Evolutionary fingerprints of EMT in pancreatic cancers

Mesenchymal plasticity has been extensively described in advanced and metastatic epithelial cancers; however, its functional role in malignant progression, metastatic dissemination and therapy response is controversial. More importantly, the role of epithelial mesenchymal transition (EMT) and cell plasticity in tumor heterogeneity, clonal selection and clonal evolution is poorly understood. Functionally, our work clarifies the contribution of EMT to malignant progression and metastasis in pancreatic cancer. We leveraged ad hoc somatic mosaic genome engineering, lineage tracing and ablation technologies and dynamic genetic reporters to trace and ablate tumor-specific lineages along the phenotypic spectrum of epithelial to mesenchymal plasticity. The experimental evidences clarify the essential contribution of mesenchymal lineages to pancreatic cancer evolution and metastatic dissemination. Spatial genomic analysis combined with single cell transcriptomic and epigenomic profiling of epithelial and mesenchymal lineages reveals that EMT promotes with the emergence of chromosomal instability (CIN). Specifically tumor lineages with mesenchymal features display highly conserved patterns of genomic evolution including complex structural genomic rearrangements and chromotriptic events. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross species analysis of pancreatic and other human epithelial cancers. Mechanistically, we discovered that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, which in turn results in delayed mitosis and catastrophic cell division. Therefore, EMT favors the emergence of high-fitness tumor cells, strongly supporting the concept of a cell-state, lineage-restricted patterns of evolution, where cancer cell sub-clonal speciation is propagated to progenies only through restricted functional compartments. Restraining those evolutionary routes through genetic ablation of clones capable of mesenchymal plasticity and extinction of the derived lineages completely abrogates the malignant potential of one of the most aggressive form of human cancer.

Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer

Molecular routes to metastatic dissemination are critical determinants of aggressive cancers. Through in vivo CRISPR-Cas9 genome editing, we generated somatic mosaic genetically engineered models that faithfully recapitulate metastatic renal tumors. Disruption of 9p21 locus is an evolutionary driver to systemic disease through the rapid acquisition of complex karyotypes in cancer cells. Cross-species analysis revealed that recurrent patterns of copy number variations, including 21q loss and dysregulation of the interferon pathway, are major drivers of metastatic potential. In vitro and in vivo genomic engineering, leveraging loss-of-function studies, along with a model of partial trisomy of chromosome 21q, demonstrated a dosage-dependent effect of the interferon receptor genes cluster as an adaptive mechanism to deleterious chromosomal instability in metastatic progression. This work provides critical knowledge on drivers of renal cell carcinoma progression and defines the primary role of interferon signaling in constraining the propagation of aneuploid clones in cancer evolution.

SMARCB1 regulates the hypoxic stress response in sickle cell trait

Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor suppressor SMARCB1. Because renal ischemia induced by red blood cell sickling exacerbates chronic renal medullary hypoxia in vivo, we investigated whether the loss of SMARCB1 confers a survival advantage under the setting of SCT. Hypoxic stress, which naturally occurs within the renal medulla, is elevated under the setting of SCT. Our findings showed that hypoxia-induced SMARCB1 degradation protected renal cells from hypoxic stress. SMARCB1 wild-type renal tumors exhibited lower levels of SMARCB1 and more aggressive growth in mice harboring the SCT mutation in human hemoglobin A (HbA) than in control mice harboring wild-type human HbA. Consistent with established clinical observations, SMARCB1-null renal tumors were refractory to hypoxia-inducing therapeutic inhibition of angiogenesis. Further, reconstitution of SMARCB1 restored renal tumor sensitivity to hypoxic stress in vitro and in vivo. Together, our results demonstrate a physiological role for SMARCB1 degradation in response to hypoxic stress, connect the renal medullary hypoxia induced by SCT with an increased risk of SMARCB1-negative RMC, and shed light into the mechanisms mediating the resistance of SMARCB1-null renal tumors against angiogenesis inhibition therapies.

Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis

Mitochondria are hubs where bioenergetics, redox homeostasis, and anabolic metabolism pathways integrate through a tightly coordinated flux of metabolites. The contributions of mitochondrial metabolism to tumor growth and therapy resistance are evident, but drugs targeting mitochondrial metabolism have repeatedly failed in the clinic. Our study in pancreatic ductal adenocarcinoma (PDAC) finds that cellular and mitochondrial lipid composition influence cancer cell sensitivity to pharmacological inhibition of electron transport chain complex I. Profiling of patient-derived PDAC models revealed that monounsaturated fatty acids (MUFAs) and MUFA-linked ether phospholipids play a critical role in maintaining ROS homeostasis. We show that ether phospholipids support mitochondrial supercomplex assembly and ROS production; accordingly, blocking de novo ether phospholipid biosynthesis sensitized PDAC cells to complex I inhibition by inducing mitochondrial ROS and lipid peroxidation. These data identify ether phospholipids as a regulator of mitochondrial redox control that contributes to the sensitivity of PDAC cells to complex I inhibition.

Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAFV600E inhibition resistance in melanoma

Targeted cancer therapies have revolutionized treatment but their efficacies are limited by the development of resistance driven by clonal evolution within tumors. We developed "CAPTURE", a single-cell barcoding approach to comprehensively trace clonal dynamics and capture live lineage-coupled resistant cells for in-depth multi-omics analysis and functional exploration. We demonstrate that heterogeneous clones, either preexisting or emerging from drug-tolerant persister cells, dominated resistance to vemurafenib in BRAFV600E melanoma. Further integrative studies uncovered diverse resistance mechanisms. This includes a previously unrecognized and clinically relevant mechanism, chromosome 18q21 gain, which leads to vulnerability of the cells to BCL2 inhibitor. We also identified targetable common dependencies of captured resistant clones, such as oxidative phosphorylation and E2F pathways. Our study provides new therapeutic insights into overcoming therapy resistance in BRAFV600E melanoma and presents a platform for exploring clonal evolution dynamics and vulnerabilities that can be applied to study treatment resistance in other cancers.

Immune landscape of a genetically engineered murine model of glioma compared with human glioma

Novel therapeutic strategies targeting glioblastoma (GBM) often fail in the clinic, partly because preclinical models in which hypotheses are being tested do not recapitulate human disease. To address this challenge, we took advantage of our previously developed spontaneous Qk/Trp53/Pten (QPP) triple-knockout model of human GBM, comparing the immune microenvironment of QPP mice with that of patient-derived tumors to determine whether this model provides opportunity for gaining insights into tumor physiopathology and preclinical evaluation of therapeutic agents. Immune profiling analyses and single-cell sequencing of implanted and spontaneous tumors from QPP mice and from patients with glioma revealed intratumoral immune components that were predominantly myeloid cells (e.g., monocytes, macrophages, and microglia), with minor populations of T, B, and NK cells. When comparing spontaneous and implanted mouse samples, we found more neutrophils and T and NK cells in the implanted model. Neutrophils and T and NK cells were increased in abundance in samples derived from human high-grade glioma compared with those derived from low-grade glioma. Overall, our data demonstrate that our implanted and spontaneous QPP models recapitulate the immunosuppressive myeloid-dominant nature of the tumor microenvironment of human gliomas. Our model provides a suitable tool for investigating the complex immune compartment of gliomas.

Abstract 2611: The NEDD8 pathway as a therapeutic target in HER2-amplified colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease with a wide spectrum of clinical outcomes, from indolent resectable disease to aggressive-metastatic cases. Primary and acquired resistance limits the efficacy of available treatments, and the identification of effective drug combinations is needed to further improve patients' outcomes. We previously found that the NEDD8-activating enzyme inhibitor pevonedistat induced tumor stabilization in preclinical models of poorly differentiated, clinically aggressive CRC resistant to available therapies. To identify drugs that can be effectively combined with pevonedistat, we performed a "drop-out" loss-of-function synthetic lethality screening with an shRNA library covering 200 drug-target genes in four different CRC cell lines. Multiple screening hits were found to be involved in the EGFR signaling pathway, suggesting that, rather than inhibition of a specific gene, interference with the EGFR pathway at any level could be effectively leveraged for combination therapies based on pevonedistat. Exploiting both BRAF-mutant and RAS/RAF wild-type CRC models, we validated the therapeutic relevance of our findings by showing that combined blockade of NEDD8 and EGFR pathways led to increased growth arrest and apoptosis both in vitro and in vivo. Pathway modulation analysis showed that compensatory feedback loops induced by single treatments were blunted by the combinations. Our results suggested possible therapeutic opportunities in specific CRC clinical settings. We further focused on HER2 amplified CRC cells and we observed cooperation between pevonedistat and HER2/EGFR blockade by the trastuzumab + lapatinib combination -the current standard treatment for HER2-amplified CRC. In addition, to confirm cooperation in reducing colony formation in vitro, we explored the effect of pevonedistat on long-term persisters, i.e., cell surviving to several weeks of HER2/EGFR blockade. Interestingly, we observed a marked decrease of cell colonies when pevonedistat was added to persisters survived to three weeks of trastuzumab + lapatinib treatment. These results unveil the possibility of testing in vivo the addition of pevonedistat subsequently to tumor stabilization or reduction by HER2/EGFR blockade, to promote further tumor regression.

Citation Format: Federica Invrea, Alessandro Carugo, Sabrina Arena, Alberto Bardelli, Giulio F. Draetta, Enzo Medico. The NEDD8 pathway as a therapeutic target in HER2-amplified colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2611.

