PAK signalling drives acquired drug resistance to MAPK inhibitors in BRAF-mutant melanomas

Targeted BRAF inhibition (BRAFi) and combined BRAF and MEK inhibition (BRAFi and MEKi) therapies have markedly improved the clinical outcomes of patients with metastatic melanoma. Unfortunately, the efficacy of these treatments is often countered by the acquisition of drug resistance. Here we investigated the molecular mechanisms that underlie acquired resistance to BRAFi and to the combined therapy. Consistent with previous studies, we show that resistance to BRAFi is mediated by ERK pathway reactivation. Resistance to the combined therapy, however, is mediated by mechanisms independent of reactivation of ERK in many resistant cell lines and clinical samples. p21-activated kinases (PAKs) become activated in cells with acquired drug resistance and have a pivotal role in mediating resistance. Our screening, using a reverse-phase protein array, revealed distinct mechanisms by which PAKs mediate resistance to BRAFi and the combined therapy. In BRAFi-resistant cells, PAKs phosphorylate CRAF and MEK to reactivate ERK. In cells that are resistant to the combined therapy, PAKs regulate JNK and β-catenin phosphorylation and mTOR pathway activation, and inhibit apoptosis, thereby bypassing ERK. Together, our results provide insights into the molecular mechanisms underlying acquired drug resistance to current targeted therapies, and may help to direct novel drug development efforts to overcome acquired drug resistance.

ATG5 Mediates a Positive Feedback Loop between Wnt Signaling and Autophagy in Melanoma

Autophagy mediates resistance to various anticancer agents. In melanoma, resistance to targeted therapy has been linked to expression of Wnt5A, an intrinsic inhibitor of β-catenin, which also promotes invasion. In this study, we assessed the interplay between Wnt5A and autophagy by combining expression studies in human clinical biopsies with functional analyses in cell lines and mouse models. Melanoma cells with high Wnt5A and low β-catenin displayed increased basal autophagy. Genetic blockade of autophagy revealed an unexpected feedback loop whereby knocking down the autophagy factor ATG5 in Wnt5A^high cells decreased Wnt5A and increased β-catenin. To define the physiologic relevance of this loop, melanoma cells with different Wnt status were treated in vitro and in vivo with the potent lysosomotropic compound Lys05. Wnt5A^high cells were less sensitive to Lys05 and could be reverted by inducing β-catenin activity. Our results suggest the efficacy of autophagy inhibitors might be improved by taking the Wnt signature of melanoma cells into account. Cancer Res; 77(21); 5873-85. ©2017 AACR.

Abstract 758: Capture and characterization of circulating tumor cell clusters in patients with metastatic castrate-resistant prostate cancer

Introductory Sentence indicating purpose of study: Circulating tumor cell (CTC) clusters have been shown to have higher metastatic potential than single CTCs in breast, pancreatic, and other cancers, yet these clusters have not been extensively described in metastatic castrate-resistant prostate cancer (MCRPC). Here we sought to determine the feasibility of capturing and characterizing CTC clusters in prostate cancer patients.

Description of Experimental Procedures: Fifty-five blood samples from 29 MCRPC patients, ages 50 to 81 (median age 68), were obtained prior to the patient starting or switching to androgen receptor inhibitor or 17 alpha lyase inhibitor therapies. Eighteen patients received enzalutamide and 11 received abiraterone. The majority of patients had a Gleason score > 7 (22; 75.9%), bone metastases (19; 65.5%), and an ECOG status of 0 (21; 72.4%). All patients had previously undergone, or were receiving at time of enrollment, androgen deprivation therapy. Eleven patients (37.9%) had been on a prior 2nd generation anti-androgen therapy. CTC single cells and clusters (2 or more cells together in one image) were enumerated using the CellSearch system and stained to detect expression of androgen receptor (AR), glucocorticoid receptor (GR), and neuroendocrine (NE) markers.

Summary of Data: Five or more single CTCs, a measure which has previously been associated with an unfavorable prognosis, were detected in 13 of 29 patients (44.8%), and in 19 of 55 blood samples (34.5%). Altogether, a total of 282 CTC clusters was detected, with 1 or more clusters found in 10 patients (34.5%) and 13 samples (23.6%). The number of clusters per 7.5ml of blood ranged from 0-150, and clusters contained anywhere from 2 to 16 cells. Most CTC clusters (268; 95.0%) contained only CTCs and no leukocytes. Just over half the detected clusters (162; 57.4%) contained only 2 CTCs. Cluster staining patterns were fairly homogenous with 29.4% of clusters having uniform expression of either AR, GR, or NE markers, i.e., all CTCs in the cluster expressed the marker of interest. Most clusters (67.7%) were uniformly marker negative and the remaining 2.8% demonstrated a mix of marker positive and marker negative CTCs. Serum Chromogranin A levels, as determined by standard of care clinical blood testing, were found to be positively associated with the number of CTC clusters per 7.5ml of blood (p<0.0001).

Statement of Conclusions: The capture and characterization of CTC clusters in the blood of MCRPC patients can be successfully performed using the CellSearch system. Further investigation into the clinical implications of these clusters is warranted, including whether cluster characteristics are associated with more aggressive disease.

