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Owonikoko T, Dahlberg S, Sica G, Poirier J, Byers L, Rudin C, Wistuba I, Ramalingam S. P3.12-06 SLFN11 Expression and Efficacy of PARP Inhibitor Therapy in Extensive Stage Small Cell Lung Cancer: ECOG-ACRIN 2511 Study. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Rusch V, Chaft J, Johnson B, Wistuba I, Kris M, Lee J, Bunn P, Kwiatkowski D, Reckamp K, Finley D, Haura E, Waqar S, Doebele R, Garon E, Blasberg J, Nicholas A, Schulze K, Phan S, Gandhi M, Carbone D. MA04.09 Neoadjuvant Atezolizumab in Resectable Non-Small Cell Lung Cancer (NSCLC): Updated Results from a Multicenter Study (LCMC3). J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wistuba I. ES08.04 Neoadjuvant Therapy. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Expósito F, Villalba M, Pajares M, Redrado M, Sainz C, Wistuba I, Behrens C, Redin E, Andrea C, Cirauquiz C, Montuenga L, Pio R, Calvo A. P1.03-24 TMPRSS4: A Novel Prognostic Biomarker and Therapeutic Target in NSCLC. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kris M, Aisner D, Sholl L, Berry L, Rossi M, Chen H, Fujimoto J, Moreira A, Ramalingam S, Villaruz L, Otterson G, Haura E, Politi K, Glisson B, Cetnar J, Garon E, Schiller J, Waqar S, Sequist L, Brahmer J, Shyr Y, Kugler K, Wistuba I, Johnson B, Minna J, Bunn P, Kwiatkowski D. P3.03-007 LCMC2: Expanded Profiling of Lung Adenocarcinomas Identifies ROS1 and RET Rearrangements and TP53 Mutations as a Negative Prognostic Factor. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Guijarro I, Poteete A, Fan Y, Cho S, Tong P, Roarty E, Nilsson M, Rodriguez-Canales J, Mino B, Cuentas EP, Wistuba I, Wang J, Heymach J. P3.03-027 LKB1 Loss Is Associated with Resistance to Anti-Angiogenic Therapy in Non-Small Cell Lung Cancer Mouse Models. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wistuba I. MS 15.02 Molecular Testing Using NGS. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hu X, Fujimoto J, Ying L, Reuben A, Chen R, Chow C, Rodriguez-Canales J, Sun W, Hu J, Parra E, Carmen B, Wu C, Mao X, Song X, Li J, Gumbs C, Swisher S, Zhang J, Heymach J, Hong W, Wistuba I, Futreal A, Su D, Zhang J. P2.02-013 Investigation of Genomic and TCR Repertoire Evolution of AAH, AIS, MIA to Invasive Lung Adenocarcinoma by Multiregion Exome and TCR Sequencing. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang J, Gong Y, Nong J, Yi Y, Guan Y, Yang L, Jia H, Zhang S, Yi X, Liao Z, Lam V, Papadimitrakopoulou V, Wistuba I, Heymach J, Glisson B, Futreal A, Xia X, Zhang J. MA 01.03 The Potential of ctDNA Sequencing in Disease Monitoring and Depicting Genomic Evolution of Small-Cell Lung Cancer Under Therapy. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chen L, Diao L, Yang Y, Yi X, Rodriguez B, Li Y, Rodriguez-Canales J, Liu X, Huang A, Zhao Q, Peng D, Fradette J, Tong P, Ungewiss C, Fan Y, Peng D, Villalobos P, Dmitrovsky E, Papadimitrakopoulou V, Wang J, Byers L, Heymach J, Ullrich S, Wistuba I, Qin X, Gibbons D. OA 13.01 CD38-Mediated Immunometabolic Suppression as a Mechanism of Resistance to PD-1/PD-L1 Axis Blockade. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Martinez-Terroba E, Behrens C, De Miguel F, Agorreta J, Monsó E, Millares L, Mesa-Guzman M, Perez-Gracia J, Lozano M, Zulueta J, Pio R, Wistuba I, Pajares M, Montuenga L. P2.02-061 Two Novel Protein-Based Prognostic Signatures Improve Risk Stratification of Early Lung ADC and SCC Patients. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Skoulidis F, Albacker L, Hellmann M, Awad M, Gainor J, Goldberg M, Schrock A, Gay L, Elvin J, Ross J, Rizvi H, Carter B, Erasmus J, Halpenny D, Plodkowski A, Long N, Nishino-Habatu M, Denning W, Rodriguez-Canales J, Villalobos P, Cuentas EP, Sholl L, Sauter J, Elamin Y, Zhang J, Leonardi G, Wong K, Stephens P, Papadimitrakopoulou V, Wistuba I, Wolchok J, Shaw A, Jänne P, Rudin C, Miller V, Heymach J. MA 05.02 STK11/LKB1 Loss of Function Genomic Alterations Predict Primary Resistance to PD-1/PD-L1 Axis Blockade in KRAS-Mutant NSCLC. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhao X, Huffman K, Fujimoto J, Canales J, Girard L, Guangjun N, Heymach J, Wistuba I, Minna J, Yu Y. Quantitative Proteomic Analysis of Core-Needle Biopsy of Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sepesi B, Cuentes EP, Canales J, Behrens C, Correa A, Antonoff M, Gibbons D, Heymach J, Hofstetter W, Mehran R, Rice D, Roth J, Vaporciyan A, Walsh G, Weissferdt A, Kalhor N, Moran C, Swisher S, Wistuba I. Tumor-Infiltrating Lymphocytes and Overall Survival in Surgically Resected Stage II and III Non–Small Cell Lung Cancer. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.01.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Allenson K, Castillo J, San Lucas FA, Scelo G, Kim DU, Bernard V, Davis G, Kumar T, Katz M, Overman MJ, Foretova L, Fabianova E, Holcatova I, Janout V, Meric-Bernstam F, Gascoyne P, Wistuba I, Varadhachary G, Brennan P, Hanash S, Li D, Maitra A, Alvarez H. High prevalence of mutant KRAS in circulating exosome-derived DNA from early-stage pancreatic cancer patients. Ann Oncol 2017; 28:741-747. [PMID: 28104621 PMCID: PMC5834026 DOI: 10.1093/annonc/mdx004] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Indexed: 02/03/2023] Open
Abstract
Background Exosomes arise from viable cancer cells and may reflect a different biology than circulating cell-free DNA (cfDNA) shed from dying tissues. We compare exosome-derived DNA (exoDNA) to cfDNA in liquid biopsies of patients with pancreatic ductal adenocarcinoma (PDAC). Patients and methods Patient samples were obtained between 2003 and 2010, with clinically annotated follow up to 2015. Droplet digital PCR was performed on exoDNA and cfDNA for sensitive detection of KRAS mutants at codons 12/13. A cumulative series of 263 individuals were studied, including a discovery cohort of 142 individuals: 68 PDAC patients of all stages; 20 PDAC patients initially staged with localized disease, with blood drawn after resection for curative intent; and 54 age-matched healthy controls. A validation cohort of 121 individuals (39 cancer patients and 82 healthy controls) was studied to validate KRAS detection rates in early-stage PDAC patients. Primary outcome was circulating KRAS status as detected by droplet digital PCR. Secondary outcomes were disease-free and overall survival. Results KRAS mutations in exoDNA, were identified in 7.4%, 66.7%, 80%, and 85% of age-matched controls, localized, locally advanced, and metastatic PDAC patients, respectively. Comparatively, mutant KRAS cfDNA was detected in 14.8%, 45.5%, 30.8%, and 57.9% of these individuals. Higher exoKRAS MAFs were associated with decreased disease-free survival in patients with localized disease. In the validation cohort, mutant KRAS exoDNA was detected in 43.6% of early-stage PDAC patients and 20% of healthy controls. Conclusions Exosomes are a distinct source of tumor DNA that may be complementary to other liquid biopsy DNA sources. A higher percentage of patients with localized PDAC exhibited detectable KRAS mutations in exoDNA than previously reported for cfDNA. A substantial minority of healthy samples demonstrated mutant KRAS in circulation, dictating careful consideration and application of liquid biopsy findings, which may limit its utility as a broad cancer-screening method.
