Heterogeneity and transcriptional drivers of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.

Multiple screening approaches reveal HDAC6 as a novel regulator of glycolytic metabolism in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a subtype of breast cancer without a targeted form of therapy. Unfortunately, up to 70% of patients with TNBC develop resistance to treatment. A known contributor to chemoresistance is dysfunctional mitochondrial apoptosis signaling. We set up a phenotypic small-molecule screen to reveal vulnerabilities in TNBC cells that were independent of mitochondrial apoptosis. Using a functional genetic approach, we identified that a "hit" compound, BAS-2, had a potentially similar mechanism of action to histone deacetylase inhibitors (HDAC). An in vitro HDAC inhibitor assay confirmed that the compound selectively inhibited HDAC6. Using state-of-the-art acetylome mass spectrometry, we identified glycolytic substrates of HDAC6 in TNBC cells. We confirmed that inhibition or knockout of HDAC6 reduced glycolytic metabolism both in vitro and in vivo. Through a series of unbiased screening approaches, we have identified a previously unidentified role for HDAC6 in regulating glycolytic metabolism.

Abstract PO-53: Combined EZH2 and BCL2 inhibitors as precision therapy for genetically defined DLBCL subtypes

Molecular alterations in the histone methyltransferase EZH2 and the antiapoptotic protein BCL2 frequently co-occur in diffuse large B-cell lymphoma (DLBCL). We hypothesized that EZH2 inhibition and BCL2 inhibition would be synergistic in DLBCL. To test this, we evaluated the EZH2 inhibitor tazemetostat and the BCL2 inhibitor venetoclax in DLBCL cells, 3D lymphoma organoids, and patient-derived xenografts (PDXs). We found that tazemetostat and venetoclax are synergistic in DLBCL cells that harbor both an EZH2 mutation and a BCL2/IGH translocation, as demonstrated by CI values <1 (CI: 0.034, 0.259 and 0.074 in SUDHL-6, WSU-DLCL2, and OCI-Ly1 respectively), but not in wild-type cells. Since cell lines in suspension do not reflect lymph node architecture, we developed a 3D lymphoma organoid culture system that consists of extracellular matrix, lymphoma cells, and stromal cells (Tian et al., Biomaterials 2015). We observed synergy between the two agents in two organoid model systems: 1) OCI-LY1; 2) PDX derived from a DLBCL with BCL2/IGH translocation and EZH2 mutation. To investigate mechanisms of synergy, we evaluated previously published RNA-seq profiles of DLBCL cell lines (n=26) treated with vehicle or tazemetostat to investigate changes in BCL2 family members (Brach et al., Mol Can Ther 2017). Tazemetostat-treated cells showed enhanced expression of proapoptotic BCL2 family members including BCL2L11 (p=0.012), BMF (p<0.001), and BCL2L14 (p=0.002), suggesting that these may be direct or indirect EZH2 target genes that are de-repressed upon EZH2 inhibition. To assess mitochondrial priming to apoptosis as a result of EZH2 inhibition, we performed BH3 profiling of DLBCL PDX organoids treated with vehicle vs. tazemetostat. Tazemetostat-treated cells had increased priming as evidenced by cytochrome c release in response to general apoptotic signaling peptides BIM and PUMA (p<0.0001) and to the BCL2 specific peptide BAD (p<0.0001), suggesting that pretreatment with tazemetostat increases mitochondrial sensitivity to BCL2 inhibition. We next evaluated combination therapy in vivo. In SUDHL-6 xenografts, the combination resulted in attenuation of tumor growth compared to either drug alone (combination vs. venetoclax p<0.0001, combination vs. tazemetostat p=0.0004) and improved overall survival. In DLBCL PDXs, combination therapy resulted in complete resolutions of tumors, which were durable over time and associated with improved overall survival. Strikingly, after 197 days of follow-up there was no detectable disease in any combination-treated animal. In summary, we demonstrate that combined BCL2 and EZH2 inhibition results in synergistic anti-lymphoma effects. We expect this combination to be especially effective as precision therapy for the newly identified cluster 3/EZB DLBCL subtype, which frequently harbors both EZH2 and BCL2 alterations. A clinical trial of this combination is currently in development.

Citation Format: Hanna Scholze, Regan E. Stephenson, Raymond Reynolds, Shivem Shah, Rishi Puri, Matthew R. Teater, Herman van Besien, Destini Gibbs-Curtis, Hideki Ueno, Salma Parvin, Anthony G. Letai, Susan Mathew, Ankur Singh, Ethel Cesarman, Ari Melnick, Lisa Giulino-Roth. Combined EZH2 and BCL2 inhibitors as precision therapy for genetically defined DLBCL subtypes [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-53.