Citation Format: Samantha L. Savitch, Stephanie S. Yee, Devon Soucier, Denis Smirnov, Chandra Rao, Steve Gross, Ravi K. Amaravadi, David J. Vaughn, Naomi B. Haas, Erica L. Carpenter. Capture and characterization of circulating tumor cell clusters in patients with metastatic castrate-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 758. doi:10.1158/1538-7445.AM2017-758

Targeting Autophagy in Cancer: Update on Clinical Trials and Novel Inhibitors

Eukaryotes use autophagy as a mechanism for maintaining cellular homeostasis by degrading and recycling organelles and proteins. This process assists in the proliferation and survival of advanced cancers. There is mounting preclinical evidence that targeting autophagy can enhance the efficacy of many cancer therapies. Hydroxychloroquine (HCQ) is the only clinically-approved autophagy inhibitor, and this systematic review focuses on HCQ use in cancer clinical trials. Preclinical trials have shown that HCQ alone and in combination therapy leads to enhancement of tumor shrinkage. This has provided the base for multiple ongoing clinical trials involving HCQ alone and in combination with other treatments. However, due to its potency, there is still a need for more potent and specific autophagy inhibitors. There are multiple autophagy inhibitors in the pre-clinical stage at various stages of development. Additional studies on the mechanism of HCQ and other autophagy inhibitors are still required to answer questions surrounding how these agents will eventually be used in the clinic.

Phase II trial of the autophagy inhibitor hydroxychloroquine with FOLFOX and bevacizumab in front line treatment of metastatic colorectal cancer

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Background: Colorectal cancer (CRC) cells can become resistant to chemotherapy and anti-angiogenic therapy through autophagy. The antimalarial agent hydroxychloroquine (HCQ) is a potent inhibitor of autophagy, and in vivo studies in CRC cell models show significant decrease tumor volume when these autophagy inhibitors were combined with oxaliplatin and bevacizumab. We previously reported safety with HCQ 600mg BID in combination with standard front-line FOLFOX and bevacizumab in a Phase I study in metastatic CRC patients. We report the results of a single-arm phase II trial of patients with previously untreated stage IV CRC with good performance status and adequate hematologic and biochemical indices. Methods: Patients were treated with standard doses of mFOLFOX6 and bevacizumab with HCQ 600mg BID. Imaging was obtained every 2 months. Results: 37 patients were enrolled, 62% male, 89% Caucasian, median age 61, 65% ECOG PS 0, and 73% colon primary. Twenty-eight patients were evaluable for response as 2 patients did not start therapy and 7 patients withdrew prior to first response assessment. The ORR was 68% with an 11% CR rate. The median time to response was 3.1 months. Responses were independent of genomic aberrations within tumor tissue, specifically KRAS, TP53, BRAF, and PIK3CA. Median PFS and duration of response were not interpretable given that only 25% of patients came off trial for progression; all other patients withdrew to pursue surgery or liver embolization therapy, to receive therapy elsewhere, or due to toxicity associated with chemotherapy. The 1 year OS rate was 74%, and median OS has not been reached. The most common G3 or higher adverse events included neutropenia (31%), fatigue (11%), thromboembolism (9%), and cardiac events (9%). HCQ-attributable side effects included G1-3 insomnia (26%), G1-3 anxiety (20%), G1 visual disturbances (11%) and G3 allergy (3%). The majority of patients had increase in both LC3 and p62 in peripheral blood mononuclear cells and exhibited an increase in autophagosomes within the cytosol by electron microscopy. Conclusions: These data are promising and further evaluation in a randomized controlled trial is planned. Clinical trial information: NCT01206530.

Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

Therapeutic blocking of the PD1 pathway results in significant tumor responses, but resistance is common. We demonstrate that prolonged interferon signaling orchestrates PDL1-dependent and PDL1-independent resistance to immune checkpoint blockade (ICB) and to combinations such as radiation plus anti-CTLA4. Persistent type II interferon signaling allows tumors to acquire STAT1-related epigenomic changes and augments expression of interferon-stimulated genes and ligands for multiple T cell inhibitory receptors. Both type I and II interferons maintain this resistance program. Crippling the program genetically or pharmacologically interferes with multiple inhibitory pathways and expands distinct T cell populations with improved function despite expressing markers of severe exhaustion. Consequently, tumors resistant to multi-agent ICB are rendered responsive to ICB monotherapy. Finally, we observe that biomarkers for interferon-driven resistance associate with clinical progression after anti-PD1 therapy. Thus, the duration of tumor interferon signaling augments adaptive resistance and inhibition of the interferon response bypasses requirements for combinatorial ICB therapies.

Autophagy supports generation of cells with high CD44 expression via modulation of oxidative stress and Parkin-mediated mitochondrial clearance

High CD44 expression is associated with enhanced malignant potential in esophageal squamous cell carcinoma (ESCC), amongst the deadliest of all human carcinomas. Although alterations in autophagy and CD44 expression are associated with poor patient outcomes in various cancer types, the relationship between autophagy and cells with high CD44 expression remains incompletely understood. In transformed esophageal keratinocytes, CD44^Low-CD24^High (CD44L) cells give rise to CD44^High-CD24^−/Low (CD44H) cells via epithelial-mesenchymal transition (EMT) in response to transforming growth factor (TGF)-β. We couple patient samples and xenotransplantation studies with this tractable in vitro system of CD44L to CD44H cell conversion to investigate the functional role of autophagy in generation of cells with high CD44 expression. We report that high expression of the autophagy marker cleaved LC3 expression correlates with poor clinical outcome in ESCC. In ESCC xenograft tumors, pharmacological autophagy inhibition with chloroquine derivatives depletes cells with high CD44 expression while promoting oxidative stress. Autophagic flux impairment during EMT-mediated CD44L to CD44H cell conversion in vitro induces mitochondrial dysfunction, oxidative stress and cell death. During CD44H cell generation, transformed keratinocytes display evidence of mitophagy, including mitochondrial fragmentation, decreased mitochondrial content and mitochondrial translocation of Parkin, essential in mitophagy. RNA interference-mediated Parkin depletion attenuates CD44H cell generation. These data suggest that autophagy facilitates EMT-mediated CD44H generation via modulation of redox homeostasis and Parkin-dependent mitochondrial clearance. This is the first report to implicate mitophagy in regulation of tumor cells with high CD44 expression, representing a potential novel therapeutic avenue in cancers where EMT and CD44H cells have been implicated, including ESCC.

