Disruptive and Truncating TP53 Mutations Are Associated with African-Ancestry and Worse Prognosis in Brazilian Patients with Lung Adenocarcinoma

INTRODUCTION

TP53 is the most frequently mutated gene in lung tumors, but its prognostic role in admixed populations, such as Brazilians, remains unclear. In this study, we aimed to evaluate the frequency and clinicopathological impact of TP53 mutations in non-small cell lung cancer (NSCLC) patients in Brazil.

METHODS

We analyzed 446 NSCLC patients from Barretos Cancer Hospital. TP53 mutational status was evaluated through targeted next-generation sequencing (NGS) and the variants were biologically classified as disruptive/nondisruptive and as truncating/nontruncating. We also assessed genetic ancestry using 46 ancestry-informative markers. Analysis of lung adenocarcinomas from the cBioportal dataset was performed. We further examined associations of TP53 mutations with patients' clinicopathological features.

RESULTS

TP53 mutations were detected in 64.3% (n = 287/446) of NSCLC cases, with a prevalence of 60.4% (n = 221/366) in lung adenocarcinomas. TP53 mutations were associated with brain metastasis at diagnosis, tobacco consumption, and higher African ancestry. Disruptive and truncating mutations were associated with a younger age at diagnosis. Additionally, cBioportal dataset revealed that TP53 mutations were associated with younger age and Black skin color. Patients harboring disruptive/truncating TP53 mutations had worse overall survival than nondisruptive/nontruncating and wild-type patients.

CONCLUSION

TP53 mutations are common in Brazilian lung adenocarcinomas, and their biological characterization as disruptive and truncating mutations is associated with African ancestry and shorter overall survival.

RNA-based next generation sequencing in non-small-cell lung cancer in a routine setting: an experience from an Italian referral center

Aim: ALK, ROS1, NTRK and RET gene fusions and MET exon 14 skipping alterations represent novel predictive biomarkers for advanced non-small-cell lung cancer (NSCLC). Therefore, testing patients for these genetic variants is crucial for choosing the best selective treatment. Over the last couple of decades, next generation sequencing (NGS) platforms have emerged as an extremely useful tool for detecting these variants. Materials & methods: In the present study, we report our NGS molecular records produced during a year of diagnostic activity. Results: Overall, our in-house developed NGS workflow successfully analyzed n = 116/131 (88.5%) NSCLC samples. Of these, eight (6.8%) and five (4.3%) out of 116 patients harbored ALK and RET gene rearrangements, respectively: one case harbored ROS1 gene fusion (0.7%). Conclusion: Our results highlight that an RNA-based NGS analysis can reliably detect gene fusion alterations, thereby playing a pivotal role in the management of NSCLC patients.

The EPICAL trial, a phase Ib study combining first line afatinib with anti-EGF vaccination in EGFR-mutant metastatic NSCLC

INTRODUCTION

Combination of anti-EGFR monoclonal antibodies or immune checkpoint inhibitors with TKIs has shown minimal benefit in EGFR mutant (EGFR-mut) NSCLC patients. Consequently, new combination approaches are needed.

PATIENTS AND METHODS

The EPICAL was a single arm, phase 1b study to evaluate safety, tolerability and anti-tumor activity of first line afatinib combined with anti-EGF vaccination in advanced EGFR-mut patients. EGFR status and mutations in liquid biopsies were determined by reverse transcriptase-polymerase chain reaction; serum biomarkers by ELISA and Western blotting analysis.

RESULTS

The assay enrolled 23 patients, 21 completed the anti-EGF immunization phase. Treatment was well tolerated and no serious adverse events (SAEs) related to the anti-EGF vaccine were reported. Objective response and disease control rates were 78.3% (95%CI = 53.6-92.5) and 95.7% (95%CI = 78.1-99.9), respectively. After a median follow-up of 24.2 months, median progression-free survival (PFS) was 14.8 months (95% CI = 9.5-20.1) and median overall survival (OS) 26.9 months (95% CI = 23.0-30.8). Among the 21 patients completing the immunization phase, PFS was 17.5 months (95% CI = 12.0-23.0) and OS 26.9 months (95% CI = 24.6-NR). At the end of the immunization phase, all 21 patients showed high serum titers of anti-EGF antibodies, while EGF levels had decreased significantly. Finally, treatment with fully immunized patient's sera inhibited the EGFR pathway in tumor cells growing in vitro.

CONCLUSIONS

Combination treatment with an anti-EGF vaccine is well tolerated; induces a sustained immunogenic effect and might enhance the clinical efficacy of EGFR TKIs.

BRCA1 Expression and Outcome in Patients With EGFR-Mutant NSCLC Treated With Gefitinib Alone or in Combination With Olaparib

Introduction

DNA repair capacity, as exemplified by BRCA1 gene expression, is related with outcome to EGFR tyrosine kinase inhibitors in patients with EGFR-mutant NSCLC. Olaparib, a PARP inhibitor, reduces BRCA1 expression. Olaparib was tested in combination with gefitinib versus gefitinib single agent, as a first-line therapy for patients with EGFR-mutant NSCLC in the GOAL study (trial registration: NCT01513174). Here, we report the results of the biomarker-related prespecified secondary objectives of the GOAL study.

Methods

We evaluated the impact of BRCA1 mRNA expression in 91 patients with EGFR-mutant NSCLC. Of those 91 patients, 51 were randomized to treatment with gefitinib and 40 were randomized to treatment with gefitinib plus olaparib. We explored in vitro whether BRCA1 mRNA levels are related with outcome to gefitinib plus olaparib. The expression levels of 53BP1, CtIP, and AXL were also explored and correlated with the treatment outcome.

Results

Overall, as what happened in the GOAL study, no statistically significant difference was observed in median progression-free survival (PFS) between the two treatment arms, for the 91 patients of the present study (p = 0.2419). For patients with high BRCA1 mRNA expression (BRCA1-high group), median PFS was 12.9 months in the gefitinib plus olaparib arm, compared with 9.2 months in the gefitinib arm (p = 0.0449). In the gefitinib arm, median PFS was 9.1 months for the BRCA1-high group and 10.2 months for the BRCA1-low group (p = 0.0193). We observed a more pronounced synergism of gefitinib plus olaparib in cells with higher BRCA1 compared with those with low BRCA1 mRNA expression.

Conclusions

High BRCA1 mRNA expression identified patients with NSCLC who benefited from gefitinib plus olaparib in the GOAL phase 2 clinical trial.

Abstract 951: Evolution of antibody titers, growth factor levels and in vitro activity in the sera of patients enrolled in the EPICAL trial of afatinib combined with anti-EGF vaccination

Background: We have recently demonstrated that antibodies generated by vaccination (anti-EGFVacAbs) potentiate the effects of EGFR TKIs in epidermal growth factor receptor mutant (EGFR-mut) non-small cell lung cancer (NSCLC) cells growing in vitro and prevent the emergence of resistance to EGFRTKIs (1). Based on these preclinical results we have started the Epical Phase Ib clinical trial(NCT03623750), testing anti-EGF vaccination in combination with EGFR TKI in advanced EGFR-mut NSCLC patients.

Methods: The EPICAL trial is a Multicenter, Open-Label, Exploratory Phase Ib Clinical Study in which 23 patients have been enrolled. Anti-EGF VacAbs is a vaccine for intramuscular administration that is designed to be used in conjunction with standard of care treatment which, in this study, is afatinib. Blood samples have been collected at baseline and every three months and sent to a central laboratory. The presence of EGFR mutations has been determined on purified DNA by 5′-nuclease real-time PCR (Taqman®) assay in presence of PNA. All the serum samples have been analyzed by ELISA to determine the levels of EGF, TGFα, HGF and GAS6, together with anti-EGF antibody titers. Sera of patients were added to EGFR-mutant cell lines growing in vitro and Western blot was used to analyze EGFR, AKT andERK activation.

Results: Median EGF levels in the sera of enrolled patients was 179.5 pg/mL at baseline and no anti-EGFantibodies were detected. Three months after first immunization, median serum EGF levels decreased to30.8 pg/mL (p=0.0008) while the anti-EGF vaccination titers increased to 1:6000 (p=0.0012). Anti-EGF titers remained high and EGF levels low in the patient's sera for the duration of the trial. Regarding serum TGFα and HGF levels baseline were 19.4 pg/mL and 861.2 pg/mL, respectively, and after three months dropped to 7.9 pg/mL (p=0.0037) and 341.3 pg/mL (p=0.0259). In EGFR-mutant cell lines in culture, the activation of the EGFR, AKT or ERK was abrogated by the sera of immunized patients.

Conclusions: Anti-EGF vaccination induces high anti-EGF antibody titers and effectively reducing the levels of EGF and other growth factors in the blood of advanced NSCLC patients.

1J Thorac Oncol. 2018 Sep;13(9):1324-1337.

Citation Format: Silvia Garcia-Roman, Jordi Codony, Miguel Angel Molina-Vila, Nuria Jordana-Ariza, Beatriz Garcia, Monica Garzon, Clara Mayo de las Casas, Maria Jose Catalan, Andres Aguilar, Santiago Viteri, Andres F. Cardona, Delvys Rodríguez, Manuel Cobo, Noemi Reguart, Erik d'Hondt, Rafael Rosell. Evolution of antibody titers, growth factor levels and in vitro activity in the sera of patients enrolled in the EPICAL trial of afatinib combined with anti-EGF vaccination [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 951.

Abstract 1107: Precision phosphoproteomic analysis in Chr22q11.2 amplified NSCLC cells reveals distinct signaling corruption and response to Aurora kinase B inhibition

Background: NSCLC cells carrying EGFR mutations can gain resistance to cognate TKIs through amplification of Chr22q11.2 (Chr22amp), a chromosome segment containing CRKL. This also specifically associates with exquisite sensitivity to inhibitors of Aurora Kinase B (AZD2811), potentially mediated by other Chr22 genes. Furthermore, a phenotypic rewiring occurs in the response to AZD2811, from a senescent polyploidy in wildtype (WT) cells to apoptosis in Chr22amp cells. Here, we aimed to elucidate the underlying signaling alterations in this background by phosphoproteomic pathway analysis.

Methods: The EGFR mutant cell line PC9 and 8 TKI resistant derivatives were profiled (4 Chr22amp and 4 WT). Kinetics of response to AZD2811 (100nM) and osimertinib (160 nM) were identified by flow cytometry. Samples (n=3) were prepared for phosphoproteomics, after 6, 24, and 48 h AZD2811 and 1 h osimertinib, with time matched controls. Cells were washed and lysed in urea, then digested with trypsin. Phosphorylated peptides were enriched with TiO2 and analyzed by Orbitrap LC-MS/MS. Computational analyses quantified peptides across samples. KScanTM bioinformatics identified differential phosphopeptides between Chr22amp and WT to determine kinase substrate profiles by KSEA, putative downstream targets (PDT) and differential compound target activity markers (CTAM).

