values, 0.07-0.86). Treatment of Rb-intact LAR TNBC cells with palbociclib monotherapy suppressed Rb phosphorylation and resulted in adaptive phosphorylation/activation of S473 AKT and AKT substrates GSKβ and PRAS40 at 24h. These responses were not observed in Rb-null CAL-148 cells. Palbociclib-induced phosphorylation of AKT substrates as well as induction P-S6 and P-4EBP1 were better suppressed by capivasertib than by alpelisib over a dose range. Addition of the PI3Kβ/δ inhibitor AZD8186 to alpelisib markedly enhanced the inhibition of P-AKT, P-PRAS40 and P-Sin, suggesting inhibition of PI3Kα is inadequate to block the adaptive response to palbociclib in these cells. Mean CI values showed that the combination of palbociclib/capivasertib was more synergistic against LAR TNBC cells compared to palbociclib/alpelisib (mean CI, 0.29 vs. 0.78). ARE reporter activity did not change upon inhibition of PI3K or AKT with alpelisib or capivasertib, respectively. Conclusions: Our results suggest that addition of an AKT inhibitor to palbociclib suppresses the rebound activation of AKT following treatment with the CDK4/6i and is effective in LAR TNBC with wild type Rb. In vivo studies are underway to investigate the antitumor activity of the combination of palbociclib and capivasertib in LAR TNBC xenografts.

Citation Format: Gun Min Kim, Kyung-min Lee, Dhivya Sudhan, Albert Lin, Arnaldo Marin, Sumanta Chatterjee, Dan Ye, Vishal Kandagatla, Saurabh Mendiratta, Ariella Hanker, Carlos Arteaga. Combined inhibition of CDK4/6 and AKT is effective in Rb-intact triple-negative breast cancer of the luminal androgen receptor (LAR) subtype [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 PD3-07.

Abstract PD2-01: A platform of CDK4/6 inhibitor-resistant patient-derived breast cancer organoids illuminates mechanisms of resistance and therapeutic vulnerabilities

CDK4/6 inhibitors (CDK4/6i) in combination with antiestrogens have revolutionized the treatment of ER+ metastatic breast cancer (MBC), significantly prolonging survival. However, this combination is not curative, and tumors eventually acquire resistance. Following progression on this combination, patients are left with limited treatment options. A diverse array of mechanisms of resistance to CDK4/6i + antiestrogens have been described. However, laboratory models that capture this heterogeneity of resistance mechanisms are lacking. Patient-derived organoids (PDOs) provide a rapid, robust and reliable platform that recapitulates intra-tumor heterogeneity, partially mimics the cancer microenvironment, and accurately predicts drug response. We aspired to generate a platform of CDK4/6i-resistant breast cancer PDOs to serve as models for understanding acquired resistance to CDK4/6i + antiestrogens and identifying therapies to overcome resistance. We successfully established 16 PDOs out of 32 biopsies (50% efficiency) of metastates from patients with ER+ MBC progressing on CDK4/6i (palbociclib or abemaciclib) + antiestrogens (letrozole or fulvestrant; median response to combination = 9 months). Our collection includes PDOs derived from lobular (n=3) and inflammatory (n=2) breast cancers and reflects racial/ethnic diversity (50% white/not Hispanic; 18.8% Hispanic; 12.5% Black; 12.5% other/unknown). Next-gen sequencing reports were available for 10 patients from which organoids were established, revealing alterations associated with CDK4/6i and/or antiestrogen resistance, including ESR1 (n=2), HER2/ERBB2 (n=2), PTEN (n=2), CCNE1 (n=1), NF1 (n=1), and ARID1A (n=1). Furthermore, one biopsy and its derived organoid lost ER expression, and 5 harbored PIK3CA activating mutations. Thus far, we have performed targeted DNA-sequencing on 7 PDOs and found 13/15 (86.7%) concordance with driver mutations from tumor NGS reports. PDOs established from CDK4/6i-resistant biopsies maintained resistance to palbociclib or abemaciclib ± fulvestrant (500 nM each) in 3D cell viability assays (6 days of treatment). In contrast, control PDOs established from primary ER+ breast cancer surgical samples (n=2) were sensitive to each CDK4/6i ± fulvestrant (median viability for combination=25.6-31.5% for control vs 65.2-80.5% for resistant). GSEA analysis of RNA-seq data from control (n=2) and CDK4/6i-resistant (n=6) PDOs cultured in estrogen-depleted media ± 200 nM palbociclib revealed that palbociclib treatment resulted in downregulation of E2F target and G2M checkpoint signatures in control but not resistant PDOs. Next, we performed a high-throughput screen of 1,000 compounds in 3 resistant PDOs. One PDO showed exquisite sensitivity to G2/M cell cycle checkpoint components, including CDK1, PLK1, Aurora kinase, ATR, Chk1, and Wee1 inhibitors. Finally, treatment of 10 resistant PDOs with the CDK2/4/6 inhibitor PF-06873600 revealed that the CCNE1 (cyclin E1)-amplified PDO was highly sensitive (IC50=130 nM vs >1000 nM), supporting that CCNE1-amplified tumors are vulnerable to CDK2 inhibition. Conclusions: PDOs can be successfully established from ER+ MBC biopsies, maintain the resistant phenotype in culture, retain driver alterations found in tumors from which they were derived, and fail to suppress E2F targets following treatment with CDK4/6i. Therefore, these PDOs represent valuable models to understand and explore diverse mechanisms of CDK4/6i resistance and therapeutic vulnerabilities.