Abstract A81: Identifying cellular immune components that correlate with response to immunotherapy in breast cancer using murine models

The heterogeneity of the tumor microenvironment may contribute to the lack of durable responses of immunotherapy in breast cancer. To understand factors that contribute to tumor immune cell heterogeneity, we report a detailed analysis and comparison of the immune tumor microenvironment of the autochthonous MMTV-PyMT murine breast cancer model resembling luminal B breast cancer and corresponding syngeneic models. We obtained tumors from MMTV-PyMT mice and used them to generate syngeneic models using either 1E6, 1E5, or 1E4 cells injected into the mammary fat pad of FVB/NJ wild-type mice. When tumors reached 100 mm3, tumors were harvested and quantitative flow-cytometry and NanoString analysis was performed. We have identified that the number of cells inoculated to generate syngeneic tumors significantly influences tumor latency, the tumor immune microenvironment, and the response to immune checkpoint blockade (ICB). Compared to the autochthonous model, the 1E6 and 1E5 model had significantly more tumor-infiltrating lymphocytes (TILs; CD3+, CD4+, and CD8+) and the highest proportion of PD-L1-positive myeloid cells. We found that increased TILs and expression of PD-L1 on myeloid cells were the best predictors of response to PD-L1 or CTLA-4 therapy but that tumor cell expression of PD-L1 and T-cell expression of PD-1 did not correspond to beneficial outcome of treatment. Both the 1E6 and 1E5 models responded to PD-L1 and/or CTLA-4 ICB therapy, whereas the 1E4 and autochthonous models were resistant. These matched sensitive and resistant tumor models represent a unique opportunity to further interrogate the TME in breast cancer.

Citation Format: Anita K. Mehta, Jessica A. Castrillion, Alaba Sotayo, Elizabeth A. Mittendorf, Anthony G. Letai, Jennifer L. Guerriero, Emily Cheney. Identifying cellular immune components that correlate with response to immunotherapy in breast cancer using murine models [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A81.

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies

Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.

Abstract 2496: Dynamic BH3 profiling identifies active combinations with conventional chemotherapy in non-small cell lung cancer

Mitochondrial apoptotic priming (referred to as priming) determines a cell’s ‘readiness’ for cell death and is regulated by the B-cell lymphoma 2 (BCL-2) family of proteins. It has been shown in multiple disease settings such as acute lymphoblastic leukemia, acute myeloid leukemia, multiple myeloma and ovarian cancer, that chemosensitivity correlates with priming. Patients with highly primed tumors exhibited superior clinical response to chemotherapy. In contrast, chemoresistant cancers and normal tissues were poorly primed. Priming is relative and can be measured using BH3 profiling. BH3 profiling is a functional assay which uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only BCL-2 family members to provoke a response from viable mitochondria. To identify drugs that enhance priming, tumor cells can be incubated with drugs prior to BH3 profiling, a method called dynamic BH3 profiling (DBP). DBP is a functional approach to precision medicine and measures early changes in death signaling after drug perturbation. An increase in priming after short term drug treatment (8-24 hours) has been shown to result in cell death days later. Moreover, it has been shown to predict in vivo response to therapy. Therefore, DBP can predict efficacious therapies within 24 hours.We hypothesized that drugs that enhance priming would render cancers more sensitive to conventional chemotherapy. To determine whether drugs that increase priming enhanced sensitivity to docetaxel and etoposide in non-small cell lung cancer (NSCLC), we first identified agents that enhanced priming via DBP. We found that targeted agents that increased priming of NSCLC tumor cells resulted in increased chemosensitivity in vitro. To assess whether targeted agents that increase priming might enhance the efficacy of cytotoxic agents in vivo, we carried out an efficacy study in PC9 xenograft mouse model. The BH3 mimetic navitoclax, which inhibits BCL-xL, BCL-w and BCL-2, consistently primed NSCLC tumors in vitro and in vivo. The BH3 mimetic venetoclax, which inhibits BCL-2, did not. In vivo navitoclax reduced tumor burden whilst mice were treated but as soon as therapy was stopped tumors recovered comparable to vehicle treated mice. Etoposide as a single agent had no effect on tumors. However, combining navitoclax with etoposide significantly reduced tumor burden after treatment was stopped, increasing mouse survival. Adding venetoclax to etoposide had no effect on tumor burden. These data suggest that targeted agents that increase priming, increased chemosensitivity resulting in reduction of tumor burden in vivo.

Citation Format: Danielle S. Potter, Anthony G. Letai. Dynamic BH3 profiling identifies active combinations with conventional chemotherapy in non-small cell lung 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 2496.

Abstract 675: Network modeling of drug resistance mechanisms and drug combinations in breast cancer

Durable control of invasive solid tumors is thwarted by the lack of knowledge of effective drug combinations and of the acquired and intrinsic resistance mechanisms of drugs. In an effort to tackle this problem, the SU2C-NSF-TVF Drug Combination Convergence Team is using mechanistic models of cancer cell signaling based on therapeutic and cell line data in order to identify elements within cancer cells that might eventually be exploited through therapeutic combinations.