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Tang C, Amer A, Hobbs B, Li X, Behrens C, Para Cuentas E, Rodriguez Canales J, Chang J, Hong D, Welsh J, Wistuba I, Koay E. Pathology-Based Non-Small Cell Lung Cancer Radiomics Signature Describing the Local Tumor Immune Environment: Discovery and Validation. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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San Lucas FA, Allenson K, Bernard V, Castillo J, Kim DU, Ellis K, Ehli EA, Davies GE, Petersen JL, Li D, Wolff R, Katz M, Varadhachary G, Wistuba I, Maitra A, Alvarez H. Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes. Ann Oncol 2015; 27:635-41. [PMID: 26681674 PMCID: PMC4803451 DOI: 10.1093/annonc/mdv604] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/07/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The ability to perform comprehensive profiling of cancers at high resolution is essential for precision medicine. Liquid biopsies using shed exosomes provide high-quality nucleic acids to obtain molecular characterization, which may be especially useful for visceral cancers that are not amenable to routine biopsies. PATIENTS AND METHODS We isolated shed exosomes in biofluids from three patients with pancreaticobiliary cancers (two pancreatic, one ampullary). We performed comprehensive profiling of exoDNA and exoRNA by whole genome, exome and transcriptome sequencing using the Illumina HiSeq 2500 sequencer. We assessed the feasibility of calling copy number events, detecting mutational signatures and identifying potentially actionable mutations in exoDNA sequencing data, as well as expressed point mutations and gene fusions in exoRNA sequencing data. RESULTS Whole-exome sequencing resulted in 95%-99% of the target regions covered at a mean depth of 133-490×. Genome-wide copy number profiles, and high estimates of tumor fractions (ranging from 56% to 82%), suggest robust representation of the tumor DNA within the shed exosomal compartment. Multiple actionable mutations, including alterations in NOTCH1 and BRCA2, were found in patient exoDNA samples. Further, RNA sequencing of shed exosomes identified the presence of expressed fusion genes, representing an avenue for elucidation of tumor neoantigens. CONCLUSIONS We have demonstrated high-resolution profiling of the genomic and transcriptomic landscapes of visceral cancers. A wide range of cancer-derived biomarkers could be detected within the nucleic acid cargo of shed exosomes, including copy number profiles, point mutations, insertions, deletions, gene fusions and mutational signatures. Liquid biopsies using shed exosomes has the potential to be used as a clinical tool for cancer diagnosis, therapeutic stratification and treatment monitoring, precluding the need for direct tumor sampling.
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Lin S, Gudikote J, Giri U, Fujimoto J, Wang J, Wei C, Chen H, Farnia B, Gomez D, Story M, Komaki R, Swisher S, Wistuba I, Heymach J. RAD50 Expression Predicts for Locoregional Failure and Distant Metastatic Recurrence After Postoperative Radiation Therapy in Resected Non-Small Cell Lung Cancer. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.08.321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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An E, Liao W, Thyparambil S, Rodriguez J, Salgia R, Wistuba I, Burrows J, Hembrough T. 489 Development and clinical validation of a quantitative mass spectrometric assay for PD-L1 protein in FFPE NSCLC samples. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70615-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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D'Arcangelo M, Brustugun O, Xiao Y, Choi Y, Behrens C, Solis L, Wang Y, Firestein R, Boyle T, Lund-Iversen M, Rivard C, Helland Å, Wistuba I, Hirsch F, Shames D. Prevalence and Prognostic Significance of Sodium-Dependent Phosphate Transporter 2B (Napi2B) Protein Expression in Non-Small Cell Lung Cancer (Nsclc). Ann Oncol 2014. [DOI: 10.1093/annonc/mdu326.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Shames D, Kowanetz M, Xiao Y, Choi Y, D'Arcangelo M, Behrens C, Solis L, Koeppen H, Firestein R, Wang Y, Mocci S, Boyle T, Lund-Iversen M, Bowden C, Amler L, Brustugun O, Wistuba I, Hirsch F. Prevalence, Prognostic Significance, and Overlap of Actionable Biomarkers in Nsclc. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu326.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Komaki R, Kim Y, Wistuba I, Tang X, Meyn R, Allen P, Wei X, Lee I, O’Reilly M, Blumenschein G, Hong W. 104: Vimentin (EMT Marker Protein) Score As One of Predictors Resistance to Erlotinib and Radiotherapy for Patients with Stage III Non-Small Cell Lung Cancer on A Prospective Phase II Trial. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)34125-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Doroshow J, Liu ET, Pellini M, Miller V, Palmer G, Averbuch S, Green G, Novotny J, Paoletti P, Patel K, Hoos A, Gaynor R, Melemed S, Reinhard C, Teh BT, Hong WK, Kim E, Herbst R, Papadimitrakopoulou V, Gold K, Wistuba I, Lee J, Lippman S, Jackson JR, Zitvogel L, Meisel C, Workman P, Dalton WS, Botwood N, Davis BJ, Batist G, Assouline S, Camlioglu E, Tetu B, Spatz A, Diaz Z, Aguilar-Mahecha A, Basik M, Rodon J, Dienstmann R, Cortes J, Saura C, Aura C, Hernandez-Losa J, Vivancos A, Joan J, del Campo J, Felip E, Seoane J, Tabernero JT, Friend SH, Tsimberidou AM, Hong DS, Wheler JJ, Ye Y, Fu S, Piha-Paul SA, Naing A, Falchook GS, Janku F, Luthra R, Wen S, Kurzrock R, Naley M, Johnson P, Schuerer K, Lopes M, Hood LE, Yarden Y, Quackenbush J. Lectures. Ann Oncol 2012. [DOI: 10.1093/annonc/mds160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hong W, Kim E, Herbst R, Papadimitrakopoulou V, Gold K, Wistuba I, Lee J, Lippman S. L4.1 Evolution of Battle Trials at Md Anderson Cancer Center. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)31272-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Singh SP, Han L, Murali R, Solis L, Roth J, Ji L, Wistuba I, Kundra V. SSTR2-based reporters for assessing gene transfer into non-small cell lung cancer: evaluation using an intrathoracic mouse model. Hum Gene Ther 2010; 22:55-64. [PMID: 20653396 DOI: 10.1089/hum.2010.109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The most common cause of cancer-related deaths in North America is lung cancer, 85% of which is non-small cell lung cancer (NSCLC). Gene therapy is a promising approach, but has been hindered by lack of methods for localizing and quantifying gene expression in vivo. Human somatostatin receptor subtype-2 (SSTR2)-based reporters can be used to follow gene expression in vivo using ligands with greater affinity for this subtype. NSCLCs can express SSTR subtypes, which may interfere with SSTR2-based reporters. We assessed whether a SSTR2-based reporter can serve as a reporter of gene transfer into NSCLCs. SSTR subtype expression was assessed in NSCLC cell lines A549, H460, and H1299 using RT-PCR. After infection with an adenovirus containing hemagglutinin-A-tagged-SSTR2 (Ad-HA-SSTR2) or control insert, expression was assessed by immunologic techniques and binding to clinically-approved (111)In-octreotide. In vivo, after magnetic resonance (MR) imaging, intrathoracic H460 tumors were injected with Ad-HA-SSTR2 or control virus (n = 6 mice/group) under ultrasound guidance. Intravenous injection of (111)In-octreotide 2 days later was followed by planar and single-photon emission computed tomography (SPECT) imaging. Biodistribution into tumors was assessed in vivo using anatomic MR and functional gamma-camera images and ex vivo using excised organs/tumors. In human lung tumor samples (n = 70), SSTR2 expression was assessed using immunohistochemistry. All three NSCLC cell lines expressed different SSTR subtypes, but none expressed SSTR2. Upon Ad-HA-SSTR2 infection, HA-SSTR2 expression was seen in all three cell lines using antibodies targeting the HA domain or (111)In-octreotide targeting the receptor domain (p < 0.05). Intrathoracic tumors infected with Ad-HA-SSTR2 were clearly visible by gamma-camera imaging; expression was quantified by both in vivo and ex vivo biodistribution analysis and demonstrated greater uptake in tumors infected with Ad-HA-SSTR2 compared with control virus (p < 0.05). Immunohistochemistry found that 78% of NSCLCs are negative for and 13% have low levels of SSTR2 expression. It is concluded that SSTR2-based reporters can serve as reporters of gene transfer into NSCLCs.
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