BID expression determines the apoptotic fate of cancer cells after abrogation of the spindle assembly checkpoint by AURKB or TTK inhibitors

BACKGROUND

Drugs targeting the spindle assembly checkpoint (SAC), such as inhibitors of Aurora kinase B (AURKB) and dual specific protein kinase TTK, are in different stages of clinical development. However, cell response to SAC abrogation is poorly understood and there are no markers for patient selection.

METHODS

A panel of 53 tumor cell lines of different origins was used. The effects of drugs were analyzed by MTT and flow cytometry. Copy number status was determined by FISH and Q-PCR; mRNA expression by nCounter and RT-Q-PCR and protein expression by Western blotting. CRISPR-Cas9 technology was used for gene knock-out (KO) and a doxycycline-inducible pTRIPZ vector for ectopic expression. Finally, in vivo experiments were performed by implanting cultured cells or fragments of tumors into immunodeficient mice.

RESULTS

Tumor cells and patient-derived xenografts (PDXs) sensitive to AURKB and TTK inhibitors consistently showed high expression levels of BH3-interacting domain death agonist (BID), while cell lines and PDXs with low BID were uniformly resistant. Gene silencing rendered BID-overexpressing cells insensitive to SAC abrogation while ectopic BID expression in BID-low cells significantly increased sensitivity. SAC abrogation induced activation of CASP-2, leading to cleavage of CASP-3 and extensive cell death only in presence of high levels of BID. Finally, a prevalence study revealed high BID mRNA in 6% of human solid tumors.

CONCLUSIONS

The fate of tumor cells after SAC abrogation is driven by an AURKB/ CASP-2 signaling mechanism, regulated by BID levels. Our results pave the way to clinically explore SAC-targeting drugs in tumors with high BID expression.

Insights into EGFR Mutations and Oncogenic KRAS Mutations in Non-Small-Cell Lung Cancer

Genetic mutations can activate different sets of proto-oncogenes and tumor suppressors genes [...].

Abstract 1032: Development of a plasma circRNA signature for the discrimination of malign lung nodules using the nCounter platform

Introduction: The evaluation of suspicious lung nodules detected by imaging techniques is currently being performed by invasive methods, such as surgical biopsy or fine-needle aspiration (FNA). Liquid biopsies could offer a minimally invasive alternative in this setting. Some circRNAs have recently been investigated as biomarkers for the early detection of lung cancer and other solid tumors. In this project, we are evaluating the levels of whole plasma circRNAs using the nCounter technology in order to develop a prognostic signature that can aid the clinician to differentiate benign vs. malign nodules.

Methods: Plasma samples from patients with malign lung nodules (n=135) and controls (n=149), including patients with benign nodules (n=66/149) have been collected. RNA was purified using the QIAsymphony DSP Virus/Pathogen Midi Kit in a QIAsymphony robot (Qiagen). The nCounter Low RNA Input Amplification Kit (NanoString) was used to retrotranscribe and pre-amplify 4 μL of plasma RNA. Overnight hybridization and posterior nCounter processing (NanoString) steps were carried out following the manufacturer’s instructions. Differential expression and machine learning (ML) methods were performed for the development of a lung cancer signature.

Results: Preliminary analysis of the 88 samples first included in the study shown a cluster of 6 circRNAs differentially expressed in lung cancer. Among these circRNAs, circSMAD2, circCOL11A1, circCHST15, and circFUT8 were upregulated, while circACP3 and circLYPLAL1 were found downregulated in plasma of lung cancer patients. In addition, a 64-circRNA signature selected by ML was able to differentiate NSCLC patients from controls, including those with benign nodules, The algorithm assigned signature scores to samples, which ranged from 0 to 1. Using a cut-off value of 0.5, preliminary signature was able to classify samples with an AUC ROC of 0.90 and accuracy of 78.41% (CI = 68.35% - 86.47%) with the final model.

Conclusion: Using ML on nCounter analysis of 88 samples, we have generated a preliminary 64-circRNA signature in plasma predictive of early-stage NSCLC. Final results in the entire cohort of 294 samples will be presented at the meeting.

Citation Format: Carlos Pedraz Valdunciel, Giovanna Casagrande, Elizabeth Martínez-Pérez, Ana Gimenez-Capitán, Joselyn Valarezo, Pablo Rubinstein, Andrés Aguilar-Hernández, Leticia Ferro-Leal, Cristina Marino-Buslje, Rui Reis, Rafael Rosell, Miguel Ángel Molina-Vila. Development of a plasma circRNA signature for the discrimination of malign lung nodules using the nCounter platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1032.

Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer

BACKGROUND

The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. However, standardized and robust protocols need to be developed to boost their potential in the clinical setting. Although nCounter has been used for the analysis of other liquid biopsy substrates and biomarkers, it has never been employed for EV-circRNA analysis of LC patients.