Results: Single cell time-course analysis of phenotypic response to AZD2811 in Chr22amp cells showed that >60% of cells become Annexin V+ by 48 h post-treatment. We took earlier timepoints of 6, 24 and 48 h post treatment. We focused the phosphoproteomic analysis on three comparisons of Chr22amp amplified cells to: 1) the basal signaling state compared to WT; 2) the signaling response to osimertinib in parental PC9; and 3) the altered kinetics of signaling in response to AZD2811 compared to WT. At the basal level, Chr22amp had CK1e, CDK2, p38a substrates differentially enriched, and MTOR inhibitor and Aurora B inhibitor modulated sites (p<10-3). The response to osimertinib was largely differential in the maintenance of ERK1/2 signaling to P90RSK1 but not MEK1 in Chr22amp cells. In cells treated with AZD2811, alterations in signaling were associated with Aurora B in all cells as expected. However in amplified cells, we observed key differences at 24h such in cell death and metabolic processes in specific hierarchical clusters of temporally modulated sites, underpinned by relative down regulation of multiple signaling nodes such as ARAF (z = 4.87, p<10-2), ERN1 (z = 4.56, p<10-2), and CDK2 (z = 4.30, p<10-2).

Conclusions: Here, we identified significant pathway deregulation in Chr22amp cells that subverted EGFR inhibition and enhanced sensitivity to AZD2811. Intriguingly, we detected enhanced Aurora B activity in Chr22amp cells at basal levels, and surprising impact of AZD2811 on the EGFR pathway.

Citation Format: Arran Dokal, Jordi Bertran-Alamillo, Edmund Wilkes, Hilary Lewis, Ana Gimenez-Capitan, Calum Greenhalgh, Ruth Osuntola, Maruan Higazi-Vega, Shona Ellison, Vinothini Rajeeve, Giulia Fabbri, Urszula Polanska, J. Elizabeth Pease, Pedro Rodriguez-Cutillas, Jelena Urosevic, Miguel Angel Molina-Vila, David Britton, Jon Travers. Precision phosphoproteomic analysis in Chr22q11.2 amplified NSCLC cells reveals distinct signaling corruption and response to Aurora kinase B inhibition [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 1107.

Abstract 469: Comprehensive, large scale analysis of ALK, ROS1, RET, NTRK1 and NRG1 transcripts in lung cancer reveals over-expressing, potentially targetable patients

Background: Fusion involving anaplastic lymphoma kinase (ALK), RET proto-oncogene (RET) or ROSproto-oncogene 1, receptor tyrosine kinase (ROS1), neurotrophic receptor tyrosine kinase 1 (NTRK1)and neuregulin 1 (NRG1) are present in lung cancer (LC) and represent important biomarkers fortargeted therapies. However, little is known about the RNA expression levels of some of these genesregardless of fusions.

Methods: We used a custom nCounter panel (NanoString Technologies) designed to detect fusionsand mRNA expression levels of ALK, ROS1, RET, NTRK1 and NRG1 in formalin-fixed paraffin embedded(FFPE) samples. RNA was purified from lung cancer tumor samples and analyzed with the panel. Thecounts corresponding to the 3' probes were normalized using the geometrical mean of thehousekeeping genes and then added to evaluate total mRNA expression levels. Cut-off values for veryhigh expression levels were established as the average counts in all samples (s.) studied for each geneplus three times the standard deviation.

Results: A total of 580 LC s. from two different institutions were retrospectively analyzed for ALK,ROS1, RET and NTRK1 mRNA levels. Very high levels of ALK mRNA were found in 76 s. (13%). Of them,69/76 were also positive for EML4-ALK fusions and 61/76 had adenocarcinoma histology (ADC). OneALK-translocated patient with a sample with low levels of ALK mRNA did not respond to therapy.Twenty-two s. (3.8%) showed very high levels of ROS1 mRNA and 17/22 were ADC. In contrast withALK, only 4/22 had a concomitant ROS1 fusion. Among the remaining 16 s. with very high levels ofROS1 mRNA, 11 were ALK or EGFR positive and two were wt for the more common lung ADC geneticalteration. Regarding RET, very high expression levels were found in 11 s. (2%), only one of themshowed a RET fusion. Among the remaining 10 s., 6 presented neuroendocrine features and only 2were ADC. Regarding NTRK1, 4 s. showed very high expression levels of mRNA and only one of themwas positive for NTRK1 translocation. Finally, 116 LC s were analyzed for NRG1; very high mRNA levelswere detected in 2 cases, none of them translocated.

Conclusions: Very high expression of ALK mRNA in NSCLC is associated with EML4-ALK translocations.In contrast, a significant number of fusion negative patients show high ROS1, RET and NTRK1 mRNAvery high levels. Further research is warranted to determine the clinical relevance of this finding.

Citation Format: Cristina Aguado, Cristina Teixido, Ana Gimenez Capitan, Elba Marin, Ruth Roman, Sonia Rodriguez, Irene Moya, Roxana Reyes, Nuria Viñolas, Santiago Viteri, Andres Aguilar, Rafael Rosell, Noemi Reguart, Miguel Angel Molina-Vila. Comprehensive, large scale analysis of ALK, ROS1, RET, NTRK1 and NRG1 transcripts in lung cancer reveals over-expressing, potentially targetable patients [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 469.

Abstract 290: Comparison of clinically relevant fusions detection using two multiplexing RNA based platforms: nCounter and GeneReader

Background: Fusions involving the tyrosine kinase receptor genes ALK, ROS1, RET, NTRK or MET exon 14 skipping variant (METex14) are present in a significant percentage of advanced solid tumors and their accurate identification is critical to guide targeted therapies. While FISH has traditionally been considered the gold standard for fusion analysis, it is costly and shows biases. GeneReader Next Generation Sequencing (NGS) (Qiagen) and nCounter (Nanostring) are two technologies allowing simultaneous detection of fusion transcripts and splicing variants. In this work we compared the performance of both platforms for fusion and splicing variant detection in advanced solid tumor patients.

Methods: RNAs from 40 selected solid tumors were purified using High Pure FFPET RNA Isolation Kit (Hoffman-La Roche) and prospectively analyzed by GeneReader and nCounter. The custom nCounter codeset used targets fusions involving ALK, ROS1, RET, NTRK1-3, NRG1 and MET exon 14 skipping variant based on a dual strategy: detection of specific fusion transcripts and imbalances between the 3' and 5' mRNA regions, enabling the recognition of even those fusions not identified with the specific primers. Reporter counts from nCounter were collected with the nSolver Analysis software (Nanostring) and analyzed using an algorithm developed in the laboratory. The design of QIAact Lung Fusion Custom GeneReader panel contains specific junction probes for the detection of fusions in ALK, ROS1, RET, FGFR1- 3, NRG1, NTRK1- 3, EGFR, BRAF, and MET exon 14 skipping variant. GeneReader analysis and interpretation were performed with the QCI-Analyze and QCI-Interpret software's (Qiagen).

Results: Valid results were obtained for 40/40 (100%) of samples tested. Paired analysis showed a 97.5% concordance (39/40 cases) between the results obtained by nCounter and GeneReader NGS, corresponding to a Cohen's kappa of 0.935 [CI=0.809-1.0]. Overall, 8 samples tested positive for fusion transcripts, namely EML4-ALK (n=4), CCDC6-RET (n=1), KIF5B-RET (n=1), EZR-ROS1 (n=1) and ETV6-NTRK3 (n=1). In addition, MET exon 14 skipping variant was detected in two samples. The discordant case between nCounter and NGS corresponded to a rare RET fusion only detected by 3'-5' imbalance using nCounter, while the remaining 29 patients were pan-negative. In one of them, an uncommon HLA-DRB1-MET fusion not included in the nCounter codeset, was found by the GeneReader custom panel.

Conclusions: RNA-based NGS and nCounter show excellent concordance for detection of gene fusions and MET splicing variant in advanced solid tumors.

Citation Format: Mónica Garzón Ibañez, Ana Gimenez-Capitán, Marta Vives Usano, Ruth Román Lladó, Sonia Rodriguez, Erika Aldeguer, Beatriz García Pelaez, Nuria Jordana Ariza, Cristina Aguado, Santiago Viteri, Andrés Aguilar, Irene Moya, Carlos Cabrera, Maria Jose Catalán, Maria Gonzalez cao, Silvia Garcia-Roman, Jordi Bertran Alamillo, Florencia Garcia Casabal, Rafael Rosell, Miguel Angel Molina-Vila, Clara De La Caridad Mayo De Las Casas. Comparison of clinically relevant fusions detection using two multiplexing RNA based platforms: nCounter and GeneReader [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 290.

Dihydroartemisinin overcomes the resistance to osimertinib in EGFR-mutant non-small-cell lung cancer

Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (TKI), is commonly used to treat EGFR-mutant non-small-cell lung cancer (NSCLC). However, acquired resistance to mutant EGFR (T790M) can evolve following osimertinib treatment. High reactive oxygen species (ROS) levels in lung cancer cells can influence heme levels and have an impact on osimertinib resistance. Here, we found that heme levels were increased in osimertinib resistant EGFR-mutant NSCLC cell lines and plasma heme levels were also elevated in osimertinib-treated EGFR-mutant NSCLC patients. The antimalarial drug dihydroartemisinin (DHA), which has anticancer effects and requires heme, was tested to determine its potential to revert osimertinib resistance. DHA downregulated the expression of heme oxygenase 1 and inhibited cell proliferation in osimertinib-resistant EGFR-mutant NSCLC cells (PC9-GR4-AZD1), which was further enhanced by addition of 5-aminolevulinic acid, protoporphyrin IX and hemin. DHA was synergistic with osimertinib in inhibiting cell proliferation and colony formation of all osimertinib-resistant cell lines tested. Combination treatment with osimertinib and DHA also increased the levels of ROS, downregulated the phosphorylation or protein levels of several RTKs that often are overexpressed in osimertinib-resistant EGFR-mutant NSCLC cells, and inhibited tumor growth without toxicity in a PC9-GR4-AZD1 xenograft mouse model. The results suggest that DHA is able to reverse the resistance to osimertinib in EGFR-mutant NSCLC by elevating ROS level and impair heme metabolism.

Molecular profiling by NGS upon progression disease in advanced stage NSCLC patients

e21196

Background: Non-small cells lung cancer (NSCLC) patients treated with Tyrosine Kinase Inhibitors (TKI) at first-line ultimately develop disease progression after 10 to 14 months. Mechanisms underlying TKI-resistance are not complete understood. Tumor re-biopsy is often unfeasible for NSCLC patients and liquid biopsy is a suitable alternative in identify mechanism by which tumors progress. Methods: 113 plasma samples were collected from advanced stage EGFR positive NSCLC patients upon disease progression according to RECIST V1.1. cfDNA NGS profiling was carried out using the Oncomine™ Pan-Cancer Cell-Free Assay and sequenced on an Ion GeneStudio S5 Plus System. Variant calling and annotation were performed with Torrent Suite and Ion Reporter (v5.16) software, respectively. In addition, we developed a bioinformatic pipeline, using RStudio for variant filtering. Results: Overall, 344 somatic variants were detected with an average number of variants per patient of 2.32 and a median Mutant Allele Frequency (MAF) of 0.83%. Most mutated genes were EGFR (63.72%), TP53 (60.18%), APC (16.81%), MAP2K1 (11.50%), PIK3CA (10.62%), FGFR3 (7.08%), KRAS (7.08%) and BRAF (6.19%). As expected, SNPs were the most frequent mutation type (72.67%), following by INDELs (24.41%) and CNVs (2.91%). We found high co-occurrence between MYC-GNA11, MYC-CCND2, HRAS-AR and EGFR-TP53 genes using Jaccard’s score (0.5, 0.5, 0.5 and 0.46, respectively). Within EGFR-mutated patients, 40% had T790M resistance mutation. Finally, we found KRAS mutations and missense PIK3CA mutations were mutually exclusive. Conclusions: Molecular profiling of liquid biopsies collected upon disease progression using NGS help to identify molecular mechanisms underlying treatment failure.