Association of High-Intensity Exercise with Renal Medullary Carcinoma in Individuals with Sickle Cell Trait: Clinical Observations and Experimental Animal Studies

Renal medullary carcinoma (RMC) is a lethal malignancy affecting individuals with sickle hemoglobinopathies. Currently, no modifiable risk factors are known. We aimed to determine whether high-intensity exercise is a risk factor for RMC in individuals with sickle cell trait (SCT). We used multiple approaches to triangulate our conclusion. First, a case-control study was conducted at a single tertiary-care facility. Consecutive patients with RMC were compared to matched controls with similarly advanced genitourinary malignancies in a 1:2 ratio and compared on rates of physical activity and anthropometric measures, including skeletal muscle surface area. Next, we compared the rate of military service among our RMC patients to a similarly aged population of black individuals with SCT in the U.S. Further, we used genetically engineered mouse models of SCT to study the impact of exercise on renal medullary hypoxia. Compared with matched controls, patients with RMC reported higher physical activity and had higher skeletal muscle surface area. A higher proportion of patients with RMC reported military service than expected compared to the similarly-aged population of black individuals with SCT. When exposed to high-intensity exercise, mice with SCT demonstrated significantly higher renal medulla hypoxia compared to wild-type controls. These data suggest high-intensity exercise is the first modifiable risk factor for RMC in individuals with SCT.

Oxidative Phosphorylation Is a Metabolic Vulnerability in Chemotherapy-Resistant Triple-Negative Breast Cancer

Oxidative phosphorylation (OXPHOS) is an active metabolic pathway in many cancers. RNA from pretreatment biopsies from patients with triple-negative breast cancer (TNBC) who received neoadjuvant chemotherapy demonstrated that the top canonical pathway associated with worse outcome was higher expression of OXPHOS signature. IACS-10759, a novel inhibitor of OXPHOS, stabilized growth in multiple TNBC patient-derived xenografts (PDX). On gene expression profiling, all of the sensitive models displayed a basal-like 1 TNBC subtype. Expression of mitochondrial genes was significantly higher in sensitive PDXs. An in vivo functional genomics screen to identify synthetic lethal targets in tumors treated with IACS-10759 found several potential targets, including CDK4. We validated the antitumor efficacy of the combination of palbociclib, a CDK4/6 inhibitor, and IACS-10759 in vitro and in vivo. In addition, the combination of IACS-10759 and multikinase inhibitor cabozantinib had improved antitumor efficacy. Taken together, our data suggest that OXPHOS is a metabolic vulnerability in TNBC that may be leveraged with novel therapeutics in combination regimens. SIGNIFICANCE: These findings suggest that triple-negative breast cancer is highly reliant on OXPHOS and that inhibiting OXPHOS may be a novel approach to enhance efficacy of several targeted therapies.

Targeting mitochondrial respiration and the BCL2 family in high-grade MYC-associated B-cell lymphoma

Multiple molecular features, such as activation of specific oncogenes (e.g., MYC, BCL2) or a variety of gene expression signatures, have been associated with disease course in diffuse large B‐cell lymphoma (DLBCL), although their relationships and implications for targeted therapy remain to be fully unraveled. We report that MYC activity is closely correlated with—and most likely a driver of—gene signatures related to oxidative phosphorylation (OxPhos) in DLBCL, pointing to OxPhos enzymes, in particular mitochondrial electron transport chain (ETC) complexes, as possible therapeutic targets in high‐grade MYC‐associated lymphomas. In our experiments, indeed, MYC sensitized B cells to the ETC complex I inhibitor IACS‐010759. Mechanistically, IACS‐010759 triggered the integrated stress response (ISR) pathway, driven by the transcription factors ATF4 and CHOP, which engaged the intrinsic apoptosis pathway and lowered the apoptotic threshold in MYC‐overexpressing cells. In line with these findings, the BCL2‐inhibitory compound venetoclax synergized with IACS‐010759 against double‐hit lymphoma (DHL), a high‐grade malignancy with concurrent activation of MYC and BCL2. In BCL2‐negative lymphoma cells, instead, killing by IACS‐010759 was potentiated by the Mcl‐1 inhibitor S63845. Thus, combining an OxPhos inhibitor with select BH3‐mimetic drugs provides a novel therapeutic principle against aggressive, MYC‐associated DLBCL variants.

Epithelial memory of inflammation limits tissue damage while promoting pancreatic tumorigenesis

Inflammation is a major risk factor for pancreatic ductal adenocarcinoma (PDAC). When occurring in the context of pancreatitis, KRAS mutations accelerate tumor development in mouse models. We report that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, pancreatic epithelial cells display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thereby limiting tissue damage through a rapid decrease of zymogen production. We propose that because activating mutations of KRAS maintain an irreversible ADM, they may be beneficial and under strong positive selection in the context of recurrent pancreatitis.

miR-9 modulates and predicts the response to radiotherapy and EGFR inhibition in HNSCC

Radiotherapy (RT) plus the anti-EGFR monoclonal antibody Cetuximab (CTX) is an effective combination therapy for a subset of head and neck squamous cell carcinoma (HNSCC) patients. However, predictive markers of efficacy are missing, resulting in many patients treated with disappointing results and unnecessary toxicities. Here, we report that activation of EGFR upregulates miR-9 expression, which sustains the aggressiveness of HNSCC cells and protects from RT-induced cell death. Mechanistically, by targeting KLF5, miR-9 regulates the expression of the transcription factor Sp1 that, in turn, stimulates tumor growth and confers resistance to RT+CTX in vitro and in vivo. Intriguingly, high miR-9 levels have no effect on the sensitivity of HNSCC cells to cisplatin. In primary HNSCC, miR-9 expression correlated with Sp1 mRNA levels and high miR-9 expression predicted poor prognosis in patients treated with RT+CTX. Overall, we have discovered a new signaling axis linking EGFR activation to Sp1 expression that dictates the response to combination treatments in HNSCC. We propose that miR-9 may represent a valuable biomarker to select which HNSCC patients might benefit from RT+CTX therapy.

Sequential Administration of XPO1 and ATR Inhibitors Enhances Therapeutic Response in TP53-mutated Colorectal Cancer

BACKGROUND & AIMS

Understanding the mechanisms by which tumors adapt to therapy is critical for developing effective combination therapeutic approaches to improve clinical outcomes for patients with cancer.

METHODS

To identify promising and clinically actionable targets for managing colorectal cancer (CRC), we conducted a patient-centered functional genomics platform that includes approximately 200 genes and paired this with a high-throughput drug screen that includes 262 compounds in four patient-derived xenografts (PDXs) from patients with CRC.

RESULTS

Both screening methods identified exportin 1 (XPO1) inhibitors as drivers of DNA damage-induced lethality in CRC. Molecular characterization of the cellular response to XPO1 inhibition uncovered an adaptive mechanism that limited the duration of response in TP53-mutated, but not in TP53-wild-type CRC models. Comprehensive proteomic and transcriptomic characterization revealed that the ATM/ATR-CHK1/2 axes were selectively engaged in TP53-mutant CRC cells upon XPO1 inhibitor treatment and that this response was required for adapting to therapy and escaping cell death. Administration of KPT-8602, an XPO1 inhibitor, followed by AZD-6738, an ATR inhibitor, resulted in dramatic antitumor effects and prolonged survival in TP53-mutant models of CRC.

CONCLUSIONS

Our findings anticipate tremendous therapeutic benefit and support the further evaluation of XPO1 inhibitors, especially in combination with DNA damage checkpoint inhibitors, to elicit an enduring clinical response in patients with CRC harboring TP53 mutations.

Medium-chain acyl CoA dehydrogenase protects mitochondria from lipid peroxidation in glioblastoma

Glioblastoma (GBM) is highly resistant to chemo- and immune-based therapies and targeted inhibitors. To identify novel drug targets, we screened orthotopically implanted, patient-derived glioblastoma sphere-forming cells (GSCs) using an RNAi library to probe essential tumor cell metabolic programs. This identified high dependence on mitochondrial fatty acid metabolism. We focused on medium-chain acyl-CoA dehydrogenase (MCAD), which oxidizes medium-chain fatty acids (MCFAs), due to its consistently high score and high expression among models and upregulation in GBM compared to normal brain. Beyond the expected energetics impairment, MCAD depletion in primary GBM models induced an irreversible cascade of detrimental metabolic effects characterized by accumulation of unmetabolized MCFAs, which induced lipid peroxidation and oxidative stress, irreversible mitochondrial damage, and apoptosis. Our data uncover a novel protective role for MCAD to clear lipid molecules that may cause lethal cell damage, suggesting that therapeutic targeting of MCFA catabolism could exploit a key metabolic feature of GBM.

Abstract PD9-05: A tiered algorithm using mid-therapy ultrasound (US) response assessment and a novel gene expression signature (GES) improves the prediction of pathologic complete response (pCR) to neoadjuvant therapy (NAT) in triple-negative breast cancer (TNBC): Results from the ARTEMIS trial (NCT02276443)

Background: The heterogeneity of TNBC results in mixed responses to NAST: 30-60% of patients (pts) have a pCR to standard chemotherapy with an excellent prognosis. Several methods have been used to predict pCR, most yielding a positive predictive value (PPV) of no greater that 70%. To improve prediction of pCR to NAT, we hypothesized that we can integrate mid-treatment US with molecular profiling to generate a GES, thus reducing the need for escalation of therapy (example: immunotherapy) in select patients. We used data from ARTEMIS, a prospective trial that uses molecular profiling and imaging assessment of TNBC response during therapy to personalize NAT. Methods: Patients begin a planned 4 cycles of AC. Those with substantial volumetric reduction (>=70%) of the primary tumor by US (SVR-US) after AC receive standard taxane-based therapy as the second phase of NAT, while those with resistant disease (including disease progression during AC) are offered therapeutic trials based upon molecular profiling of the pre-treatment biopsy. Pathologic response is assessed at surgical resection. Results: 167 patients had RNAseq, US and pCR data. Overall pCR was 36%. TNBCs with SVR-US after AC (n=101) had significantly higher pCR (55 vs 6%, p<0.001). SVR-US had a PPV of 0.55 and NPV of 0.94 for prediction of pCR. Given the strong NPV, we focused on improving the PPV. In the 101 TNBCs that had SVR-US after AC, we performed differential gene expression comparing those with pCR vs residual disease using 74 TNBCs as a training set and 29 as a validation/test set. Differentially expressed genes (N=500-1000) served as a feature set for a series of machine learning models, including GBM (gradient boosting machines), GLM (generalized linear models), SVM (support vector machines) and CNN (convolutional neural networks) (N train=74). CNN and GLM had similar accuracy, NPV and PPV on the validation set (N=29), therefore GLM was selected as the final model because of ease of interpretability. By combining with SVR-US, we were able to increase the PPV of the tiered model from 0.55 (SVR-US after AC) to 0.89 (SVR-US after AC+GES/GLM) (validation set). Our analysis has validated the predictive value of the GES in patients with SVR-US to 4 cycles of AC, but the entire algorithm (including TNBCs without SVR-US) requires a second validation cohort. However, if the PPV and NPV remain consistent, the impact of this strategy to determine which TNBCs require therapy escalation beyond ACàT is estimated in Table 1. Conclusions: We have created an integrative, tiered model combining two complementary modalities (mid-treatment US assessment of response and GES) that has substantially improved the PPV in assessing pCR to NAST using the ARTEMIS strategy.

