Targeting CD73 with AB680 (Quemliclustat), a Novel and Potent Small-Molecule CD73 Inhibitor, Restores Immune Functionality and Facilitates Antitumor Immunity

T cells play a critical role in the control of cancer. The development of immune checkpoint blockers (ICB) aimed at enhancing antitumor T-cell responses has revolutionized cancer treatment. However, durable clinical benefit is observed in only a subset of patients, prompting research efforts to focus on strategies that target multiple inhibitory signals within the tumor microenvironment (TME) to limit tumor evasion and improve patient outcomes. Adenosine has emerged as a potent immune suppressant within the TME, and CD73 is the major enzyme responsible for its extracellular production. CD73 can be co-opted within the TME to impair T-cell-mediated antitumor immunity and promote tumor growth. To target this pathway and block the formation of adenosine, we designed a novel, selective, and potent class of small-molecule inhibitors of CD73, including AB680 (quemliclustat), which is currently being tested in patients with cancer. AB680 effectively restored T-cell proliferation, cytokine secretion, and cytotoxicity that were dampened by the formation of immunosuppressive adenosine by CD73. Furthermore, in an allogeneic mixed lymphocyte reaction where CD73-derived adenosine had a dominant suppressive effect in the presence of PD-1 blockade, AB680 restored T-cell activation and function. Finally, in a preclinical mouse model of melanoma, AB680 inhibited CD73 in the TME and increased the antitumor activity of PD-1 blockade. Collectively, these data provide a rationale for the inhibition of CD73 with AB680 in combination with ICB, such as anti-PD-1, to improve cancer patient outcomes.

Intrinsic and acquired drug resistance to LSD1 inhibitors in small cell lung cancer occurs through a TEAD4-driven transcriptional state

Small-cell lung cancer (SCLC) is a heterogeneous disease, consisting of intratumoral and intertumoral neuroendocrine (ASCL1 and/or NEUROD1), mesenchymal-like, and YAP-driven transcriptional states. Lysine-specific demethylase 1 (LSD1; also known as KDM1A) inhibitors have recently been progressed to clinical trials in SCLC based on a promising preclinical antitumor activity. A potential clinical limitation of LSD1 inhibitors is the heterogeneous drug responses that have been observed in SCLC cell lines and patient-derived models. Based on these observations, we studied molecular and transcriptional signatures that predict patient response to this class of drug. Employing SCLC patient-derived transcriptional signatures, we define that SCLC cell lines sensitive to LSD1 inhibitors are enriched in neuroendocrine transcriptional markers, whereas cell lines enriched in a mesenchymal-like transcriptional program demonstrate intrinsic resistance to LSD1 inhibitors. We have identified a reversible, adaptive resistance mechanism to LSD1 inhibitors through epigenetic reprogramming to a TEAD4-driven mesenchymal-like state. Our data suggest that only a segment of SCLC patients, with a defined neuroendocrine differentiation state, will likely benefit from LSD1 inhibitors. It provides novel evidence for the selection of a TEAD4-driven mesenchymal-like subpopulation resistant to LSD1 inhibitors in SCLC patients that may require effective drug combinations to sustain effective clinical responses.

Ablation of atrioventricular-nodal-reentrant- tachycardia in a patient with left-sided superior vena cava and dilated coronary sinus

Atrioventricular (AV)-nodal-reentrant-tachycardia is a rare association in a patient with persistent left-sided superior vena cava and dilated coronary sinus. There are a few inherent difficulties in ablation in this condition, viz., difficulty in localization of good site for ablation and difficulty in stabilization of the ablation catheter at the designated site, making it difficult to produce transmural lesions and increasing risk of producing AV block. We hereby present a case highlighting the difficulties and possible solutions for them.

Atrial tachycardia from an unusual site-Left atrial appendage tachycardia: Challenges in ablation

Left atrial appendage (LAA) tachycardia are rarely encountered in clinical practice (2.1% of focal atrial tachycardia). Out of these, the ones arising from the distal part of LAA are difficult to ablate due to higher risk of LAA perforation and thromboembolism. We hereby present a patient with LAA tachycardia mapped to the tip of LAA with the help of the CARTO system and ablated. This case highlights the inherent challenges faced in such a scenario.