Citation Format: Ariella B. Hanker, Sumanta Chatterjee, Yunguan Wang, Dan Ye, Dhivya R. Sudhan, Brian M. Larsen, Lauren C. Smith, Yilin Zhang, Vishal Kandagatla, Kuntal Majmudar, Ezequiel Renzulli, Saurabh Mendiratta, Kimberly Blackwell, Alana L. Welm, Sunati Sahoo, Nisha Unni, Cheryl M. Lewis, Tao Wang, Ameen A. Salahudeen, Carlos L. Arteaga. A platform of CDK4/6 inhibitor-resistant patient-derived breast cancer organoids illuminates mechanisms of resistance and therapeutic vulnerabilities [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 PD2-01.

Abstract GS3-09: Loss of ASXL1 tumor suppressor promotes resistance to CDK4/6 inhibitors in ER+ breast cancer

Background: CDK4/6 inhibitors (CDK4/6i) in combination with antiestrogens have prolonged survival of patients with ER+ metastatic breast cancer. However, this combination is not curative mainly due to acquired drug resistance. Knowledge about mechanisms of such resistance remains quite incomplete. We report herein a forward-genetics screen to discover a broad spectrum of novel somatic mutations causal to CDK4/6i resistance. Methods: We used CRISPR/Cas9 to delete the DNA mismatch repair (MMR) gene MSH2 in MCF7 and T47D ER+ breast cancer cells. Deficiency of DNA MMR proteins such as MSH2 results in a high nucleotide substitution rate which, in turn, predisposes cells to acquire drug resistance-associated mutations. MSH2-/- MCF7 and T47D cells were infected with a lentiviral barcode library containing ~1000 unique DNA barcodes. MSH2-/- barcoded cells were expanded for ~25 doublings to allow the accumulation of random mutations. Clones resistant to CDK4/6i were selected in the presence of IC90 of palbociclib (200 nM) or abemaciclib (500 nM) for 4-6 weeks. CDK4/6i resistant clones with unique barcode IDs were subjected to whole exome sequencing (WES). Results: Following drug selection, ~73 uniquely barcoded resistant colonies emerged from MCF7 and T47D MSH2-/- clonal lines. As expected, MCF7 and T47D MSH2-/- clones harbored a high mutation burden compared to parental cells. Candidate variants were distilled based on (a) functionality prediction and (b) mutation frequency in Project GENIE. We observed RB1 (5/73 clones; 6.8%) mutations in CDK4/6i resistant clones, providing proof-of-principle that this approach can identify clinically-relevant drug resistant alterations. Overall, we identified non-synonymous alterations in 2,206 genes in T47D palbociclib-resistant, 2,195 genes in T47D abemaciclib-resistant, and 1,312 genes in MCF7 palbociclib-resistant lines. A secondary screen of the 10 genes recurrently mutated in all three CDK4/6i resistant groups identified loss of ASXL1 as top hit. ASXL1 encodes a polycomb repressive complex protein that regulates chromatin accessibility. Loss of ASXL1 has been implicated in myeloid transformation through epigenetic reprogramming. WES of 76 CDK4/6i resistant tumor biopsies (DFCI/MBCproject cohort) identified ASXL1 alterations in two and four patients with acquired and primary resistance, respectively (6/76=7.9%). One of the tumors that progressed after an initial response to palbociclib had acquired the same ASXL1 R549C mutation that was identified in our screen. Among 1,769 tumors from patients treated with CDK4/6i (TEMPUS database), 37 exhibited ASXL1 alterations (4 frameshift, 6 truncating, 3 in-frame del, 24 missense mutations). DNAseq of patient-derived organoids established from post-CDK4/6i metastases identified ASXL1 mutations in 2/7 organoids (29%). ASXL1-/- MCF7 and T47D cells were cross-resistant to fulvestrant. GSEA analysis of RNA-seq data showed upregulation of E2F targets in palbociclib-treated cells stably transduced with ASXL1 shRNA but not control shRNA (Enrichment score=0.75, q=1.00E-09). This was associated with maintenance of RB phosphorylation in the presence of CDK4/6i, markedly higher levels of CDK2, CDK6, cyclins E and A, and downregulation of p21 and p27. Finally, siRNAs targeting CDK2 or cyclin A reduced the viability of ASXL1-deficient T47D cells by 50% and 90%, respectively. Conclusions: An accelerated mutagenesis approach using MMR-deficient ER+ breast cancer cells identified loss of ASXL1 as a novel mechanism of resistance to CDK4/6i. ASXL1 alterations were found in ~8% of tumors from patients with de novo or acquired resistance to CDK4/6i. Knockdown of CDK2 and cyclin A restored sensitivity to CDK4/6i and reduced viability of ASXL1 deficient cells, suggesting CDK2 inhibitors are a treatment approach against these drug-resistant tumors.