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

Despite the success of monotherapies based on blockade of programmed cell death 1 (PD-1) in human melanoma, most patients do not experience durable clinical benefit. Pre-existing T-cell infiltration and/or the presence of PD-L1 in tumours may be used as indicators of clinical response; however, blood-based profiling to understand the mechanisms of PD-1 blockade has not been widely explored. Here we use immune profiling of peripheral blood from patients with stage IV melanoma before and after treatment with the PD-1-targeting antibody pembrolizumab and identify pharmacodynamic changes in circulating exhausted-phenotype CD8 T cells (T_ex cells). Most of the patients demonstrated an immunological response to pembrolizumab. Clinical failure in many patients was not solely due to an inability to induce immune reinvigoration, but rather resulted from an imbalance between T-cell reinvigoration and tumour burden. The magnitude of reinvigoration of circulating T_ex cells determined in relation to pretreatment tumour burden correlated with clinical response. By focused profiling of a mechanistically relevant circulating T-cell subpopulation calibrated to pretreatment disease burden, we identify a clinically accessible potential on-treatment predictor of response to PD-1 blockade.

Targeting the unfolded protein response in cancer

Cancer cells are exposed to various intrinsic and extrinsic factors that disrupt protein homeostasis, producing endoplasmic reticulum (ER) stress. To cope with these situations, cancer cells evoke a highly conserved adaptive mechanism called the unfolded protein response (UPR) to restore the ER homeostasis. Recently, several pharmacological agents have been found to exhibit anti-tumor activity by targeting the UPR components. The development of potent and specific compounds that target the UPR components has not only shed light on the regulation of the UPR in cancer cells, but also brought the field closer to clinical drug candidates. Here we present an overview of the milestones in the field of UPR biology in cancer with a focus on new strategies for pharmacological inhibition.

Multidrug Analyses in Patients Distinguish Efficacious Cancer Agents Based on Both Tumor Cell Killing and Immunomodulation

The vision of a precision medicine-guided approach to novel cancer drug development is challenged by high intratumor heterogeneity and interpatient diversity. This complexity is rarely modeled accurately during preclinical drug development, hampering predictions of clinical drug efficacy. To address this issue, we developed Comparative In Vivo Oncology (CIVO) arrayed microinjection technology to test tumor responsiveness to simultaneous microdoses of multiple drugs directly in a patient's tumor. Here, in a study of 18 canine patients with soft tissue sarcoma (STS), CIVO captured complex, patient-specific tumor responses encompassing both cancer cells and multiple immune infiltrates following localized exposure to different chemotherapy agents. CIVO also classified patient-specific tumor resistance to the most effective agent, doxorubicin, and further enabled assessment of a preclinical autophagy inhibitor, PS-1001, to reverse doxorubicin resistance. In a CIVO-identified subset of doxorubicin-resistant tumors, PS-1001 resulted in enhanced antitumor activity, increased infiltration of macrophages, and skewed this infiltrate toward M1 polarization. The ability to evaluate and cross-compare multiple drugs and drug combinations simultaneously in living tumors and across a diverse immunocompetent patient population may provide a foundation from which to make informed drug development decisions. This method also represents a viable functional approach to complement current precision oncology strategies. Cancer Res; 77(11); 2869-80. ©2017 AACR.

Ischemia Induces Quiescence and Autophagy Dependence in Hepatocellular Carcinoma

Purpose To characterize hepatocellular carcinoma (HCC) cells surviving ischemia with respect to cell cycle kinetics, chemosensitivity, and molecular dependencies that may be exploited to potentiate treatment with transarterial embolization (TAE). Materials and Methods Animal studies were performed according to institutionally approved protocols. The growth kinetics of HCC cells were studied in standard and ischemic conditions. Viability and cell cycle kinetics were measured by using flow cytometry. Cytotoxicity profiling was performed by using a colorimetric cell proliferation assay. Analyses of the Cancer Genome Atlas HCC RNA-sequencing data were performed by using Ingenuity Pathway Analysis software. Activation of molecular mediators of autophagy was measured with Western blot analysis and fluorescence microscopy. In vivo TAE was performed in a rat model of HCC with (n = 5) and without (n = 5) the autophagy inhibitor Lys05. Statistical analyses were performed by using GraphPad software. Results HCC cells survived ischemia with an up to 43% increase in the fraction of quiescent cells as compared with cells grown in standard conditions (P < .004). Neither doxorubicin nor mitomycin C potentiated the cytotoxic effects of ischemia. Gene-set analysis revealed an increase in mRNA expression of the mediators of autophagy (eg, CDKN2A, PPP2R2C, and TRAF2) in HCC as compared with normal liver. Cells surviving ischemia were autophagy dependent. Combination therapy coupling autophagy inhibition and TAE in a rat model of HCC resulted in a 21% increase in tumor necrosis compared with TAE alone (P = .044). Conclusion Ischemia induces quiescence in surviving HCC cells, resulting in a dependence on autophagy, providing a potential therapeutic target for combination therapy with TAE. ^© RSNA, 2017 Online supplemental material is available for this article.

