Non-small Cell Lung Cancer Biopsies Research Articles

Abstract 4954: Decoding tumor microenvironment to enhance NSCLC targeted therapy

Abstract Background: Tyrosine kinase inhibitors (TKI) have yielded promising responses in non-small-cell lung cancer (NSCLC) with EGFR mutations and ALK translocations. However, these and other targeted therapies are limited by intrinsic and acquired drug resistance. The previous study from our group investigated tumor autonomous resistance mechanisms by developing patient-derived cancer models (PDCs). In this study, we aimed to decipher the non-autonomous resistance mechanisms via tumor microenvironment by developing patient-derived fibroblast (PDF) models. Method: Cancer-associated fibroblast cell lines are established directly from individual EGFR mutant NSCLC biopsies. These cell lines, as representative of each patient's tumor microenvironment, are further subjected to functional analysis. An imaging-based high-throughput platform is developed to screen for non-autonomous resistance by co-culturing PDC and PDF models in vitro. In the parallel, two independent approaches are performed to further identify mechanisms underlying the non-autonomous resistance. These include a drug screen to determine the pathway maintaining the cancer cells' survival, and a secretomic analysis on the PDFs to identify the plausible cytokine(s) responsible for the resistance. Result: By co-culturing screening, non-autonomous resistance can be found in a wide spectrum of models. The subsequent drug screen reveals both a canonical HGF dependent and novel HGF independent mechanisms contributing to EGFR TKI resistance. Both of these can be explained by the PDF's variable cytokine secretion and can be overcome by specific therapeutic combinations. Moreover, the microenvironment-driven EGFR TKI resistance has also been validated in vivo. And the prevalence of the identified cytokine is further tested in clinical specimens. Conclusion: PDFs provide a new avenue to explore non-autonomous resistance for targeted therapy. Applying this approach, we identified both the canonical HGF dependent and novel HGF independent mechanisms that putatively conferring EGFR TKI resistance. Taking EGFR TKI therapy as a paradigm, these findings will be valuable to optimize targeted therapy and to inform the design of personalized pharmaceutical interventions. Citation Format: Haichuan Hu, Lecia Sequist, Zosia Piotrowska, David Kodack, Aaron Hata, Matt Niederst, Cyril Benes, Jeffrey Engelman. Decoding tumor microenvironment to enhance NSCLC targeted therapy [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 4954.

P3.01-082 Surgical Rebiopsy in Advanced Non-Small Cell Lung Cancer Resistant to Previous Chemotherapy

To optimize the personalized medicine for advanced non-small cell lung cancer (NSCLC), sufficient tumor tissue is mandatory to analyze molecular and genetic profile. The demand for repeat biopsy in NSCLC is increasing, it is more difficult to obtain specimen after initial treatment. The aim of this study was to evaluate the impact of surgical rebiopsy in advanced NSCLC. From Jan 2014 to Mar 2017, 146 consecutive patients underwent surgical rebiopsy for NSCLC which was resistant to prior chemotherapy. Their medical records were reviewed retrospectively. There were 60 male and 86 female patients with mean age of 57 years (range 30-83). Adenocarcinoma was most common histologic type (n=142, 93%). Among them, 107 patients represent EGFR mutation before chemotherapy, deletion in exon 19 (n=73) was most frequently observed. Before surgical rebiopsy, 121 patients (83%) were treated with EGFR-TKIs. The mean number of change in chemotherapy regimen was 2 (range 1-6) and 24% of patients underwent more than 3 different chemotherapy before rebiopsy. The median time between initial treatment and rebiopsy was 17.4 months (IQR 9-25). Surgical rebiopsy was possible in all cases. One hundred and seven patients (73%) underwent pleura biopsy, 22 underwent lung resection and 12 patients underwent both pleural and lung resection. Most procedure underwent video-assisted thoracic surgery (n=136, 93%), 10 patients required mini-thoracotomy. Median postoperative hospital stay was 4 days (IQR, 3-6) and the 30-day mortality was 2.7%. All specimens were confirmed as NSCLC and adequate for mutational and genetic analysis except 2 patients. One patient was failed to mutational analysis, other patients was failed to genetic sequencing due to low tumor volume. After surgery, 129 patients can resume chemotherapy. Of those, 85 patients were enrolled clinical trial or treated with new target agent. Thirty nine patients were treated with cytotoxic chemotherapy and 5 patients continued with prior target agent. Surgical rebiopsy can detect changes in cancer characteristics and may be used in therapeutic decision making in advanced NSCLC resistant to previous treatment.