METHODS

EVs were isolated from early-stage LC patients (n = 36) and controls (n = 30). Different volumes of plasma, together with different number of pre-amplification cycles, were tested to reach the best nCounter outcome. Differential expression analysis of circRNAs was performed, along with the testing of different machine learning (ML) methods for the development of a prognostic signature for LC.

RESULTS

A combination of 500 μL of plasma input with 10 cycles of pre-amplification was selected for the rest of the study. Eight circRNAs were found upregulated in LC. Further ML analysis selected a 10-circRNA signature able to discriminate LC from controls with AUC ROC of 0.86.

CONCLUSIONS

This study validates the use of the nCounter platform for multiplexed EV-circRNA expression studies in LC patient samples, allowing the development of prognostic signatures.

Abstract 1424: Prospective validation of a mRNA signature in plasma for the diagnosis of early stage lung cancer

Background: Non-small cell lung cancer (NSCLC) is usually diagnosed at stages IIIB-IV, with a median overall survival that does not exceed two years. In contrast, patients diagnosed at early and locally advanced stages (I-IIIA) can undergo surgery and have a significantly better prognosis. Imaging technologies often detect lung nodules of unknown significance that pose a diagnostic challenge. In a proof-of-concept study, based on a 76-patient cohort, we developed a preliminary mRNA expression signature in plasma that discriminated healthy individuals from early-stage NSCLC patients with AUC=0.98. Here, we aimed to expand the training cohort, to refine the diagnostic signature and to prospectively validate the final signature in the clinical setting.

Methods: Two hundred and thirty individuals with pulmonary nodules suspicious of lung cancer have been enrolled in the training cohort. All of them underwent bronchoscopy, fine needle aspiration, percutaneous or surgical biopsy to confirm the diagnosis. Circulating-free RNA (cfRNA) has been isolated from plasma using an automatic extraction method (Qiasymphony, Qiagen). Purified cfRNA has been quantified using Qubit®, retrotranscribed and pre-amplified with 14 cycles using the Low RNA Input Amplification kit (NanoString Technologies). Gene expression analysis has been performed on the nCounter platform using the PanCancer IO360࣪ panel (NanoString Technologies), which can detect 770 transcripts related to tumor biology, micro-environment and the immune system.

Results: One hundred twenty-six patients have been analyzed so far; plasma samples have been successfully analyzed by nCounter in all cases. Ongoing analysis reveal differential patterns of gene expression in early-stage NSCLC patients versus non-cancer individuals. Using a bioinformatics recursive feature elimination algorithm, we have selected a diagnostic signature with an area under the ROC curve of 0.89. The signature scores derived from the algorithm are significantly different between the non-cancer and NSCLC cases. Final results of the training and validation cohort will be presented at the meeting

Conclusions: Plasma RNA expression signatures can be a useful tool to guide clinical decision in patients with pulmonary nodules suspicious of malignancy, orienting towards surgery or observation.

Citation Format: Ana María Giménez Capitán, Pablo Rubisntein, Andrés Aguilar-Hernández, María González-cao, Irene Moya, Santiago Viteri, Carlos Cabrera, Santiago Ramón y Cajal, Karina Loor, Mario Culebras, Irene Sansano, Federico Rubisntein, Joselyn Valarezo, Clara Mayo-de las-Casas, Carlos Pedraz, Joseph Beechem, Sarah Warren, Rafael Rosell, Miguel Ángel Molina-Vila. Prospective validation of a mRNA signature in plasma for the diagnosis of early stage lung 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 1424.

Abstract 1610: Primary cultures from malignant pleural effusions and ascites for drug screening in personalized therapy

Background: A significant percentage of patients (p.) with solid tumors present with pleural effusion or ascitic fluid during disease history. Although isolation of viable malignant cells from these fluids for drug screening and other experimental purposes have been described in the literature, the success rate in obtaining pure cultures is low and the technique is rarely employed in the clinical setting. Here, we present the results of the implementation in our hospital of routine primary culture and subsequent drug testing from pleural effusions and ascites.

Methods: 22 pleural effusions (PE) and 11 ascitic fluid from 33 p. were collected; three colon, one esophagous, one melanoma, eight ovarian, one pancreatic and 19 lung cancer. Total cells were isolated by centrifugation, erythrocytes discarded by density gradient and the remaining cells cultured in RPMI + 20%FBS. Primary cultures were genotyped by next generation sequencing (NGS), FISH, qPCR and nCounter. The antitumor effects of several drugs were tested by MTT, including tyrosine kinase, PARP and KRAS inhibitors and chemotherapeutic agents such as cis-platinum or pemetrexed.

Results: Primary cultures were attempted from 33 malignant pleural effusions and ascites samples. Cells grew ≥3 passages and were genotyped in 28/33 cases (84%). Eleven primary cultures were pan-negative by NGS, suggesting that they derived either from non-tumor cells or from a minor sub-clone within the tumor. In contrast, 17 primary cultures showed alterations in oncogenes or tumor supressor genes, allelic fractions were ≥70% in 11 cases. Synchronous liquid biopsies or FFPE biopsies were available for the 17 primary cultures; the same genetic alterations were present in all cases. Five primary cultures with drivers at ≥70% allelic fraction (KRAS G12C; ALK and ROS1 fusions; MET and FGFR1 amplifications) were used for MTT assays. In the three cases where the patient was administered the same drugs tested in primary cultures, results were concordant.