Table 1: PPV and NPV used to estimate the impact in escalation of therapy*Correct decision: 88% of ptsIncorrect decision: 12% of ptsPredicted pCR=pCR (True positives) Therapy correctly not escalatedPredicted non-pCR=non-pCR (True negatives) Therapy correctly escalatedUnder treatmentOver treatmentPredicted pCR does not=pCR (False positives) Therapy incorrectly not escalatedPredicted non-pCR =pCR (False negatives) Therapy incorrectly escalated34%54%8%4%*example of escalated regimen= taxane + novel agent on clinical trial or taxane + immunotherapy (if FDA approved)

Citation Format: Sahil Seth, Gaiane M Rauch, Beatriz Adrada, Helen Piwnica-Worms, Lei Hou, Alastair M Thompson, William F Symmans, Bora Lim, Jason White, Giulio F Draetta, Andrew Futreal, Jeffrey Chang, Stacy Moulder. A tiered algorithm using mid-therapy ultrasound (US) response assessment and a novel gene expression signature (GES) improves the prediction of pathologic complete response (pCR) to neoadjuvant therapy (NAT) in triple-negative breast cancer (TNBC): Results from the ARTEMIS trial (NCT02276443) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-05.

Loss of ARID1A Promotes Epithelial-Mesenchymal Transition and Sensitizes Pancreatic Tumors to Proteotoxic Stress

Cellular dedifferentiation is a key mechanism driving cancer progression. Acquisition of mesenchymal features has been associated with drug resistance, poor prognosis, and disease relapse in many tumor types. Therefore, successful targeting of tumors harboring these characteristics is a priority in oncology practice. The SWItch/Sucrose non-fermentable (SWI/SNF) chromatin remodeling complex has also emerged as a critical player in tumor progression, leading to the identification of several SWI/SNF complex genes as potential disease biomarkers and targets of anticancer therapies. AT-rich interaction domain-containing protein 1A (ARID1A) is a component of SWI/SNF, and mutations in ARID1A represent one of the most frequent molecular alterations in human cancers. ARID1A mutations occur in approximately 10% of pancreatic ductal adenocarcinomas (PDAC), but whether these mutations confer a therapeutic opportunity remains unclear. Here, we demonstrate that loss of ARID1A promotes an epithelial-mesenchymal transition (EMT) phenotype and sensitizes PDAC cells to a clinical inhibitor of HSP90, NVP-AUY922, both in vitro and in vivo. Although loss of ARID1A alone did not significantly affect proliferative potential or rate of apoptosis, ARID1A-deficient cells were sensitized to HSP90 inhibition, potentially by promoting the degradation of intermediate filaments driving EMT, resulting in cell death. Our results describe a mechanistic link between ARID1A defects and a quasi-mesenchymal phenotype, suggesting that deleterious mutations in ARID1A associated with protein loss exhibit potential as a biomarker for patients with PDAC who may benefit by HSP90-targeting drugs treatment. SIGNIFICANCE: This study identifies ARID1A loss as a promising biomarker for the identification of PDAC tumors that are potentially responsive to treatment with proteotoxic agents.

Allosteric SHP2 Inhibitor, IACS-13909, Overcomes EGFR-Dependent and EGFR-Independent Resistance Mechanisms toward Osimertinib

Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.

Discovery of IACS-9439, a Potent, Exquisitely Selective, and Orally Bioavailable Inhibitor of CSF1R

Tumor-associated macrophages (TAMs) have a significant presence in the tumor stroma across multiple human malignancies and are believed to be beneficial to tumor growth. Targeting CSF1R has been proposed as a potential therapy to reduce TAMs, especially the protumor, immune-suppressive M2 TAMs. Additionally, the high expression of CSF1R on tumor cells has been associated with poor survival in certain cancers, suggesting tumor dependency and therefore a potential therapeutic target. The CSF1-CSF1R signaling pathway modulates the production, differentiation, and function of TAMs; however, the discovery of selective CSF1R inhibitors devoid of type III kinase activity has proven to be challenging. We discovered a potent, highly selective, and orally bioavailable CSF1R inhibitor, IACS-9439 (1). Treatment with 1 led to a dose-dependent reduction in macrophages, promoted macrophage polarization toward the M1 phenotype, and led to tumor growth inhibition in MC38 and PANC02 syngeneic tumor models.

Abstract 1935: The NEDD8 and EGFR pathways are independent therapeutic targets in colorectal cancer

Colorectal cancer (CRC) develops and progresses through an accumulation of genetic and epigenetic alterations in multiple molecular pathways. Currently, targeted therapies combined with standard chemotherapy are the first-line therapy for metastatic CRC; nevertheless, the effectiveness of these drugs is limited by primary and acquired resistance. Since pathways are highly interconnected, the development of rational combinations of targeted therapies can be exploited to circumvent resistance mechanisms. As a possible alternative pathway for CRC treatment, an attractive option is the blockade of the NEDD8-ubiquitin like protein conjugation pathway. We previously found that the NEDD8-inhibitor pevonedistat has significant in vitro and in vivo activity on a subset of CRCs. However, the in vivo response is limited to tumor stabilization rather than regression, highlighting the need for therapeutic combinations. When the optimal drug combination cannot be readily predicted, functional genetic screens represent a powerful tool for unbiased exploration. We therefore carried out a synthetic lethality screening with an shRNA library covering 200 genes associated with FDA-approved drugs. The screening was aimed at identifying shRNAs that would be depleted only in the presence of pevonedistat: such constructs were expected to target genes that could harbor synergistic effects with NEDD8 inhibition. After shRNA library transduction, CRC cell lines were grown in the absence or presence of low-dose pevonedistat; Next Generation Sequencing and bioinformatics analysis allowed comparing the transduced library repertoire with or without pevonedistat, and identifying candidate synthetic lethal genes. The screening results revealed a strong, pevonedistat-dependent depletion of constructs targeting different tyrosine kinases (i.e. EGFR, BRAF, FYN and FLT4) in specific CRC cell lines (CAR1, WIDR, LIM2099 and DIFI, respectively). Firstly, we focused on the remarkable drop-out of EGFR-targeting shRNAs in CAR1 cells, which represent a subgroup of aggressive tumors refractory to cetuximab treatment, despite the lack of currently known markers of resistance. We discovered an independent and additive effect of anti-EGFR drugs (cetuximab and lapatinib) combined with pevonedistat, which was then validated in vitro on further cell lines (HCA7 and HROC69) and in vivo on HCA7-transplanted mice. Furthermore, we considered the depletion of constructs targeting BRAF, a member of EGFR pathway, observed in WIDR BRAF-mutant cells: we found an additive effect of BRAF inhibitor vemurafenib and pevonedistat in reducing in vitro cell growth. Altogether our results suggest that the concomitant pharmacological inhibition of NEDD8 and EGFR-pathway could be a novel effective approach to treat clinically aggressive CRCs, worthy of further characterization.

Citation Format: Federica Invrea, Alessandro Carugo, Consalvo Petti, Cristopher Bristow, Michael Peoples, Carlotta Cancelliere, Alessia Corrado, Alberto Bardelli, Claudio Isella, Giulio F. Draetta, Enzo Medico. The NEDD8 and EGFR pathways are independent therapeutic targets in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1935.

Abstract 1497: Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized trial (ARTEMIS; NCT02276443)

Background: The heterogeneity of TNBC results in a spectrum of responses to NAST: 30-40% of patients (pts) have a pathologic complete response (pCR) with an excellent prognosis. Several methods have been used to measure and evaluate residual disease, including ultrasound, MRI scans, histo-pathology. In addition to these, we hypothesize that comprehensive molecular profiling of longitudinal biopsies, with an integrative evaluation of sub-clonal selection and changes in molecular pathways, will serve as a critical biomarker for chemotherapy, and subsequent targeted therapy trials.

Methods: Pts with stage I-III TNBC began a planned 4 cycles of Adriamycin-based chemo (AC). Biopsies were performed pre (mandatory) and post (optional) AC. Volumetric change by ultrasound (VUS) at completion of AC (or progression) was calculated. Pts with sensitive disease received subsequent taxane-based (T) therapy. Pts with insensitive disease were offered phase II trials. Pathologic response was assessed at surgical resection in 85 pts (Training N=55, Validation N=30). Matched samples, pre and post AC (N = 85 pts) underwent transcriptomic and genomic profiling. Samples were classified into six previously identified ARTEMIS subtypes of TNBC (ART-Type) and immune deconvolution and estimation were performed using RNA-Seq profiles. Multiplex IHC using the Vectra platform is being used to validate results from bulk RNASeq experiments. Somatic mutations and copy-number changes were evaluated using, Mutect2, Sequenza (and FACETs), and PhyloWGS (and PyClone).