Autophagy Inhibition Enhances Sunitinib Efficacy in Clear Cell Ovarian Carcinoma

Clear cell ovarian carcinoma (CCOC) is an aggressive form of epithelial ovarian cancer that exhibits low response rates to systemic therapy and poor patient outcomes. Multiple studies in CCOC have revealed expression profiles consistent with increased hypoxia, and our previous data suggest that hypoxia is correlated with increased autophagy in CCOC. Hypoxia-induced autophagy is a key factor promoting tumor cell survival and resistance to therapy. Recent clinical trials with the molecular-targeted receptor tyrosine kinase (RTK) inhibitor sunitinib have demonstrated limited activity. Here, it was evaluated whether the hypoxia-autophagy axis could be modulated to overcome resistance to sunitinib. Importantly, a significant increase in autophagic activity was found with a concomitant loss in cell viability in CCOC cells treated with sunitinib. Pharmacologic inhibition of autophagy with the lysosomotropic analog Lys05 inhibited autophagy and enhanced sunitinib-mediated suppression of cell viability. These results were confirmed by siRNA targeting the autophagy-related gene Atg5 In CCOC tumor xenografts, Lys05 potentiated the antitumor activity of sunitinib compared with either treatment alone. These data reveal that CCOC tumors have an autophagic dependency and are an ideal tumor histotype for autophagy inhibition as a strategy to overcome resistance to RTK inhibitors like sunitinib.Implications: This study shows that autophagy inhibition enhances sunitinib-mediated cell death in a preclinical model of CCOC. Mol Cancer Res; 15(3); 250-8. ©2017 AACR.

Lysosomal Biology in Cancer

Cells depend on the lysosome for sequestration and degradation of macromolecules in order to maintain metabolic homeostasis. These membrane-enclosed organelles can receive intracellular and extracellular cargo through endocytosis, phagocytosis, and autophagy. Lysosomes establish acidic environments to activate enzymes that are able to break down biomolecules engulfed through these various pathways. Recent advances in methods to study the lysosome have allowed the discovery of extended roles for the lysosome in various diseases, including cancer, making it an attractive and targetable node for therapeutic intervention. This review focuses on key aspects of lysosomal biology in the context of cancer and how these properties can be exploited for the development of new therapeutic strategies. This will provide a contextual framework for how advances in methodology could be applied in future translational research.

Abstract PR05: Peripheral blood immune profiling of anti-PD-1 therapy in human melanoma reveals a link between T cell re-invigoration and tumor burden that predicts response

Despite the clinical success of PD-1 based therapies in human melanoma patients, the majority of patients do not have durable clinical benefit from anti-PD-1 monotherapy. A major challenge remains identifying which patients will respond to anti-PD-1 therapy and defining the underlying reasons for successful response versus treatment failure. Pre-existing T cell infiltration and/or PD-L1 expression in tumors may predict clinical responses; however, the use of blood-based profiling to understand the immunologic mechanism of PD-1 blockade has been less explored. Here we used detailed immune profiling of peripheral blood from stage IV melanoma patients before and after pembrolizumab (pembro), and identified pharmacodynamic changes in circulating exhausted-phenotype CD8 T cells (TEX). Robust induction of Ki67 in this subset of circulating CD8 T cells post-therapy (re-invigoration) occurred in 78% of patients indicating strong, on target immunological effects of PD-1 blockade in most patients studied here. Despite this high immunological response rate, the objective clinical response rate in this cohort was less than 40%. Ki67 in CD8 T cells alone did not predict clinical outcomes and, in fact, higher systemic immune activation at baseline was associated with lower overall survival. Rather, the magnitude of re-invigoration of circulating TEX in relation to pre-treatment tumor burden correlated with clinical response. We identified a TEX re-invigoration to tumor burden ratio which could be used to predict clinical response and overall survival as early as 6 weeks post therapy. Consistent observations were found in a second independent cohort and suggest that clinical failure of PD-1 blockade in many patients may not solely be due to an inability to induce immune re-invigoration but rather, an imbalance between T cell re-invigoration and tumor burden. Thus, by focused profiling of a mechanistically relevant circulating T cell subpopulation calibrated to pre-treatment disease burden, we identify a clinically accessible predictor of response to PD-1 blockade. These findings also provide a framework for dissecting distinct types of treatment failures in melanoma and have implications for stratifying patients into additional immunotherapeutic treatment approaches.

Citation Format: Alexander Huang, Michael A. Postow, Robert J. Orlowski, Rosemarie Mick, Bertram Bengsch, Sasi Manne, Wei Xu, Shannon Harmon, Matthew Adamow, Deborah Kuk, Katherine Panangeas, Cristina Carerra, Phillip Wong, Felix Quagliarello, Kristen E. Pauken, Ramin S. Herati, Suzanne McGettigan, Shawn Kothari, Sangeeth M. George, Brandon Wenz, Kurt D'Andrea, Xiaowei Xu, Ravi K. Amaravadi, Giorgos Karakousis, Lynn M. Schuchter, Katherine L. Nathanson, Jedd D. Wolchok, Tara C. Gangadhar, John Wherry. Peripheral blood immune profiling of anti-PD-1 therapy in human melanoma reveals a link between T cell re-invigoration and tumor burden that predicts response [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR05.