Here we present a comprehensive mechanistic network model of signal transduction in ER+ PIK3CA-mutant breast cancer. Focusing on PI3K inhibitors, the model recapitulates known resistance mechanisms and predicts other possibilities for resistance: loss of RB1, FOXO3, P27, or PRAS40. To test these predictions, we analyzed genome-wide CRISPR screens of two breast cell lines in the presence of PI3K inhibitors (BYL719 and GDC0032) and found that the predicted genes (RB1, FOXO3, P27, and PRAS40) were significantly enriched in the screens. Some of these resistance genes (e.g. loss of RB1) were found to be cell-line specific and follow-up experiments in RB1-KO cells confirmed the cell-line-specific nature of PI3K-inhibitor resistance. The model also reveals known and novel combinatorial interventions that are more effective than PI3K inhibition alone. For example, the model predicts that the combination of PI3K inhibitors with inhibitors of anti-apoptotic protein MCL1 would be effective. Follow up experiments in cell lines using cell viability assays, cell death analyses, and dynamic BH3 profiling experiments to determine increases in apoptotic priming upon treatment confirmed that MCL1 inhibitors (S63845) enhance the effect of PI3K inhibitors (BYL719) and that this combinatorial effect is cell-line-specific, similarly to what was found in the resistance genes case.

In conclusion, the model predicted drug resistance mechanisms and effective drug combinations, some of which were verified experimentally and found to be cell-line-specific. Next iterations of the model will incorporate the identified discrepancies and newly identified resistance mechanisms to drugs of clinical interest.

Citation Format: Jorge Gómez Tejeda Zañudo, Pingping Mao, Joan Montero, Guotai Xu, Kailey J. Kowalski, Gabriela N. Johnson, José Baselga, Maurizio Scaltriti, Anthony G. Letai, Nikhil Wagle, Reka Albert. Network modeling of drug resistance mechanisms and drug combinations in 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 675.

PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia

Mitochondrial apoptotic priming predicts response to cancer chemotherapy, but the mechanisms underlying variability in this mitochondrial phenotype among closely related tumors are poorly understood. Ariës et al. show that PRC2 loss-of-function mutations induce resistance to mitochondrial apoptosis in T-ALL.

The tendency of mitochondria to undergo or resist BCL2-controlled apoptosis (so-called mitochondrial priming) is a powerful predictor of response to cytotoxic chemotherapy. Fully exploiting this finding will require unraveling the molecular genetics underlying phenotypic variability in mitochondrial priming. Here, we report that mitochondrial apoptosis resistance in T cell acute lymphoblastic leukemia (T-ALL) is mediated by inactivation of polycomb repressive complex 2 (PRC2). In T-ALL clinical specimens, loss-of-function mutations of PRC2 core components (EZH2, EED, or SUZ12) were associated with mitochondrial apoptosis resistance. In T-ALL cells, PRC2 depletion induced resistance to apoptosis induction by multiple chemotherapeutics with distinct mechanisms of action. PRC2 loss induced apoptosis resistance via transcriptional up-regulation of the LIM domain transcription factor CRIP2 and downstream up-regulation of the mitochondrial chaperone TRAP1. These findings demonstrate the importance of mitochondrial apoptotic priming as a prognostic factor in T-ALL and implicate mitochondrial chaperone function as a molecular determinant of chemotherapy response.

Overcoming mutational complexity in acute myeloid leukemia by inhibition of critical pathways

Numerous variant alleles are associated with human acute myeloid leukemia (AML). However, the same variants are also found in individuals with no hematological disease, making their functional relevance obscure. Through NOD.Cg-Prkdc^scidIl2rg^tmlWjl/Sz (NSG) xenotransplantation, we functionally identified preleukemic and leukemic stem cell populations present in FMS-like tyrosine kinase 3 internal tandem duplication-positive (FLT3-ITD)⁺ AML patient samples. By single-cell DNA sequencing, we identified clonal structures and linked mutations with in vivo fates, distinguishing mutations permissive of nonmalignant multilineage hematopoiesis from leukemogenic mutations. Although multiple somatic mutations coexisted at the single-cell level, inhibition of the mutation strongly associated with preleukemic to leukemic stem cell transition eliminated AML in vivo. Moreover, concurrent inhibition of BCL-2 (B cell lymphoma 2) uncovered a critical dependence of resistant AML cells on antiapoptotic pathways. Co-inhibition of pathways critical for oncogenesis and survival may be an effective strategy that overcomes genetic diversity in human malignancies. This approach incorporating single-cell genomics with the NSG patient-derived xenograft model may serve as a broadly applicable resource for precision target identification and drug discovery.

