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WINTHER – A Study of Therapy Based on Tumor and Normal-Matched Biopsies: The Lung Cancer Experience
S1540
Journal of Thoracic Oncology
Vol. 12 No. 8S
Immune Checkpoint Protein Expression at Multiple Metastatic Sites of Lung Cancer
miRNA for Early Detection of Lung Cancer: Comparison of Tissue, Sputum and Plasma Signatures
T.A. Boyle, T. Munoz-Antonia, M.B. Schabath, A. Shaffer, C. Pratt, A. Luisa D, Q.P. Quinn, E.B. Haura H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, US
C. Rivard,1 L. Rozeboom,1 W. Feser,1 A. Baron,1 Y. Miller,2 P. Bunn,1 F. Hirsch1 1University of Colorado Denver, Denver, CO, US, 2Denver Veterans Affairs Medical Center, Denver, CO, US
Background: Translational research in advanced lung cancer is often hindered by the limited availability of specimens for advanced molecular techniques. We launched a thoracic rapid tissue donation (RTD) program to enable lung cancer research with rapid collection (<48 hours) of tissue at multiple tumor sites within hours after death. Hematoxylin and eosin (H&E) and immunohistochemistry staining were performed to evaluate RTD tissue quality and variability of immune checkpoint expression (PD-L1, TIM3, LAG3, iNOS, BTLA, and A2AR) at multiple metastatic sites. Results: H&E staining from seven RTD cases confirmed high quality tissue with minimal evidence of post-mortem tissue damage. PD-L1 expression was observed in four of five cases with evaluable tumor tissue and revealed heterogenous expression both within each tumor site (intra-tumoral) and between multiple tumor sites (inter-tumoral). Evaluation of other immune checkpoints is ongoing. Conclusions: Rapid tissue donation of post-mortem tissue from patients is feasible with collection of valuable tissue for research. The observed heterogeneous PD-L1 protein expression pattern illustrates the need to interpret PD-L1 results with caution. Post-mortem tissue collection from multiple tumor sites facilitates understanding of differences in tumor behavior and biomarker expression between primary and metastatic sites. We are grateful to the patients and families who contributed to this study. This work was funded by NIH/NCI R21 CA194932.
Background: miRNAs have shown exceptional promise as biomarkers to detect lung cancer; however, no miRNA signatures have yet reached the clinic. A panel of 50 miRNAs previously identified in at least two published studies for distinguishing lung cancer from non-cancer was used for analysis. Results: Total RNA was isolated from tissue, sputum and plasma and miRNA measured by RT-qPCR using Taqman custom microfluidics cards. Combinations of 3-4 miRNAs were evaluated for the highest median areaunder the receiver operating curve (AUC). Signatures were identified for lung cancer tumor tissue, and sputum and plasma from nodule patients with an AUC of 0.81 (plasma), 0.93 (sputum) and 0.97 (tissue). miRNA signatures for tissue and plasma had 145, 183 and 486 in common. All signatures including sputum contained miR-145. Conclusions: These data identified a signature of 3-4 miRNAs for tissue, sputum and plasma that demonstrate excellent potential for detecting early-stage lung cancer. Each of these miRNAs has been replicated in at least two previous lung cancer studies, suggesting a high likelihood of achieving clinical validation. Of interest is the identification of miR-145 which is common to tissue, sputum and plasma signatures. Final validation of plasma test set data and additional sputum projects are in process.
Proteogenomic Landscape of Squamous Cell Lung Cancer P.A. Stewart, R.J.C. Slebos, E.A. Welsh, L. Cen, Y. Zhang, Z. Chen, C.-H. Cheng, F. Pettersson, A. Berglund, G. Zhang, B. Fang, V. Izumi, S. Yoder, K. Fellows, Y.A. Chen, J.K. Teer, S.A. Eschrich, J.M. Koomen, E.B. Haura Moffitt Cancer Center, Tampa, FL, US Background: Patients with squamous cell lung cancer (SQLC) have few viable treatment options and a high degree of medical need. To generate novel approaches for molecular classification of this disease and to create new therapeutic opportunities, we performed a proteogenomic characterization (DNA, RNA, protein) of 116 surgically resected squamous cell lung cancer tumors with full clinical follow up data. Results: Targeted exon sequencing revealed the most mutations in TP53 (78%), MLL2 (32%), and NRF2 (24%). Consensus clustering of preliminary gene expression identifies four patient subtypes. Proteomic characterization identified more than 8,000 protein groups, and proteomics-based consensus clustering indicates another potential set of molecular subtypes when compared to gene-based clustering. Using 7,327 gene-protein expression pairs, we found an average Spearman’s correlation of 0.22 (similar to other proteogenomic studies). Strongly correlated pathways included NRF2, glycolysis, and pentose phosphate, while poorly correlated pathways included EGFR, mRNA processing, and nonsense-mediated decay. Conclusions: Our results highlight the challenges in trying to link between the genome and proteome in SQLC, suggesting that efforts to develop new SQLC therapeutics require a holistic approach integrating results from analysis of both the genome and proteome.