Results: Predominately, tumors reacted to AC in 4 different patterns with variation in immune and EMT related pathways. Enrichment of EMT (Group 4) was associated with poor prognosis and higher RCB (10.3% vs 42% pCR rates, p<0.05). The global changes in transcription led to ART-Type switching in all subtypes (44% of pts), except LAR subtype. This subtype was enriched in Group 3 (low overall change), and associated with PIK3CA mutations. MYC amplification was more prevalent (40%) in Group 4, associated with higher EMT and poor prognosis than other groups (28%). Multiple time points were leveraged to constrain sub-clonal clustering and enhance the accuracy of phylogenetic tree construction. Significant sub-clonal selection was detected in 22% of evaluable cases with pre and post biopsies (N=55), with analysis of the validation cohort underway. Molecular subtypes were marginally associated with overall and progression-free survival.

Conclusions: Molecular profiling of longitudinal TNBC samples reveals distinct response patterns in tumors and their micro-environments upon treatment with AC. Integrative analysis of genomic and transcriptomic changes can lead to better stratification of response to NAST. These patterns were indicative of pathologic response in the initial cohort (N=55). Analysis of the second cohort (N=30) will be presented as a validation cohort.

Citation Format: Sahil Seth, Lei Huo, Gaiane M. Rauch, Beatriz Adrada, Helen Piwnica-Worms, Bora Lim, Alastair M. Thompson, Elizabeth A. Mittendorf, Timothy Heffernan, Jennifer K. Litton, William F. Symmans, Giulio F. Draetta, Andrew P. Futreal, Jeffrey T. Chang, Stacy L. Moulder. Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized trial (ARTEMIS; NCT02276443) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1497.

Immune landscape of genetically-engineered murine models of glioma relative to human glioma by single-cell sequencing

Glioblastoma (GBM) is the most frequent and deadliest primary brain tumor, with a <10% 5-year overall survival rate. Despite promising results in other disease contexts, deployment of immune system-targeted therapies against GBM has not been successful thus far. In this regard, few preclinical models effectively recapitulate the human GBM immune microenvironment, hindering our ability to identify potentially targetable vulnerabilities. In this study, we characterized tumor immune microenvironment of the Qk/trp53/Pten (QPP) triple-knockout mouse model, harboring alterations common in human GBM and found that tumor infiltrates contain a predominantly myeloid cell population of monocytes, macrophages, and resting dendritic cells, with minor populations of T, B, and NK cells. Notable differences between spontaneous QPP tumors and tumors derived by implanting established QPP cell lines included T-cell enrichment and a larger proportion of myeloid-derived suppressive cells (MDSCs) in implanted tumors. Profiles of myeloid cells subtypes in QPP tumors paralleled findings in human GBMs, suggesting that this model effectively recapitulates the complexity of the myeloid-cell compartment and other human GBM immune cell populations.

Functional Genomics Reveals Synthetic Lethality between Phosphogluconate Dehydrogenase and Oxidative Phosphorylation

The plasticity of a preexisting regulatory circuit compromises the effectiveness of targeted therapies, and leveraging genetic vulnerabilities in cancer cells may overcome such adaptations. Hereditary leiomyomatosis renal cell carcinoma (HLRCC) is characterized by oxidative phosphorylation (OXPHOS) deficiency caused by fumarate hydratase (FH) nullizyogosity. To identify metabolic genes that are synthetically lethal with OXPHOS deficiency, we conducted a genetic loss-of-function screen and found that phosphogluconate dehydrogenase (PGD) inhibition robustly blocks the proliferation of FH mutant cancer cells both in vitro and in vivo. Mechanistically, PGD inhibition blocks glycolysis, suppresses reductive carboxylation of glutamine, and increases the NADP⁺/NADPH ratio to disrupt redox homeostasis. Furthermore, in the OXPHOS-proficient context, blocking OXPHOS using the small-molecule inhibitor IACS-010759 enhances sensitivity to PGD inhibition in vitro and in vivo. Together, our study reveals a dependency on PGD in OXPHOS-deficient tumors that might inform therapeutic intervention in specific patient populations.

Abstract C036: Discovery of IACS-13909, an allosteric SHP2 inhibitor that overcomes multiple mechanisms underlying osimertinib resistance

Osimertinib, a third generation EGFR inhibitor, is a front-line therapy for EGFR mutated non-small lung cancer (NSCLC). The long-term effectiveness of osimertinib is limited by acquired resistance. Clinically identified resistance mechanisms include EGFR-dependent mechanisms such as mutations on EGFR that preclude drug binding, and EGFR-independent activation of the MAPK pathway, for instance via activation of alternate RTKs. It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between the multiple resistance mechanisms will restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. SHP2 (Src homology 2 domain-containing phosphatase) is a phosphatase that mediates the signaling of multiple RTKs and is required for full activation of the MAPK pathway. Here we report IACS-13909 - a specific and potent allosteric inhibitor of SHP2 - suppresses the signaling of RTK/MAPK pathway. IACS-13909 potently impedes the proliferation of tumors with a broad spectrum of RTKs as the oncogenic driver. Importantly, in NSCLC models with acquired resistance to osimertinib, IACS-13909 administered as a single agent or in combination with osimertinib potently reduces tumor cell proliferation in vitro and in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFR inhibitor-resistant NSCLC. Currently, a compound that potently inhibits SHP2 has been selected as the clinical development candidate and is undergoing IND-enabling studies with a projected first-in-human target of early 2020.

Citation Format: Yuting Sun, Brooke A Meyers, Sarah B Johnson, Angela L Harris, Barbara Czako, Jason B Cross, Paul G Leonard, Faika Mseeh, Maria E Di Francesco, Connor A Parker, Qi Wu, Christopher A Bristow, Jason P Burke, Caroline C Carrillo, Christopher L Carroll, Qing Chang, Ningping Feng, Sonal Gera, Gao Guang, Justin Kwang-Lay Huang, Yongying Jiang, Zhijun Kang, Jeffrey J Kovacs, Xiaoyan Ma, Pijus K Mandal, Timothy McAfoos, Robert A Mullinax, Michael D Peoples, Vandhana Ramamoorthy, Sahil Seth, Erika Suzuki, Christopher Conrad Williams, Simon S Yu, Andy M Zuniga, Giulio F Draetta, Joseph R Marszalek, Timothy P Heffernan, Nancy E Kohl, Philip Jones. Discovery of IACS-13909, an allosteric SHP2 inhibitor that overcomes multiple mechanisms underlying osimertinib resistance [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C036. doi:10.1158/1535-7163.TARG-19-C036

YAP1 oncogene is a context-specific driver for pancreatic ductal adenocarcinoma

Transcriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, the squamous subtype is relatively independent of oncogenic KRAS signaling and typically displays much more aggressive clinical behavior versus the progenitor subtype. Here, we identified that yes-associated protein 1 (YAP1) activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and YAP1 activity in human PDAC and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated a YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.

Predictive Signatures Inform the Effective Repurposing of Decitabine to Treat KRAS-Dependent Pancreatic Ductal Adenocarcinoma

Mutated KRAS protein is a pivotal tumor driver in pancreatic cancer. However, despite comprehensive efforts, effective therapeutics that can target oncogenic KRAS are still under investigation or awaiting clinical approval. Using a specific KRAS-dependent gene signature, we implemented a computer-assisted inspection of a drug-gene network to in silico repurpose drugs that work like inhibitors of oncogenic KRAS. We identified and validated decitabine, an FDA-approved drug, as a potent inhibitor of growth in pancreatic cancer cells and patient-derived xenograft models that showed KRAS dependency. Mechanistically, decitabine efficacy was linked to KRAS-driven dependency on nucleotide metabolism and its ability to specifically impair pyrimidine biosynthesis in KRAS-dependent tumors cells. These findings also showed that gene signatures related to KRAS dependency might be prospectively used to inform on decitabine sensitivity in a selected subset of patients with KRAS-mutated pancreatic cancer. Overall, the repurposing of decitabine emerged as an intriguing option for treating pancreatic tumors that are addicted to mutant KRAS, thus offering opportunities for improving the arsenal of therapeutics for this extremely deadly disease. SIGNIFICANCE: Decitabine is a promising drug for cancer cells dependent on RAS signaling.

Critical questions in ovarian cancer research and treatment: Report of an American Association for Cancer Research Special Conference

Substantial progress has been made in understanding ovarian cancer at the molecular and cellular level. Significant improvement in 5-year survival has been achieved through cytoreductive surgery, combination platinum-based chemotherapy, and more effective treatment of recurrent cancer, and there are now more than 280,000 ovarian cancer survivors in the United States. Despite these advances, long-term survival in late-stage disease has improved little over the last 4 decades. Poor outcomes relate, in part, to late stage at initial diagnosis, intrinsic drug resistance, and the persistence of dormant drug-resistant cancer cells after primary surgery and chemotherapy. Our ability to accelerate progress in the clinic will depend on the ability to answer several critical questions regarding this disease. To assess current answers, an American Association for Cancer Research Special Conference on "Critical Questions in Ovarian Cancer Research and Treatment" was held in Pittsburgh, Pennsylvania, on October 1-3, 2017. Although clinical, translational, and basic investigators conducted much of the discussion, advocates participated in the meeting, and many presentations were directly relevant to patient care, including treatment with poly adenosine diphosphate ribose polymerase (PARP) inhibitors, attempts to improve immunotherapy by overcoming the immune suppressive effects of the microenvironment, and a better understanding of the heterogeneity of the disease.