Autophagy levels are elevated in barrett's esophagus and promote cell survival from acid and oxidative stress

Autophagy is a highly conserved mechanism that is activated during cellular stress. We hypothesized that autophagy may be induced by acid reflux, which causes injury, and inflammation, and therefore, contributes to the pathogenesis of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Currently, the role of autophagy in BE and EAC is poorly studied. We quantitatively define autophagy levels in human BE cell lines, a transgenic mouse model of BE, and human BE, and EAC biopsies. Human non-dysplastic BE had the highest basal number of autophagic vesicles (AVs), while AVs were reduced in normal squamous cells and dysplastic BE cells, and nearly absent in EAC. To demonstrate a functional role for autophagy in BE pathogenesis, normal squamous (STR), non-dysplastic BE (CPA), dysplastic BE (CPD), and EAC (OE19) cell lines were exposed to an acid pulse (pH 3.5) followed by incubation in the presence or absence of chloroquine, an autophagy inhibitor. Acid exposure increased reactive oxygen species (ROS) levels in STR and CPA cells. Chloroquine alone had a small impact on intracellular ROS or cell survival. However, combination of chloroquine with the acid pulse resulted in a significant increase in ROS levels at 6 h in STR and CPA cells, and increased cell death in all cell lines. These findings establish increased numbers of AVs in human BE compared to normal squamous or EAC, and suggest that autophagy functions to improve cell survival after acid reflux injury. Autophagy may thus play a critical role in BE pathogenesis and progression. © 2015 Wiley Periodicals, Inc.

Abstract 1018: Structural features of novel dimeric quinacrines that have single-agent antitumor activity determine the mechanism of action: destabilization of mTORC1/lysosomal interaction versus DNA damage

The safety and preliminary activity of hydroxychloroquine in phase I cancer clinical trials have established the feasibility and rationale for targeting the lysosome in cancer. We previously reported a more potent lysosomal inhibitor Lys05, which is a dimeric chloroquine (CQ) linked with a triamine linker. Here we report that high throughput screening of &gt;100 Lys05 derivatives (72-hour viability assay) revealed extending linker length between the CQ motifs markedly enhanced anti-proliferative potency (IC50 &lt;500 nM v. 5 μM Lys05). Longer linker dimeric CQs produced significantly greater autophagy inhibition (2-5 fold improved v. Lys05; mCherry-eGFP-LC3 reporter) and apoptosis (2-8 fold improved v. Lys05) in human pancreatic cancer, melanoma and in KRAS mutant P53-/- mouse pancreatic cells. We then substituted the CQ heterocycle of Lys05 with other antimalarial heterocycles including those found in mefloquine, primaquine and quinacrine. Dimeric quinacrines (DQ’s) were exquisitely cytotoxic to cancer cell lines (IC50 9 - 90nM; ≥40 fold improvement v. quinacrine). These agents were renamed DQ221-661, where the first and second digit of each compound indicates the number of carbons flanking the central nitrogen and the third digit reflects whether the central nitrogen in the dimeric molecule is methylated (1) or not (0). Inherent fluorescence of the DQs uncovered a striking pattern of subcellular localization dependent on central nitrogen methylation. All of the methylated DQs localized to the lysosome and inhibited autophagic flux (bafilomycin clamp assay), while all of the unmethylated DQ's localized to the nucleus, produced pH2AX-positive DNA damage, and induced autophagy. Methylated DQs produced lysosomal membrane permeabilization (LMP; galectin-3 puncta), and equal cytotoxicity in ATG5 WT and ATG5-null MEFs, indicating their cytotoxicity is not dependent on functional upstream canonical autophagy. Reverse phase protein array analysis of dimeric CQs Lys05, Lys75 and DQ661 revealed a signature associated with inactivation of mTORC1 (decreased phosphorylation of S6K, 4E-BP1, PRAS40). DQ661 disrupted mTOR/LAMP2 co-localization and induced greater levels of apoptosis compared to BRAF/MEK inhibition in BRAF-MT melanoma cells, gemcitabine in pancreatic cancer cells, or early stage autophagy inhibitors Spautin-1 and SBI-0206965. Unlike quinacrine, which had no effect, or DQ660, which produced a modest but significant growth impairment, DQ661 produced significant tumor regression in a melanoma xenograft model, establishing the therapeutic potential of this compound in cancer. Our data identifies a new class of lysosomal inhibitors, the centrally methylated dimeric quinacrines, devoid of DNA damaging properties, that are capable of concurrently inhibiting autophagy-lysosome function and mTORC1 through LMP.

Citation Format: Vito W. Rebecca, Michael Nicastri, Noel McGlaughlin, Quentin McAfee, Gao Zhang, Gretchen M. Alicea, Shengfu Piao, Colin Fennelly, Sengottuvelan Murugan, Zhi Wei, Gordon B. Mills, Yiling Lu, Meenhard Herlyn, Jeffrey D. Winkler, Ravi K. Amaravadi. Structural features of novel dimeric quinacrines that have single-agent antitumor activity determine the mechanism of action: destabilization of mTORC1/lysosomal interaction versus DNA damage. [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 1018.