Critical issues in the clinical application of liquid biopsy in non-small cell lung cancer.

Current therapeutic options for non-small cell lung cancer (NSCLC) patients are chemotherapy and targeted therapy directed mainly against epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements. Targeted therapy relies on the availability of tumor biopsies for molecular profiling at diagnosis and to longitudinally monitor treatment response and resistance development. Unfortunately, tumor biopsy might be invasive, recover poor material of suboptimal quality, and cause sample bias due to tumor heterogeneity. Many studies have illustrated the potential of liquid biopsy as minimal invasive approach to respond to the urgent need for real time monitoring, stratification, and personalized optimized treatment in NSCLC patients. In principle, the liquid biopsy could provide the genetic landscape of primary and metastatic cancerous lesions, detecting "druggable" genomic alterations or associated with treatment resistance. Moreover, it would guarantee the prognostic/predictive biomarkers evaluation in patients for whom biopsies are inaccessible or difficult to repeat. At this regard, the prognostic value of circulating tumor cells (CTCs) in NSCLC patients has been largely investigated, but still their clinical utility as tumor biomarker is hampered by the lack of a consensus on the criteria necessary and sufficient to define them and on the standard operating procedures (SOPs) for their assessment. This review will summarize current developments on liquid biopsy in NSCLC, addressing the technology issues that contribute to the poor ability to track CTCs in the blood of NSCLC patients, thus limiting their extensive use in the clinical practice, and analyzing the solutions adopted to overcome such limits, on the road towards the clinical validation.

Abstract LB-250: Liquid biopsy in NSCLC: EpCAM+ and EpCAM- circulating tumor cells, tumor derived extracellular vesicles and cell-free circulating tumor DNA

Abstract Introduction The need for a liquid biopsy in non-small cell lung cancer (NSCLC) patients is rapidly increasing as more and more targeted therapies become available. Presence in blood of circulating tumor cells (CTC), tumor derived extracellular vesicles (tdEV) and cell-free circulating tumor DNA (ctDNA) measured with different approaches are being explored for their potential to represent a liquid biopsy in the European and Dutch CANCER-ID projects (https://www.cancer-id.eu/ & https://www.utwente.nl/tnw/cancer-id/). Here, we determine in just one 7.5 mL tube of blood the presence of CTC, tdEV and ctDNA and investigate the relation with survival of metastatic NSCLC patients. Methods In total 106 advanced NSCLC patients were enrolled in the study. In 86 patients EpCAM+ CTC, EpCAM- CTC & tdEV were enumerated and in 50 patients EpCAM+ CTC, EpCAM- CTC, tdEV & ctDNA, all from one CellSave blood tube. ctDNA from a separate plasma tube is available for all patients but not yet analyzed. Before placing the sample in the CellSearch system, plasma was aspirated and stored at -80°C. EpCAM+ CTC were enumerated by CellSearch and EpCAM- CTC after filtration of the EpCAM+ CTC depleted blood through 5µm pore filters, as described by de Wit et al. (Sci. Rep. doi: 10.1038/srep12270, 2015). tdEV were defined by a multidimensional gate as cytokeratin+/DAPI-/CD45- vesicles and identified in the CellSearch images, using the open source image analysis program ACCEPT. The stored plasma was used for ctDNA quantification with the FAST-SeqS approach, described by Belic et al. (ClinChem 61, 838, 2015). In several patients with EpCAM- CTC, fluorescent in situ hybridization was performed on the filter to establish the cancerous origin of the EpCAM- CTC. Results In 24% of the patients ≥1 EpCAM+ CTC as well as ≥1 EpCAM- CTC were detected in 7.5 mL of blood. In 30% of the patients tdEV were present at a frequency >45 per 7.5 mL. This frequency is based on the mean + 2SD from 42 healthy controls. In 20% of the patients >10% ctDNA load was found. No significant correlation was found between the presence of these biomarkers. Presence of all four biomarkers was detected in 6% of patients and at least one of four was found in 52% of patients. One or more EpCAM+ CTC were associated with poor overall survival (p=0.010 for 86 patients and p=0.019 for 50 patients), whereas EpCAM- CTC were not (p=0.495 n=86; p=0.571 n=50). The latter is surprising since some CTC were shown to be cytogenetically aberrant, conform the primary tumor. The presence of >45 tdEV (p=0.271 n=50) and >10% ctDNA (p=0.082 n=50) did not reach significance. Conclusions In this study EpCAM+ CTC, EpCAM- CTC, tdEV or ctDNA was detected in one tube of blood in 52% of the NSCLC patients. Only the presence of EpCAM+ CTC was associated with poor overall survival, raising the question whether or not the extraction of molecular information from these other biomarkers can be used to predict response to treatment in NSCLC. To increase the percentage of patients from which a liquid biopsy can be obtained, the analyzed blood volume will need to be increased. Citation Format: Sanne de Wit, Menno Tamminga, Joost F. Swennenhuis, Leonie L. Zeune, Ellen Heitzer, Michael Speicher, T Jeroen N. Hiltermann, Leon WMM Terstappen, Harry JM Groen. Liquid biopsy in NSCLC: EpCAM+ and EpCAM- circulating tumor cells, tumor derived extracellular vesicles and cell-free circulating tumor DNA [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 LB-250. doi:10.1158/1538-7445.AM2017-LB-250

