Abstract 2606: A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer

Background: 80% of non-small cell lung cancer (NSCLC) cases are diagnosed at stages IIIB-IV and have a dismal prognosis with a median life expectancy that does not exceed 2 years. In contrast, patients diagnosed at early and locally advanced stages (I-IIIA) can undergo surgery and have the potential to be totally cured. Imaging technologies often detect lung nodules of unknown significance that pose a diagnostic challenge; some patients with benign nodules are submitted to unnecessary surgical interventions while others with small tumors are just kept in observation, risking a significant delay for treatment. A diagnostic test that could differentiate between benign and malignant masses would be of great help in this setting.

Methods: Circulating-free RNA (cfRNA) was isolated from the plasma of healthy individuals (N=21), early(I-II) stage (N=22) and stage IIIA (N=12) NSCLC patients, using an automatic extraction method(Qiasymphony, Qiagen). Purified cfRNA was quantified using Qubit, retrotranscribed and pre-amplified (14cycles) using the Low RNA Input Amplification kit (NanoString Technologies). Gene expression analysis was performed on the nCounter platform using the PanCancer IO360TM (NanoString Technologies), which can detect 770 transcripts related to tumor biology, micro-environment and the immune system.

Results: Gene expression analysis revealed differential patterns for some cf-mRNAs from localized stage NSCLC patients versus healthy controls. A bioinformatics recursive feature elimination algorithm selected a 16-gene mRNA signature that was able to distinguish between localized NSCLC and control samples with an area under the ROC curve of 0.91 to 0.95. Furthermore, the signature scores derived from the algorithm were significantly different between the two cohorts.

Conclusions: We have found an 16-gene signature that can differentiate between cfRNA of localized stages NSCLC patients and control individuals. Our results warrant validation studies in larger cohorts.

Citation Format: Ana Giménez Capitán, Jillian Bracht, Nicolas Potie, María González-Cao, Santiago Viteri, Alejandro Martínez-Bueno, Carlos Cabrera-Gálvez, Pablo Rubinstein, Clara Mayo-de-las-Casas, Joselyn Valarezo, Chung-Ying Huang, Carlos Pedraz, Richard Boykind, Sarah Warren, Rafael Rosell, Miguel Ángel Molina-Vilaa, Andrés Aguilar-Hernández. A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2606.

Abstract 809: nCounter for detection of clinically relevant alterations in exosomes of non-small cell lung cancer cells and patients

Background: ALK, ROS1 and RET fusions and MET exon 14 skipping variant (METex14) are present in 10-15% of advanced non-small-cell lung cancer (NSCLC) patients and their accurate identification is critical to guide targeted therapies. In a significant number of cancer patients, the tumor tissue available is insufficient for genetic analysis and repeated tissue biopsies for monitoring the course of the disease and the emergence of resistance are not feasible. Liquid biopsies constitute the only alternative available in these cases, but NGS techniques have shown insufficient sensitivity for fusion detection in blood samples. The nCounter technology has been adapted to detect fusions and skipping variants in FFPE tumor biopsies and we aimed to validate it for exosomes.

Methods: Exosomes were purified using a miRCURY kit (Qiagen) and RNA was extracted using the TRI reagent (MRC Inc). A customized nCounter panel (Nanostring) for detection ALK, ROS1 and RET fusion transcripts and MET ex14 mRNA was used with a 10-cycles preamp step. First, proof-of-concept experiments were run by testing exosomes isolated from the culture medium of cell lines. Next, we tested exosomes isolated from the blood of NSCLC patients with know genotypes.

Results: nCounter fusion probes successfully detected ALK, RET and ROS1 fusion transcripts in exosomes isolated from the culture medium of the cell lines H3122 (EML4-ALKv1), H2228 (EML4-ALKv3), HCC78 (SLC34A2-ROS1) and LC/2-Ad (CCDC6-RET). Exosomes from a cell line established from a patient progressing to alectinib were also positive for EML4-ALKv1and showed high MET expression levels, while exosomes from the fusion-negative cell lines A549 and H23 tested negative. Finally, fusion transcripts were detected in exosomes purified from the blood of fusion positive NSCLC patients but not in fusion negative cases.