Abstract 4980: Altered pan-Ras pathway and activating mutations in EGFR result in elevated CD73 in multiple cancers

Background: Adenosine production mediated by CD73 and/or TNAP is a potential mechanism of immune suppression across many cancer types. We have previously shown that AB928, a dual A2aR/A2bR antagonist, in combination with anti-PD-1 or chemotherapy, rescues the immunosuppressive effects of adenosine in experimental tumor models. Oncogene-driven cancers are targeted with specific tyrosine kinase inhibitors, typically leading to the development of several resistance mechanisms that bypass the kinase signaling. These oncogene-driven cancers tend to be non-responsive to PD(L)-1 inhibition. We hypothesized that oncogenic drivers might be regulating adenosine production machinery as a mechanism to suppress and evade the immune system. Here we show that pan-RAS, BRAF and EGFR alterations drive the expression of CD73, which may contribute to suppressed anti-tumor immunity.

Methods and Results: We used linear models to evaluate the ability of 299 pan-cancer consensus oncogenic drivers (Bailey et al, 2018) to predict CD73 expression independent of tumor type in PanCanAtlas TCGA dataset. We defined a given gene as either wild type or altered if it exhibited a SNV/copy number/fusion event in a given patient. Out of the 299 oncogenes, we identified 20 oncogenes that upregulated and 26 that downregulated CD73 expression (FDR < 0.05). Alterations in KRAS, BRAF and EGFR were the top 3 oncogenes upregulating CD73 expression, followed by other kinases such as RASA1, MET, RET, SMAD4 and CDK4. In KRAS/BRAF/EGFR altered tumors, CD73 expression was significantly higher compared to respective wild-type patients in all cancers combined, as well as in individual tumor types (BRCA, LUAD, LUSC, CRC, PAAD, HNSCC, UBC, CESC, ESCA, STAD, UCEC and LGG). Furthermore, the pan-cancer Ras activation classifier score (Way et.al 2018) was highly predictive of CD73 expression independent of tumor type (p-value < 2e-16). KRAS, HRAS, BRAF, EGFR as well as pan-Ras mutant cancer cell lines exhibited a significantly higher level of CD73 expression than wild-type cell lines, independent of cancer type.

Conclusions: Activating mutations in KRAS and HRAS that result in deregulation of the Ras pathway serve as oncogenic drivers in a variety of cancer types such as CRC, NSCLC, gastric-esophageal, cervical, bladder and HNSCC and upregulate CD73. BRAF mutations are enriched in breast, CRC, NSCLC, and low-grade gliomas that exhibit higher CD73 expression. Finally, EGFR mutations are prominent in RCC, low-grade gliomas and NSCLC, which drive CD73 expression. Oncogene-driven cancers are largely unresponsive to PD-(L)1 inhibition and are targeted with kinase inhibitors resulting in significant but not durable clinical responses. Our data strongly suggests that CD73 inhibition with AB680 and/or A2R antagonism with AB928 might be effective in Ras pathway mutant and EGFR mutant cancers, either in TKI-naïve or relapsed settings.

Citation Format: Akshata R. Udyavar, Daniel DiRenzo, Devika Ashok, Amy E. Anderson, Stephen W. Young, Matt J. Walters, Joanne Bl Tan. Altered pan-Ras pathway and activating mutations in EGFR result in elevated CD73 in multiple cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4980.

Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

Small cell lung cancer (SCLC) is a devastating disease due to its propensity for early invasion and refractory relapse after initial treatment response. Although these aggressive traits have been associated with phenotypic heterogeneity, our understanding of this association remains incomplete. To fill this knowledge gap, we inferred a set of 33 transcription factors (TF) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes. The topology of this SCLC TF network was derived from prior knowledge and was simulated using Boolean modeling. These simulations predicted that the network settles into attractors, or TF expression patterns, that correlate with NE or ML phenotypes, suggesting that TF network dynamics underlie the emergence of heterogeneous SCLC phenotypes. However, several cell lines and patient tumor specimens failed to correlate with either the NE or ML attractors. By flow cytometry, single cells within these cell lines simultaneously expressed surface markers of both NE and ML differentiation, confirming the existence of a "hybrid" phenotype. Upon exposure to standard-of-care cytotoxic drugs or epigenetic modifiers, NE and ML cell populations converged toward the hybrid state, suggesting possible escape from treatment. Our findings indicate that SCLC phenotypic heterogeneity can be specified dynamically by attractor states of a master regulatory TF network. Thus, SCLC heterogeneity may be best understood as states within an epigenetic landscape. Understanding phenotypic transitions within this landscape may provide insights to clinical applications. Cancer Res; 77(5); 1063-74. ©2016 AACR.

Altered TGF-α/β signaling drives cooperation between breast cancer cell populations

The role of tumor heterogeneity in regulating disease progression is poorly understood. We hypothesized that interactions between subpopulations of cancer cells can affect the progression of tumors selecting for a more aggressive phenotype. We developed an in vivo assay based on the immortalized nontumorigenic breast cell line MCF10A and its Ras-transformed derivatives AT1 (mildly tumorigenic) and CA1d (highly tumorigenic). CA1d cells outcompeted MCF10A, forming invasive tumors. AT1 grafts were approximately 1% the size of CA1d tumors when initiated using identical cell numbers. In contrast, CA1d/AT1 mixed tumors were larger than tumors composed of AT1 alone (100-fold) or CA1d (3-fold), suggesting cooperation in tumor growth. One of the mechanisms whereby CA1d and AT1 were found to cooperate was by modulation of TGF-α and TGF-β signaling. Both of these molecules were sufficient to induce changes in AT1 proliferative potential in vitro. Reisolation of AT1 tumor-derived (AT1^-TD) cells from these mixed tumors revealed that AT1^-TD cells grew in vivo, forming tumors as large as tumorigenic CA1d cells. Cooperation between subpopulations of cancer epithelium is an understudied mechanism of tumor growth and invasion that may have implications on tumor resistance to current therapies.-Franco, O. E., Tyson, D. R., Konvinse, K. C., Udyavar, A. R., Estrada, L., Quaranta, V., Crawford, S. E., Hayward, S. W. Altered TGF-α/β signaling drives cooperation between breast cancer cell populations.

Abstract 3761: Distinct transcriptional programs drive phenotypic heterogeneity in small cell lung cancer

Small-cell lung cancer (SCLC), a lethal neuroendocrine cancer, lacks targetable oncogenes and is monolithically treated with standard combination chemotherapy. Interestingly, distinct subpopulations of neuroendocrine and non-neuroendocrine cells have been identified in mouse models of SCLC, but their existence in human SCLC remains unknown. Phenotypic heterogeneity, an important phenomenon in cellular reprogramming and therapeutic resistance, can arise from cell state transitions (i.e. network-level changes dynamically controlled by transcriptional regulators). The motivation for this study is to determine whether phenotypically distinct cell states exist in human SCLC, and investigate transcription factor (TF) dynamics that maintain these states.

We implemented a mixed bioinformatics and experimental approach that defines inter-tumor heterogeneity in SCLC patients and cell lines as a spectrum of neuroendocrine (NE) and mesenchymal (MC) differentiation delineated by two anti-correlated gene co-expression networks. Features such as adhesion, surface markers and kinases effectively summarize heterogeneity in SCLC cell lines and patients as three distinct phenotypic states: NE, MC and intermediate.

To characterize the transcriptional influence that governs these distinct phenotypic states, we constructed a TF regulatory network using the mutual information based method ARACNE. Boolean network model dynamics of the top 19 predicted TFs of the NE and MC networks gives rise to 3 distinct clusters of stable phenotypic states or ‘attractors’, each given by a unique TF network configuration. These TF network states were validated at both gene and protein level in SCLC cell lines and patients, identifying specific network states governing NE, MC and intermediate attractors. In silico TF perturbation experiments (single or combination TF activation/knockdown) performed to explore the possibility of state transitions, indicated that the NE state is more easily reprogrammable via single TF manipulations than the MC state, which required a combination of 3-4 simultaneous TF manipulations. SOX2, FOXA2 and OVOL2 were identified as master regulators of MC → NE state transitions while NOTCH1, MYC, SMAD3, and NFKB1 were master regulators of the NE → MC state transitions. Experimentally, phenotypic state transitions such as NE → Intermediate and MC → Intermediate were successfully induced using HDAC inhibitors, but not with demethylating agents or cisplatin. Etoposide treatment could also induce NE → Intermediate state transitions in NE cell lines but MC cell lines were resistant. Drug rebound experiments reveal that the transitioned cells fall back into NE/MC differentiated states upon removal of the drug.