Academic Discovery of Anticancer Drugs: Historic and Future Perspectives

The identification and prosecution of meritorious anticancer drug targets and the discovery of clinical candidates represent an extraordinarily time- and resource-intensive process, and the current failure rate of late-stage drugs is a critical issue that must be addressed. Relationships between academia and industry in drug discovery and development have continued to change over time as a result of technical and financial challenges and, most importantly, to the objective of translating impactful scientific discoveries into clinical opportunities. This Golden Age of anticancer drug discovery features an increased appreciation for the high-risk, high-innovation research conducted in the nonprofit sector, with the goals of infusing commercial drug development with intellectual capital and curating portfolios that are financially tenable and clinically meaningful. In this review, we discuss the history of academic-industry interactions in the context of antidrug discovery and offer a view of where these interactions are likely headed as we continue to reach new horizons in our understanding of the immense complexities of cancer biology.

p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid Tumors

Alterations in chromatin remodeling genes have been increasingly implicated in human oncogenesis. Specifically, the biallelic inactivation of the SWI/SNF subunit SMARCB1 results in the emergence of extremely aggressive pediatric malignancies. Here, we developed embryonic mosaic mouse models of malignant rhabdoid tumors (MRTs) that faithfully recapitulate the clinical-pathological features of the human disease. We demonstrated that SMARCB1-deficient malignancies exhibit dramatic activation of the unfolded protein response (UPR) and ER stress response via a genetically intact MYC-p19^ARF-p53 axis. As a consequence, these tumors display an exquisite sensitivity to agents inducing proteotoxic stress and inhibition of the autophagic machinery. In conclusion, our findings provide a rationale for drug repositioning trials investigating combinations of agents targeting the UPR and autophagy in SMARCB1-deficient MRTs.

Collapsing the Tumor Ecosystem: Preventing Adaptive Response to Treatment by Inhibiting Transcription

<b/> Adaptation and resistance to treatment are the results of a multitude of (epi)genetic events unmasked or directly triggered by therapies targeting the genetic driver(s) of a dominant cell population within a tumor mass. Rusan and colleagues report that drug-tolerant cells are sensitive to THZ1, a dual CDK7/12 inhibitor, which, by impairing the transcriptional machinery, can prevent cellular rewiring to survive therapeutic attack. Cancer Discov; 8(1); 17-9. ©2018 AACRSee related article by Rusan et al., p. 59.

Abstract B40: Perturbation of proteostasis is lethal in SMARCB1-deficient tumors

Alterations in the SWI/SNF chromatin remodeling complex have been implicated in human malignancies. Biallelic inactivation of the core subunits SMARCB1 and SMARCA4 are associated with particularly aggressive forms of pediatric cancer known as malignant rhabdoid tumors (MRTs) and atypical theratoid/rhabdoid tumors (AT/RTs). MRTs and AT/RTs are characterized by simple genomes and lack of somatic events, suggesting that dysregulation of SWI/SNF machinery is sufficient to induce a highly malignant state. However, the lack of a conditional genetic model of MRT has precluded the investigation of the molecular bases and dependencies associated with SMARCB1 loss. To this aim, we have developed a novel embryonic mosaic mouse model of MRTs of the liver. Using this mouse model, we performed a systematic functional investigation of vulnerabilities in the context of SMARCB1 loss in order to identify novel treatments for these diseases. Embryonic mosaic models of MRTs of the liver were generated by transuterine delivery of adenoviral vectors carrying the Cre recombinase under a tissue-specific promoter (Adx-Alb-Cre) to target SMARCB1LoxP/LoxP embryos at embryonic day E12-14 in order to study the effect of SMARCB1 ablation on development and tumorigenesis. Such an approach allowed us to target the developing liver epithelial compartment and to bypass the perinatal lethality observed with tissue-specific Cre deleter strains. This approach results in postnatal expansion of the epithelial compartment and in the emergence of rhabdoid tumors in a subset of cases. Upon investigation of the early effects of SMARCB1 ablation during mouse development and tumorigenesis, we found that livers in these embryonic mosaic murine models undergo profound metabolic changes resulting in a dramatic activation of cellular programs involved in the maintenance of proteostasis in response to ER stress and autophagy. To functionally validate the hypothesis that SMARCB1 loss confers sensitivity to proteotoxic agents, embryonic mosaic murine models of MRTs of the liver were treated with combinations of bortezomib and chloroquine, resulting in suppression of tumor growth and prolonged survival. Murine transplantation models of MRT treated with combinations of bortezomib and chloroquine also resulted in a significant increase in survival. Additionally, immunohistochemical studies of pediatric MRTs showed significant accumulation of markers of ER stress, and autophagy in comparison to normal tissue. The use of a novel embryonic mosaic models of MRT demonstrated that SMARCB1 disruption during liver embryogenesis caused activation of anabolic pathways and an increase in UPR, ER stress response, and autophagy. Overall, our preclinical study provides the rationale for a novel therapeutic approach aimed at exploiting a “collateral proteopathy” characteristic of SMARCB1-deficient malignancies and at the repositioning of existing drugs that have already shown acceptable toxicity profiles.

Citation Format: Melinda Soeung, Alessandro Carugo, Frederick Scott Robinson, Rosalba Minelli, Federica Carbone, Anirban Maitra, Andrea Viale, Charles W.M. Roberts, Nizar Tannir, Giulio F. Draetta, Giannicola Genovese. Perturbation of proteostasis is lethal in SMARCB1-deficient tumors [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B40.

Abstract 2856: Targeting OXPHOS with IACS-010759 to eliminate standard of care resistant tumor cells

Tumors are comprised of heterogenous populations of tumor cells that rely on both glycolysis and oxidative phosphorylation (OXPHOS) for bioenergy and synthetic processes in support of cell proliferation. Over the past few years, we and others have reported that there is a subpopulation of tumors cells that are resistant to standard of care treatment or targeted therapies, and that these so-called persistent tumor cells possess stem cell like properties. Of note, these cells have elevated levels of mitochondria and are dependent on OXPHOS for survival. We have previously disclosed the discovery of IACS-010759, a potent, selective inhibitor of complex I of the electron transport chain, which is orally bioavailable and has excellent PK and physicochemical properties in preclinical species. IACS-010759 is currently in phase I clinical trials in relapsed/refractory AML and solid tumors where initial safety, pharmacokinetics, efficacy and pharmacodynamic impacts on tumor cell biology are being evaluated. As part of the development of IACS-010759, we were interested to explore the impact of the compound to target the persistent tumor cells, in particular by treating AML, TNBC and PDAC PDX models post-chemotherapy with IACS-010759. For all three contexts, IACS-010759 extended progression free survival, consistent with IACS-010759 targeting the recently described metabolically adapted residual tumor cells. For solid tumor indications, we have utilized innovative barcoding and clonal tracking strategies to confirm dependency of a specific subpopulation of tumor cells on OXPHOS. We show that OXPHOS inhibition extends survival and limits AML growth in secondary transplantation by stimulating terminal differentiation of putative stem cells. Taken together, these data provide rationale for multiple Phase II/III clinical trials where IACS-010759 will be used to target persistent tumor cell population and extend survival.

Citation Format: Joseph R. Marszalek, Sahil Seth, Denise Corti, Qi Zhang, Gloria V. Echeverria, Lina Han, Yuting Sun, Jennifer Molina, Sonal Gera, Edward Chang, Tin O. Khor, Mikhila Mahendra, Ningping Feng, Jason P. Gay, Timothy McAfoos, Virginia Giuliani, Xi Shi, Sabrina Jeter-Jones, Sarah Loponte, Chieh-Yuan Li, Christopher A. Bristow, Maria Emilia Di Francesco, Helen Piwnica-Worms, Marina Konopleva, Alessandro Carugo, Andrea Viale, Philip Jones, Timothy P. Heffernan, Giulio F. Draetta. Targeting OXPHOS with IACS-010759 to eliminate standard of care resistant tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2856.

An inhibitor of oxidative phosphorylation exploits cancer vulnerability

Metabolic reprograming is an emerging hallmark of tumor biology and an actively pursued opportunity in discovery of oncology drugs. Extensive efforts have focused on therapeutic targeting of glycolysis, whereas drugging mitochondrial oxidative phosphorylation (OXPHOS) has remained largely unexplored, partly owing to an incomplete understanding of tumor contexts in which OXPHOS is essential. Here, we report the discovery of IACS-010759, a clinical-grade small-molecule inhibitor of complex I of the mitochondrial electron transport chain. Treatment with IACS-010759 robustly inhibited proliferation and induced apoptosis in models of brain cancer and acute myeloid leukemia (AML) reliant on OXPHOS, likely owing to a combination of energy depletion and reduced aspartate production that leads to impaired nucleotide biosynthesis. In models of brain cancer and AML, tumor growth was potently inhibited in vivo following IACS-010759 treatment at well-tolerated doses. IACS-010759 is currently being evaluated in phase 1 clinical trials in relapsed/refractory AML and solid tumors.

EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming

Acquired and intrinsic resistance to receptor tyrosine kinase inhibitors (RTKi) represents a major hurdle in improving the management of clear cell renal cell carcinoma (ccRCC). Recent reports suggest that drug resistance is driven by tumor adaptation via epigenetic mechanisms that activate alternative survival pathways. The histone methyl transferase EZH2 is frequently altered in many cancers, including ccRCC. To evaluate its role in ccRCC resistance to RTKi, we established and characterized a spontaneously metastatic, patient-derived xenograft model that is intrinsically resistant to the RTKi sunitinib, but not to the VEGF therapeutic antibody bevacizumab. Sunitinib maintained its antiangiogenic and antimetastatic activity but lost its direct antitumor effects due to kinome reprogramming, which resulted in suppression of proapoptotic and cell-cycle-regulatory target genes. Modulating EZH2 expression or activity suppressed phosphorylation of certain RTKs, restoring the antitumor effects of sunitinib in models of acquired or intrinsically resistant ccRCC. Overall, our results highlight EZH2 as a rational target for therapeutic intervention in sunitinib-resistant ccRCC as well as a predictive marker for RTKi response in this disease. Cancer Res; 77(23); 6651-66. ©2017 AACR.