Abstract 1024: Expression pattern of ALDH1A1 and HLTF predicts sensitivity to lysosomal autophagy inhibitors in cancer cells

Autophagy inhibition with hydroxychloroquine (HCQ)is cytotoxic to only a subset of cancer cell lines. Clinical trials involving HCQ in cancer patients are underway, but predictive biomarkers to identify patients most likely to respond are unavailable. To identify determinants of sensitivity to HCQ, an mRNA microarray analysis of HCQ-sensitive(S) compared to HCQ- resistant (R) colon and lung cancer cell lines identified differentially expressed genes in HCQ-S cells. Immunoblotting against the 2 most upregulated (Lysozyme (LYZ); aldehyde dehydrogenase 1 (ALDH1A1)) and 2 most down regulated proteins (helicase like transcription factor (HLTF); p-glycoprotein (ABCB1)) was performed in 35 human cancer cell lines. The IC50 and slope of the HCQ dose response curve (72 h MTT) were used to create a composite score to categorize cell lines as -S or -R, and correlated to protein expression of the 4 genes. Classification and regression tree (CART) analysis determined that high expression of the stem cell marker ALDH1A1 or low expression of both ALDH1A1 and HLTF identified 100% of sensitive cell lines. To understand how ALDH1A1 mechanistically interacts with HCQ, the aldefluor assay determined that a more potent dimeric CQ (Lys21) did not impair ALDH1A1 enzymatic function, however knockdown or chemical inhibition of ALDH1A1 impaired cellular uptake of fluorescently tagged Lys21 and conferred resistance to HCQ. Overexpression of ALDH1A1 conferred HCQ sensitivity in HCQ-R cells. To understand the interaction between HLTF and HCQ, we determined that HLTF promoter methylation correlated with silenced expression and sensitivity to HCQ. Forced expression of HLTF or treatment with a demethylating agent conferred resistance to HCQ-S cells. Knockdown of HLTF in HCQ-R cells conferred sensitivity. HCQ produced reactive oxygen species (ROS) irrespective of HLTF status. Cotreatment with a ROS scavenger mitigated HCQ cytotoxicity in HLTF silenced cells. DNA damage (p-H2AX) was observed at 100-fold lower HCQ concentrations in HLTF silenced compared to HLTF expressed cells. Overexpression of HLTF significantly reduced HCQ associated double strand breaks (Rad52 foci). Knockdown of DNA polymerase eta, a low fidelity DNA polymerase involved in translesion synthesis (TLS) completely abrogated HLTF-associated HCQ resistance. In vivo expression of HLTF mitigated the antitumor activity of the dimeric CQ Lys05 in a HCQ-S colon cancer xenograft. These results indicate ALDH1A1 acts as a sink for CQ derivatives to enter the cell, localize to the lysosome, and produce ROS-mediated DNA damage. The DNA damage can be counteracted by intact HLTF/Pol eta-dependent TLS. Analysis of the TCGA found that the ALDH1A1 high and HLTF low phenotype is prevalent across 10 human cancers. In conclusion this study identifies a 2 gene signature that can be translated into an IHC-based assay to identify patients most likely to respond to lysosomal autophagy inhibitors.

Citation Format: Shengfu Piao, Arabinda Samanta, Xiaohong Ma, Quentin W. Mcafee, Vito W. Rebecca, Meghan Buckley, Eric J. Brown, Phyllis A. Gimotty, Ravi K. Amaravadi. Expression pattern of ALDH1A1 and HLTF predicts sensitivity to lysosomal autophagy inhibitors in cancer cells. [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 1024.

Targeting mitochondrial biogenesis to overcome drug resistance to MAPK inhibitors

Targeting multiple components of the MAPK pathway can prolong the survival of patients with BRAFV600E melanoma. This approach is not curative, as some BRAF-mutated melanoma cells are intrinsically resistant to MAPK inhibitors (MAPKi). At the systemic level, our knowledge of how signaling pathways underlie drug resistance needs to be further expanded. Here, we have shown that intrinsically resistant BRAF-mutated melanoma cells with a low basal level of mitochondrial biogenesis depend on this process to survive MAPKi. Intrinsically resistant cells exploited an integrated stress response, exhibited an increase in mitochondrial DNA content, and required oxidative phosphorylation to meet their bioenergetic needs. We determined that intrinsically resistant cells rely on the genes encoding TFAM, which controls mitochondrial genome replication and transcription, and TRAP1, which regulates mitochondrial protein folding. Therefore, we targeted mitochondrial biogenesis with a mitochondrium-targeted, small-molecule HSP90 inhibitor (Gamitrinib), which eradicated intrinsically resistant cells and augmented the efficacy of MAPKi by inducing mitochondrial dysfunction and inhibiting tumor bioenergetics. A subset of tumor biopsies from patients with disease progression despite MAPKi treatment showed increased mitochondrial biogenesis and tumor bioenergetics. A subset of acquired drug-resistant melanoma cell lines was sensitive to Gamitrinib. Our study establishes mitochondrial biogenesis, coupled with aberrant tumor bioenergetics, as a potential therapy escape mechanism and paves the way for a rationale-based combinatorial strategy to improve the efficacy of MAPKi.

HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors

The stress-inducible chaperone protein HSP70 (HSPA1) is implicated in melanoma development, and HSP70 inhibitors exert tumor-specific cytotoxic activity in cancer. In this study, we documented that a significant proportion of melanoma tumors express high levels of HSP70, particularly at advanced stages, and that phospho-FAK (PTK2) and BRAF are HSP70 client proteins. Treatment of melanoma cells with HSP70 inhibitors decreased levels of phospho-FAK along with impaired migration, invasion, and metastasis in vitro and in vivo Moreover, the HSP70 inhibitor PET-16 reduced levels of mutant BRAF, synergized with the BRAF inhibitor PLX4032 in vitro, and enhanced the durability of response to BRAF inhibition in vivo Collectively, these findings provide strong support for HSP70 inhibition as a therapeutic strategy in melanoma, especially as an adjuvant approach for overcoming the resistance to BRAF inhibitors frequently observed in melanoma patients. Cancer Res; 76(9); 2720-30. ©2016 AACR.