Abstract 1012: Patient-derived tumor microenvironment models uncover nonautonomous TKI resistance mechanisms in NSCLC

Abstract Background: Tyrosine kinase inhibitors (TKI) have yielded great responses in non-small-cell lung cancer (NSCLC) with EGFR mutations and ALK translocations, however these and other targeted therapies are limited by intrinsic and acquired drug resistance. Previous study from our group was looking into tumor autonomous resistance mechanisms by developing patient-derived cancer models (PDCs). In this study, we aimed to decipher the non-autonomous resistance mechanisms via tumor microenvironment by developing patient-derived fibroblast (PDF) cell lines. Method: Cancer-associated fibroblast cells are isolated directly from EGFR mutant and ALK translocated NSCLC biopsies. Over 30 PDFs models have been established, which represent different clinical features and response profiles. Result: By co-culturing the PDCs with PDFs, we found that there is considerable variability in both models for their magnitude and mechanism by which the TKI treatment is desensitized. Both HGF dependent and HGF independent resistance mechanisms can be overcome by specific therapeutic combinations. Conclusion: Together, our results indicate that PDFs are clinically relevant models for deciphering non-autonomous resistance mechanisms, that they are heterogeneous in protecting cancer cells from TKI treatment, and that the resistance mediated by PDFs can be overcome by specific therapeutic combinations. Citation Format: Haichuan Hu, Hillary Mulvey, Sundus Noeen, Kodack David, Aaron Hata, Matthew Niederst, Cyril Benes, Jeffrey Engelman. Patient-derived tumor microenvironment models uncover nonautonomous TKI resistance mechanisms in 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 1012. doi:10.1158/1538-7445.AM2017-1012

Concordance of PD-L1 expression detection in non-small cell lung cancer (NSCLC) tissue biopsies between OncoTect iO single cell PD-L1 quantification assay and immunohistochemistry (IHC).

e23172 Background: PD-1/PD-L1 therapy has been shown to be effective in patients with NSCLC, specifically those with 50% PD-L1 expression or greater by IHC. Response rates for those with lower PD-L1 expression do not consistently correlate with PD-L1 amount. The OncoTect iO Lung PD-L1 Assay was designed to provide non-subjective quantification of PD-L1 expression on tumor cells and immune cells from a multitude of tumor types. The objective of this study was to compare OncoTect iO and the current method of PD-L1 testing by immunohistochemistry (IHC) in NSCLC biopsies. Methods: Eleven NSCLC tissues were obtained from two IRB approved sites. Fresh tissues were processed into single cell suspensions using the IVD IncellPREP Kit (IncellDx, Inc). Normal lung tissue adjacent to tumor sites was obtained for 9 of the samples. Cell suspensions were tested with the OncoTect iO Lung Assay which contains antibodies directed against PD-L1 (28-8), CD45, CD3, and CD8. Suspensions are fixed and permeabilized, labeled with the antibodies, and then stained with DAPI to identify intact, single cells, and to analyze cell cycle including aneuploidy.Matched FFPE sections were taken from the tissue biopsies and were tested at BioReference Laboratories with the Dako PD-L1 IHC 28-8 PharmDx Kit. Results: A cut-off of 4% was used for the OncoTect iO Assay and a positive result for the Dako assay is ≥ 5% of the tumor cells (equivalent to 5 cells out of 100). PD-L1 expression ranged from 0% to 75% in the tumor samples which is consistent with reported ranges. Seven samples were positive by OncoTect iO Lung and 6 were positive by IHC. Twelve samples were negative by OncoTect iO Lung and 13 were negative by IHC demonstrating a concordance of 95%. Of note, one tumor that was negative by OncoTect iO and IHC demonstrated 5% of aneuploidy tumor cells that were positive and most likely very rare to be detected in the assays. Conclusions: In this study, the concordance between Oncotect iO and IHC was 95%, however, the Oncotect iO Single Cell PD-L1 Quantification Assay was fast ( < 3 hours), non-subjective, and provided addition expression information for aneuploid tumor cells.