WINTHER e A Study of Therapy Based on Tumor and Normal-Matched Biopsies: The Lung Cancer Experience Tal Sella, Amir Onn Sheba Medical Center, IL, Tel HaShomer, Israel Background: Patient-tailored therapy based on tumor genomics is limited to 30-40% of the patients whose tumor harbor actionable DNA mutations or amplifications.WINTHER is an international open label non-randomized clinical trial developed by the WIN consortium. Matched tumor and normal tissue biopsies are collected and analyzed by NGS (Foundation Medicine) or by functional genomics utilizing a prediction model of efficacy developed at Ben Gurion University. Results: 56 patients were biopsied. 29 (52%) had lung cancer. Successful biopsies yielding sufficient material for full genomic analyses were achieved in 29 subjects (53%). Lung biopsy success rates were 71% and 61% respectively for normal and tumor specimens. To date, 11 lung cancer patients were treated with chemotherapy (1) or biologic agents (11). Targeted genomic alterations included EGFR (3), RET (2), KRAS (2), ALK (1), ErbB2 (1), ErbB3 (1), BRAF (1). Clinical benefit rate (CBR) was 55% (6/11) with 1 subject achieving compete response, 2 partial response and 3 stable disease. Response durations were 7, 14 and 18 months. Conclusions: Tumor genomic analysis based on the comparison of matched tumor and normal biopsies is acceptable and feasible. The experience of the multidisciplinary team is an important contributor to the program’s success.
Quantitative Proteomic Analysis of Core-Needle Biopsy of Lung Cancer X. Zhao,1 K. Huffman,1 J. Fujimoto,2 J. Canales,2 L. Girard,1 N. Guangjun,3 J. Heymach,2 I. Wistuba,2 J. Minna,1 Y. Yu1 1University of Texas Southwestern Medical Center, Dallas, TX, US, 2MD Anderson Cancer Center, Houston, TX, US, 3National Center for Nanoscience and Technology, Beijing, CN Background: It is becoming increasingly appreciated that proper pretreatment diagnostics are essential for determining the appropriate
Journal of Thoracic Oncology
Vol. 12 No. 8S
Immune Checkpoint Protein Expression at Multiple Metastatic Sites of Lung Cancer
miRNA for Early Detection of Lung Cancer: Comparison of Tissue, Sputum and Plasma Signatures
T.A. Boyle, T. Munoz-Antonia, M.B. Schabath, A. Shaffer, C. Pratt, A. Luisa D, Q.P. Quinn, E.B. Haura H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, US
C. Rivard,1 L. Rozeboom,1 W. Feser,1 A. Baron,1 Y. Miller,2 P. Bunn,1 F. Hirsch1 1University of Colorado Denver, Denver, CO, US, 2Denver Veterans Affairs Medical Center, Denver, CO, US
Background: Translational research in advanced lung cancer is often hindered by the limited availability of specimens for advanced molecular techniques. We launched a thoracic rapid tissue donation (RTD) program to enable lung cancer research with rapid collection (<48 hours) of tissue at multiple tumor sites within hours after death. Hematoxylin and eosin (H&E) and immunohistochemistry staining were performed to evaluate RTD tissue quality and variability of immune checkpoint expression (PD-L1, TIM3, LAG3, iNOS, BTLA, and A2AR) at multiple metastatic sites. Results: H&E staining from seven RTD cases confirmed high quality tissue with minimal evidence of post-mortem tissue damage. PD-L1 expression was observed in four of five cases with evaluable tumor tissue and revealed heterogenous expression both within each tumor site (intra-tumoral) and between multiple tumor sites (inter-tumoral). Evaluation of other immune checkpoints is ongoing. Conclusions: Rapid tissue donation of post-mortem tissue from patients is feasible with collection of valuable tissue for research. The observed heterogeneous PD-L1 protein expression pattern illustrates the need to interpret PD-L1 results with caution. Post-mortem tissue collection from multiple tumor sites facilitates understanding of differences in tumor behavior and biomarker expression between primary and metastatic sites. We are grateful to the patients and families who contributed to this study. This work was funded by NIH/NCI R21 CA194932.