Abstract PR14: Polycomb repressive complex 2 inactivation induces primary chemotherapy resistance in T-ALL by upregulating the TRAP1 mitochondrial chaperone

The tendency of mitochondria to undergo or resist BCL2-controlled apoptosis (so-called mitochondrial priming) is a powerful predictor of the outcome of cytotoxic chemotherapy for cancer. To fully exploit this finding, it will be important to understand the molecular genetic contexts responsible for the relative mitochondrial priming of chemotherapy-sensitive versus resistant cell populations. Here we report that mitochondrial apoptosis resistance in T-cell acute lymphoblastic leukemia (T-ALL) is mediated by inactivation of polycomb repressive complex 2 (PRC2) and consequent downstream upregulation of the TRAP1 gene, which encodes a mitochondrial chaperone protein of the HSP90 family. In clinical samples from 47 T-ALL patients, we found that loss-of-function mutations in any of three core components of PRC2 (EZH2, EED or SUZ12) were associated with resistance to mitochondrial apoptosis, as assessed by BH3 profiling (P = 0.015). In human T-ALL cells, PRC2 depletion induced resistance to mitochondrial apoptosis induction, as assessed by caspase 3/7 activation or annexin V/PI staining, in response to multiple antileukemic drugs with distinct mechanisms of action, including dexamethasone, doxorubicin, vincristine, and asparaginase (P < 0.01). In mouse immature T-cell progenitors, haploinsufficiency for the PRC2 components Ezh2 or Eed was sufficient to induce resistance to mitochondrial apoptosis, as assessed by BH3 profiling analysis (P ≤ 0.01). PRC2 is a histone-modifying complex whose activity is strongly associated with transcriptional repression. We found that PRC2 represses transcription of TRAP1, a nuclearly encoded, mitochondrially localized chaperone of the HSP90 family. Importantly, TRAP1 overexpression was necessary to induce resistance to chemotherapy-induced apoptosis downstream of PRC2 inactivation (P < 0.001), while pharmacologic inhibition of TRAP1 synergized with antileukemic drugs in PRC2-deficient leukemic cells. These findings demonstrate the importance of relative mitochondrial apoptotic priming as a prognostic factor in T-ALL, and implicate mitochondrial chaperone function as a molecular determinant of response to cancer chemotherapy, suggesting a rationale for targeted therapeutic intervention.

This abstract is also being presented as Poster 07.

Citation Format: Ingrid Aries, Triona Ni Chonghaile, Salmaan Karim, Sebastian Balbach, Melissa Burns, Gayle Pouliot, Stevenson Kristen, Donna Neuberg, Meenakshi Devidas, Loh Mignon, Stephen Hunger, Stuart Winter, David Teachey, Karen Rabin, Kimberly Dunsmore, Brent Wood, Lewis Silverman, Stephen Sallan, Peter Van Vlierberghe, Stuart H. Orkin, Anthony G. Letai, Alejandro Gutierrez. Polycomb repressive complex 2 inactivation induces primary chemotherapy resistance in T-ALL by upregulating the TRAP1 mitochondrial chaperone [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR14.

Abstract IA19: Directing blood cancer therapy with mitochondrial BH3 profiling

Connecting the right drugs to the right tumor is the fundamental job of cancer precision medicine. While there is a tendency to equate precision medicine with genomics, we are surrounded by examples where very effective modern targets are deployed effectively in disease without genomic guidance. One example is in chronic lymphocytic leukemia (CLL) where there have been several recent FDA approvals for drugs targeting CD20, PI3K, BTK, and BCL-2. Combinations of these highly active agents will likely dramatically alter practice, yet their discovery and assignment to CLL was not guided by genomics, as CLL generally lacks genetic alterations in any of these pathways. Instead, use in CLL was guided by the identification of vulnerabilities that had more to do with lineage than with genetics. In this talk, I will describe how my laboratory is using a probe of apoptotic signaling at the mitochondrion to identify drugs that provoke apoptotic signaling in cancer cells. This approach, called “BH3 profiling,” has so far been effective in guiding clinical trials of the BCL-2 inhibitor venetoclax in CLL and acute myelogenous leukemia. I will describe how we can deploy this tool as a predictive biomarker or as a discovery tool to directly identify drug vulnerabilities of cancer cells.

Citation Format: Anthony G. Letai. Directing blood cancer therapy with mitochondrial BH3 profiling [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA19.