Panels and models for accurate prediction of tumor mutation burden in tumor samples

Immune checkpoint blockade (ICB) is becoming standard-of-care in many types of human malignancies, but patient selection is still imperfect. Tumor mutation burden (TMB) is being evaluated as a biomarker for ICB in clinical trials, but most of the sequencing panels used to estimate it are inadequately designed. Here, we present a bioinformatics-based method to select panels and mathematical models for accurate TMB prediction. Our method is based on tumor-specific, forward-step selection of genes, generation of panels using a linear regression algorithm, and rigorous internal and external validation comparing predicted with experimental TMB. As a result, we propose cancer-specific panels for 14 malignancies which can offer reliable, clinically relevant estimates of TMBs. Our work facilitates a better prediction of TMB that can improve the selection of patients for ICB therapy.

Comprehensive analysis of the clinicopathological features, targetable profile, and prognosis of mucinous adenocarcinoma of the lung

PURPOSE

The clinicopathological or genetic features related to the prognosis of mucinous adenocarcinoma are unknown because of its rarity. The clinicopathological or targetable features were investigated for better management of patients with mucinous adenocarcinoma of the lung.

METHODS

We comprehensively evaluated the clinicopathological and genetic features of 60 completely resected mucinous lung adenocarcinomas. Targetable genetic variants were explored using nCounter and polymerase chain reaction, PD-L1 and TTF-1 expression were evaluated using immunohistochemistry. We analyzed the prognostic impact using the Kaplan-Meier method and log-rank test.

RESULTS

Of the 60 enrolled patients, 13 (21.7%) had adenocarcinoma in situ/minimally invasive adenocarcinoma, and 47 (78.3%) had invasive mucinous adenocarcinoma (IMA). Fifteen patients (25%) showed a pneumonic appearance on computed tomography (CT). CD74-NRG1 fusion, EGFR mutations, and BRAF mutation were detected in three (5%), four (6.7%), and one (1.7%) patient(s), respectively. KRAS mutations were detected in 31 patients (51.7%). Two patients (3.5%) showed immunoreactivity for PD-L1. No in situ or minimally invasive cases recurred. IMA patients with pneumonic appearance had significantly worse recurrence-free survival (RFS) and overall survival (OS) (p < 0.001). Furthermore, IMA patients harboring KRAS mutations had worse RFS (p = 0.211). Multivariate analysis revealed that radiological pneumonic appearance was significantly associated with lower RFS (p < 0.003) and OS (p = 0.012). KRAS mutations served as an unfavorable status for RFS (p = 0.043).

CONCLUSION

Mucinous adenocarcinoma had a low frequency of targetable genetic variants and PD-L1 immunoreactivity; however, KRAS mutations were frequent. Pneumonic appearance on CT imaging and KRAS mutations were clinicopathological features associated with a worse prognosis.

RNA-Based Assay for Next-Generation Sequencing of Clinically Relevant Gene Fusions in Non-Small Cell Lung Cancer

Gene fusions represent novel predictive biomarkers for advanced non-small cell lung cancer (NSCLC). In this study, we validated a narrow NGS gene panel able to cover therapeutically-relevant gene fusions and splicing events in advanced-stage NSCLC patients. To this aim, we first assessed minimal complementary DNA (cDNA) input and the limit of detection (LoD) in different cell lines. Then, to evaluate the feasibility of applying our panel to routine clinical samples, we retrospectively selected archived lung adenocarcinoma histological and cytological (cell blocks) samples. Overall, our SiRe RNA fusion panel was able to detect all fusions and a splicing event harbored in a RNA pool diluted up to 2 ng/µL. It also successfully analyzed 46 (95.8%) out of 48 samples. Among these, 43 (93.5%) out of 46 samples reproduced the same results as those obtained with conventional techniques. Intriguingly, the three discordant results were confirmed by a CE-IVD automated real-time polymerase chain reaction (RT-PCR) analysis (Easy PGX platform, Diatech Pharmacogenetics, Jesi, Italy). Based on these findings, we conclude that our new SiRe RNA fusion panel is a valid and robust tool for the detection of clinically relevant gene fusions and splicing events in advanced NSCLC.

Combination of gefitinib and olaparib versus gefitinib alone in EGFR mutant non-small-cell lung cancer (NSCLC): A multicenter, randomized phase II study (GOAL)

OBJECTIVES

Progression-free survival (PFS) and response rate to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) varies in patients with non-small-cell lung cancer (NSCLC) driven byEGFR mutations, suggesting that other genetic alterations may influence oncogene addiction. Low BRCA1 mRNA levels correlate with longer PFS in erlotinib-treated EGFR-mutant NSCLC patients. Since the poly (ADP-ribose) polymerase (PARP) inhibitor, olaparib, may attenuate and/or prevent BRCA1 expression, the addition of olaparib to gefitinib could improve outcome in EGFR-mutant advanced NSCLC.

MATERIALS AND METHODS

GOAL was a multicenter, randomized phase IB/II study performed in two countries, Spain and Mexico. Eligible patients were 18 years or older, treatment-naïve, pathologically confirmed stage IV NSCLC, with centrally confirmed EGFR mutations and measurable disease. Patients were randomly allocated (1:1) to receive gefitinib 250 mg daily or gefitinib 250 mg daily plus olaparib 200 mg three times daily in 28-day cycles. The primary endpoint was PFS. Secondary endpoints included overall survival (OS), response rate, safety and tolerability.

RESULTS

Between September 2013, and July 2016, 182 patients underwent randomization, 91 received gefitinib and 91 received gefitinib plus olaparib. There were no differences in gender, age, smoking status, performance status, presence of bone and brain metastases or type ofEGFR mutation. Median PFS was 10.9 months (95 % CI 9.3-13.3) in the gefitinib arm and 12.8 months (95 % CI 9.1-14.7) in the gefitinib plus olaparib arm (HR 1.38, 95 % CI 1.00-1.92; p = 0.124). The most common adverse events were anemia, 78 % in gefitinib plus olaparib group, 38 % in gefitinib arm, diarrhea, 65 % and 60 %, and fatigue, 40 % and 32 %, respectively.

CONCLUSIONS

The gefitinib plus olaparib combination did not provide significant benefit over gefitinib alone. The combination's safety profile showed an increase in hematological and gastrointestinal toxicity, compared to gefitinib alone, however, no relevant adverse events were noted.

SRC and PIM1 as potential co-targets to overcome resistance in MET deregulated non-small cell lung cancer

Background

The role of MET alterations in non-small cell lung cancer (NSCLC) is increasing and several targeted agents are under evaluation. MET exon 14 skipping mutations and MET amplifications are associated with potential sensitivity to MET inhibition, though resistance mechanisms are emerging. In MET addicted cells, MET inhibition leads to activation of proviral integration site for Moloney murine leukemia virus-1 (PIM1). PIM1 and proto-oncogene tyrosine-protein kinase Src (SRC) can regulate the expression of receptor tyrosine kinases (RTKs), potentially inducing resistance to MET inhibition through cross-activation.

Methods

We evaluated the activity of class I–II MET inhibitors, the SRC inhibitor dasatinib, and pan-PIM inhibitors in four MET addicted cell lines. We assessed the effect of the dual MET/PIM and MET/SRC inhibition on cell viability and at the protein level. We evaluated RNA expression profiles of the cell lines. Advanced NSCLCs were also screened for MET alterations.

Results

All cell lines were sensitive to class I–II MET inhibitors. All cell lines were resistant to single PIM and SRC inhibition. Dual MET/PIM inhibition was synergistic or additive in MET amplified cell lines and dual MET/SRC inhibition was highly synergistic in all MET addicted cell lines. The addition of an SRC inhibitor partially prevents the RTKs cross-activation. MET alterations were found in 9 out of 97 evaluable samples (9.3%); median overall survival in MET altered patients was 5 months (95% CI, 3 m–NA).

Conclusions

We identified a potential role of PIM inhibition in MET amplified tumors and of SRC inhibition in MET addicted tumors. Potential applications of this new treatment strategy warrant further evaluation.

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 929: Transcriptomic analysis of pre-treatment tissue samples to predict clinical benefit to durvalumab in HIV-infected cancer patients

Introduction: Treatment with anti PD-1/PD-L1 antibodies has demonstrated clinical activity in different types of solid tumors, but only 20 to 30% of patients (pts) respond to these immune checkpoint inhibitors (ICIs). Therefore, predictive biomarkers of response that can assist in pt selection are urgently needed. Single biomarker expression, like PD-L1, may not provide enough information about cancer cells and the tumor microenviroment. Novel technologies, analyzing hundreds of genes at the same time, are needed to yield better predictive gene signatures of ICI response. The DURVAST trial analyzed the feasibility of durvalumab treatment in HIV-infected cancer pts, which are usually excluded from ICI clinical trials. The trial included 20 patients with different tumor types and yielded a disease control rate of 56%.

Methods: Pre-ICI-treatment FFPE tumor tissue samples from 14 HIV-infected cancer pts (including 11 lung, 1 melanoma, 1 anal and 1 bladder cancer) were analyzed using the nCounter NanoString platform with the IO360 panel, including 770 genes involved in tumor biology, microenvironment and immune response. Gene expression results were correlated with clinical benefit (CB) (objective response and stable disease of more than 24 weeks by RECIST1.1 criteria), and compared to other predictive markers.

Results: Exploratory analysis of pre-treatment gene expression profiles (GEPs) revealed differentially expressed genes (DEGs) between the pts with- and without CB. Panel-incorporated biological signatures related to tumor and immune activities were evaluated and some of the most DEGs (based on higher log2FC values and nominal p-values ≤0.05) were shown to be involved in cytokine and chemokine signaling. Although not significant, pts without CB tend to have lower expression of genes involved in cytokine and chemokine signaling (p = 0.097). In contrast, pts without CB tended to have a higher TGF beta signature scores (p = 0.318). When combining both signatures, we obtained an aggregated signature score that was significantly different between pts with- and without CB (p = 0.017). While the positive predictive values were the same for all tests, our signature score outperformed PD-L1 expression positivity by immunohistochemistry and PD-L1 RNA expression as predictors for clinical benefit with a two-fold higher sensitivity and negative predictive value.

Conclusion: Gene expression analysis of pre-treatment tumor samples revealed distinct GEPs between HIV-infected cancer pts with- and without CB, where combined high baseline recruitment and activation of immune cells by cytokine and chemokine signaling pathways and low immunosuppressive TGF beta signaling pathways predict CB from durvalumab treatment. This predictive score outperformed other predictive markers of CB. These findings need further validation in an external and non-HIV infected pt cohort, in addition to a pt cohort treated with other ICIs.

Citation Format: Jillian Wilhelmina Bracht, Maria Gonzalez-Cao, Teresa Moran, Judith Dalmau, Javier Garcia-Corbacho, Reyes Bernabe, Oscar Juan, Javier de Castro, Ana Gimenez-Capitan, Remedios Blanco, Erika Aldeguer, Sonia Rodriguez, Ana Drozdowskyj, Jordi Argilaguet, Julian Blanco, Julia Prado, Christian Brander, Jorge Carrillo, Bonaventura Clotet, Bartomeu Massuti, Mariano Provencio, Chung-Ying Huang, Clara Mayo de las Casas, Monica Garzon, Andres Felipe Cardona, Oscar Arrieta, Andreas Meyerhans, Miguel Angel Molina-Vila, Javier Martinez-Picado, Rafael Rosell. Transcriptomic analysis of pre-treatment tissue samples to predict clinical benefit to durvalumab in HIV-infected cancer 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 929.