Targeting the lysosome in cancer

Lysosomes are membrane-bound intracellular organelles that receive macromolecules delivered by endocytosis, phagocytosis, and autophagy for degradation and recycling. Over the last decade, advances in lysosome research have established a broad role for the lysosome in the pathophysiology of disease. In this review, we highlight the recent discoveries in lysosome biology, with an emphasis on their implications for cancer therapy. We focus on targeting the lysosome in cancer by exploring lysosomal biogenesis and its role in the crosstalk between apoptosis and autophagy. We also discuss how lysosomal inhibition could emerge as a new therapeutic strategy to overcome drug resistance in cancer.

A Phase I Study of the SMAC-Mimetic Birinapant in Adults with Refractory Solid Tumors or Lymphoma

The inhibitor of apoptosis (IAP) family of antiapoptotic proteins has been identified as a target for small molecule inhibitors in cancer. Second mitochondrial-derived activator of caspases (SMAC) efficiently and naturally antagonizes IAPs, and preclinical studies have determined that SMAC mimetics have potent anticancer properties. Here, we report a first-in-human trial designed to determine the maximum tolerated dose (MTD), safety, and pharmacokinetics/pharmacodynamics (PK/PD) of birinapant, a novel SMAC mimetic. Patients with advanced solid tumors or lymphoma were enrolled in a 3+3 dose escalation design with birinapant administered intravenously from 0.18 to 63 mg/m(2) once weekly every 3 of 4 weeks. Fifty patients were enrolled to 12 dose cohorts. Birinapant 47 mg/m(2) was determined to be the MTD. At 63 mg/m(2), dose-limiting toxicities included headache, nausea, and vomiting. Two cases of Bell's palsy (grade 2) also occurred at 63 mg/m(2). Birinapant had a plasma half-life of 30 to 35 hours and accumulated in tumor tissue. Birinapant suppressed cIAP1 and increased apoptosis in peripheral blood mononuclear cells and tumor tissue. Prolonged stable disease was observed in 3 patients: non-small cell lung cancer (5 months), colorectal cancer (5 months), and liposarcoma (9 months). Two patients with colorectal cancer had radiographic evidence of tumor shrinkage. In conclusion, birinapant was well tolerated with an MTD of 47 mg/m(2) and exhibited favorable PK and PD properties. Several patients demonstrated stable disease and evidence of antitumor activity. These results support the ongoing clinical trials of birinapant in patients with cancer.

Abstract SY01-04: Chloroquine derivatives as anticancer agents

Mouse models of cancer have demonstrated that therapy-induced autophagy in advanced cancer can promote tumor cell survival and resistance to therapy. Chloroquine derivatives impair autophagy by impairing lysosomal function. Preclinical studies in many, but not all, cancer models have shown that combining chloroquine derivatives with other anticancer agents produces autophagic vesicle accumulation followed by enhanced cancer cell death. Based on these results, clinical trials involving the hydroxychloroquine (HCQ) have been launched for patients with refractory malignancies. The results of the first 6 HCQ clinical trials (5 in humans, 1 in dogs) represent the first deliberate attempt to modulate autophagy therapeutically in patients. These studies indicate that autophagy can be modulated therapeutically with HCQ in patients. While the majority of patients did not experience unexpected toxicity, specific HCQ- chemotherapy combinations did produce enhanced myelosuppression, indicating treatment with HCQ and other chloroquine derivatives should continue to only be considered in the context of clinical trials. Encouraging antitumor activity of HCQ based combinations was observed in patients with melanoma, colon cancer, renal cell carcinoma, and in pet dogs, but randomized studies will be needed to determine if the activity can be attributed to the addition of HCQ. Preliminary results of currently enrolling or more recently completed clinical trials involving hydroxychloroquine will be highlighted. A serum-based approach based on secretome analysis of melanoma cells grown in three dimensional culture has identified potential quantitative biomarkers of low and high tumor cell autophagy. This approach could potentially lead to predictive and pharmacodynamic assays of response to autophagy modulation. To improve the potency of chloroquine derivatives against cancer we have previously reported a dimeric chloroquine Lys05, which is being evaluated for clinical development. Based on analysis of 70 new derivatives of Lys05, compounds which localize to the lysosome, inhibit autophagy and exhibit nanomolar cytotoxicity profiles have been identified. Finally we will discuss ongoing efforts to develop a more detailed understanding of the mechanism of action chloroquine as an anticancer agent.

Citation Format: Ravi K. Amaravadi. Chloroquine derivatives as anticancer agents. [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 SY01-04. doi:10.1158/1538-7445.AM2015-SY01-04

Abstract 2858: Radiation and dual immune checkpoint blockade overcome tumor resistance and distinctly improve immunity