Conclusions: nCounter can detect ALK, RET and ROS1 fusion transcripts in exosomes purified from the blood of advanced NSCLC patients

Citation Format: Ana Giménez Capitán, Jill Bracht, Chung-Ying Huang, Cristina Teixidó, Noemí Reguart, Rich Boykin, Sarah Warren, Joseph M Beechem, Santiago Viteri Ramirez, Juan José García, Andrés Aguilar, Rafael Rosell Costa, Jay Gerlach, Miguel Angel Molina-Vila. nCounter for detection of clinically relevant alterations in exosomes of non-small cell lung cancer cells and patients [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 809.

Abstract 4601: Astrocytic elevated gene 1 (AEG1) a target for pharmacological anticancer intervention

AEG1 is highly expressed in solid tumors; hyperexpression confers multidrug resistance, increased tumor proliferation, angiogenesis, metastatic potential and poor outcome in most solid tumors. AEG1 activates multiple protumorogenic signal transduction pathways like PIK3/ALT, NFKB, MAMPK, WNT and is a rational target for therapeutic intervention in solid tumors.Also AEG1 functionality is instrumental in the natural history of brain tumors. Our data in NSCLCs confirm AEG1 overexpression as the main parameter (uni and multivariate analysis) indicative of outcome to targeted and cytotoxic therapy. We designed an in silico model based on inhibition of AEG1-p65 crosstalk, identifying a possible interacting interface between the 2 proteins that could be modeled as a three-dimensional structure. This interface was further reduced and transformed into a 3-point pharmacophore for virtual screening comparing both molecular interaction fields and the pharmacophore. A total of 217.000 chemical entities (CEs) were tested in this model giving a Hercules® affinity ranking. Sixty CEs with the highest Hercules® ranking were identified for a second (16 CEs) and third (5 CEs) selection to implement the first round of in vitro studies in our human solid tumor panel. Twenty analogs were generated to seek for a lead according to prospective selection criteria. PB0412-3 (PB3), a small molecule polyheterocyclic compound, was selected for further development. PB3 displays antitumor activity in the human solid tumor panel (median IC50 1.3 uM) and PB3-induced growth inhibition appears independent of EGFR, KRAS & p53 mutational status, Her2 amplification, PIK3 mutations and BRCA1 expression;tumor cell lines bearing highest AEG1-mRNA expression levels were sensititive to PB3. Median IC50 in our glioblastoma (GBM) panel was 60 nM with no impact of MGMT methylation status on PB3's molar potency (MP). IC50s delta solid vs brain tumors were significant (p<.0001) representing a 25-fold increase in MP. Data from nitrosureas in the same GBM panel indicate PB3 is 250 times more potent than BCNU and temozolamide. Median IC50s in human non cancer lines is 2 uM. PB3 was re-screened in the in silico model; PB3 fully matches the AEG1 binder pharmacophore model and was screened in the Chemical Space web tool; results confirm PB3 as first-in-class CE. Functional studies are ongoing; preliminary data in PC9 NSCLC cell line demonstrate significant PB3-induced downregulation of AEG1 mRNA expression. Expansion of the CNS tumor panel, cell kinetics, drug-induced cell death & in vivo/PK-PD studies in SC orthotopic models is ongoing. To the best of our knowledge, this is the first successful attempt at the Pharmacological intervention against the AEG1 pathway. A dual developmental plan for PB3 as local brain drug delivery and systemic therapy is proposed.

Citation Format: Jose M. Jimeno, Gerardo Acosta, Miguel Ángel Molina, Nicky Karachaliou, Cristina Teixidó, Carlos Obiol, Oriol Villacañas, Jordi Bertran, María Sánchez Rouco, Ana Giménez Capitán, Santiago Ramón y Cajal, Miquel Taron, Rafael Rosell, Fernando Albericio. Astrocytic elevated gene 1 (AEG1) a target for pharmacological anticancer intervention. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4601. doi:10.1158/1538-7445.AM2014-4601