Abstract 760: miRNA and mRNA detection in plasma-derived extracellular vesicles (EVs) using the nCounter NanoString platform

Introduction: Although genetic and transcriptomic analysis of tumor tissue can provide useful information for prognosis and treatment decision making, 5-20% of advanced-stage lung cancer patients cannot be biopsied, or the amount of tumor tissue is insufficient for successful analysis. In addition, repeated sampling is often not possible. Liquid biopsies have shown potential to be used as minimally invasive, safe and sensitive alternative for tissue biopsies, but lack of standardized protocols is hampering implementation in the clinic. The nCounter platform could provide the solution for this problem, with an easy-to-use technical workflow and straightforward data analysis. Extracellular vesicles (EVs) are mediators of intercellular communication and may play a role in early cancer development. Therefore, RNA found within EVs can be used as a biomarker for cancer development and progression. In addition, the lipid bilayer of EVs makes their cargo particularly stable and allows the use of biobank stored samples.

Methods: EVs were isolated from 600 μL plasma of 19 cancer patients and 10 healthy donors, using the miRCURY® Exosome Serum/Plasma Kit (Qiagen), and total RNA was extracted using TRI Reagent® (MRC Inc) or the automated QIAsymphony® System (Qiagen) with the DSP Virus/Pathogen Kit, after RNAse A (Sigma-Aldrich) treatment to remove plasma cell-free RNA. The Human Immune V2 panel (NanoString Technologies), including 600 mRNA targets, was used to analyze EV-derived mRNA after a pre-amplification (pre-amp) step with the Low RNA Input Amplification Kit. In addition, the Human V3 miRNA panel (NanoString Technologies), including 800 miRNA targets, was used to analyze the same EV samples without pre-amp.

Results: Total amount of RNA isolated from EVs was found to be significantly higher using TRI Reagent®, versus automated RNA isolation. In addition, the conditions for the pre-amp step were tested and optimized. A pre-amp of 10 cycles for the mRNA panel was shown to be sufficient to detect mRNA targets in EVs without saturation, and the NanoString retrotranscription (RT) enzyme outperformed the other RT enzyme tested. In addition, supernatant collected during EV isolation was also analyzed, and results showed that the RNA targets were derived from within the EVs. On average, 337 mRNA targets were detected within the EVs, while 157 miRNA targets were detected in the same samples without pre-amp, with no significant differences between cancer patients and healthy donors. Interestingly, most differentially expressed (DE) mRNAs were shown to be lower expressed in cancer patients, while most DE miRNAs were found to be higher expressed in cancer patients.

Conclusion: Our results demonstrate that the nCounter NanoString platform can be used for miRNA and mRNA detection in plasma-derived EVs from cancer patients and healthy donors. Further studies will focus on specific mRNA and miRNA expression differences between these two cohorts.

Citation Format: Jillian Wilhelmina Bracht, Ana Gimenez-Capitan, Chung-Ying Huang, Carlos Pedraz-Valdunciel, Joselyn Valarezo, Sarah Warren, Rafael Rosell, Miguel Angel Molina-Vila. miRNA and mRNA detection in plasma-derived extracellular vesicles (EVs) using the nCounter NanoString platform [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 760.

Non-Small-Cell Lung Cancer Signaling Pathways, Metabolism, and PD-1/PD-L1 Antibodies

Treatment of advanced (metastatic) non-small-cell lung cancer (NSCLC) is currently mainly based on immunotherapy with antibodies against PD-1 or PD-L1, alone, or in combination with chemotherapy. In locally advanced NSCLC and in early resected stages, immunotherapy is also employed. Tumor PD-L1 expression by immunohistochemistry is considered the standard practice. Response rate is low, with median progression free survival very short in the vast majority of studies reported. Herein, numerous biological facets of NSCLC are described involving driver genetic lesions, mutations ad fusions, PD-L1 glycosylation, ferroptosis and metabolic rewiring in NSCLC and lung adenocarcinoma (LUAD). Novel concepts, such as immune-transmitters and the effect of neurotransmitters in immune evasion and tumor growth, the nascent relevance of necroptosis and pyroptosis, possible new biomarkers, such as gasdermin D and gasdermin E, the conundrum of K-Ras mutations in LUADs, with the growing recognition of liver kinase B1 (LKB1) and metabolic pathways, including others, are also commented. The review serves to charter diverse treatment solutions, depending on the main altered signaling pathways, in order to have effectual immunotherapy. Tumor PDCD1 gene (encoding PD-1) has been recently described, in equilibrium with tumor PD-L1 (encoded by PDCD1LG1). Such description explains tumor hyper-progression, which has been reported in several studies, and poises the fundamental criterion that IHC PD-L1 expression as a biomarker should be revisited.

Abstract B03: Urine cell-free DNA (cfDNA) concentration and stability test for future clinical use

Introduction: Urine was shown to be a liquid biopsy source with high sensitivity for cfDNA mutation detection in both early- and late-stage cancer patients, outperforming plasma cfDNA and tissue samples in some patients. In addition, obtaining a urine sample is completely noninvasive. Limitations of using urine samples in the clinical setting include their unknown nucleic acid stability and the large total volume of one deposit, and therefore the presence of highly diluted cfDNA. Urine volume concentration, cfDNA stability, cfDNA quantity, and detection of wild-type (wt) EGFR alleles were explored to determine the future suitability of urine cfDNA as a diagnostic or prognostic biosource.

Methods: First-void urine samples, with a higher fraction of nucleic acids due to overnight concentration, were collected from 5 healthy donors and 5 cancer patients. Cell-free urine samples were concentrated using Amicon filter tubes to determine differences in cfDNA concentration. In addition, we tested the ability to detect wild-type EGFR exon 19 in cfDNA from concentrated and unconcentrated urine samples using a peptide nucleic acid (PNA) Taqman Assay. Hereafter, stability of urine cfDNA was explored using variable storage temperatures and times and addition of a urine cfDNA preservative directly after sample collection. cfDNA was extracted using the automated QIAsymphony system with the DSP virus/pathogen kit and quantified using the Qubit dsDNA HS Assay in all experiments.

Results: Amicon filter-based concentration of urine samples from 15 mL to 1.2 mL yielded a two-fold increase in cfDNA concentration. Importantly, while wild-type EGFR could not be detected in first-void urine using a PNA Taqman Assay, detection was possible using concentrated urine samples. Therefore, in all following experiments, samples were concentrated unless specified otherwise. Stability tests indicated that storage temperature matters when samples are not processed within two hours, with nearly doubled cfDNA concentrations found in samples stored at four degrees for 26 hours, compared to room temperature (RT). Addition of a cfDNA preservative yielded a six-fold higher cfDNA concentration after 26 hours of storage at RT, compared to samples without a preservative added. For this reason, we tested the use of only cfDNA preservative without concentrating the sample and found a four-fold increase in cfDNA concentration when adding only preservative, versus a 15-fold increase when using both after sample storage at RT for 24 hours.

Conclusion: Patient urine samples should be either concentrated and processed within two hours, or a urine cfDNA preservative should be added directly after sample collection to prevent cfDNA degradation. Depending on the downstream application, samples where preservative was added may be concentrated to enhance the cfDNA yield, for example, when downstream NGS analysis will be performed.

Citation Format: Jillian W. P. Bracht, Niki Karachaliou, Jordi Berenguer, Manuel Fernandez-Bruno, Mónica Garzón, Ana Gimenez-Capitan, Clara Mayo-de-las-Casas, Miguel Angel Molina-Vila, Rafael Rosell. Urine cell-free DNA (cfDNA) concentration and stability test for future clinical use [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B03.

Comprehensive cross-platform comparison of methodologies for noninvasive EGFR mutation testing: Results of the RING observational trial

e21518

Background: Several platforms for non-invasive EGFR testing are currently used in the clinical setting, with sensitivities ranging from 30 to 100%. Comparison studies in prospective cohorts remain limited and reports evaluating mutant allelic fractions (MAFs) are particularly scarce. The RING observational trial (ClinicalTrials.gov identifier NCT03363139) was designed to comprehensively analyze the concordance between methodologies for EGFR mutation detection in blood. Methods: Seventy-two EGFR mutant NSCLC patients were enrolled in the trial. Plasma samples were prospectively collected at progression to first line Tyrosine Kinase Inhibitor and tested for EGFR mutations by 7 methodologies; cobas EGFR Mutation Test v2, Therascreen EGFR Plasma RGQ PCR Kit, QuantStudio 3D Digital PCR System, a 5-nuclease real-time PCR assay in presence of PNA, OncoBEAM EGFR and NGS with two different gene panels, Ion Torrent Oncomine and GeneRead QIAact Lung DNA UMI Cancer Panel. Results: The agreement between all methodologies for was almost perfect for the detection of deletions in exon 19 (K = 0.86; 95%CI: 0.76-0.96) and substantial for exon 21 point mutations (K = 0.76; 95%CI: 0.63-0.89). Regarding the p.T790M resistance mutation, concordance was lower but still substantial (K = 0.68; 95%CI: 0.57-0.79). If only NGS-based technologies were considered, the agreement was almost perfect for sensitizing mutations and substantial for the resistance mutation (K = 0.84; 95%CI: 0.68-1.00, K = 0.86; 95%CI: 0.69-1.00 and K = 0.77; 95%CI: 0.60-0.95 for exon 19, exon 21 and p.T790M, respectively). Most discordant samples between methodologies had mutant allele fractions (MAFs) ≤0.5%. Sensitizing mutations were always present at higher MAFs than concomitant p.T790M, explaining the lower concordance observed for this variant. MAFs obtained by different methodologies showed an excellent reproducibility (intraclass correlation coeficients 0.85-0.97). Similarly, Passing–Bablok regression analysis showed a high correlation between methodologies when assessing MAFs. Conclusions: Our results support the use of liquid biopsies for non-invasive EGFR testing in the clinical setting and highlight the need to systematically report MAFs.

Precision medicine and its implementation in patients with NTRK fusion genes: perspective from developing countries

Precision oncology is the field that places emphasis on the diagnosis and treatment of tumors that harbor specific genomic alterations susceptible to inhibition or modulation. Although most alterations are only present in a minority of patients, a substantial effect on survival can be observed in this subgroup. Mass genome sequencing has led to the identification of a specific driver in the translocations of the tropomyosin receptor kinase family (NTRK) in a subset of rare tumors both in children and in adults, and to the development and investigation of Larotrectinib. This medication was granted approval by the US Food and Drug Administration for NTRK-positive tumors, regardless of histology or age group, as such, larotrectinib was the first in its kind to be approved under the premise that molecular pattern is more important than histology in terms of therapeutic approach. It yielded significant results in disease control with good tolerability across a wide range of diseases including rare pediatric tumors, salivary gland tumors, gliomas, soft-tissue sarcomas, and thyroid carcinomas. In addition, and by taking different approaches in clinical trial design and conducting allocation based on biomarkers, the effects of target therapies can be isolated and quantified. Moreover, and considering developing nations and resource-limited settings, precision oncology could offer a tool to reduce cancer-related disability and hospital costs. In addition, developing nations also present patients with rare tumors that lack a chance of treatment, outside of clinical trials. This, in turn, offers the possibility for international collaboration, and contributes to employment, education, and health service provisions. The reviews of this paper are available via the supplemental material section.