Citation Format: Dhivya R. Sudhan, Sumanta Chatterjee, Jiwoong Kim, Yunguan Wang, Vishal Kandagatla, Dan Ye, Chang-Ching Lin, Jorge Gomez Tejeda Zanudo, Esha Jain, Arnaldo Marin, Alberto Servetto, Kyung-min Lee, Juan Manuel Povedano, David McFadden, Alex Barrett, Nikhil Wagle, Ariella B. Hanker, Carlos L. Arteaga. Loss of ASXL1 tumor suppressor promotes resistance to CDK4/6 inhibitors in ER+ breast cancer [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 GS3-09.

A Single-Center Trial to Evaluate the Efficacy and Tolerability of Four Microneedling Treatments on Fine Lines and Wrinkles of Facial and Neck Skin in Subjects With Fitzpatrick Skin Types I-IV: An Objective Assessment Using Noninvasive Devices and 0.33-mm Microbiopsies

BACKGROUND

Although ablative techniques are the standard of care for the treatment of fine lines and wrinkles, microneedling offers a minimally invasive alternative.

OBJECTIVES

The purpose of this study was to assess the efficacy of microneedling on facial and neck fine lines and wrinkles.

METHODS

Thirty-five subjects between 44 and 65 years old with Fitzpatrick skin types I to IV received 4 monthly microneedling treatments over the face and neck. Subjects returned 1 and 3 months posttreatment. At every visit, high-resolution ultrasonography and optical coherence tomography were performed, and transepidermal water loss and skin elasticity were measured. Microbiopsies (0.33 mm) were collected pretreatment, before the fourth treatment and 3 months posttreatment.

RESULTS

Thirty-two subjects (30 females, 2 males) completed all 7 visits. Facial dermal and epidermal density increased 101.86% and 19.28%, respectively, from baseline at 3 months posttreatment. Facial elasticity increased 28.2% from baseline at 3 months posttreatment. Facial attenuation coefficient increased 15.65% and 17.33% at 1 and 3 months posttreatment, respectively. At study completion, blood flow at a depth of 300 µm decreased 25.8% in the face and 42.3% in the neck. Relative collagen type III and elastin gene expression was statistically higher 3 months posttreatment. However, total elastin protein levels were unchanged from baseline values. Dermal muscle formation was observed in 58% of biopsies extracted 3 months posttreatment compared with 15.3% at baseline.

CONCLUSIONS

The results illustrate the effects of microneedling treatments. Noninvasive measurements and biopsy data showed changes in skin architecture and collagen/elastin gene expression, suggesting skin rejuvenation, with new extracellular matrix production and muscle formation.

LEVEL OF EVIDENCE: 3