Optimal results with immune checkpoint inhibitors such as CTLA4 and PD-1 will likely require combination therapy. This raises important questions about tumor resistance and non-redundant mechanisms of action. Pre-clinical and clinical data indicate that radiation (RT) may augment responses to immune checkpoint inhibition. We therefore evaluated this combination for metastatic melanoma using parallel studies in mice and humans. In a phase I clinical trial with 19 patients with multiple melanoma metastases, a single index lesion was irradiated with hypofractionated RT, delivered over two or three fractions, followed by four cycles of the anti-CTLA4 antibody ipilimumab. We reproduced this therapy in mice using the melanoma cell line B16-F10. For this, each flank of C57BL/6 mice was implanted with tumors to model multiple metastases. Mice received anti-CTLA4 (on days 5, 8, and 11), irradiation of one tumor using an image-guided micro-irradiator (20 Gy x 1 on day 8), or both treatments. Mechanistic studies were performed on material obtained from patients and mice at baseline and thereafter. Overall, treatment in the phase I study was well tolerated and toxicity was similar to that reported for anti-CTLA4. Major tumor regressions were observed in a subset of patients with metastatic melanoma treated with anti-CTLA4 + RT. In mice, although combined treatment enhanced the CD8 T cell to Treg ratios and improved responses in irradiated and unirradiated tumors, resistance was common. Genome-wide and unbiased analyses revealed that resistant tumors have increased PD-L1, interferon-stimulated genes, and exhausted T cells that depress the CD8/Treg ratio. Patients and mice with high PD-L1 tumors that were treated with RT + anti-CTLA4 poorly reinvigorated exhausted T cells, did not respond, and rapidly progressed. In mice, adding anti-PD-L1/PD-1 to RT + anti-CTLA4 reinvigorated exhausted T cells, leading to complete responses and immunity across multiple cancer types. The extent of T cell exhaustion/reinvigoration predicts response and can be assessed through peripheral blood. Resistance to RT + anti-CTLA4 results from depression in the CD8/Treg ratio due to elevated tumor PD-L1 and persistent T cell exhaustion. Both clinical and pre-clinical data suggest that the combination of RT with CTLA4 and PD-1 checkpoint blockade is a rational, non-redundant approach to overcoming tumor resistance and improving immunity in multiple cancer types.

Citation Format: Andrew J. Rech, Christina Twyman-Saint Victor, Amit Maity, Ramesh Rengan, Kristen E. Pauken, Erietta Stelekati, Joseph Benci, Bihui Xu, Hannah Dada, Pamela M. Odorizzi, Ramin S. Herati, Kathleen D. Mansfield, Dana Patsch, Ravi K. Amaravadi, Lynn M. Schuchter, Hemant Ishwaran, Rosemarie Mick, Daniel Pryma, Xiaowei Xu, Michael D. Feldman, Tara C. Gangadhar, Stephen M. Hahn, E. John Wherry, Andy J. Minn, Robert H. Vonderheide. Radiation and dual immune checkpoint blockade overcome tumor resistance and distinctly improve immunity. [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 2858. doi:10.1158/1538-7445.AM2015-2858

Multiple Gastrointestinal Polyps in Patients Treated with BRAF Inhibitors

PURPOSE

BRAF inhibitors (BRAFi) extend survival in BRAF-mutant melanoma but can promote the growth of Ras-mutant neoplasms. This study determined if gastrointestinal polyps found in BRAFi-treated patients harbored Ras mutations.

EXPERIMENTAL DESIGN

Colonic and gastric polyps were identified and resected from BRAFi-treated melanoma patients. Next-generation sequencing (NGS) was performed on polyps. The ability of BRAFi to promote polyp formation was functionally characterized in Apc Min(+/-) mice. MAPK and β-catenin pathway activity was assessed by immunohistochemistry in mouse and human polyps.

RESULTS

Fourteen patients treated with BRAFi underwent endoscopy to assess for polyps. Seven out of 7 patients >40 years of age and treated for >2 years were found to have colonic tubular adenomas with 4 out of the 7 patients having 5 or more polyps. One patient presented with bleeding from hyperplastic gastric polyps that recurred 6 months after BRAFi rechallenge. NGS performed on polyps found no mutations in MAPK pathway genes, but found APC mutations in all tubular adenomas. A significant increase in the number of polyps was observed in BRAFi-treated compared with control-treated Apc Min(+/-) mice (20.8 ± 9.2 vs 12.8 ± 0.1; P = 0.016). No polyps were observed in BRAFi-treated wild-type mice.

CONCLUSIONS

BRAFi may increase the risk of developing hyperplastic gastric polyps and colonic adenomatous polyps. Due to the risk of gastrointestinal bleeding and the possibility of malignant transformation, further studies are needed to determine whether or not endoscopic surveillance should be recommended for patients treated with BRAFi.

Phase I/II Trial of Imatinib and Bevacizumab in Patients With Advanced Melanoma and Other Advanced Cancers

BACKGROUND

Vascular endothelial growth factor and platelet-derived growth factor signaling in the tumor microenvironment appear to cooperate in promoting tumor angiogenesis.

PATIENTS AND METHODS

We conducted a phase I trial combining bevacizumab (i.v. every 2 weeks) and imatinib (oral daily). Once a recommended phase II dose combination was established, a phase II trial was initiated in patients with metastatic melanoma. A Simon 2-stage design was used with 23 patients required in the first stage and 41 patients in total should the criteria to proceed be met. We required that 50% of the patients be progression-free at 16 weeks. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and power Doppler ultrasonography were performed in patients with metastatic tumors amenable to imaging with these methods at baseline and after 4 weeks.

RESULTS

A total of 17 patients were accrued to 4 dose and combination levels. Bevacizumab 10 mg/kg every 2 weeks could be safely combined with imatinib 800 mg daily. Common toxicities included fatigue, nausea, vomiting, edema, proteinuria, and anemia, but were not commonly severe. A total of 23 patients with metastatic melanoma (48% with American Joint Commission on Cancer stage M1c; median age, 63 years) were enrolled in the first stage of phase II. The 16-week progression-free survival rate was 35%, leading to termination of phase II after the first stage. In the small subset of patients who remained on study with lesions evaluable by DCE-MRI, significant decreases in tumor vascular permeability were noted, despite early disease progression using the Response Evaluation Criteria In Solid Tumors.

CONCLUSION

Bevacizumab and imatinib can be safely combined at the maximum doses used for each agent. We did not observe significant clinical activity with this regimen in melanoma patients.