Hsp90 inhibitors enhance the antitumoral effect of osimertinib in parental and osimertinib-resistant non-small cell lung cancer cell lines

Background

Osimertinib improve therapy for non-small cell lung cancer (NSCLC). However, invariable acquired resistance appears.

Methods

MTT assay was used to analyze cell viability. Protein expression and activation was detected by Western blotting. In addition, the effects of heat shock protein 90 (Hsp90) inhibitors and osimertinib were studied in colony formation assays.

Results

Our laboratory generated osimertinib resistant cell lines from PC9 cell line and overexpression or activation of several proteins was detected. Hsp90 inhibitors, ganetespib and luminespib, inhibited cell viability and colony formation in H1975, PC9 and PC9-derived osimertinib-resistant cell lines and combination of these inhibitors with osimertinib achieved to enhance this cell viability and colony formation inhibition. Luminespib downregulated the expression of the several proteins involved in osimertinib-resistance and the combination of this compound plus osimertinib caused an important decrease of expression of several of these proteins, such as Stat3, Yap, Akt, EGFR and Met. Osimertinib activated the phosphorylation of several membrane receptors and downstream molecules that was partially inhibited by luminespib. In addition, a lung cancer patient with an EGFR eon 20 mutation had a partial radiographic response to ganetespib.

Conclusions

Hsp90 inhibitors and osimertinib exhibits a good efficiency to inhibit cell viability, colony formation and inhibits expression and activation of proteins involved in osimertinib-resistance and may represent an effective strategy for NSCLC with intrinsic resistance to osimertinib inhibition.

Abstract 131: Concordance of mRNA expression (nCounter) and protein expression (IHC) for the detection of PD-L1 in patients with advanced non-small cell lung cancer (NSCLC)

Background: PD-L1 immunohistochemistry (IHC) staining is currently accepted as the gold-standard biomarker for immune therapy in advanced non-small cell lung cancer (NSCLC). However, the use of various antibodies and cut-offs as well as certain degree of subjectivity in pathological evaluation has overshadowed the clear-cut predictive performance of PD-L1 expression. Multiplexed technologies can be of help in this setting providing an objective measurement of PD-L1 levels. On the other hand, gene expression signatures incorporating not only PD-L1 but also other components of the stroma might better capture the immune-context of the molecular heterogeneity of NSCLC tumors. nCounter gene expression technology is an alternative method to measure PD-L1 gene expression by digital counting proving a direct measurement of mRNA levels.

Methods: A 7-gene ‘immune signature’ comprising CD4, CD8, programmed cell death-1 (PD-1), programmed death-ligand 1 (PD-L1), interferon gamma (IFNG), granzyme M (GZMM) and forkhead box P3 (FOXP3) were included in a customized nCounter panel (NanoString Technologies), used in our institution on a routine basis to simultaneously screen for relevant oncogenic-drivers (ALK, ROS1, RET, NTRK1 gene fusions and METΔ14 mutation). Total RNA obtained from formalin-fixed paraffin embedded (FFPE) samples was used for PD-L1 digital counting (nCounter) which was normalised with six housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, SF3A1, GAPDH) and compared with PD-L1 protein IHC evaluation using whole tissue section with 22C3 monoclonal mouse anti-PD-L1 antibody measured on tumor cells.

Results: A total of 425 FFPE samples from advanced NSCLC were analyzed with the nCounter panel. Among them, 25 samples were not evaluable (5.9%). PD-L1 IHC was available for 163 FFPE samples and were compared with nCounter PD-L1 expression results. By IHC, 63/163 samples (38.65%) were scored as negative for PD-L1 protein expression, whereas 100/163 (61.35%) were evaluated as positive. Among positive, 62 (38.04%) and 38 (23.31%) presented a moderate (≥ 1-49%) and high PD-L1 staining (≥50%) respectively. Using an appropriate cut-off value (IHC≥1%), PD-L1 mRNA expression levels correlated with PD-L1 IHC evaluation with a 76% of concordance and a 0.755 Cohen’s kappa (confidence interval 95% 0.651- 0.858). Unsupervised clustering across of mRNA expression data from 395 samples using the seven-immune-related genes and correlations between each immune gene were performed and a high correlation was found between PD-1 and FOXP3 (r=0.9) and PD-1 with GZMM (r=0.8).

Conclusions: PD-L1 mRNA gene expression shows promising in predicting PD-L1 protein expression in NSCLC. Further clinical validation is ongoing to confirm if PD-L1 gene expression by nCounter can be an alternative to IHC to select patients’ candidates for immune check-point inhibitors.

Citation Format: Cristina Teixido, Elba Marin, Cristina Aguado, Laia Pare, Ana Gimenez-Capitan, Sandra Lopez-Prades, Andres Felipe Cardona, Carlos Cabrera, Elena Gonzalvo, Laura Lopez, Ruth Roman, Daniel Martinez, Ivana Sullivan, Pedro Jares, Aleix Prat, Miguel Angel Molina-Vila, Noemi Reguart. Concordance of mRNA expression (nCounter) and protein expression (IHC) for the detection of PD-L1 in patients with advanced non-small cell lung cancer (NSCLC) [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 131.

Abstract 1384: nCounter for detection of clinically relevant alterations in liquid biopsies of solid tumor patients

Background: With the advent of precision medicine, screening for clinically relevant mutations and gene fusions is mandatory in many tumor types. However, in a significant number of cancer patients, the tumor tissue available is insufficient for genetic analysis. In addition, repeated tissue biopsies for monitoring the course of the disease and the emergence of mechanisms of resistance to targeted therapies are not feasible. Liquid biopsies constitute the only alternative available in these cases. The nCounter technology has been adapted to detect mutations and gene fusions in FFPE biopsies from cancer patients with a minimum requirement of tumor material and sample handling, a short turnaround time and a straightforward data analysis. However, nCounter has not been tested in liquid biopsy samples.

Methods: For mutation analysis, the SNV Solid Tumor Panel was used, which allows for detection of 97 driver mutations in 24 genes. For fusions, a customized panel for ALK, ROS1, RET, and NTRK1 fusion transcripts was used with a 14-cycles preamp step. First, proof-of-concept experiments were run by spiking plasma samples with a mixture of genomic DNAs or RNAs from positive cell lines. Next, 65 circulating-free DNA (cfDNA) samples from advanced cancer patients, previously genotyped by other techniques, were analyzed using the SNV panel. Of those, 60 had been purified from plasma, 4 from ascites and 1 from the pleural effusion. Nineteen were positive for EGFR mutations, 20 for KRAS, 13 for BRAF, 5 for PIK3CA, 2 for NRAS, and 6 were pan-negative. Finally, 8 circulating cell-free RNA samples isolated from plasma were tested with the nCounter Low RNA Input Kit and the lung fusion panel. Of those, 6 corresponded to lung cancer patients harboring ALK or ROS1 rearrangements in tumor tissue, but previous RT-PCR only detected fusions transcripts in 2.

Results: Spiking experiments revealed that the nCounter SNV Panel was able to detect mutations at allelic fractions as low as 0.2% for most of the drivers. When testing liquid biopsies, 63/65 cfDNA samples from cancer patients were evaluable, despite having DNA concentrations lower than 1 ng/µL. The SNV Panel successfully detected EGFR, KRAS, BRAF, PIK3CA and NRAS mutations with a concordance rate of 97.5% with previous genotyping by NGS, Therascreen® or Taqman® with PNA, corresponding to a Cohen’s kappa of 0,913. In the case of the lung fusion panel, ALK, ROS1 and RET fusion transcripts were detected in all spiked plasma cfRNA. Two samples from lung cancer patients with positive RT-PCR results were also detected by the nCounter low-input lung fusion panel. Research is ongoing to further improve the performance of the nCounter low-input fusion panel in liquid biopsy samples.

Conclusions: Our results demonstrate the feasibility of mutation analysis in the cfDNA of advanced cancer patients using nCounter. The nCounter technology also shows promise for the detection of gene fusions in cfRNA

Citation Format: Ana A. Giménez-Capitán, Chung-Ying Huang, Jill Bracht, Rich Boykin, Clara Mayo-de-las-Casas, Joseph M. Beechem, Cristina Teixidó, Ariadna Balada-Bel, Beatriz Garcia-, Sergio Villatoro, Monica Garzón, Nuria Jordana-Ariza, Cristina Aguado, Santiago Viteri, Juan José García, Rafael Rosell, Jay Gerlach, Noemi Reguart, Miguel Angel Molina-Vila. nCounter for detection of clinically relevant alterations in liquid biopsies of solid tumor patients [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 1384.

Abstract 4905: Comprehensive characterization of MET alterations in a large cohort of 610 advanced non-small cell lung cancer patients

Background: A variety of alterations in MET have been described in advanced non-small cell lung cancer (NSCLC) patients, including gene amplification, protein overexpression, splicing variants and point mutations. MET alterations are receiving increasing attention as targets in precision medicine, and several clinical trials of anti-MET agents are ongoing in NSCLC.

Methods: A cohort of 610 patients with stage IIIb-IV NSCLC from two institutions was retrospectively analyzed for MET alterations by next-generation sequencing (NGS) (Ion Torrent PGM® or GeneReader®), nCounter, reverse transcriptase polymerase chain reaction (RT-PCR) or immunohistochemistry (IHC) during a 2-year period. Patients positive for MET amplification by NGS or MET overexpression by nCounter and/or IHC were submitted to fluorescence in situ hybridization (FISH). Representative patients positive for MET exon 14-skipping (METΔex14) mutations by nCounter and/or RT-PCR were confirmed by sequencing exons 13-15 of the METgene.

Results: Overall, MET alterations were found in 116/610 patients (19%). Some patients had ≥2 MET aberrations. The most frequent finding was MET overexpression (58/333; 17.6%), followed by METΔex14 (31/610; 5.1%) and MET point mutations (3/129; 2.3%). Regarding MET amplification, it was found in 24/157 patients (15.3%). MET positivity by IHC (3+, &gt;50%) showed a 90.8% concordance with MET mRNA overexpression by nCounter, with a 0.768 Cohen’s kappa (confidence interval, CI 95% 0.575-0.961). A moderate agreement between RT-PCR and nCounter was found for METΔex14 (Cohen’s kappa 0.629; CI 95% 0.434-0.825). METamplification by FISH was found in the subset of MET-overexpressing patients with the highest mRNA levels by nCounter. Interestingly, a patient with a concomitant EGFR mutation and MET overexpression derived two years clinical benefit from crizotinib.

Conclusions: MET aberrations are present in 19% of advanced NSCLC patients and represent one of the most frequent targetable alterations in this malignancy. A comprehensive testing of MET alterations in advanced NSCLC patients, including NGS and nCounter techniques, is needed to identify a broader number of patients’ candidates for targeted therapies.

Citation Format: Cristina Aguado Esteban, Cristina Teixidó, Ruth Román, Ana María Gimenez Capitán, Carlos Cabrera, Mireia García, Clara D. Mayo De Las Casas, Ainara Arcocha, Sonia Rodriguez, Roxana Reyes, Elba Marín, Ana Perez Rosado, Niki Karachaliou, Aleix Prat, Rafael Rosell, Alejandro Martinez-Bueno, Miguel Angel Molina-Vila, Noemi Reguart. Comprehensive characterization of MET alterations in a large cohort of 610 advanced non-small cell lung cancer patients [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 4905.