Background: miRNAs have shown exceptional promise as biomarkers to detect lung cancer; however, no miRNA signatures have yet reached the clinic. A panel of 50 miRNAs previously identified in at least two published studies for distinguishing lung cancer from non-cancer was used for analysis. Results: Total RNA was isolated from tissue, sputum and plasma and miRNA measured by RT-qPCR using Taqman custom microfluidics cards. Combinations of 3-4 miRNAs were evaluated for the highest median areaunder the receiver operating curve (AUC). Signatures were identified for lung cancer tumor tissue, and sputum and plasma from nodule patients with an AUC of 0.81 (plasma), 0.93 (sputum) and 0.97 (tissue). miRNA signatures for tissue and plasma had 145, 183 and 486 in common. All signatures including sputum contained miR-145. Conclusions: These data identified a signature of 3-4 miRNAs for tissue, sputum and plasma that demonstrate excellent potential for detecting early-stage lung cancer. Each of these miRNAs has been replicated in at least two previous lung cancer studies, suggesting a high likelihood of achieving clinical validation. Of interest is the identification of miR-145 which is common to tissue, sputum and plasma signatures. Final validation of plasma test set data and additional sputum projects are in process.
Proteogenomic Landscape of Squamous Cell Lung Cancer P.A. Stewart, R.J.C. Slebos, E.A. Welsh, L. Cen, Y. Zhang, Z. Chen, C.-H. Cheng, F. Pettersson, A. Berglund, G. Zhang, B. Fang, V. Izumi, S. Yoder, K. Fellows, Y.A. Chen, J.K. Teer, S.A. Eschrich, J.M. Koomen, E.B. Haura Moffitt Cancer Center, Tampa, FL, US Background: Patients with squamous cell lung cancer (SQLC) have few viable treatment options and a high degree of medical need. To generate novel approaches for molecular classification of this disease and to create new therapeutic opportunities, we performed a proteogenomic characterization (DNA, RNA, protein) of 116 surgically resected squamous cell lung cancer tumors with full clinical follow up data. Results: Targeted exon sequencing revealed the most mutations in TP53 (78%), MLL2 (32%), and NRF2 (24%). Consensus clustering of preliminary gene expression identifies four patient subtypes. Proteomic characterization identified more than 8,000 protein groups, and proteomics-based consensus clustering indicates another potential set of molecular subtypes when compared to gene-based clustering. Using 7,327 gene-protein expression pairs, we found an average Spearman’s correlation of 0.22 (similar to other proteogenomic studies). Strongly correlated pathways included NRF2, glycolysis, and pentose phosphate, while poorly correlated pathways included EGFR, mRNA processing, and nonsense-mediated decay. Conclusions: Our results highlight the challenges in trying to link between the genome and proteome in SQLC, suggesting that efforts to develop new SQLC therapeutics require a holistic approach integrating results from analysis of both the genome and proteome.
WINTHER e A Study of Therapy Based on Tumor and Normal-Matched Biopsies: The Lung Cancer Experience Tal Sella, Amir Onn Sheba Medical Center, IL, Tel HaShomer, Israel Background: Patient-tailored therapy based on tumor genomics is limited to 30-40% of the patients whose tumor harbor actionable DNA mutations or amplifications.WINTHER is an international open label non-randomized clinical trial developed by the WIN consortium. Matched tumor and normal tissue biopsies are collected and analyzed by NGS (Foundation Medicine) or by functional genomics utilizing a prediction model of efficacy developed at Ben Gurion University. Results: 56 patients were biopsied. 29 (52%) had lung cancer. Successful biopsies yielding sufficient material for full genomic analyses were achieved in 29 subjects (53%). Lung biopsy success rates were 71% and 61% respectively for normal and tumor specimens. To date, 11 lung cancer patients were treated with chemotherapy (1) or biologic agents (11). Targeted genomic alterations included EGFR (3), RET (2), KRAS (2), ALK (1), ErbB2 (1), ErbB3 (1), BRAF (1). Clinical benefit rate (CBR) was 55% (6/11) with 1 subject achieving compete response, 2 partial response and 3 stable disease. Response durations were 7, 14 and 18 months. Conclusions: Tumor genomic analysis based on the comparison of matched tumor and normal biopsies is acceptable and feasible. The experience of the multidisciplinary team is an important contributor to the program’s success.
Quantitative Proteomic Analysis of Core-Needle Biopsy of Lung Cancer X. Zhao,1 K. Huffman,1 J. Fujimoto,2 J. Canales,2 L. Girard,1 N. Guangjun,3 J. Heymach,2 I. Wistuba,2 J. Minna,1 Y. Yu1 1University of Texas Southwestern Medical Center, Dallas, TX, US, 2MD Anderson Cancer Center, Houston, TX, US, 3National Center for Nanoscience and Technology, Beijing, CN Background: It is becoming increasingly appreciated that proper pretreatment diagnostics are essential for determining the appropriate