Thus, classification of human SCLC into 3 distinct phenotypic states - NE, MC and intermediate serves as a useful mapping tool for defining heterogeneity that could lead into personalized treatment strategies.

Citation Format: Akshata R. Udyavar, Megan Hoeksema, David J. Wooten, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Jonathan Irish, Pierre Massion, Vito Quaranta. Distinct transcriptional programs drive phenotypic heterogeneity in small cell lung cancer. [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 3761. doi:10.1158/1538-7445.AM2015-3761

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer

Background

Oncogenic mechanisms in small-cell lung cancer remain poorly understood leaving this tumor with the worst prognosis among all lung cancers. Unlike other cancer types, sequencing genomic approaches have been of limited success in small-cell lung cancer, i.e., no mutated oncogenes with potential driver characteristics have emerged, as it is the case for activating mutations of epidermal growth factor receptor in non-small-cell lung cancer. Differential gene expression analysis has also produced SCLC signatures with limited application, since they are generally not robust across datasets. Nonetheless, additional genomic approaches are warranted, due to the increasing availability of suitable small-cell lung cancer datasets. Gene co-expression network approaches are a recent and promising avenue, since they have been successful in identifying gene modules that drive phenotypic traits in several biological systems, including other cancer types.

Results

We derived an SCLC-specific classifier from weighted gene co-expression network analysis (WGCNA) of a lung cancer dataset. The classifier, termed SCLC-specific hub network (SSHN), robustly separates SCLC from other lung cancer types across multiple datasets and multiple platforms, including RNA-seq and shotgun proteomics. The classifier was also conserved in SCLC cell lines. SSHN is enriched for co-expressed signaling network hubs strongly associated with the SCLC phenotype. Twenty of these hubs are actionable kinases with oncogenic potential, among which spleen tyrosine kinase (SYK) exhibits one of the highest overall statistical associations to SCLC. In patient tissue microarrays and cell lines, SCLC can be separated into SYK-positive and -negative. SYK siRNA decreases proliferation rate and increases cell death of SYK-positive SCLC cell lines, suggesting a role for SYK as an oncogenic driver in a subset of SCLC.

Conclusions

SCLC treatment has thus far been limited to chemotherapy and radiation. Our WGCNA analysis identifies SYK both as a candidate biomarker to stratify SCLC patients and as a potential therapeutic target. In summary, WGCNA represents an alternative strategy to large scale sequencing for the identification of potential oncogenic drivers, based on a systems view of signaling networks. This strategy is especially useful in cancer types where no actionable mutations have emerged.

Abstract 5216: Gene co-expression network analysis of small cell lung cancer (SCLC) identifies new subclasses and novel therapeutic targets including Src family kinase Fyn and Spleen Tyrosine Kinase Syk