Consistency and reproducibility of next-generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimens

BACKGROUND

Artificial genomic reference standards in a cytocentrifuge/cytospin format with well-annotated genomic data are useful for validating next-generation sequencing (NGS) on routine cytopreparations. Here, reference standards were optimized to be stained by different laboratories before DNA extraction and to contain a lower number of cells (2 × 10⁵ ). This was done to better reflect the clinical challenge of working with insufficient cytological material.

METHODS

A total of 17 worldwide laboratories analyzed customized reference standard slides (slides A-D). Each laboratory applied its standard workflow. The sample slides were engineered to harbor epidermal growth factor receptor (EGFR) c.2235_2249del15 p.E746_A750delELREA, EGFR c.2369C>T p.T790M, Kirsten rat sarcoma viral oncogene homolog (KRAS) c.38G>A p.G13D, and B-Raf proto-oncogene, serine/threonine kinase (BRAF) c.1798_1799GT>AA p.V600K mutations at various allele frequencies (AFs).

RESULTS

EGFR and KRAS mutation detection showed excellent interlaboratory reproducibility, especially on slides A and B (10% and 5% AFs). On slide C (1% AF), either the EGFR mutation or the KRAS mutation was undetected by 10 of the 17 laboratories (58.82%). A reassessment of the raw data in a second-look analysis highlighted the mutations (n = 10) that had been missed in the first-look analysis. BRAF c.1798_1799GT>AA p.V600K showed a lower concordance rate for mutation detection and AF quantification.

CONCLUSIONS

The data show that the detection of low-abundance mutations is still clinically challenging and may require a visual inspection of sequencing reads to detect. Genomic reference standards in a cytocentrifuge/cytospin format are a valid tool for regular quality assessment of laboratories performing molecular studies on cytology with low-AF mutations.

Ubiquinol-cytochrome C reductase core protein II promotes tumorigenesis by facilitating p53 degradation

Background

Ubiquinol-cytochrome C reductase core protein II (QCR2) is essential for mitochondrial functions, yet, its role in cancer development has remained elusive.

Methods

The expression of QCR2 in cancer patients was assessed by immunohistochemistry. The proliferation of cancer cells was assessed by CCK-8 assay, EdU staining and Flow cytometry analysis. The biological function of QCR2 and PHB were determined using western blotting, RT-qPCR, microarray analysis and xenografts. The interactions between proteins and the ubiquitination of p53 were assessed by immunoprecipitation, mass spectrometry analysis and GST pull down. The subcellular location of PHB and QCR2 was assessed by immunoblotting and immunofluorescence.

Finding

The expression of QCR2 is upregulated in multiple human tumors. Suppression of QCR2 inhibits cancer cell growth by activating p53 signaling and inducing p21-dependent cell cycle arrest and senescence. QCR2 directly interacts with PHB in the mitochondria. Overexpression of QCR2 inhibits PHB binding to p53 in the nucleus, and facilitates p53 ubiquitination and degradation, consequently leading to tumorigenesis. Also, increased QCR2 and decreased PHB protein levels are well correlated with decreased expression of p21 in cervical cancer tissues.

Interpretation

These results identify a novel role for QCR2, together with PHB, in negative regulation of p53 stability and activity, thus promote cervical carcinogenesis.

Fund

“973” Program of China, the National Science-technology Supporting Plan Projects, the National Natural Science Foundation of China, National Science and Technology Major Sub-Project and Technical Innovation Special Project of Hubei Province.

Comutation and exclusion analysis in human tumors: A tool for cancer biology studies and for rational selection of multitargeted therapeutic approaches

Malignant tumors originate from somatic mutations and other genomic and epigenomic alterations, which lead to loss of control of the cellular circuitry. These alterations present patterns of co-occurrence and mutual exclusivity that can influence prognosis and modify response to drugs, highlighting the need for multitargeted therapies. Studies in this area have generally focused in particular malignancies and considered whole genes instead of specific mutations, ignoring the fact that different alterations in the same gene can have widely different effects. Here, we present a comprehensive analysis of co-dependencies of individual somatic mutations in the whole spectrum of human tumors. Combining multitesting with conditional and expected mutational probabilities, we have discovered rules governing the codependencies of driver and nondriver mutations. We also uncovered pairs and networks of comutations and exclusions, some of them restricted to certain cancer types and others widespread. These pairs and networks are not only of basic but also of clinical interest, and can be of help in the selection of multitargeted antitumor therapies. In this respect, recurrent driver comutations suggest combinations of drugs that might be effective in the clinical setting, while recurrent exclusions indicate combinations unlikely to be useful.

Abstract 837: Antitumor effects of anti-EGF antibodies generated by vaccination in NSCLC tumor cells

Background: Immunization against Epidermal Growth Factor (EGF) has demonstrated clinical efficacy in a phase III trial including unselected NSCLC patients. We are currently analyzing if anti-EGF antibodies generated by vaccination (anti-EGF VacAbs) showed antitumor activity in EGFR-mutant, Kras-mutant (mut) and Anaplastic Lymphoma Kinase (ALK) translocated non-small cell lung cancer cells (NSCLC), alone or in combination with tyrosine kinase inhibitors (TKI). In an EGFR-mut and in an ALK translocated cell lines we are also studying if the anti-EGF VacABs can delay the emergence of resistance to TKIs.

Methods: Anti-EGF VacAbs were obtained by immunizing rabbits with recombinant EGF. Cell lines were treated with anti-EGF VacABs alone and in combination with TKIs in EGFR (PC9, H1975) and ALK translocated (H3122, H2228) cell lines. In KRAS-mut cells (A549, H23) the combination was with chemotherapy agents. Cell viability was analyzed by MTT and apoptosis and cell cycle by fluorescence-activates cell sorting analysis (FACS). Changes of total and phosphorylated proteins were determined by Western blot. Sera from advanced NSCLC patients immunized with anti-EGF vaccine were also tested

Results: Anti-EGF VacAbs suppressed EGF-induced cell proliferation and inhibited downstream EGFR signaling in all cell lines tested. In combination, the anti-EGF VacAbs significantly enhanced the antitumor activity of gefitinib, erlotinib, osimertinib and afatinib in EGFR-mut cells, potentiated Erk ½ phosphorylation, arrested cell cycle progression and increased apoptosis. In addition, anti-EGF VacAbs blocked the activation of STAT3, downregulated the expression of proteins related to EGFR resistance, such as AXL, and significantly delayed the emergence in vitro of clones resistant to EGFR TKI. Sera from patients vaccinated against EGF also suppressed Erk ½ phosphorylation. Results for the combination of ALK TKIs and chemotherapy agents in ALK translocated and KRAS-mut cell lines will be presented at the meeting.

Conclusions: Anti-EGF VacAbs decreased cell proliferation and inhibited the activation of EGFR-pathway downstream proteins in EGFR-mut, KRAS-mut and ALK translocated cell lines. Also, they potentiate the effects of TKIs and prevent the emergence of resistance in EGFR-mut NSCLC cells. Two clinical trials are currently testing anti-EGF vaccination in EGFR-wt and EGFR-mut advanced NSCLC patients.

Citation Format: Silvia Garcia-Roman, Jordi Codony-Servat, Miguel Angel Molina-Vila, Jordi Bertran-Alamillo, Ana Gimenez-Capitán, Niki Karachaliou, Erik d'Hondt, Rafael Rosell. Antitumor effects of anti-EGF antibodies generated by vaccination in NSCLC 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 837.

Large scale, prospective screening of EGFR mutations in the blood of advanced NSCLC patients to guide treatment decisions

Background

In a significant percentage of advanced non-small-cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses. We prospectively analyzed if circulating-free DNA (cfDNA) purified from blood can be used as a surrogate in this setting to select patients for treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs).

Patients and methods

Blood samples were collected in 119 hospitals from 1138 advanced NSCLC patients at presentation (n = 1033) or at progression to EGFR-TKIs (n = 105) with no biopsy or insufficient tumor tissue. Serum and plasma were sent to a central laboratory, cfDNA purified and EGFR mutations analyzed and quantified using a real-time PCR assay. Response data from a subset of patients (n = 18) were retrospectively collected.

Results

Of 1033 NSCLC patients at presentation, 1026 were assessable; with a prevalence of males and former or current smokers. Sensitizing mutations were found in the cfDNA of 113 patients (11%); with a majority of females, never smokers and exon 19 deletions. Thirty-one patients were positive only in plasma and 11 in serum alone and mutation load was higher in plasma and in cases with exon 19 deletions. More than 50% of samples had <10 pg mutated genomes/µl with allelic fractions below 0.25%. Patients treated first line with TKIs based exclusively on EGFR positivity in blood had an ORR of 72% and a median PFS of 11 months. Of 105 patients screened after progression to EGFR-TKIs, sensitizing mutations were found in 56.2% and the p.T790M resistance mutation in 35.2%.

Conclusions

Large-scale EGFR testing in the blood of unselected advanced NSCLC patients is feasible and can be used to select patients for targeted therapy when testing cannot be done in tissue. The characteristics and clinical outcomes to TKI treatment of the EGFR-mutated patients identified are undistinguishable from those positive in tumor.

Common Co-activation of AXL and CDCP1 in EGFR-mutation-positive Non-smallcell Lung Cancer Associated With Poor Prognosis

Epidermal growth factor receptor (EGFR)-mutation-positive non-small cell lung cancer (NSCLC) is incurable, despite high rates of response to EGFR tyrosine kinase inhibitors (TKIs). We investigated receptor tyrosine kinases (RTKs), Src family kinases and focal adhesion kinase (FAK) as genetic modifiers of innate resistance in EGFR-mutation-positive NSCLC. We performed gene expression analysis in two cohorts (Cohort 1 and Cohort 2) of EGFR-mutation-positive NSCLC patients treated with EGFR TKI. We evaluated the efficacy of gefitinib or osimertinib with the Src/FAK/Janus kinase 2 (JAK2) inhibitor, TPX0005 in vitro and in vivo. In Cohort 1, CUB domain-containing protein-1 (CDCP1) was an independent negative prognostic factor for progression-free survival (hazard ratio of 1.79, p = 0.0407) and overall survival (hazard ratio of 2.23, p = 0.0192). A two-gene model based on AXL and CDCP1 expression was strongly associated with the clinical outcome to EGFR TKIs, in both cohorts of patients. Our preclinical experiments revealed that several RTKs and non-RTKs, were up-regulated at baseline or after treatment with gefitinib or osimertinib. TPX-0005 plus EGFR TKI suppressed expression and activation of RTKs and downstream signaling intermediates. Co-expression of CDCP1 and AXL is often observed in EGFR-mutation-positive tumors, limiting the efficacy of EGFR TKIs. Co-treatment with EGFR TKI and TPX-0005 warrants testing.

•

AXL and CDCP1 are co-expressed in treatment-naïve EGFR-mutation-positive NSCLC patients.

•

AXL and CDCP1 are related to shorter progression-free survival with EGFR inhibitors and shorter overall survival.

•

Src family kinases and YAP1 are regulatory nodes for AXL and CDCP1 expression.

•

The combination of EGFR TKI with TPX-0005 is synergistic in EGFR-mutation-positive lung tumors in culture and in vivo.