Webinar | Deciphering cancer: Investigating cell death mechanisms

Cell death, including autophagy, necroptosis, and apoptosis, is a physiological process critical for normal development and function of multicellular organisms. Many of the signals that elicit cell death converge on mitochondria, which regulate cell death by a pivotal process called mitochondrial outer membrane permeabilization (MOMP). In apoptosis, MOMP is tightly regulated by the Bcl-2 family of proteins, composed of both proapoptotic (Bax, Bak, Bid, Bim) and antiapoptotic (Bcl-2, Bcl-xL, Bcl-W) members, which act in part by governing mitochondrial death signaling through cytochrome C release and subsequent activation of caspases. Irrespective of caspase activity, MOMP can lead to cell death by causing a progressive decline in mitochondrial function. Under certain circumstances, however, a cell can survive cell death; its survival may have pathophysiological consequences leading to cancer, autoimmunity, neurodegeneration, and resistance to cancer therapies. This webinar will examine how identification of dysregulated cell-death mechanisms underpinning various pathologies can be exploited to develop novel treatments for cancer and neurodegenerative diseases that directly activate the cell-death machinery.

Cristae remodeling causes acidification detected by integrated graphene sensor during mitochondrial outer membrane permeabilization

The intrinsic apoptotic pathway and the resultant mitochondrial outer membrane permeabilization (MOMP) via BAK and BAX oligomerization, cytochrome c (cytc) release, and caspase activation are well studied, but their effect on cytosolic pH is poorly understood. Using isolated mitochondria, we show that MOMP results in acidification of the surrounding medium. BAK conformational changes associated with MOMP activate the OMA1 protease to cleave OPA1 resulting in remodeling of the cristae and release of the highly concentrated protons within the cristae invaginations. This was revealed by utilizing a nanomaterial graphene as an optically clear and ultrasensitive pH sensor that can measure ionic changes induced by tethered mitochondria. With this platform, we have found that activation of mitochondrial apoptosis is accompanied by a gradual drop in extra-mitochondrial pH and a decline in membrane potential, both of which can be rescued by adding exogenous cytc. These findings have importance for potential pharmacological manipulation of apoptosis, in the treatment of cancer.

Abstract SY43-01: Precision cancer medicine using BH3 profiling

The job of precision medicine is to match the right patient to the right drug(s). While the term “precision medicine” is often considered synonymous with “cancer genomics,” -omics approaches have thus far enjoyed only inconsistent success in assigning therapy to patients, despite the abundance of data such approaches generate. We favor functional approaches that allow for perturbation of the cancer cells of interest. BH3 profiling can measure the state of the apoptotic pathway of a cancer cell before and after brief exposures to drugs. By identifying drugs that enhance apoptotic signaling in brief ex vivo exposures, we can identify agents that are active in vivo. An advantage to dynamic BH3 profiling is that its measurements can be made in less than 24 hours, removing the requirement for longer term ex vivo culture that has typically proved a major stumbling block for ex vivo approaches.

Citation Format: Anthony G. Letai. Precision cancer medicine using BH3 profiling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr SY43-01.

Abstract 5030: Polarizing tumor associated macrophages (TAMs) towards an anti-tumor phenotype with a novel compound reveals a new subset of TAMs within breast tumors which facilitate tumor regression

Manipulation of the innate immune system is a relatively understudied strategy for anti-cancer immunotherapy. The current focus on immunotherapy is centered on the adaptive immune system. However, there is growing evidence that manipulation of the innate immune system, including macrophages, is also a promising method to combat cancer.

Tumor associated macrophages (TAMs) are one of the major infiltrating leukocyte populations associated with solid tumors. There are two major types of macrophages: classically activated macrophages, which can kill bacteria, pathogens, and similarly tumor cells; and alternatively activated macrophages which facilitate wound repair and are generally found in the tumor microenvironment. TAMs are generally alternatively activated cells with immunosuppressive properties that have been shown to enhance tumorogenesis by facilitating metastasis, angiogenesis, and inhibiting a protecting adaptive immune response. The presence of macrophages in the tumor microenvironment correlates with poor prognosis. Here we describe a novel, first in class compound that activates macrophages to an anti-tumor phenotype. While this compound has no direct cytotoxic activity, we show in the PyMT mouse model of breast cancer that breast tumors regress in response to therapy in a manner dependent on myeloid cells. Through the use of flow cytometry, we have been able to identify different subpopulations of TAMs using the markers CD45, MHCII, and CD11b. Correlating with tumor regression, we see an increase in PARP and cleaved caspase 3, indicating apoptotic cell death. Here we show that a novel compound effectively polarize macrophages to an anti-tumor phenotype to induce tumor regression. This strategy may have great therapeutic promise.