Abstract 414: Identifying selective vulnerabilities in colorectal cancer molecular subtypes using in vivo functional genomic screens

Colorectal cancer (CRC) is a leading cause of cancer-related morbidity and mortality with significantly heterogeneous features and drug responses. Recently, the international Colorectal Cancer Subtyping Consortium identified four robust consensus molecular subtypes of CRC (CMS1-4) using large-scale gene expression data. These findings may enable us to identify molecularly homogenous subsets of CRC patients and accelerate effective drug development strategies. To identify potential therapeutic targets and novel selective vulnerabilities in CRC molecular subtypes, we developed an in vivo loss-of-function genomic screen using CRC patient-derived xenografts (PDXs) for each molecular subtype. Our PDX-derived CRC models underwent comprehensive integrated molecular characterization of mRNA profiles, DNA mutations, and histochemical profiles upon confirmed serial retransplantation to determine whether characteristics of the subtypes are recapitulated in vivo. Because the original CMS classification algorithm was trained and validated using Affymetrix data, profiling the PDX-derived cell lines using this technology provided the most robust analysis of the CMS subtypes. In vivo pooled short hairpin RNA (shRNA) screens rely on specific elimination of individual shRNAs in a cell population and require that the infected tumor cell population is adequately endowed with engraftment capacity when implanted into recipient mice. Therefore, we determined the transduction efficiency of the PDX models, the frequency of tumor-initiating cells, and the maximum library complexity allowed by each model. To identify targets that represent selective vulnerabilities in specific CRC molecular subtypes, we screened each model in vivo with an shRNA library targeting about 200 genes specifically belonging to U.S. Food and Drug Administration-approved targeted therapies (FDAome; 10 shRNAs/gene ). We leveraged redundant shRNA activity analysis to evaluate “hits” (or top-scoring genes) emerging from our screening. We further applied ranking-based analytics in combination with integromic approaches (use of computational packages to unravel relationships between -omics) to inform on selective CMS specific top-scoring genes. One of the benefits of using an FDAome library is the direct correspondence of target genes with clinically available drugs. We therefore tested these drugs for validation in fully annotated PDXs. These efforts, in association with systematic profiling of the CMS subtypes at the patient level through adaptation of NanoString technology, may enable us to stratify CRC patients who will benefit from selective U.S. Food and Drug Administration-approved drugs and to rapidly design successful preclinical and clinical trials in CRC patients.

Citation Format: Akira Inoue, Bahar Salimian Rizi, Alessandro Carugo, Sahil Seth, Christopher Bristow, Giannicola Genovese, Andrea Viale, David G. Menter, Scott Kopetz, Giulio F. Draetta. Identifying selective vulnerabilities in colorectal cancer molecular subtypes using in vivo functional genomic screens [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 414. doi:10.1158/1538-7445.AM2017-414

Abstract 4170: Targeting androgen receptor overcomes resistance to tyrosine kinase inhibitors in advanced clear cell renal cell carcinoma

Background: Advanced renal cell carcinoma (RCC) responds initially to anti-angiogenic therapies but eventually develop resistance which may be driven by the expression of key intratumoral pro-survival protein and overall kinome reprogramming. Androgen receptor (AR) expression has been reported in clear cell renal cell carcinoma (ccRCC) but its biological role remains elusive and its association with resistance to tyrosine kinase inhibitors (TKIs) has not been studied. Here we report the role of AR and its association with resistance to TKIs in advanced RCC. Methods: Human RCC cell lines; 786-0, 786-0R (with induced sunitinib resistance), ACHN, URMC2 (with intrinsic sunitinib resistance) were used to assess the combination effect of sunitinib and the AR antagonist enzalutamide in vitro. In vivo studies utilizing 786-0 tumors assessed the combination effect of enzalutamide and sunitinib following acquired resistance to sunitinib. AR expression was detected by qRT-PCR and Western blot analysis, and AR localization by immunofluorescence in treated and non-treated cells. Gene array was used to assess 93 AR associated genes in sensitive and resistant cells. Results: Quantitative RT-PCR data revealed a significant increase in AR expression with sunitinib resistance (&gt;100 folds; p&gt;0.001). In vitro and in vivo studies indicated significant increase in nuclear and cytoplasmic expression of AR with sunitinib treatment in resistant cells which was abrogated with single agent enzalutamide and combination treatment. More interestingly, combination treatment of enzalutamide and sunitinib significantly decreased cell growth and induced tumor regression in vitro and in vivo, respectively. Conclusion: Our data suggest the role of AR both in intrinsic and acquired sunitinib resistance in ccRCC and provide a rationale for combination strategies to restore TKI sensitivity that can be tested in the clinical setting.

Citation Format: Remi M. Adelaiye-Ogala, Sreenivasulu Chintala, Ashley Orillion, May Elbanna, Ben Elzey, Nur Damayanti, Kiersten M. Miles, Chinghai Kao, Piergiorgio Pettazzoni, Giulio F. Draetta, Roberto Pili. Targeting androgen receptor overcomes resistance to tyrosine kinase inhibitors in advanced clear cell renal cell carcinoma [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 4170. doi:10.1158/1538-7445.AM2017-4170

Abstract 415: In vivo shRNA library screening to identify novel targets for head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a diverse group of tumors from the upper aerodigestive tract that are treated primarily with surgery, chemotherapy, and/or radiation. Recent genomic studies have characterized the genomic alterations in HNSCC but they failed to identify novel oncogenic drivers for therapeutic targeting. In order to identify novel targets we have utilized an in vivo shRNA library screening platform in a panel of genomically characterized HNSCC cell lines. The screens were performed alone or in combination with platinum-based chemotherapy or radiation, and the screening libraries included known druggable targets, DNA repair genes, and HNSCC candidate driver genes. Initial results indicate that this in vivo screening is able to identify targets that may not be found through traditional in vitro screening approaches and related to tumor-stromal interactions and metabolism. These genes emphasize the importance of including the tumor microenvironment in studies to understand driver genes and identify novel therapeutic interventions.

Citation Format: Curtis R. Pickering, Tongxin Xie, Manish Kumar, Ramya L. Parimi, Liang P. Yang, Jiping Wang, Sahil Seth, Christopher A. Bristow, Alessandro Carugo, Frederick S. Robinson, Giulio F. Draetta, Heath Skinner, Mitchell J. Frederick, Jeffrey N. Myers. In vivo shRNA library screening to identify novel targets for head and neck squamous cell carcinoma [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 415. doi:10.1158/1538-7445.AM2017-415

How Much Longer Will We Put Up With $100,000 Cancer Drugs?

The spiraling cost of new drugs mandates a fundamentally different approach to keep lifesaving therapies affordable for cancer patients. We call here for the formation of new relationships between academic drug discovery centers and commercial partners, which can accelerate the development of truly transformative drugs at sustainable prices.

Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer

Malignant neoplasms evolve in response to changes in oncogenic signalling. Cancer cell plasticity in response to evolutionary pressures is fundamental to tumour progression and the development of therapeutic resistance. Here we determine the molecular and cellular mechanisms of cancer cell plasticity in a conditional oncogenic Kras mouse model of pancreatic ductal adenocarcinoma (PDAC), a malignancy that displays considerable phenotypic diversity and morphological heterogeneity. In this model, stochastic extinction of oncogenic Kras signalling and emergence of Kras-independent escaper populations (cells that acquire oncogenic properties) are associated with de-differentiation and aggressive biological behaviour. Transcriptomic and functional analyses of Kras-independent escapers reveal the presence of Smarcb1-Myc-network-driven mesenchymal reprogramming and independence from MAPK signalling. A somatic mosaic model of PDAC, which allows time-restricted perturbation of cell fate, shows that depletion of Smarcb1 activates the Myc network, driving an anabolic switch that increases protein metabolism and adaptive activation of endoplasmic-reticulum-stress-induced survival pathways. Increased protein turnover renders mesenchymal sub-populations highly susceptible to pharmacological and genetic perturbation of the cellular proteostatic machinery and the IRE1-α-MKK4 arm of the endoplasmic-reticulum-stress-response pathway. Specifically, combination regimens that impair the unfolded protein responses block the emergence of aggressive mesenchymal subpopulations in mouse and patient-derived PDAC models. These molecular and biological insights inform a potential therapeutic strategy for targeting aggressive mesenchymal features of PDAC.

Abstract B43: PILOT: a patient-oriented in vivo functional platform to identify new lethalities and optimize cancer treatment