Evaluation of Merkel cell polyomavirus in non-small cell lung cancer and adjacent normal cells.

Several risk factors have been linked to lung cancer (LC). Nevertheless, a viral etiology has been mentioned for a subset of patients developing LC. The aim of this study was to evaluate the effect of Merkel cell polyomavirus (MCPyV) on developing non-small cell lung cancer (NSCLCs). In total, 96 paraffin-embedded NSCLC biopsies and 96 adjacent non-LC normal specimens were analyzed by quantitative real-time polymerase chain reaction (PCR) for the existence of the MCPyV DNA and the expressions of RNA transcripts. Among the 96 enrolled participants, 42 patients were adenocarcinomas (ADs) and 54 patients were squamous cell carcinoma (SCC). Of the 42 ADs, MCPyV DNA was determined in 15 (35.7%) samples and of the 54 SCC, MCPyV DNA was detected in 22 (40.7%) samples. Only one non-cancerous sample in SCC subjects was positive for MCPyV LT-Ag DNA load (0.216×10-3). In MCPyV-positive subjects, the median MCPyV copy number was higher in the patients with ADs (0.016×10-3 copies/cell) compared to SCCs (0.005×10-3 copies/cell); but this difference was not statistically significant (P=0.913). In the seven stages of LC, the MCPyV LT-Ag was quantified in stage IV (0.204×10-3 copies/cell) more than in other stages. There was statistically significant difference between stages of cancer and MCPyV LT-Ag DNA load (P=0.002). These results revealed for the first time the presence of MCPyV in a subset of patients with NSCLCs in Iran. Further studies should be carried out to clarify the role of MCPyV in lung carcinogenesis.

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology.

Background:Next-generation sequencing (NGS) with a multi-gene panel is now available for patients with lung adenocarcinoma, but the performance characteristics and clinical utility of this testing are not well-described. We present the results of an extended 467 gene panel in a series of advanced, highly selected nonsmall cell lung cancer (NSCLC) patients using a range of specimens, including predominantly small biopsy and cytology specimens.Materials and Methods:A retrospective review of 22 NSCLC biopsies sent for NGS using an extended gene panel from January 2014 to July 2015. The customized NGS panel sequences 467 cancer-associated genes with exonic and intronic sequences obtained from purified tumor DNA. Genomic alterations, patient characteristics, and success of testing were determined.Results:The majority of samples tested were metastatic lung adenocarcinoma on final pathology. Of the 22 specimens tested, 5 (22.7%) were surgical resections and 17 (77.3%) were small biopsy and cytology specimens. Twenty-one (95%) of the specimens were adequate for full sequencing and yielded a total of 204 genomic alterations (average 8.9 per tumor), of which 17 (average 0.81 per tumor) were actionable and/or clinically relevant. Genomic alterations were found most commonly in the TP53, EGFR, EPHB1, MLL3, APC, SETD2, KRAS, DNMT3A, RB1, CDKN2A, ARID1A, EP300, KDM6B, RAD50, STK11, and BRCA2 genes.Conclusions:NGS using a comprehensive gene panel was performed successfully in 95% of all NSCLC cases in this series, including 94% small biopsy and cytology specimens and 100% surgical resections. This custom assay was performed on a range of tumor specimens and demonstrates that small specimens are able to provide a similar depth of information as larger ones. As many patients present at an advanced stage and only small specimens are obtained, the information these provide has the potential for guiding treatment in highly selected patients with advanced lung adenocarcinoma.