Citation Format: Alaba O. Sotayo, Jennnifer L. Guerriero, Holly E. Ponichtera, Anthony G. Letai. Polarizing tumor associated macrophages (TAMs) towards an anti-tumor phenotype with a novel compound reveals a new subset of TAMs within breast tumors which facilitate tumor regression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5030. doi:10.1158/1538-7445.AM2015-5030

Abstract SY20-01: Conventional chemotherapy cures people by exploiting apoptotic priming

Conventional chemotherapy has an amazing track record that is often under-appreciated in today's world of genomics and targeted pathway inhibitors. Conventional chemotherapy is responsible for curing millions of cancer patients over the past 5 decades. That is, millions of patients have presented to their doctors with an otherwise fatal malignancy, were given a finite course of chemotherapy (largely DNA and microtubule perturbing agents) and had their cancer eradicated, never to return. Perhaps as remarkable as the magnitude of the achievement of conventional chemotherapy is the magnitude of our ignorance of why it should ever work, and why it works far better in some tumors than in others. Textbook explanations rely on concepts of differential proliferation rates in cancers that are incompletely supported in the clinical literature. Successful chemotherapy treatments usually kill via the mitochondrial pathway of apoptosis. We have found that simple functional measurements of the pre-treatment state of the tumor cell can be rapidly made with BH3 profiling. These measurements demonstrate that a major, if not the major, reason for a therapeutic index for cancer chemotherapy is that chemo-sensitive cancer cells are simply more primed for apoptosis than normal cells. Moreover, apoptotic priming can be measured to make clinical predictions regarding quality of response on an individualized basis. Enhancing pretreatment priming of cancer cells with selectively acting targeted agents is a promising strategy to extend the demonstrated curative power of conventional chemotherapy.

Citation Format: Anthony G. Letai. Conventional chemotherapy cures people by exploiting apoptotic priming. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY20-01. doi:10.1158/1538-7445.AM2015-SY20-01

Modulation of Mcl-1 sensitizes glioblastoma to TRAIL-induced apoptosis

Glioblastoma (GBM) is the most aggressive form of primary brain tumour, with dismal patient outcome. Treatment failure is associated with intrinsic or acquired apoptosis resistance and the presence of a highly tumourigenic subpopulation of cancer cells called GBM stem cells. Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) has emerged as a promising novel therapy for some treatment-resistant tumours but unfortunately GBM can be completely resistant to TRAIL monotherapy. In this study, we identified Mcl-1, an anti-apoptotic Bcl-2 family member, as a critical player involved in determining the sensitivity of GBM to TRAIL-induced apoptosis. Effective targeting of Mcl-1 in TRAIL resistant GBM cells, either by gene silencing technology or by treatment with R-roscovitine, a cyclin-dependent kinase inhibitor that targets Mcl-1, was demonstrated to augment sensitivity to TRAIL, both within GBM cells grown as monolayers and in a 3D tumour model. Finally, we highlight that two separate pathways are activated during the apoptotic death of GBM cells treated with a combination of TRAIL and R-roscovitine, one which leads to caspase-8 and caspase-3 activation and a second pathway, involving a Mcl-1:Noxa axis. In conclusion, our study demonstrates that R-roscovitine in combination with TRAIL presents a promising novel strategy to trigger cell death pathways in glioblastoma.

Selective BCL-2 inhibition by ABT-199 causes on-target cell death in acute myeloid leukemia

B-cell leukemia/lymphoma 2 (BCL-2) prevents commitment to programmed cell death at the mitochondrion. It remains a challenge to identify those tumors that are best treated by inhibition of BCL-2. Here, we demonstrate that acute myeloid leukemia (AML) cell lines, primary patient samples, and murine primary xenografts are very sensitive to treatment with the selective BCL-2 antagonist ABT-199. In primary patient cells, the median IC50 was approximately 10 nmol/L, and cell death occurred within 2 hours. Our ex vivo sensitivity results compare favorably with those observed for chronic lymphocytic leukemia, a disease for which ABT-199 has demonstrated consistent activity in clinical trials. Moreover, mitochondrial studies using BH3 profiling demonstrate activity at the mitochondrion that correlates well with cytotoxicity, supporting an on-target mitochondrial mechanism of action. Our protein and BH3 profiling studies provide promising tools that can be tested as predictive biomarkers in any clinical trial of ABT-199 in AML.

Abstract CN04-01: Poking cancer cells with BH3 profiling to personalize cancer therapy

Nearly all attempts to understand and predict response of patient cancer cells to therapeutics rely on measurements of static properties at a single time point such as protein abundance, gene expression profiling, or genetic code. While these approaches have doubtless yielded useful information to guide therapy, it is often the case that observing how a system responds to systematic perturbation can be a more powerful guide to understanding and predicting behavior. Using BH3 profiling, we systematically perturb the mitochondria of cancer cells with BH3 peptides and can make predictions about response to therapy based on the response observed. So far, we have successfully applied BH3 profiling to understanding and predicting clinical response to conventional chemotherapy, targeted pathway inhibitors and direct inhibitors of anti-apoptotic proteins like BCL-2. Since BH3 profiling can provide results within a single day, it is applicable to studying primary cancer cells from patient biopsies without the need for prolonged ex vivo culture. BH3 profiling has the potential to provide a predictive biomarker for any cancer therapeutic that kills cancer cells via the mitochondrial pathway of apoptosis.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):CN04-01.