Large-scale genomics efforts have provided the opportunity to access a comprehensive catalog of genetic alterations in multiple cancers. However, it has also become apparent that very few driver mutations are emerging and as a consequence of that, limited opportunities exist to target mutated oncogenic proteins. It is imperative therefore to develop alternative approaches to therapy that can leverage the selective vulnerabilities of tumor cells resulting from the engagement of abnormal pathway connectivity. These can be best exploited in vivo, in a context that is closer to the environment tumors strive in. To identify new relevant actionable dependencies we have developed PILOT (Patient-oriented In vivo Lethality to Optimize Treatment), a loss-of-function in vivo platform for rapid identification of potential therapeutic targets in Patient-Derived Xenografts (PDXs). By optimizing primary tumor explant and expansion, determination of tumor-initiating cell frequency trough retroviral-mediated transduction, in vivo RNA interference screens, next-generation sequencing and analytic pipelines, we have been able to establish a comprehensive “patient-centric” approach oriented towards the identification of the highest priority genetic targets in specific clinico-pathological and mutational settings. So far, the main limitation for the systematic exploitation of in vivo functional genomics systems to elucidate patient vulnerabilities in the PDX models come from the limited number of human cells contributing to tumor establishment in a transplantation setting. The frequency of these tumors initiating cells (TICs) is commonly estimated by time-consuming limiting dilution assays and may consistently vary between different tumor origins. With this in mind, we have integrated in our platform a system based on scrambled barcoded libraries that allows to directly assess the required coverage of screening libraries in each model and adjust the RNAi screens for this factor. Our coverage study demonstrated to be a powerful tool to identify the minimal number of cells/barcode required to sustain a complex library in PDX models and at the same time a step forward to personalize the in vivo screening patient-by-patient. As proof of concept, we applied our PILOT platform to systematically interrogate context-specific epigenetic dependencies in pancreatic ductal adenocarcinoma (PDAC). In addition to the well-known genetic alterations (KRAS, TP53, CDKN2A/p16, SMAD4), some epigenetic mechanisms demonstrated to play a central role in PDAC progression and some of them could intriguingly represent new points of vulnerability, due to the low-frequency of mutation (ex. collateral or synthetic lethality). Our screening system utilized fully annotated low-passage PDAC xenografts and a lentiviral library of pooled shRNAs targeting 230 potentially “druggable” epigenetic regulators adjusted for the coverage study in each PDX. Hairpin-associated molecular barcodes were quantified by massively parallel sequencing and clustered according to their depletion or enrichment in comparison to a control population before transplantation. To date, we have completed a total of 5 in vivo screens using diverse PDAC xenograft models and, applying our comprehensive mutational and functional data analytics pipeline, we have developed a high-throughput validation scheme to triage “hits” that emerge from each screen. Focusing on epigenetic regulators, we identified WDR5, a core member of the COMPASS histone H3 Lys4 (H3K4) MLL (1-4) methyltransferase complex, as a top tumor maintenance hit required across multiple PDAC tumors and associated with the presence of G1-checkpoint alterations (p53 or p16). Mechanistically, WDR5 functions to sustain proper execution of DNA replication in PDAC cells, as previously suggested by replication stress studies involving MLL1, a critical ATR substrate, and c-Myc, also found to interact with WDR5. We indeed demonstrated that the WDR5-Myc interaction is critical for this replicative function and protects the PDAC cells from the excessive DNA damage accumulation and mitotic catastrophe. Intriguingly, this checkpoint function executed by the WDR5-Myc axis to protect the S-phase seems to be an addiction of the cancer cells, that have more active replication forks to stabilize in order to sustain the abnormal proliferative burst. To confirm this new cancer-associated lethality, we demonstrated that normal cells display less sensitivity to this replication checkpoint in virtue of their proficient G1-checkpoints and reduced time spent in S-phase compared to cancer cells. So, our PILOT platform was able to illuminate new therapeutic vulnerabilities that can be rapidly evaluated in the clinic through the development of WDR5-Myc inhibitors. In the near future, we plan to extend this platform in syngeneic mouse models, where one can probe the effects of target inhibition in the context of an intact immune response and in the presence of immune checkpoint activators, and in association with approved drugs, to identify new therapeutic options for recalcitrant tumor populations.

Citation Format: Alessandro Carugo, Giannicola Genovese, Sahil Seth, Luigi Nezi, Angelo Cicalese, Daniela Bossi, Johnathon L. Rose, Andrea Viale, Luisa Lanfrancone, Timothy P. Heffernan, Giulio F. Draetta. PILOT: a patient-oriented in vivo functional platform to identify new lethalities and optimize cancer treatment. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B43.

Abstract 2126: Androgen receptor expression is associated with sunitinib resistance in renal cell carcinoma models

Background: Androgen receptor (AR) expression has been reported in renal cell carcinoma but its biological role remains elusive. Sunitinib is a potent anti-angiogenic drug approved for the treatment of advanced renal cell carcinoma (RCC). However, eventually RCC tumors develop drug resistance. We have hypothesized that tumor cells resistance to sunitinib is associated with kinome reprograming and anti-apoptotic genes upregulation. To date, there is no report on the association between AR expression and resistance to TKI such as sunitinib in RCC. Our study was designed to investigate the role of AR in sunitinib resistance in RCC. We used our previously reported sunitinib resistant ccRCC cells and patient derived xenograft models. Methods: Human RCC cell lines; 786-0, 786-0R (sunitinib resistant), C2, C2R (sunitinib resistant), ACHN and Caki 2 were utilized to determine sensitivity or resistance to sunitinib. Patient derived xenograft (PDX) models of advance and metastatic RCC and RCC cell lines, sensitive and resistant tumors were used to detect AR expression by qRT-PCR, immunohistochemistry and Western blot analysis. Reverse phase protein array (RPPA) was used to assess 249 protein including AR in sunitinib sensitive and resistant tumors. Results: Our qRT-PCR data showed an increase by 1000 folds in mRNA levels of AR in our sunitinib resistant cell lines. Similarly, RPPA data revealed AR to be increased in sunitinib resistant RCC PDX tumors. This observation was confirmed by Western blot analysis. Conclusion: Overall our data suggest the potential role of AR and its association with resistance to sunitinib. Ongoing studies are testing the in vitro and in vivo combination treatment of RCC models with sunitinib and AR antagonists.

Citation Format: Remi M. Adelaiye-Ogala, Sreenivasulu Chintala, Ashley Orillion, Piergiorgio Pettazzoni, May Elbanna, Bennett Elzey, Kiersten Marie Miles, Chinghai Kao, Giulio F. Draetta, Roberto Pili. Androgen receptor expression is associated with sunitinib resistance in renal cell carcinoma models. [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 2126.

Genetics and biology of pancreatic ductal adenocarcinoma

Ying et al. review pancreatic ductal adenocarcinoma (PDAC) genetics and biology, particularly altered cancer cell metabolism, the complexity of immune regulation in the tumor microenvironment, and impaired DNA repair processes.

With 5-year survival rates remaining constant at 6% and rising incidences associated with an epidemic in obesity and metabolic syndrome, pancreatic ductal adenocarcinoma (PDAC) is on track to become the second most common cause of cancer-related deaths by 2030. The high mortality rate of PDAC stems primarily from the lack of early diagnosis and ineffective treatment for advanced tumors. During the past decade, the comprehensive atlas of genomic alterations, the prominence of specific pathways, the preclinical validation of such emerging targets, sophisticated preclinical model systems, and the molecular classification of PDAC into specific disease subtypes have all converged to illuminate drug discovery programs with clearer clinical path hypotheses. A deeper understanding of cancer cell biology, particularly altered cancer cell metabolism and impaired DNA repair processes, is providing novel therapeutic strategies that show strong preclinical activity. Elucidation of tumor biology principles, most notably a deeper understanding of the complexity of immune regulation in the tumor microenvironment, has provided an exciting framework to reawaken the immune system to attack PDAC cancer cells. While the long road of translation lies ahead, the path to meaningful clinical progress has never been clearer to improve PDAC patient survival.

In Vivo Genetic Screens of Patient-Derived Tumors Revealed Unexpected Frailty of the Transformed Phenotype

The identification of genes maintaining cancer growth is critical to our understanding of tumorigenesis. We report the first in vivo genetic screen of patient-derived tumors, using metastatic melanomas and targeting 236 chromatin genes by expression of specific shRNA libraries. Our screens revealed unprecedented numerosity of genes indispensable for tumor growth (∼50% of tested genes) and unexpected functional heterogeneity among patients (<15% in common). Notably, these genes were not activated by somatic mutations in the same patients and are therefore distinguished from mutated cancer driver genes. We analyzed underlying molecular mechanisms of one of the identified genes, the Histone-lysine N-methyltransferase KMT2D, and showed that it promotes tumorigenesis by dysregulating a subset of transcriptional enhancers and target genes involved in cell migration. The assembly of enhancer genomic patterns by activated KMT2D was highly patient-specific, regardless of the identity of transcriptional targets, suggesting that KMT2D might be activated by distinct upstream signaling pathways.

SIGNIFICANCE

Drug targeting of biologically relevant cancer-associated mutations is considered a critical strategy to control cancer growth. Our functional in vivo genetic screens of patient-derived tumors showed unprecedented numerosity and interpatient heterogeneity of genes that are essential for tumor growth, but not mutated, suggesting that multiple, patient-specific signaling pathways are activated in tumors. Cancer Discov; 6(6); 650-63. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 561.

Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair

CRISPR/Cas9 induces DNA double-strand breaks that are repaired by cell-autonomous repair pathways, namely, non-homologous end-joining (NHEJ), or homology-directed repair (HDR). While HDR is absent in G1, NHEJ is active throughout the cell cycle and, thus, is largely favored over HDR. We devised a strategy to increase HDR by directly synchronizing the expression of Cas9 with cell-cycle progression. Fusion of Cas9 to the N-terminal region of human Geminin converted this gene-editing protein into a substrate for the E3 ubiquitin ligase complex APC/Cdh1, resulting in a cell-cycle-tailored expression with low levels in G1 but high expression in S/G2/M. Importantly, Cas9-hGem(1/110) increased the rate of HDR by up to 87% compared to wild-type Cas9. Future developments may enable high-resolution expression of genome engineering proteins, which might increase HDR rates further, and may contribute to a better understanding of DNA repair pathways due to spatiotemporal control of DNA damage induction.

Tumors and mitochondrial respiration: a neglected connection

For decades, tumor cells have been considered defective in mitochondrial respiration due to their dominant glycolytic metabolism. However, a growing body of evidence is now challenging this assumption, and also implying that tumors are metabolically less homogeneous than previously supposed. A small subpopulation of slow-cycling cells endowed with tumorigenic potential and multidrug resistance has been isolated from different tumors. Deep metabolic characterization of these tumorigenic cells revealed their dependency on mitochondrial respiration versus glycolysis, suggesting the existence of a common metabolic program active in slow-cycling cells across different tumors. These findings change our understanding of tumor metabolism and also highlight new vulnerabilities that can be exploited to eradicate cancer cells responsible for tumor relapse.