Abstract A24: Evaluation of the expression of immune functional markers in the tumor microenvironment

Abstract Recent clinical successes with immune checkpoint blockades have provided promising immune-based therapeutic approaches for controlling malignancy. While therapeutic antibodies against CTLA-4 and PD-1/PD-L1 have resulted in potent and durable clinical responses in many patients, there still remains an urgent need to develop biomarker based assays to identify patients who may benefit from these approaches while avoiding toxicity and without compromising efficacy. While gene and protein expression of immune cell and checkpoint markers can be obtained through traditional techniques, insight regarding spatial and cell-specific expression within the tumor microenvironment is lacking, particularly in regards to secreted proteins with key immune functions. RNAscope® is an advanced in situ hybridization assay that allows for the visualization of single-cell gene expression, targeting mRNA sequences directly in tissues. The probes designed for this approach permit the detection of secreted markers, including cytokines and chemokines. In our investigation of 60 archived formalin-fixed paraffin embedded non-small cell lung cancer biopsies, expression profiles of immune checkpoint markers and immune functional molecules were evaluated in the tissue environment by RNAscope®. Each of the tumors displayed distinct co-expression patterns of immune checkpoint markers as well as varying levels of cytokines (TGFβ, IFNγ, and TNFα) and chemokines, which were measured in respect to their relative location in the tumor or stromal regions. Additionally, the detection of immune cell markers were used to pinpoint the location of infiltrating lymphocytes. The methods and findings in this study provide a valuable glimpse into the understanding of key immune functional markers in the tumor microenvironment to potentially advance treatment opportunities in this era of immuno-oncology therapies. Citation Format: Jeffrey Kim, Na Li, Mingxiao He, Bingqing Zhang, Nan Su, Xiao-Jun Ma, Emily Park. Evaluation of the expression of immune functional markers in the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A24.

Association of microRNA-33a Molecular Signature with Non-Small Cell Lung Cancer Diagnosis and Prognosis after Chemotherapy.

ObjectiveThis study aims to explore the expression pattern and prognostic significance of miR-33a in non-small cell lung cancer (NSCLC) treated with adjuvant chemotherapy.MethodsMiR-33aexpression in NSCLC was analyzed in silico using the GEO database and was subsequently confirmed by quantitative RT-PCR in 147 NSCLC biopsies. Among these, 32 of these biopsies were paired with adjacent non-neoplastic tissues. The survival analysis of NSCLC by Kaplan-Meier estimates was stratified based on miR-33a expression. In addition, multivariate survival analysis in corresponding groups of NSCLC patients was conducted by Cox proportional hazards regression model.ResultsThe in silico analysis of miR-33a expression in NSCLC resulted to its down-regulation in different tumor types. The expression level of miR-33a was lower in each grade of NSCLC tumor biopsies than in normal lung tissues. Univariate and multivariate survival analysis further established that low miR-33a expression was an important risk factor for overall survival and disease free survival in NSCLC patients.ConclusionOur study implied that miR-33a expression levels may have an essential role in NSCLC progression, and could act as a specific and sensitive biomarker for NSCLC patients who have undergone adjuvant chemotherapy.

Identification of miR‑124a as a novel diagnostic and prognostic biomarker in non‑small cell lung cancer for chemotherapy.

Previous studies have suggested that dysregulation of microRNA (miR) −124a is associated with various types of human cancer. However, there are few studies reporting the level of miR-124a expression in non-small cell lung cancer (NSCLC). The present study investigated the association between miR-124a and NSCLC by analyzing the differential expression of miR-124a in NSCLC using the GEO database, as well as subsequently performing reverse transcription-quantitative polymerase chain reaction analysis on 160 NSCLC biopsies, 32 of which were paired with adjacent normal tissues. The results indicated that mir-124a expression levels were decreased in NSCLC tumor biopsies compared with adjacent normal tissues. The overall survival (OS) in patients with a high expression of miR-124a was prolonged relative to patients with low expression of miR-124a. The expression levels of miR-124a were associated with clinical characteristics, including lymph-node metastasis, tumor differentiation, tumor node metastasis (TNM) stage and diameter. Frequently, lymph-node metastasis, TNM stage, diameter and lack of chemotherapy have been associated with a worse prognosis in patients. In addition, the present study identified that high expression of miR-124awith chemotherapy may increase OS. In conclusion, the current study demonstrated that miR-124a was downregulated in NSCLC, and miR-124a was a potential prognostic tumor biomarker response to chemotherapy.