Citation Format: Joan Montero, Triona Ni Chonghaile, Kris Sarosiek, Jeremy A. Ryan, Hogdal Leah, Anthony G. Letai. Poking cancer cells with BH3 profiling to personalize cancer therapy. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr CN04-01.

Abstract 5257: Manipulating the Noxa/Bim axis undermines the multicellular resistance of 3D tumor spheroids

When grown in 3D cultures as spheroids, cancer cells acquire a multicellular resistance to apoptosis that resembles that of solid tumors. We have previously found in lung cancer and mesothelioma that multicellular resistance lies at the level of mitochondria and can be reduced by manipulating the Bcl-2 repertoire with BH3-mimetics. One mechanism for the multicellular resistance to apoptosis is the lack of up-regulation of the pro-apoptotic sensitizer Noxa upon treatment; Noxa displaces pro-apoptotic Bim from its anti-apoptotic buffering proteins allowing the Bim to induce apoptosis. Interestingly, we have found that, at the same time that cells acquire apoptotic resistance in 3D, they also acquire a pro-apoptotic potential that has been termed “apoptotic priming,” due to an elevated Bim that is sequestered by the anti-apoptotic Bcl-2 proteins. We found that multicellular resistance could be abolished either by restoring Noxa levels using a permeable Noxa peptide or by releasing Bim via inhibition of the anti-apoptotic Bcl-2 proteins using the small molecule inhibitor, ABT-737. Moreover, multicellular resistance was also abolished by the histone deacetylase inhibitor SAHA which upregulated both Noxa and Bim expression. Knockdown of Bim blocked the effect of the Noxa peptide, ABT-737 or SAHA showing the importance of Bim in the chemotherapeutic response. Our results using a clinically-relevant 3D model show that manipulation of the core apoptotic repertoire in order to release Bim may improve chemosensitivity of lung cancer and mesothelioma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5257. doi:1538-7445.AM2012-5257

The Bcl-2 repertoire of mesothelioma spheroids underlies acquired apoptotic multicellular resistance

Three-dimensional (3D) cultures are a valuable platform to study acquired multicellular apoptotic resistance of cancer. We used spheroids of cell lines and actual tumor to study resistance to the proteasome inhibitor bortezomib in mesothelioma, a highly chemoresistant tumor. Spheroids from mesothelioma cell lines acquired resistance to bortezomib by failing to upregulate Noxa, a pro-apoptotic sensitizer BH3-only protein that acts by displacing Bim, a pro-apoptotic Bax/Bak-activator protein. Surprisingly, despite their resistance, spheroids also upregulated Bim and thereby acquired sensitivity to ABT-737, an inhibitor of anti-apoptotic Bcl-2 molecules. Analysis using BH3 profiling confirmed that spheroids acquired a dependence on anti-apoptotic Bcl-2 proteins and were ‘primed for death'. We then studied spheroids grown from actual mesothelioma. ABT-737 was active in spheroids grown from those tumors (5/7, ∼70%) with elevated levels of Bim. Using immunocytochemistry of tissue microarrays of 48 mesotheliomas, we found that most (33, 69%) expressed elevated Bim. In conclusion, mesothelioma cells in 3D alter the expression of Bcl-2 molecules, thereby acquiring both apoptotic resistance and sensitivity to Bcl-2 blockade. Mesothelioma tumors ex vivo also show sensitivity to Bcl-2 blockade that may depend on Bim, which is frequently elevated in mesothelioma. Therefore, mesothelioma, a highly resistant tumor, may have an intrinsic sensitivity to Bcl-2 blockade that can be exploited therapeutically.

Abstract LB-22: A subset of small cell lung cancer (SCLC) cell lines is Mcl-1-dependent and responds to cyclin-dependent kinase (cdk)9 inhibition in vitro and in vivo