Metabolic Features of Cancer Treatment Resistance

A major barrier to achieving durable remission and a definitive cure in oncology patients is the emergence of tumor resistance, a common outcome of different disease types, and independent from the therapeutic approach undertaken. In recent years, subpopulations of slow-cycling cells endowed with enhanced tumorigenic potential and multidrug resistance have been isolated in different tumors, and mounting experimental evidence suggests these resistant cells are responsible for tumor relapse. An in-depth metabolic characterization of resistant tumor stem cells revealed that they rely more on mitochondrial respiration and less on glycolysis than other tumor cells, a finding that challenges the assumption that tumors have a primarily glycolytic metabolism and defective mitochondria. The demonstration of a metabolic program in resistant tumorigenic cells that may be present in the majority of tumors has important therapeutic implications and is a critical consideration as we address the challenge of identifying new vulnerabilities that might be exploited therapeutically.

Sugar? No Thank You, Just a Deep Breath of Oxygen for Cancer Stem Cells

Tumors are metabolically heterogeneous, and subpopulations of tumorigenic cells have been recently described to rely more on mitochondrial respiration than glycolysis for energy production. In this issue, Sancho et al. (2015) demonstrate that MYC is a master switch regulating metabolic programs in different subpopulations of pancreatic tumor cells.

Abstract 976: Metabolic eradication of treatment resistant cancer stem cells in pancreatic tumors: A clonal tracking-based platform for identifying the best personalized treatment

Pancreatic ductal adenocarcinoma (PDAC) continues to have a poor prognosis despite new drugs advancing to the clinic.

We recently characterized a population of cells able to survive the genetic and pharmacologic extinction of oncogenic pathways and demonstrated that the surviving cells (SC) are tumor stem cells (CSC) able to remain in a quiescent state for months before relapsing. In-depth transcriptomics and metabolomics analyses revealed SCs to exhibit different metabolic features compared to the bulk of tumor cells. Specifically, SC relied on mitochondrial respiration (OXPHOS) and displayed impaired glycolytic capacity. In accord with their decreased dependence on glycolysis these SC were highly sensitive to OXPHOS inhibitors, which prevented tumor recurrence.

Notably, preliminary results in patients suggest that SC resistant to conventional chemoradiation also have similar features. We analyzed specimens after neoadjuvant treatment and observed dormant cells positive for CSC markers and characterized by an increased mitochondrial mass. Evaluation of TMA of hundreds of treated tumors revealed that high mitochondrial content is a common feature of SC. Furthermore, functional metabolic characterization of human cells resistant to gemcitabine revealed that SC have a severely impaired glycolytic reserve, closely resembling mouse SC. Based on these findings, we posit that OXPHOS inhibitors may be an effective adjuvant therapy to eradicate resistant cells in patients.

To validate the efficacy of OXPHOS inhibition, we developed a new platform to study tumor evolution in response to treatments based on clonal tracking. Lentivirus-based systems have been extensively used as a tool to investigate the clonal dynamics, but they have been limited by lack of sensitivity and the impossibility of tracking identical clones in different animals. Here, using a new version of the barcoded technology coupled with deep-sequencing, we track hundreds of thousands of clones at the single-cell level. We generated patient-derived xenograft animal cohorts in which tumors were clonal replicas of each other (each tumor is maintained by the same clones of all other tumors), representing a unique tool to evaluate responses to treatments. More importantly, resistant tumor clones generated in vivo can be isolated and fully characterized and compared to pre-treatment clones to identify new mechanisms of resistance.

Our integrated analysis paves the way for new therapeutic strategies for patients to eradicate treatment-resistant CSC by specifically targeting their unique metabolism. In addition, our clonal tracking-based platform monitoring the efficacy of different treatments in eradicating resistant clones represents an unprecedented tool for exploring treatment responses at the single-cell level, which will help guide the development of personalized treatments.

Citation Format: Denise Corti, Alessandro Carugo, Seth Sahil, Matteo Marchesini, Piergiorgio Pettazzoni, Luigi Nezi, Tessa Green, Joseph R Marszalek, Maria Emilia Di Francesco, Timothy P Heffernan, Giulio F Draetta, Andrea Viale. Metabolic eradication of treatment resistant cancer stem cells in pancreatic tumors: A clonal tracking-based platform for identifying the best personalized treatment. [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 976. doi:10.1158/1538-7445.AM2015-976

Abstract 1701: Identification of epigenetic modifiers able to suppress growth of pancreatic ductal adenocarcinoma: A patient-oriented in vivo functional platform

We have seen great advances in our knowledge of the genetic regulation of various cancers in recent years, thanks in large part to large-scale genome sequencing efforts. As we catalogue and characterize the genomic aberrations associated with cancers with increasing detail and accuracy, we are faced with the challenge of having to cull bystanders from biologically active drivers and establish relevant disease context in which these drivers are rate-limiting. To address this challenge, we have adapted a loss-of-function screening approach to function in the context of an intact tumor microenvironment using patient-derived tumors that more faithfully recapitulate the human disease compared to established cell lines. Due to the genetic heterogeneity between human tumors, we have integrated independent screening approaches in a flexible platform for the interrogation of patient-derived samples as well as GEM models in exactly the same experimental conditions. The goal of this platform is to identify context-specific genetic vulnerabilities and translate these findings into drug discovery opportunities. As proof of concept, we developed an in vivo loss-of-function screen to systematically interrogate epigenetic dependencies in pancreatic ductal adenocarcinoma (PDAC). The screening system utilizes tumor cells isolated from low-passage xenograft tissue and a lentiviral library of pooled shRNAs targeting 230 “druggable” epigenetic regulators. The custom-designed shRNA library (10 shRNAs per gene) was engineered with unique molecular barcodes that allow quantitation of each clone by deep sequencing. To date, we have completed a total of 5 in vivo screens using diverse PDAC models that have informed on novel epigenetic dependencies. So far, the main limitation for the systematic exploitation of in vivo loss-of-function screens come from the limited number of human cells contributing to tumor establishment in a transplantation setting. The frequency of these tumor initiating cells (TICs) is commonly estimated by limiting dilution assays and may consistently vary between tumor origins. With this in mind, we have integrated in our platform a system based on scrambled barcoded libraries that allow to directly assess the required coverage of screening libraries in each model. Our coverage study demonstrated to be a powerful tool to identify the minimal number of cells/barcode required to sustain a complex library and at the same time a step forward to personalize the in vivo screening patient by patient. We optimized a comprehensive data analytics pipeline and developed a high-throughput validation scheme to triage “hits” that emerge from each screen. The most potent “hits” have been enrolled in both functional and clinico-pathological validation studies to determine the highest priority targets for this devastating disease. Results from these studies will be presented.

Note: This abstract was not presented at the meeting.

Citation Format: Alessandro Carugo, Giannicola Genovese, Sahil Seth, Luigi Nezi, Johnathon L. Rose, Andrea Viale, Piergiorgio F. Pettazzoni, Angelo Cicalese, Daniela Bossi, Wantong Yao, Jason B. Fleming, Luisa Lanfrancone, Timothy P. Heffernan, Giulio F. Draetta. Identification of epigenetic modifiers able to suppress growth of pancreatic ductal adenocarcinoma: A patient-oriented in vivo functional platform. [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 1701. doi:10.1158/1538-7445.AM2015-1701

Genetic events that limit the efficacy of MEK and RTK inhibitor therapies in a mouse model of KRAS-driven pancreatic cancer

Mutated KRAS (KRAS*) is a fundamental driver in the majority of pancreatic ductal adenocarcinomas (PDAC). Using an inducible mouse model of KRAS*-driven PDAC, we compared KRAS* genetic extinction with pharmacologic inhibition of MEK1 in tumor spheres and in vivo. KRAS* ablation blocked proliferation and induced apoptosis, whereas MEK1 inhibition exerted cytostatic effects. Proteomic analysis evidenced that MEK1 inhibition was accompanied by a sustained activation of the PI3K-AKT-MTOR pathway and by the activation of AXL, PDGFRa, and HER1-2 receptor tyrosine kinases (RTK) expressed in a large proportion of human PDAC samples analyzed. Although single inhibition of each RTK alone or plus MEK1 inhibitors was ineffective, a combination of inhibitors targeting all three coactivated RTKs and MEK1 was needed to inhibit proliferation and induce apoptosis in both mouse and human low-passage PDAC cultures. Importantly, constitutive AKT activation, which may mimic the fraction of AKT2-amplified PDAC, was able to bypass the induction of apoptosis caused by KRAS* ablation, highlighting a potential inherent resistance mechanism that may inform the clinical application of MEK inhibitor therapy. This study suggests that combinatorial-targeted therapies for pancreatic cancer must be informed by the activation state of each putative driver in a given treatment context. In addition, our work may offer explanative and predictive power in understanding why inhibitors of EGFR signaling fail in PDAC treatment and how drug resistance mechanisms may arise in strategies to directly target KRAS.

Oncogene ablation-resistant pancreatic cancer cells depend on mitochondrial function

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers in western countries, with a median survival of 6 months and an extremely low percentage of long-term surviving patients. KRAS mutations are known to be a driver event of PDAC, but targeting mutant KRAS has proved challenging. Targeting oncogene-driven signalling pathways is a clinically validated approach for several devastating diseases. Still, despite marked tumour shrinkage, the frequency of relapse indicates that a fraction of tumour cells survives shut down of oncogenic signalling. Here we explore the role of mutant KRAS in PDAC maintenance using a recently developed inducible mouse model of mutated Kras (Kras(G12D), herein KRas) in a p53(LoxP/WT) background. We demonstrate that a subpopulation of dormant tumour cells surviving oncogene ablation (surviving cells) and responsible for tumour relapse has features of cancer stem cells and relies on oxidative phosphorylation for survival. Transcriptomic and metabolic analyses of surviving cells reveal prominent expression of genes governing mitochondrial function, autophagy and lysosome activity, as well as a strong reliance on mitochondrial respiration and a decreased dependence on glycolysis for cellular energetics. Accordingly, surviving cells show high sensitivity to oxidative phosphorylation inhibitors, which can inhibit tumour recurrence. Our integrated analyses illuminate a therapeutic strategy of combined targeting of the KRAS pathway and mitochondrial respiration to manage pancreatic cancer.