“An RNA-seq analysis from non-small cell lung cancer biopsies suggests an important role for aberrant alternative splicing in its pathophysiology”

Lung cancer accounts for the highest fatalities amongst cancers worldwide. Within the frames of the Metaboli-Ca project, we explored the effects of non-small cell lung cancer (NSCLC) by utilizing next generation sequencing (NGS) technologies. Here, we update and expand our previous work; exploiting RNA sequencing data for the derivation of differentially expressed genes and alternatively spliced genes in cancer cells compared to the adjacent normal tissue and carry out functional analysis to discover the underlying molecular mechanisms altered in cancer cells. We used our established pipeline for quantitative analysis, which utilizes a range of state-of-the-art tools, and investigated the modifications performed in cancer cells. A significant number of 1449 genes were found as differentially expressed, while 368 genes as alternatively spliced. Focusing in alternative splicing events, a number of important molecular mechanisms emerged, such as proteasome functionality, stemness, and regulation of mitosis. Our analysis suggests several molecular players that could enhance the understanding of NSCLC pathophysiology.

QUANTITATIVE ASSESSMENT OF BETA-III TUBULIN EXPRESSION IN LUNG ADENOCARCINOMA AND SQUAMOUS CELL CARCINOMA

Background. Beta-III tubulin (TUBB3) is a tumor-specific isoform of the microtubule protein beta-tubulin. TUBB3 is considered to be a marker of adverse prognosis and tumor resistance to therapy with taxanes and Vinka alkaloids. Association between TUBB3 expression and histological type of the tumor has not been studied properly yet. Objective. The expression level of TUBB3 in non-small cell lung cancer biopsy specimens has been measured on 2 groups of patients with adenocarcinoma and squamous cell carcinoma. Materials and methods. The samples with adenocarcinoma (n = 43) and squamous cell carcinoma (n = 39) were converted to suspension, filtered, fixed with 4 % formaldehyde, stained with monoclonal antibodies for TUBB3 and DyLight 650-conjugated secondary antibodies to mouse IgG and analyzed by flow-cytometry. The method was developed in N.N. Blokhin Russian Cancer Research Center. Results. The average level of TUBB3 expression in the adenocarcinoma group is higher than in the squamous cell carcinoma group (33.1 ± 12.4 % of cells expressing the marker in adenocarcinoma vs. 26.0 ± 13.6 % in squamous cell carcinoma; differences were statistically significant). The average level of TUBB3 expression in adenocarcinoma is 29.7 ± 8.1 % in female and is 34.9 ± 13.9 % in male (differences statistically insignificant). Since the group of patients with adenocarcinoma was presented by both men and women, while the group of patients with squamous cell carcinoma was only men, from the analysis was excluded all female patients. Differences between the groups remained statistically significant. Conclusion. TUBB3 expression in tumor tissue does not depend on the gender, at least among patients with adenocarcinoma of the lung, and at the same time, the level of TUBB3 in adenocarcinoma tissue is higher in comparison with squamous cell carcinoma tissue.

Positive nuclear BAP1 immunostaining helps differentiate non-small cell lung carcinomas from malignant mesothelioma.

The differential diagnosis between pleural malignant mesothelioma (MM) and lung cancer is often challenging. Immunohistochemical (IHC) stains used to distinguish these malignancies include markers that are most often positive in MM and less frequently positive in carcinomas, and vice versa. However, in about 10–20% of the cases, the IHC results can be confusing and inconclusive, and novel markers are sought to increase the diagnostic accuracy.We stained 45 non-small cell lung cancer samples (32 adenocarcinomas and 13 squamous cell carcinomas) with a monoclonal antibody for BRCA1-associated protein 1 (BAP1) and also with an IHC panel we routinely use to help differentiate MM from carcinomas, which include, calretinin, Wilms Tumor 1, cytokeratin 5, podoplanin D2-40, pankeratin CAM5.2, thyroid transcription factor 1, Napsin-A, and p63. Nuclear BAP1 expression was also analyzed in 35 MM biopsies. All 45 non-small cell lung cancer biopsies stained positive for nuclear BAP1, whereas 22/35 (63%) MM biopsies lacked nuclear BAP1 staining, consistent with previous data. Lack of BAP1 nuclear staining was associated with MM (two-tailed Fisher's Exact Test, P = 5.4 × 10−11). Focal BAP1 staining was observed in a subset of samples, suggesting polyclonality. Diagnostic accuracy of other classical IHC markers was in agreement with previous studies. Our study indicated that absence of nuclear BAP1 stain helps differentiate MM from lung carcinomas. We suggest that BAP1 staining should be added to the IHC panel that is currently used to distinguish these malignancies.