We explore the molecular changes that occur after the application of an EGFR inhibitor in EGFR-mutation positive tumors. The tumors do not acquire secondary drivers to overcome a primary driver but, counter-regulatory nodes observable before treatment, are immediately made apparent by pathway-specific intervention. The expression of the receptor tyrosine kinase AXL and the transmembrane protein CDCP1 in baseline samples of EGFR-mutation positive NSCLC patients can provide us with information on the treatment outcome. The upfront combination of an EGFR inhibitor with a multikinase inhibitor, that controls the regulatory nodes for RTKs activation, is a therapeutic approach that deserves to be further explored.

Interferon gamma, an important marker of response to immune checkpoint blockade in non-small cell lung cancer and melanoma patients

Background

Programmed death-ligand 1 (PD-L1) may be induced by oncogenic signals or can be upregulated via interferon gamma (IFN-γ). We have explored whether the expression of IFNG, the gene encoding IFN-γ, is associated with clinical response to the immune checkpoint blockade in non-small cell lung cancer (NSCLC) and melanoma patients. The role of inflammation-associated transcription factors STAT3, IKBKE, STAT1 and other associated genes has also been examined.

Methods

Total RNA from 17 NSCLC and 21 melanoma patients was analyzed by quantitative reverse transcription PCR. STAT3 and Rantes, YAP1 and CXCL5, DNMT1, RIG1 and TET1, EOMES, IFNG, PD-L1 and CTLA4, IKBKE and NFATC1 mRNA were examined. PD-L1 protein expression in tumor and immune cells and stromal infiltration of CD8⁺ T-cells were also evaluated. Progression-free survival and overall survival were estimated.

Results

A total of 17 NSCLC patients received nivolumab and 21 melanoma patients received pembrolizumab. Progression-free survival with nivolumab was significantly longer in NSCLC patients with high versus low IFNG expression (5.1 months versus 2 months, p = 0.0124). Progression-free survival with pembrolizumab was significantly longer in melanoma patients with high versus low IFNG expression (5.0 months versus 1.9 months, p = 0.0099). Significantly longer overall survival was observed for melanoma patients with high versus low IFNG expression (not reached versus 10.2 months p = 0.0183). There was a trend for longer overall survival for NSCLC patients with high versus low IFNG expression.

Conclusions

IFN-γ is an important marker for prediction of response to immune checkpoint blockade. Further research is warranted in order to validate whether IFNG is more accurate than PD-L1.

An update on liquid biopsy analysis for diagnostic and monitoring applications in non-small cell lung cancer

INTRODUCTION

Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients. Expert commentary: Detection of somatic alterations in cfDNA is already in use in clinical practice and provides valuable information for patient management. Monitoring baseline alterations and emergence of resistance mutations is one of the most important clinical applications and can be used to non-invasively track disease evolution. Today, different technologies are available for cfDNA analysis, including whole-genome or exome sequencing and targeted methods that focus on a selection of genes of interest in a specific disease. In the case of Next Generation Sequencing (NGS) approaches, in depth coverage of candidate mutation loci can be achieved by selecting a limited number of targeted genes.

Abstract 1739: Analysis of EML4-ALK fusion transcripts in plasma and platelets to monitor response to crizotinib in EML4-ALK positive non-small cell lung cancer patients (NSCLC)

Background: Rearrangements in anaplastic lymphoma kinase (ALK) gene can be detected in 5-7% of EGFR and KRAS wild-type advanced NSCLC patients (p). Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) are currently used for screening but are unable to identify the specific fusion partner and are unpractical to monitor clinical responses due to difficulty of obtaining rebiopsies. The RT-PCR technique has the potential to overcome this pitfall and allow patient monitorization in blood.

Methods: A total of 405 formalin-fixed paraffin-embedded (FFPE) samples from advanced NSCLC were analyzed by ALK IHC (Ventana D5F3) and FISH (Vysis). Positive patients were confirmed by RT-PCR and submitted to Sanger in order to identify the variant. In a subset of 36 patients with EML4-ALK-rearranged tumors who were treated with crizotinib, fusion transcripts were analyzed by RT-PCR in mRNA purified from plasma and platelets and correlated with clinical response.

Results: ALK IHC was analyzed in 405 NSCLC patients and 37 tested positive (9.1%) whereas 25 (7.7%) were identify as translocated by FISH (n=323). ALK fusion transcripts were analyzed by RT-PCR and a new fusion variant of ALK was identified. A total of 36 p benefited from crizotinib treatment, including the p with the new variant. Monitoring of EML4-ALK fusion transcripts in the plasma ad platelets of 35 ALK positive patients revealed a good correlation with clinical outcome to crizotinib treatment, with the fusion transcripts becoming undetectable in p with good clinical responses.

Conclusions: Analysis of ALK fusion transcripts in mRNA purified from plasma and platelets can have a value in patients with no biopsy available and to monitor the course of the disease.

Citation Format: Cristina Aguado, Cristina Teixido, Ana Gimenez-Capitan, Maria de los Llanos Gil, Sonia Rodriguez, Santiago Viteri, Niki Karachaliou, Erika Aldeguer, Vicente Peg, Lidia Alonso, Miguel Angel Molina-Vila, Rafael Rosell. Analysis of EML4-ALK fusion transcripts in plasma and platelets to monitor response to crizotinib in EML4-ALK positive non-small cell lung cancer patients (NSCLC) [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 1739. doi:10.1158/1538-7445.AM2017-1739

Abstract 2723: MET exon 14 skipping mutations in advanced non-small cell lung cancer (NSCLC) are not associated with MET amplification and overexpression

Background: Activating alterations of the mesenchymal epithelial transition (MET) oncogene in NSCLC are potentially actionable with targeted MET inhibitors. MET exon 14 skipping mutations have been described in 3% of patients (p) in NSCLC,.Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) are currently used for detecting MET amplification and overexpression, respectively, but are not useful to detect MET splicing variants. On the other hand, the reverse transcription-polymerase chain reaction (RT-PCR) technique has the potential to detect this actionable alteration.

Methods: We designed and validated a custom set of 5´and 3´ primers to detect the MET exon 14 splicing variant by RT-PCR. RNA isolation from FFPE samples was performed with Roche High Pure FFPET RNA isolation kit and M-MLV Reverse Transcriptase enzyme was used in the RT-PCR. A panel of cell lines was initially employed to assess the performance of the technique. Subsequently, a total of 232 formalin-fixed paraffin-embedded (FFPE) samples from advanced NSCLC patients were analyzed. Of them, 15 were positive by RT-PCR (n=209) for the MET exon 14 variant. The bands corresponding to the splicing variant were submitted to Sanger sequencing.

Results were compared with FISH (ZytoVision Dual Color probe Z-2087-200) and IHC (Ventana CONFIRM anti-Total c-MET (SP44)). Results: A total of 232 EGFR-wt advanced NSCLC p were analyzed by IHC and 42 (18.1%) were considered as positive (cut-off 3+≥ 50%). Regarding FISH, MET amplification was detected in 13 out of 58 p (22.4%) evaluable while the MET exon 14 skipping variant was detected in 15 (7.2%) out of 209 p . Unexpectedly, only three (21.4%) of the positive MET exon 14 skipping p by RT-PCR were positive for IHC. Finally, of the 15 MET exon 14 positive p, 5 were evaluable for FISH and none of them were positive for MET amplification.

Conclusion: In our cohort of 232 EGFR-wt, advanced NSCLC p, the MET exon 14 skipping mutation had an incidence of 7.2% No correlation was found between the presence of the MET exon 14 variant by RT-PCR and MET overexpression or amplification. Detection of MET exon 14 alterations poses a challenge for diagnostic testing.

Citation Format: Ana Gimenez-Capitan, Cristina Teixidó, Cristina Aguado, Sonia Rodríguez, Jordi Bertran-Alamillo, Josep Castellví, Zaira Yeste, Ana Pérez, Rafael Rosell, Miguel Angel Molina-Vila. MET exon 14 skipping mutations in advanced non-small cell lung cancer (NSCLC) are not associated with MET amplification and overexpression [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 2723. doi:10.1158/1538-7445.AM2017-2723

Interferon-gamma (INFG), an important marker of response to immune checkpoint blockade (ICB) in non-small cell lung cancer (NSCLC) and melanoma patients

11504

Background: PD-L1 can be induced by oncogenic signals or up-regulated via INFG in a STAT1- and NFκB-dependent manner. STAT3 opposes STAT1-mediated anti-tumor immune responses. I kappa B kinase epsilon (IKBKE) is an interferon signaling inducer. We explored whether INFG expression in pre-treatment tumors is associated with to the efficacy of ICB in NSCLC and melanoma patients. The role of inflammation-associated transcription factors STAT3, IKBKE and STAT1 was also examined. Methods: Total RNA from 17 NSCLC and 21 melanoma patients, was analyzed by qRT-PCR. INFG, STAT3, IKBKE, STAT1 and PD-L1 mRNA were examined. PD-L1 protein expression in tumor and immune cells was evaluated (Ventana SP142 assay). Progression free survival (PFS) and overall survival (OS) were estimated. Results: 17 previously treated NSCLC patients received nivolumab; 71% lung adenocarcinoma, 71% male, 53% smokers, 35% KRAS mutant, 88% EGFR wild-type (wt). 21 previously treated melanoma patients received pembrolizumab; 67% male, 67% BRAF wt. PFS to nivolumab was significantly longer in NSCLC patients with high vs. low INFG expression (5.12 vs. 2mo, p = 0.0124). PFS to pembrolizumab was significantly longer in melanoma patients with high vs. low INFG expression (4.99 vs. 1.86mo, p = 0.0099). Significantly longer OS was observed for melanoma patients with high vs. low INFG expression (not reached vs. 3.10mo p = 0.0183). There was a trend for longer OS for NSCLC patients with high vs. low INFG expression (10.15 vs. 4.86mo, p = 0.0687). The other gene levels and PD-L1 protein levels in tumor and immune cells did not affect the outcome to ICB. IKBKE was positively correlated with INFG and PD-L1 expression (NSCLC Spearman’s ρ = 0.58 and 0.65; melanoma Spearman’s ρ = 0.61 and 0.59), and STAT3 expression was loosely anticorrelated with PD-L1 expression (NSCLC Spearman’s ρ = −0.21; melanoma Pearson’s ρ = −0.01). Conclusions: INFG is an important marker for qRT-PCR mediated prediction of response to ICB in NSCLC and melanoma patients. Further research is warranted in order to validate that INFG is more accurate than PD-L1.

Abstract 269: The role of BRCA1 and AEG1 mRNA expression in advanced non-small-cell lung cancer (NSCLC) patients (p) with EGFR activating and pretreatment T790M mutations receiving the combination of erlotinib plus bevacizumab (E+B) in the BELIEF trial

The BELIEF trial (NCT01562028) examined the efficacy of E+B for the 1st line treatment of European p with advanced NSCLC harboring exon 19 deletion or exon 21 L858R epidermal growth factor receptor (EGFR) mutations with or without pretreatment T790M. Median progression-free survival (mPFS) was 13.8 months (m) (95% CI 10.3-16.2) for the 109 p enrolled in the study. mPFS was 16m (95% CI 13.1-not estimable [NE]) and 10.4m (95% CI 9.2-15.6) for the 37 T790M(+) p and 72 T790M(-) p, respectively (P = 0.089). We have previously shown that low BRCA1 levels neutralize the negative effect of pretreatment T790M and are associated with longer PFS to erlotinib. Low astrocyte elevated gene 1 (AEG1) levels are associated with longer PFS to erlotinib. A secondary objective of the BELIEF trial was the assessment of the prognostic impact of BRCA1 and AEG1 mRNA expression in the baseline tumor tissue.