Conclusions: Primary culture of pleural effusions and ascites can be implemented in the clinical setting with a significant success rate. Drug testing in primary cultures can be of help in treatment selection.

Citation Format: Cristina A. Aguado, Beatriz Garcia, Andrés Aguilar-Hernández, Alejandro Martínez-Bueno, Marta Vives-Usano, Florencia Garcia-Casabal, Ruth Román, Ekaterina Meshoulam, Erika Aldeguer, Nuria Jordana-Ariza, Juan José García-Mosquera, Carlos Cabrera, Santiago Viteri, Sonia Rodríguez, Laura Berrocal-Gómez, Pablo Rubinstein, Clara Mayo-de-las-Casas, Rafael Rosell, Miguel Ángel Molina-Vila. Primary cultures from malignant pleural effusions and ascites for drug screening in personalized therapy [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 1610.

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.

Multiplex RNA-based detection of clinically relevant MET alterations in advanced non-small cell lung cancer

MET inhibitors have shown activity in non‐small‐cell lung cancer patients (NSCLC) with MET amplification and exon 14 skipping (METΔex14). However, patient stratification is imperfect, and thus, response rates have varied widely. Here, we studied MET alterations in 474 advanced NSCLC patients by nCounter, an RNA‐based technique, together with next‐generation sequencing (NGS), fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and reverse transcriptase polymerase chain reaction (RT–PCR), exploring correlation with clinical benefit. Of the 474 samples analyzed, 422 (89%) yielded valid results by nCounter, which identified 13 patients (3%) with METΔex14 and 15 patients (3.5%) with very‐high MET mRNA expression. These two subgroups were mutually exclusive, displayed distinct phenotypes and did not generally coexist with other drivers. For METΔex14, 3/8 (37.5%) samples positive by nCounter tested negative by NGS. Regarding patients with very‐high MET mRNA, 92% had MET amplification by FISH and/or NGS. However, FISH failed to identify three patients (30%) with very‐high MET RNA expression, among which one received MET tyrosine kinase inhibitor treatment deriving clinical benefit. Our results indicate that quantitative mRNA‐based techniques can improve the selection of patients for MET‐targeted therapies.

Influence of Quaternary Benzophenantridine and Protopine Alkaloids on Growth Performance, Dietary Energy, Carcass Traits, Visceral Mass, and Rumen Health in Finishing Ewes under Conditions of Severe Temperature-humidity Index

Twenty Pelibuey×Katahdin ewes (35±2.3 kg) were used to determine the effects of the consumption of standardized plant extract containing a mixture of quaternary benzophenanthridine alkaloids and protopine alkaloids (QBA+PA) on growth performance, dietary energetics, visceral mass, and ruminal epithelial health in heat-stressed ewes fed with a high-energy corn-based diet. The basal diet (13.9% crude protein and 2.09 Mcal of net energy [NE] of maintenance/kg of dry matter) contained 49.7% starch and 15.3% neutral detergent fiber. Source of QBA+PA was Sangrovit RS (SANG) which contains 3 g of quaternary benzophenathridine and protopine alkaloids per kg of product. Treatments consisted of a daily consumption of 0 or 0.5 g SANG/ewe. Ewes were grouped by weight and assigned to 10 pens (5 pens/treatment), with two ewes per pen. The experimental period lasted 70 days. The mean temperature humidity index during the course of this experiment was 81.7±1.0 (severe heat stress). There were no treatment effects on water intake. Dry matter intake was not affected (p = 0.70) by treatments, but the group fed SANG had a numerically (11.2%) higher gain in comparison to the control group, SANG improved gain efficiency (8.3%, p = 0.04), dietary NE (5.2%, p<0.01) and the observed-to-expected NE (5.9%, p<0.01). Supplemental SANG did not affect (p≥0.12) carcass characteristics, chemical composition of shoulder, and organ weights (g/kg empty body weight) of stomach complex, intestines, and heart/lung. Supplemental SANG decreased liver weight (10.3%, p = 0.02) and increased visceral fat (16.9%, p = 0.02). Rumen epithelium of ewes fed SANG had lower scores for cellular dropsical degeneration (2.08 vs 2.34, p = 0.02), parakeratosis (1.30 vs 1.82, p = 0.03) and neutrophil infiltration (2.08 vs 2.86, p = 0.05) than controls. It is concluded that SANG supplementation helped ameliorate the negative effects of severe heat on growth performance of feedlot ewes fed high-energy corn-based diets. Improvement in energetic efficiency may have been mediated, in part, by anti-inflammatory effects of supplemental SANG and corresponding enhancement of nutrient uptake.