Abstract 299: Patient-derived tumor microenvironment models uncover non-autonomous TKI resistance mechanisms in NSCLC

Abstract Background: Tyrosine kinase inhibitors (TKI) have yielded great responses in non-small-cell lung cancer (NSCLC) with EGFR mutations and ALK translocations, however these and other targeted therapies are limited by intrinsic and acquired drug resistance. Previous studies looking into relapsed samples largely expanded our understanding of tumor autonomous resistance mechanisms. In this study, we aimed to decipher the non-autonomous mechanisms in vitro by recapitulating the in vivo tumor microenvironment from patient-derived models. Method: Cancer-associated fibroblast cells are isolated directly from EGFR mutant and ALK translocated NSCLC biopsies. Over 20 patient-derived fibroblast (PDF) models have been established for studying the tumor microenvironment's effect on TKI response. Result: We found that many, but not all, PDF cells exert significant resistance to TKIs. Furthermore, there is considerable variability in the degree and secreted factor / mechanism by which they are protecting the tumor cells. These variations are further correlated with patient in vivo response. Conclusion: Together, our results indicate that PDFs are clinically relevant models for deciphering non-autonomous resistance mechanisms, that they are heterogeneous in protecting cancer cells from TKI treatment, and that the resistance mediated by PDFs can be overcome by specific therapeutic combinations. Citation Format: Haichuan Hu, Matthew Niederst, Jeffrey Engelman. Patient-derived tumor microenvironment models uncover non-autonomous TKI resistance mechanisms in NSCLC. [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 299.

Significance and evaluation of anaplastic lymphoma kinase by immunohistochemistry in non-small cell lung cancer.

We used immunohistochemistry and reverse transcription polymerase chain reaction (RT-PCR) to evaluate anaplastic lymphoma kinase (ALK) protein expression and gene rearrangements, respectively, in 283 cases of wild-type epidermal growth factor receptor (EGFR) non-small cell lung cancer biopsy specimens. Immunohistochemistry was positive for ALK in 52 cases (18.4%), and there was no significant difference in staining between various monoclonal antibodies (Roche ALK test kit, D5F3, p-ALK, and EML4-ALK). On RT-PCR, 36 cases (12.7%) were positive for ALK. Immunohistochemistry and RT-PCR were both positive in 35 cases and both negative in 230 cases, and both have a high consistency (265/283, 93.6%). Including 17 cases, immunohistochemistry was positive but RT-PCR was negative, and in one case, immunohistochemistry was negative but RT-PCR was positive. On fluorescence in situ hybridization (FISH) testing of these 18 cases, only three cases were positive (one RT-PCR was positive; two immunohistochemistry were positive). There is a high prevalence of ALK positivity in wild-type EGFR non-small cell lung cancer. Immunohistochemistry for the detection of ALK gene rearrangements was highly consistent with RT-PCR, and thus, it is a good screening tool but produces false positive results that necessitate further screening by RT-PCR or FISH.

Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform.

Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.

Increased Expression of TGFβR2 Is Associated with the Clinical Outcome of Non-Small Cell Lung Cancer Patients Treated with Chemotherapy.

To investigate the prognostic significance of TGFβR2 expression and chemotherapy in Chinese non-small cell lung cancer (NSCLC) patients, TGFβR2 expression NSCLC was analyzed in silico using the Oncomine database, and subsequently analyzed with quantitative RT-PCR in 308 NSCLC biopsies, 42 of which were paired with adjacent non-neoplastic tissues. Our results show that TGFβR2 expression was also increased in NSCLC biopsies relative to normal tissue samples and correlated with poor prognosis. TGFβR2 expression was also significantly correlated with other clinical parameters such as tumor differentiation, invasion of lung membrane, and chemotherapy. Moreover, overall survival (OS) and disease free survival (DFS) was increased in patients with low TGFβR2 expressing NSCLC and who had undergone chemotherapy. Thus, high expression of TGFβR2 is a significant risk factor for decreased OS and DFS in NSCLC patients. Thus, TGFβR2 is a potential prognostic tumor biomarker for chemotherapy.

Abstract 3563: Unlocking the potential of CD70 as a therapeutic target in non-small cell lung cancer