We assessed the baseline mRNA expression levels of BRCA1 and AEG1 and correlated them with PFS and response in the 109 EGFR-mutant NSCLC p of the BELIEF trial. BRCA1 and AEG1 mRNA levels were estimable by quantitative-real time PCR in 46 and 61 p respectively. Expression levels were divided into two groups according to their median.

No statistically significant associations were found among the expression of the two biomarkers and gender, smoking status, histology, PS or type of EGFR mutation. The association of BRCA1 and AEG1 mRNA with PFS did not differ according to T790M status (interaction P = 0.81 and 0.42, respectively). Among the T790M (+) p, those with low BRCA1 mRNA had a longer mPFS of 24.6m (95% CI: 4.9-NE) compared to 15.4 m (95% CI: 2.7-NE) for p with high BRCA1 mRNA; P = 0.63. For all and T790M (-) p, BRCA1 levels did not differentiate mPFS to E+B (low vs high BRCA1 mRNA, 11.0 m [95% CI: 6.0-NE] vs 9.5 m [95% CI: 7.2-NE]; P = 0.99 and 6.9 m [95% CI: 2.1-NE] vs 9.4 m [95% CI: 4.1-NE]; P = 0.71, respectively). Similarly, among the T790M (+) p, those with low AEG1 expression had a longer mPFS of 24.6m (95% CI: 4.9-NE) compared to 15.4 m (95% CI: 5.2-NE) for those with high AEG1 mRNA; P = 0.93. For all and T790M(-) p, AEG1 levels did not differentiate mPFS to E+B (low vs high AEG1 mRNA, 10.3 m [95% CI: 8.4-24.6] vs 15.4 m [95% CI: 6.0-33.9]; P = 0.90 and 10.3m [95% CI: 8.4-NE] vs 13.3m [95% CI: 4.7-33.9] P = 0.67). No statistically or clinically significant associations were found among BRCA1, AEG1 mRNA levels and response to E+B.

The BELIEF trial reconfirms our previous findings that pretreatment EGFR T790M is present in 34% of the patients. E+B is associated with a prolonged mPFS of 24.6m for EGFR-mutant p with both pretreatment EGFR T790M and low BRCA1 mRNA expression, as observed in our previous study with erlotinib alone. Similar results were observed for AEG1 levels though the interaction was not statistically significant for either biomarker.

Citation Format: Rafael Rosell, Niki Karachaliou, Ana Giménez-Capitán, Carles Codony-Servat, Oliver Gautschi, Enriqueta Felip, Alessandra Curioni-Fontecedro, Solange Peters, Santiago Ponce-Aix, Martin Früh, Miklos Pless, Sanjay Popat, Sinead Cuffe, Paolo Bidoli, Adolfo Favaretto, Roswitha Kammler, Urania Dafni, Zoi Tsourti, Miguel Angel Molina-Vila, Rolf A. Stahel. The role of BRCA1 and AEG1 mRNA expression in advanced non-small-cell lung cancer (NSCLC) patients (p) with EGFR activating and pretreatment T790M mutations receiving the combination of erlotinib plus bevacizumab (E+B) in the BELIEF trial. [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 269.

Abstract 265: Cotargeting EGFR, STAT3 and Src-Notch pathways: a promising approach to improve the efficacy of EGFR-TKIs in the treatment of NSCLC patients

Intrinsic or acquired resistance limits the clinical effectiveness of EGFR tyrosine kinase inhibitors (TKIs) for non-small cell lung cancer (NSCLC) patients (p) with EGFR mutations. One of the signaling mediators downstream of activated EGFR is signal transducer and activator of transcription 3 (STAT3). Not only does gefitinib not inhibit STAT3, but it also augments STAT3 tyrosine phosphorylation. EGFR blockade enriches lung cancer stem cells (CSCs) through NOTCH3-dependent signaling. A co-receptor of IL-6 (gp130) associates with Src and triggers activation of YAP and NOTCH. Our study is designed with three parallel objectives: firstly, to demonstrate that single EGFR TKI treatment cannot abrogate STAT3 and Src in EGFR mutant NSCLC cell lines; secondly, to examine whether the combination of gefitinib with compounds that target STAT3, (TPCA-1) and Src (saracatinib), suppresses the mechanisms of resistance; thirdly, to identify biomarkers in clinical tumor samples that may help us predict the outcome of EGFR TKIs and design effective combination therapies. Cell viability assay (MTT), western blotting, quantitative-real time PCR (qRT-PCR) and aldefluor assay-flow cytometry were used. We found that gefitinib increases pSTAT3 Y705 in PC-9 cells (that harbor the exon 19 deletion) in a time- and dose-dependent manner. Nine days after gefitinib treatment STAT3 mRNA level was significantly elevated. PC-9 cells showed dramatic increase in the fraction of ALDH+ cells upon treatment with gefitinib. TPCA-1 increased sensitivity to gefitinib in the PC-9 cells. Combination of gefitinib with TPCA-1 abrogated pSTAT3 Y705 but neither inhibited pPaxillin Y118 (Src induced) and pYAP S127 nor prevented the increment in the ALDH+ CSCs subpopulation. The triple combination of gefitinib, TPCA-1 and saracatinib was highly synergistic and abrogated pSTAT3 Y705, pPaxillin Y118 and pYAP S127. We performed qRT-PCR at baseline tumor samples of 64 EGFR mutant NSCLC p treated with first line EGFR TKIs and found that high expression of STAT3 and YAP were significantly correlated with shorter median progression-free survival (mPFS). mPFS was 9.6 months (m) (95% CI, 5.9 to 14.1) for p with low STAT3 and 18.4m (95% CI, 8.8 to 30.2) for p with high STAT3 mRNA expression (P&lt;0.001). mPFS was 9.6 months (95% CI, 7.7 to 15.2) for p with low YAP and 23.4 months (95% CI, 13.0 to 28.1) for p with high YAP mRNA expression (P = 0.005). A combined STAT3 and YAP risk group model was constructed since the mRNA expression of the 2 transcripts was weakly correlated (r = .0.15; P = 0.305). mPFS was 25.7 months for p with low STAT3 and YAP mRNA (95% CI, 8.5 to 60.9), 9.4 months for p with high STAT3 and YAP mRNA (95% CI, 2.8 to 15.2), and 14.1 months for others (95% CI, 8.2 to 23.4) (P = 0.004). Single EGFR TKI treatment can no longer be considered adequate for p with EGFR mutant lung cancer and a clinical trial co-targeting STAT3 and Src is warranted.

Citation Format: Niki Karachaliou, Imane Chaib, Sara Pilotto, Jordi Codony, Xueting Cai, Xuefei Li, Ana Drozdowskyj, Carles Codony, Andrés Felipe Cardona, Guillermo López-Vivanco, Alain Vergnenègre, José Miguel Sánchez, Mariano Provencio, Filippo de Marinis, Enric Carcereny, Noemí Reguart, Rosario García-Campelo, Silvia Marin, Cristina Teixido, Isabella Sperduti, Sonia Rodríguez, Roger Estrada, Raimon Puig de la Bellacasa, José Luis Ramírez, Miguel Angel Molina-Vila, Caicun Zhou, Peng Cao, Patrick Ma, Trever Bivona, Rafael Rosell. Cotargeting EGFR, STAT3 and Src-Notch pathways: a promising approach to improve the efficacy of EGFR-TKIs in the treatment of NSCLC patients. [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 265.

Association of EGFR L858R Mutation in Circulating Free DNA With Survival in the EURTAC Trial

IMPORTANCE

The EURTAC trial demonstrated the greater efficacy of erlotinib compared with chemotherapy for the first-line treatment of European patients with advanced non-small-cell lung cancer (NSCLC) harboring oncogenic epidermal growth factor receptor (EGFR) mutations (exon 19 deletion or L858R mutation in exon 21) in tumor tissue.

OBJECTIVE

To assess the feasibility of using circulating free DNA (cfDNA) from blood samples as a surrogate for tumor biopsy for determining EGFR mutation status and to correlate EGFR mutations in cfDNA with outcome.

DESIGN, SETTING, AND PARTICIPANTS

This prespecified analysis was a secondary objective of the EURTAC trial using patients included in the EURTAC trial from 2007 to 2011 with available baseline serum or plasma samples. Patients had advanced NSCLC, oncogenic EGFR mutations in the tumor, and no prior chemotherapy for metastatic disease and were treated with erlotinib or chemotherapy. EGFR mutations were examined in cfDNA isolated from 97 baseline blood samples by our novel peptide nucleic acid-mediated 5´ nuclease real-time polymerase chain reaction (TaqMan) assay.

MAIN OUTCOMES AND MEASURES

Overall survival (OS), progression-free survival (PFS), and response to therapy were correlated with type of EGFR mutations in cfDNA.

RESULTS

In samples from 76 of 97 (78%) patients with usable blood samples, EGFR mutations in cfDNA were detected. Median OS was shorter in patients with the L858R mutation in cfDNA than in those with the exon 19 deletion (13.7 [95% CI, 7.1-17.7] vs 30.0 [95% CI, 19.3-37.7] months; P < .001). Univariate analyses of patients with EGFR mutations in cfDNA identified the L858R mutation in tumor tissue or in cfDNA as a marker of shorter OS (hazard ratio [HR], 2.70 [95% CI, 1.60-4.56]; P < .001) and PFS (HR, 2.04 [95% CI, 1.20-3.48]; P = .008). For patients with the L858R mutation in tissue, median OS was 13.7 (95% CI, 7.1-17.7) months for patients with the L858R mutation in cfDNA and 27.7 (95% CI, 16.1-46.2) months for those in whom the mutation was not detected in cfDNA (HR, 2.22 [95% CI, 1.09-4.52]; P = .03). In the multivariate analysis of the 76 patients with EGFR mutations in cfDNA, only erlotinib treatment remained an independent predictor of longer PFS (HR, 0.41 [95% CI, 0.23-0.74]; P = .003).

CONCLUSIONS AND RELEVANCE

The peptide nucleic acid-mediated 5´ nuclease real-time polymerase chain reaction (TaqMan) assay used in this study can be used to efficiently assess EGFR mutations in cfDNA. The L858R mutation in cfDNA may be a novel surrogate prognostic marker.

TRIAL REGISTRATION

clinicaltrials.gov Identifier: NCT00446225.

Integrating the molecular background of targeted therapy and immunotherapy in lung cancer: a way to explore the impact of mutational landscape on tumor immunogenicity

The results of randomized clinical trials employing immune checkpoint inhibitors for pre-treated advanced non-small-cell lung cancer (NSCLC) have recently revolutionised the standard available option for this disease setting. Nevertheless, the validation of reliable predictive biomarkers, able to define that proportion of patients most likely to benefit from immunotherapy, represents a crucial and still unsolved issue. This intensive research aimed at selecting potentially predictive biomarkers for immunotherapy is developed together with a wide range of analyses investigating the molecular profiling of lung cancer, leading to the spontaneous question of how these two parallel aspects of the same disease may coexist and influence one another. The potential impact of the mutational landscape of lung cancer on tumor immunogenicity (in both oncogene-addicted and molecularly unselected disease) will be explored and discussed in this review in order to begin to answer the unsolved questions.