Oncogenic mechanisms in SCLC remain poorly understood leaving this tumor with the worst prognosis among all lung cancers. Unlike other cancer types, traditional genomic approaches have been of limited success in SCLC. For instance, no patterns of prevalent mutations associated with SCLC progression or targeted therapeutics have emerged. Gene expression profiling based on differential expression have yielded potentially useful signatures in SCLC, but they have proven to be independent of each other and with minimal overlap, reducing translational potential. Nonetheless, since integrative systems biology studies of SCLC are warranted, we hypothesized that gene co-expression analyses can unveil key signaling hubs of specific networks that regulate SCLC proliferation and survival. We applied weighted gene co-expression network analysis (WGCNA) to a lung cancer patient gene expression dataset comprising of normal lung (NL), SCLC and Non-SCLC (NSCLC) such as squamous cell carcinoma and adenocarcinoma, and identified hierarchical gene networks highly specific to SCLC. The hubs of these SCLC-specific networks formed a SCLC-specific hub network (SSHN) signature that: 1) classified SCLC from NSCLC and NL on 3 independent patient and 1 cell line datasets; 2) was validated in independent RNAseq and shotgun proteomic patient datasets; 3) identified 2 SCLC subtypes with high and low SSHN expression in patients and cell lines. Three top SSHN hubs, Fyn, Syk and BRCA1, are involved in oxidative stress (OSR) and DNA damage response (DDR), respectively. At the protein level, Fyn, Syk and BRCA1 were significantly co-expressed in tissue microarrays and classified SCLC patients into 2 subtypes: High and Low Fyn/Syk/BRCA1 (F/S/B). High F/S/B staining significantly correlated with longer recurrence-free survival of patients treated with standard chemotherapy, suggesting that efficient OSR and DDR may enhance chemo response. This possibility was tested in established SCLC cell lines, which also could be separated into high vs low F/S/B groups corresponding to the clinical subtypes. High F/S/B cell lines exhibited lower proliferative rates, suggesting that OSR and DDR may still exert influence over cell cycle. Syk knockdown in these cell lines caused significant reduction in cellular viability and proliferation, as well as increased levels of Reactive Oxygen Species (ROS). Induction of oxidative stress in High F/S/B cell lines resulted in early activation of Fyn, Syk, p38, Erk and Akt. Thus, OSR may be overactive in SCLC and play a role in its natural history and response to treatment. In summary, our WGCNA combinatorial approach yielded novel insights into SCLC pathogenesis, separated two novel SCLC molecular subtypes with distinct functional OSR and DDR properties, and pointed to unsuspected potential therapeutic targets.

Citation Format: Akshata R. Udyavar, Megan D. Hoeksema, Jonathan Clark, Yong Zou, Ming Li, Chiu-Lan (Heidi) Chen, Rosana Eisenberg, Alexander Statnikov, Daniel C. Liebler, John Field, Yu Shyr, Lourdes Estrada, Vito Quaranta, Pierre P. Massion. Gene co-expression network analysis of small cell lung cancer (SCLC) identifies new subclasses and novel therapeutic targets including Src family kinase Fyn and Spleen Tyrosine Kinase Syk. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5216. doi:10.1158/1538-7445.AM2013-5216

DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway

Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer in its clinical behavior, with a 5-year overall survival as low as 5%. Despite years of research in the field, molecular determinants of SCLC behavior are still poorly understood, and this deficiency has translated into an absence of specific diagnostics and targeted therapeutics. We hypothesized that tumor DNA copy number alterations would allow the identification of molecular pathways involved in SCLC progression. Array comparative genomic hybridization was performed on DNA extracted from 46 formalin-fixed paraffin-embedded SCLC tissue specimens. Genomic profiling of tumor and sex-matched control DNA allowed the identification of 70 regions of copy number gain and 55 regions of copy number loss. Using molecular pathway analysis, we found a strong enrichment in these regions of copy number alterations for 11 genes associated with the focal adhesion pathway. We verified these findings at the genomic, gene expression and protein level. Focal Adhesion Kinase (FAK), one of the central genes represented in this pathway, was commonly expressed in SCLC tumors and constitutively phosphorylated in SCLC cell lines. Those were poorly adherent to most substrates but not to laminin-322. Inhibition of FAK phosphorylation at Tyr(397) by a small-molecule inhibitor, PF-573,228, induced a dose-dependent decrease of adhesion and an increase of spreading in SCLC cell lines on laminin-322. Cells that tended to spread also showed a decrease in focal adhesions, as demonstrated by a decreased vinculin expression. These results support the concept that pathway analysis of genes in regions of copy number alterations may uncover molecular mechanisms of disease progression and demonstrate a new role of FAK and associated adhesion pathways in SCLC. Further investigations of FAK at the functional level may lead to a better understanding of SCLC progression and may have therapeutic implications.