Abstract Introduction: Upon interaction of CD70, a type II transmembrane protein, with its receptor CD27, the NFκB pathway is activated, leading to proliferation and survival. Hence, CD70 expression is tightly regulated and only transient on cells of the lymphoid lineage. In contrast, constitutive overexpression of CD70 has been documented in malignancies, where it appears to mediate immune escape through recruitment of CD27+ regulatory cells. Soluble CD27 (sCD27), the extracellular domain of CD27, can be released after lymphocyte activation and has been detected at increased levels in serum samples of lymphoid malignancies. To our knowledge, expression of CD70 has never been systematically characterized in non-small cell lung cancer (NSCLC). Methods: Fourty-nine primary NSCLC formalin-fixed paraffin embedded and 9 metastatic biopsies were stained by immunohistochemistry (IHC) for expression of CD70 (Clone 301731, 1/40) and CD27 (Clone 137B4, 1/40), using the Dako autostainer Link and Ventana ultra, respectively. Additionally, sCD27 levels were analyzed in 19 serum samples, taken before of biopsy, with the PeliKine Compact™ human sCD27 ELISA kit. Finally, we tested the efficacy of ARGX-110, a CD70-blocking monoclonal IgG1 SIMPLE Antibody™ endowed with enhanced ADCC properties (POTELLIGENT®), using the xCELLigence RTCA technology in CD70+ and CD70- cell lines. Results: In tumor cells, CD70 positivity (>10%) was detected in 16% of cases with a higher percentage in squamous NSCLC (27%) than in adenocarcinoma (9%). Additionally, one neuro-endocrine NSCLC was CD70+. We demonstrated identical CD70 patterns in primary and metastatic tissue in 8/10 biopsies. Furthermore, CD70 was found in the micro-environment of the tumor (23/49). IHC revealed high levels of CD27 expressing tumor infiltrating lymphocytes (TIL) in all NSCLC biopsies, with increasing FOXP3 expression and higher CD4/CD8 ratios in stromal tissue adjacent to CD70+ tumor cells. High sCD27 levels (>500U/ml) were found to be significantly associated with poor overall survival and even though sCD27 levels did not show potential as a blood-based biomarker for CD70 overexpression on tumor cells, dual positivity of CD70 and sCD27 marked even worse prognosis. We also showed that a low concentration of ARGX-110 (0.5μg/ml) induces efficient NK cell based tumor lysis in CD70+ cell lines. Conclusion: Expression of CD70 was demonstrated in tumor cells and TILs of NSCLC. Moreover, all biopsies revealed infiltration of CD27+ TIL in the micro-environment of the tumor and a trend towards increased FOXP3 expression and higher CD4/CD8 ratios in CD70+ biopsies. In addition, serum sCD27 levels have potential as a prognostic marker for NSCLC. Lastly, our in vitro results showed a maximum ADCC of ARGX-110 in CD70+ target cells stained by IHC. Hence, our data suggest that CD70 might be an interesting therapeutic target in NSCLC. Citation Format: Julie Jacobs, Patrick Pauwels, Christian Rolfo, Filip Lardon, Vanessa Deschoolmeester, Christophe Deben, Jolien Van den Bossche, Karen Zwaenepoel, Christophe Hermans, Karen Silence, Alain Thibault. Unlocking the potential of CD70 as a therapeutic target in non-small cell lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3563. doi:10.1158/1538-7445.AM2015-3563

MiR-205 and MiR-375 microRNA assays to distinguish squamous cell carcinoma from adenocarcinoma in lung cancer biopsies.

Identification of adenocarcinoma (AC) and squamous cell carcinoma (SCC) histology of non-small-cell lung cancer (NSCLC) in biopsies is clinically important but can be inaccurate by routine histopathologic examination. We quantify this inaccuracy at a cancer center, and evaluate the utility of a microRNA-based method to histotype AC/SCC in biopsies. RNA was extracted from tissue sections with greater than 90% tumor content that were macro- or micro-dissected from formalin-fixed, paraffin-embedded biopsy specimens. MicroRNAs in RNA from the biopsies and from resected tumors were quantified by TaqMan reverse transcription-polymerase chain reaction assays and normalized against the RNU6B housekeeping RNA. Publicly available microRNA expression datasets were examined. NSCLC subtyping of small biopsy specimens by routine histopathologic examination either failed or mistyped the histology of 21% of 190 cases. Using 77 resectates, an reverse transcription-polymerase chain reaction-based assay of microRNAs miR-21, miR-205, and miR-375 was developed to identify AC and SCC subtypes of NSCLC. This method identified the AC/SCC histotypes of 25 biopsies with an accuracy of 96%, and correctly histotyped all 12 cases for which the histology had been mistyped by routine histopathologic examination of the biopsy. Examination of publicly available datasets identified miR-205 and miR-375 as microRNAs with the best ability to histotype AC and SCC, and that levels of the two microRNAs in AC or SCC are unaffected by the pathologic stage of the tumor or the age or race of the patient. Histotypic microRNA assays can aid the subtyping of NSCLC biopsies as AC or SCC by standard histopathologic methods.