Small cell lung cancer (SCLC) accounts for approximately 13% of lung cancer cases, and current treatment options are limited to radiation and/or chemotherapy, which frequently lead to drug resistance. Recently, multiple SCLC cell lines have been found to be responsive to the Bcl-2/Bcl-xL inhibitor, ABT-737, both in vitro and in vivo. Clinical trials of the related orally-bioavailable compound ABT-263 have shown promising activity in SCLC patients. However, a subset of SCLC cell lines that express Mcl-1, another anti-apoptotic protein, are resistant to ABT-737. Therefore, drugs targeting Mcl-1 may be particularly useful in this disease. Here, we have investigated dependence of a panel of SCLC cell lines on Mcl-1 for survival. A subset of Mcl-1-expressing SCLC cell lines, including NCI-H82 and SHP-77, demonstrate apoptosis upon Mcl-1 knockdown. However, other SCLC cell lines, including NCI-H69 and SW1271, are not responsive to Mcl-1 knockdown. In addition, the dependence of SCLC cell lines on Mcl-1 for survival can be predicted by BH3 profiling, a methodology that measures dependence of a cell on a variety of anti-apoptotic proteins. We have also investigated the efficacy of Flavopiridol, a potent inhibitor of the transcriptional cyclin-dependent kinase (cdk)9, against the panel of SCLC cell lines. Flavopiridol acutely down-regulates Mcl-1 expression in all cell lines tested; however, only Mcl-1-dependent cells undergo abrupt apoptosis. In contrast, cells that were not found to be Mcl-1 dependent, including H69 and SW1271 cells, are not effectively killed by Flavopiridol. We have further investigated the activity of Flavopiridol against Mcl-1-dependent SCLC in vivo utilizing nude mice bearing H82 xenografts. Flavopiridol treatment results in substantial tumor growth inhibition in this aggressive and chemotherapy-refractory model. To potentially stratify patients who would be predicted to be responsive to Flavopiridol treatment, we have performed MCL-1 fluorescent in situ hybridization in SCLC cell lines and deidentified patient specimens. MCL-1 gene copy number gains exist in both patient and cell line samples, and copy number gain in cell lines correlates with Mcl-1 dependence. Finally, we have demonstrated that the combination of Flavopiridol and ABT-737 can synergistically kill both Mcl-1-dependent and – independent SCLC cells, with significantly reduced viability in SHP-77 and SW1271 cells compared to treatment with either drug alone. Taken together, our studies suggest that Flavopiridol-mediated cdk9 inhibition may effectively target Mcl-1-dependent SCLCs, including those resistant to Bcl-2/Bcl-xL inhibition.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-22. doi:10.1158/1538-7445.AM2011-LB-22

Diagnosing and exploiting cancer's addiction to blocks in apoptosis

Cancer cells survive despite violating rules of normal cellular behaviour that ordinarily provoke apoptosis. The blocks in apoptosis that keep cancer cells alive are therefore attractive candidates for targeted therapies. Recent studies have significantly increased our understanding of how interactions among proteins in the BCL2 family determine cell survival or death. It is now possible to systematically determine how individual cancers escape apoptosis. Such a determination can help predict not only whether cells are likely to be killed by antagonism of BCL2, but also whether they are likely to be sensitive to chemotherapy that kills by the intrinsic apoptotic pathway.

Pancreas-graft immunogenicity and pretreatment with anti-class II monoclonal antibodies

Pretreatment of organ allografts to reduce graft immunogenicity is an attractive and potentially clinically applicable concept. We have studied the effect of perfusing rat pancreases with anti-class II monoclonal antibody (MoAb), to remove class II- positive accessory cells from the intact organ, on prolongation of allograft survival after transplantation. The capacity of pancreatic islets obtained from these perfused organs to stimulate proliferation of allogeneic T-lymphocytes was studied in a mixed islet-lymphocyte culture (MILC). There was a significant prolongation in pancreas-allograft survival when intact pancreases were transplanted after a 3-h normothermic perfusion with MoAb reactive with class II antigens (16.2 +/- 3.6 days, n = 19) compared with control animals (11.0 +/- 1.4 days, n = 24). In vitro treatment of islets with MoAb and complement (CI) inhibited their stimulatory capacity in the MILC, as measured by [3H]thymidine uptake. Similarly, the stimulatory capacity of islets removed from perfused pancreases was also abrogated when MoAb was included in the perfusate. Although reduction in graft immunogenicity, by increasing allograft survival, was achieved by a 3-h pretreatment regimen, it was not sufficient to inhibit rejection altogether in our transplant model.

Specificity in formation of triple-stranded nucleic acid helical complexes: studies with agarose-linked polyribonucleotide affinity columns

The binding of a variety of deoxyribo and ribo homo- and copolynucleotide complementary duplexes to agarose-linked homopolynucleotide affinity columns has been studied. The results provide information concerning the specificity of recognition of complementary base pairs of nucleic acids through a mechanism that involves triple-helix formation under physiological conditions of ionic strength, pH, and temperature. The method employed made it possible, for the first time, to survey the full range of base triplets conceivable from the canonical nucleic acid bases and, in addition, hypoxanthine and thereby to differentiate between those triplets which can and cannot form. Certain previously observed features of the stereochemistry of double-helical targets for third-strand binding are confirmed, and some unrecognized features are elaborated. These include a general requirement for clusters of purine residues in one strand, protonation of third-strand C residues, the ability of natural third-strand residues to distinguish between A.T/U and G.C base pairs, and a capacity of third-strand (unnatural) I residues to recognize all base pairs within such clusters. Thus, the basis for a third-strand binding code is demonstrated.